From 0c733285b8a12f526efd44ce2e760795994a5e82 Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Thu, 28 Sep 2023 12:03:58 +0200 Subject: [PATCH 1/5] initial changes --- content/english/dashboards/RECOVAC.md | 8 +++ .../english/dashboards/covid_publications.md | 13 +++-- content/english/dashboards/post_covid.md | 56 ++++++++++--------- content/english/dashboards/vaccines.md | 10 ++-- .../covid_quantification/covid_quant_GU.md | 14 +++-- .../covid_quantification/covid_quant_KTH.md | 6 +- .../covid_quantification/covid_quant_SLU.md | 6 +- .../enteric_quantification/_index.md | 4 ++ .../influenza_quantification/_index.md | 8 +++ content/svenska/dashboards/post_covid.md | 48 ++++++---------- .../covid_quantification/covid_quant_GU.md | 18 +++--- 11 files changed, 112 insertions(+), 79 deletions(-) diff --git a/content/english/dashboards/RECOVAC.md b/content/english/dashboards/RECOVAC.md index 3a5aca635..ff09ec972 100644 --- a/content/english/dashboards/RECOVAC.md +++ b/content/english/dashboards/RECOVAC.md @@ -89,6 +89,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the +
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diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md index 033566a9a..c322727aa 100644 --- a/content/english/dashboards/covid_publications.md +++ b/content/english/dashboards/covid_publications.md @@ -5,13 +5,14 @@ banner: /dashboard_thumbs/publications.jpg toc: false plotly: true menu: - dashboard_menu: - identifier: covid_19_publications_vis - name: "COVID-19 publication overview" + dashboard_menu: + identifier: covid_19_publications_vis + name: "COVID-19 publication overview" aliases: - - /projects/dashboard/ + - /projects/dashboard/ dashboards_topics: [COVID-19, Infectious diseases] --- + The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/). Note that our database is manually curated and, as such, may not be exhaustive. The full database is available for download and use for other purposes, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details. The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). @@ -20,6 +21,10 @@ The code used to produce the visulations on this page can be found on [GitHub](h This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not. +
+ Rotating your phone may improve graph layout +
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{{< publications_per_month >}}
diff --git a/content/english/dashboards/post_covid.md b/content/english/dashboards/post_covid.md index 65d115e5d..3b155b7bb 100644 --- a/content/english/dashboards/post_covid.md +++ b/content/english/dashboards/post_covid.md @@ -5,23 +5,23 @@ banner: /dashboard_thumbs/postcovid.jpg toc: true plotly: true menu: - dashboard_menu: - identifier: post_covid - name: Post COVID-19 condition + dashboard_menu: + identifier: post_covid + name: Post COVID-19 condition aliases: - - /data_types/health_data/post_covid/ + - /data_types/health_data/post_covid/ dashboards_topics: [COVID-19, Infectious diseases] --- Since the beginning of 2020, the COVID-19 pandemic has challenged healthcare and dramatically changed daily life for people worldwide. The severity of symptoms experienced by patients during the acute infection phase of COVID-19 disease varies between individuals from mild to severe. After this phase, there are usually no indications that the disease will have any long-term effects on their health, regardless of the severity of symptoms experienced during the acute infection phase. However, some patients continue to exhibit symptoms for prolonged periods after the acute phase. The symptoms experienced by such patients are broad, but can include, for example, deep fatigue, joint pain, ‘brain fog’ (difficulty concentrating on certain tasks for longer periods of time), and heart palpitations ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8), [Marx, 2021](https://doi.org/10.1038/s41592-021-01145-z)). These symptoms can have a significant impact on the patients' quality of life. -Most studies that have explored what causes some patients to experience prolonged symptoms have been descriptive. However, several recent studies have explored potential causes in detail. For example, [Važgėlienė *et al.* (2022)](https://www.mdpi.com/2077-0383/11/21/6278) investigated potential links between prolonged symptoms after COVID-19 infection and other types of chronic disease or daily medication. They found an association between the taking of daily medication and the development of prolonged symptoms after COVID-19 infection. Other studies have found that multiple other factors, including being female, advanced age, and poor general health, are associated with an increased risk of experiencing prolonged symptoms after a COVID-19 infection ([Sudre *et al.*, 2021](https://www.nature.com/articles/s41591-021-01292-y)). +Most studies that have explored what causes some patients to experience prolonged symptoms have been descriptive. However, several recent studies have explored potential causes in detail. For example, [Važgėlienė _et al._ (2022)](https://www.mdpi.com/2077-0383/11/21/6278) investigated potential links between prolonged symptoms after COVID-19 infection and other types of chronic disease or daily medication. They found an association between the taking of daily medication and the development of prolonged symptoms after COVID-19 infection. Other studies have found that multiple other factors, including being female, advanced age, and poor general health, are associated with an increased risk of experiencing prolonged symptoms after a COVID-19 infection ([Sudre _et al._, 2021](https://www.nature.com/articles/s41591-021-01292-y)). -This condition (i.e. the presistance of symptoms following the acute phase of COVID-19 infection) has been referred to in multiple ways, including *Post COVID-19 condition*, *Post-COVID*, and *Long COVID*. On this page, we use the term *Post COVID-19 condition* for consistency. See the *[Background Information](#background)* section below for more detail about the nomenclature used and relevant research. +This condition (i.e. the presistance of symptoms following the acute phase of COVID-19 infection) has been referred to in multiple ways, including _Post COVID-19 condition_, _Post-COVID_, and _Long COVID_. On this page, we use the term _Post COVID-19 condition_ for consistency. See the _[Background Information](#background)_ section below for more detail about the nomenclature used and relevant research. -On this page, you can find visualisations of data related to *Post COVID-19 condition* in Sweden from The Swedish Board of Health and Welfare ([Socialstyrelsen](https://www.socialstyrelsen.se)), an overview of ongoing *Post COVID-19 condition* research projects in Sweden, and scientific publications regarding *Post COVID-19 condition* by researchers affiliated with Swedish universities or research institutes. +On this page, you can find visualisations of data related to _Post COVID-19 condition_ in Sweden from The Swedish Board of Health and Welfare ([Socialstyrelsen](https://www.socialstyrelsen.se)), an overview of ongoing _Post COVID-19 condition_ research projects in Sweden, and scientific publications regarding _Post COVID-19 condition_ by researchers affiliated with Swedish universities or research institutes. -For more information on *Post COVID-19 condition* in Sweden, please see [this section](https://www.socialstyrelsen.se/coronavirus-covid-19/socialstyrelsens-roll-och-uppdrag/postcovid/) of The Swedish Board of Health and Welfare (Socialstyrelsen)’s website and their [report on *Post-COVID condition* (published April 2021)](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf). More [general information](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects/index.html) is also available from the Centers for Disease Control and Prevention (CDC). +For more information on _Post COVID-19 condition_ in Sweden, please see [this section](https://www.socialstyrelsen.se/coronavirus-covid-19/socialstyrelsens-roll-och-uppdrag/postcovid/) of The Swedish Board of Health and Welfare (Socialstyrelsen)’s website and their [report on _Post-COVID condition_ (published April 2021)](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf). More [general information](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects/index.html) is also available from the Centers for Disease Control and Prevention (CDC). ## Availability of data and code @@ -37,9 +37,9 @@ All code used to produce the visualisations on this page is available on [GitHub ## Statistics on Post COVID-19 condition in Sweden -Since Post COVID-19 condition is not clearly defined, over time, it has been assigned multiple diagnosis codes for use by medical professionals/researchers. After the first cases of prolonged disease following COVID-19 infection were detected in spring 2020, The Swedish Board of Health and Welfare initiated the diagnosis *Z86.1A - COVID-19 in own medical history* (Covid-19 i den egna sjukhistorien). This diagnosis code has been used since 1st June 2020. From 1st January 2021, this diagnosis code was replaced by *U08.9 (ICD-10-SE) - COVID-19 in own medical history, unspecified* (Covid-19 i den egna sjukhistorien) in accordance with new [WHO (World Health Organization)](https://www.who.int) guidelines. This diagnosis should be used when an individual is receiving treatment for an illness/physical damage for which the patient’s history of COVID-19 infection is considered relevant (i.e. a contributory factor to the present illness/damage). Importantly, this diagnosis should only be given if the individual is no longer considered to have COVID-19, and if the current health condition is not considered to result from infection with COVID-19. *U08.9* is an additional diagnosis, as such, it should only be assigned alongside a main diagnosis; it cannot be the main diagnosis. +Since Post COVID-19 condition is not clearly defined, over time, it has been assigned multiple diagnosis codes for use by medical professionals/researchers. After the first cases of prolonged disease following COVID-19 infection were detected in spring 2020, The Swedish Board of Health and Welfare initiated the diagnosis _Z86.1A - COVID-19 in own medical history_ (Covid-19 i den egna sjukhistorien). This diagnosis code has been used since 1st June 2020. From 1st January 2021, this diagnosis code was replaced by _U08.9 (ICD-10-SE) - COVID-19 in own medical history, unspecified_ (Covid-19 i den egna sjukhistorien) in accordance with new [WHO (World Health Organization)](https://www.who.int) guidelines. This diagnosis should be used when an individual is receiving treatment for an illness/physical damage for which the patient’s history of COVID-19 infection is considered relevant (i.e. a contributory factor to the present illness/damage). Importantly, this diagnosis should only be given if the individual is no longer considered to have COVID-19, and if the current health condition is not considered to result from infection with COVID-19. _U08.9_ is an additional diagnosis, as such, it should only be assigned alongside a main diagnosis; it cannot be the main diagnosis. -From 16th October 2020, the Swedish Board of Health and Welfare initiated a new diagnosis, *U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified* (Postinfektiöst tillstånd efter covid-19, ospecificerat), in accordance with new WHO guidelines. This new diagnosis supplemented and partially replaced the *Z86.1A* diagnosis. As with *U08.9*, the *U09.9* diagnosis should only be given after the person is no longer considered to have COVID-19. This diagnosis code should be used for conditions that persist or begin after the acute infection stage has passed. *U09.9* is also an additional diagnosis, and should only be assigned alongside a separate main diagnosis. +From 16th October 2020, the Swedish Board of Health and Welfare initiated a new diagnosis, _U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified_ (Postinfektiöst tillstånd efter covid-19, ospecificerat), in accordance with new WHO guidelines. This new diagnosis supplemented and partially replaced the _Z86.1A_ diagnosis. As with _U08.9_, the _U09.9_ diagnosis should only be given after the person is no longer considered to have COVID-19. This diagnosis code should be used for conditions that persist or begin after the acute infection stage has passed. _U09.9_ is also an additional diagnosis, and should only be assigned alongside a separate main diagnosis. For more information and current guidelines regarding diagnoses used for conditions related to a history of COVID-19, see [this webpage](https://www.socialstyrelsen.se/utveckla-verksamhet/e-halsa/klassificering-och-koder/icd-10/) from The Swedish Board of Health and Welfare. @@ -113,28 +113,32 @@ The maps below show the number of people that received the diagnoses of interest #### Diagnosis U09.9 -The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the *U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified* diagnosis. In particular, the values in the table represent the amount of individuals that received the *U09.9* diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above). +The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the _U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified_ diagnosis. In particular, the values in the table represent the amount of individuals that received the _U09.9_ diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above).
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/accompdiag_table.json" height="527px" >}}
-*Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once* +_Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once_ **Code used to produce table:** [Script to produce table (English)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Script to produce table (Swedish)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). ### Contacts with healthcare -The below plot shows the number of times that patients given the diagnoses of interest have sought healthcare. Note that while the weekly data below starts from week 21 of 2020, some diagnosis codes (*U08.9* and *U09.9*) were not used until after this date (see information above). It is important to note that the data is not complete, given that data from some healthcare providers (e.g. general practitioners) are not reported to the Patient Registry due to privacy concerns. Where data is reported to registers, data from the most recent weeks should be considered preliminary, as the registers are not instantaneously updated. A delay in reporting data to registers may be particularly evident during traditional holiday periods, including over the summer months. +The below plot shows the number of times that patients given the diagnoses of interest have sought healthcare. Note that while the weekly data below starts from week 21 of 2020, some diagnosis codes (_U08.9_ and _U09.9_) were not used until after this date (see information above). It is important to note that the data is not complete, given that data from some healthcare providers (e.g. general practitioners) are not reported to the Patient Registry due to privacy concerns. Where data is reported to registers, data from the most recent weeks should be considered preliminary, as the registers are not instantaneously updated. A delay in reporting data to registers may be particularly evident during traditional holiday periods, including over the summer months.
- Scroll the plot sideways to view all data. + Rotating your phone may improve graph layout
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="300px" >}}
+ + **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py). ### Contacts with healthcare, divided by patient sex @@ -144,7 +148,7 @@ The below plots show the number of times that patients given one of the diagnose #### Diagnosis U09.9
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@@ -156,7 +160,7 @@ The below plots show the number of times that patients given one of the diagnose #### Diagnosis Z86.1A/U08.9
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@@ -167,7 +171,7 @@ The below plots show the number of times that patients given one of the diagnose ## Ongoing research projects -Below is a manually curated overview of research projects on *Post COVID-19 condition* that are funded by major funding agencies in Sweden. As it is manually curated, the list may not be exhaustive and new projects will be added as soon as possible. If you think that your project should be listed here but isn’t, please [get in touch with us](/contact/). For a list of all research projects funded by major funding agencies in Sweden [see this section of the portal](/projects/ongoing/). +Below is a manually curated overview of research projects on _Post COVID-19 condition_ that are funded by major funding agencies in Sweden. As it is manually curated, the list may not be exhaustive and new projects will be added as soon as possible. If you think that your project should be listed here but isn’t, please [get in touch with us](/contact/). For a list of all research projects funded by major funding agencies in Sweden [see this section of the portal](/projects/ongoing/). {{< display_funded_projects filter_variable="post_covid" >}} @@ -175,7 +179,7 @@ Below is a manually curated overview of research projects on *Post COVID-19 cond ## Publications -Below is a list of pre-prints and published scientific journal articles on *Post COVID-19 condition* involving at least one author affiliated with a Swedish university or research institute. Note that this list is based on a manually curated database and, as such, may not be exhaustive. If you think that a publication should be listed here but isn’t, or feel that information about a publication needs correction, please [get in touch with us](/contact/). For a list of all publications on COVID-19 and SARS-CoV-2 involving at least one author affiliated with a Swedish univerisity or research institute [see this section of the portal](/publications/). +Below is a list of pre-prints and published scientific journal articles on _Post COVID-19 condition_ involving at least one author affiliated with a Swedish university or research institute. Note that this list is based on a manually curated database and, as such, may not be exhaustive. If you think that a publication should be listed here but isn’t, or feel that information about a publication needs correction, please [get in touch with us](/contact/). For a list of all publications on COVID-19 and SARS-CoV-2 involving at least one author affiliated with a Swedish univerisity or research institute [see this section of the portal](/publications/). {{< postcovid_publications >}} @@ -185,18 +189,18 @@ Below is a list of pre-prints and published scientific journal articles on *Post ### Post COVID-19 condition -Individuals with *Post COVID-19 condition* exhibit symptoms lasting at least two months after the acute phase of COVID-19 infection ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). The particular symptoms exhibited vary between patients, as does the duration and severity of symptoms. In general though, symptoms are usually debilitating and may include persistent fatigue, myalgia (muscle aches and pains), and autonomic dysregulation, among others. Some individuals with *Post COVID-19 condition* exhibit the same symptoms as they did during the acute infection stage of COVID-19, while others with *Post COVID-19 condition* exhibit new symptoms following the acute infection phase ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis *et al.*, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido *et al.*, 2020](https://doi.org/10.1016/j.cmi.2020.07.028). +Individuals with _Post COVID-19 condition_ exhibit symptoms lasting at least two months after the acute phase of COVID-19 infection ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). The particular symptoms exhibited vary between patients, as does the duration and severity of symptoms. In general though, symptoms are usually debilitating and may include persistent fatigue, myalgia (muscle aches and pains), and autonomic dysregulation, among others. Some individuals with _Post COVID-19 condition_ exhibit the same symptoms as they did during the acute infection stage of COVID-19, while others with _Post COVID-19 condition_ exhibit new symptoms following the acute infection phase ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis _et al._, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido _et al._, 2020](https://doi.org/10.1016/j.cmi.2020.07.028). ### No consensus on definition -In September 2020, WHO established the [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) code for *Post COVID-19 condition* *U09.9 - Post COVID-19 condition, unspecified*. A [WHO report from April 2021](https://www.who.int/publications/i/item/9789240025035) stated that there is a real need to characterise and formally define *Post COVID-19 condition* in order to increase understanding about the condition and facilitate diagnosis. However, to date, *Post COVID-19 condition* still lacks a universal definition with regard to the symptoms and disease duration necessary for diagnosis. Consequently, governmental agencies and research institutes in different countries use their own definitions and terms. Related diagnoses established by WHO are *U08.9 - Personal history of COVID-19, unspecified* and *U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified*. The *U08.9* diagnosis is used to describe an earlier episode of COVID-19 (either confirmed or probable) that influenced the individual's health status, though they no longer have COVID-19. The code *U10.9* is used to describe a temporal association with COVID-19: cytokine storm, Kawasaki-like syndrome, multisystem inflammatory syndrome in children (MIS-C), and paediatric inflammatory multisystem syndrome (PIMS). +In September 2020, WHO established the [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) code for _Post COVID-19 condition_ _U09.9 - Post COVID-19 condition, unspecified_. A [WHO report from April 2021](https://www.who.int/publications/i/item/9789240025035) stated that there is a real need to characterise and formally define _Post COVID-19 condition_ in order to increase understanding about the condition and facilitate diagnosis. However, to date, _Post COVID-19 condition_ still lacks a universal definition with regard to the symptoms and disease duration necessary for diagnosis. Consequently, governmental agencies and research institutes in different countries use their own definitions and terms. Related diagnoses established by WHO are _U08.9 - Personal history of COVID-19, unspecified_ and _U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified_. The _U08.9_ diagnosis is used to describe an earlier episode of COVID-19 (either confirmed or probable) that influenced the individual's health status, though they no longer have COVID-19. The code _U10.9_ is used to describe a temporal association with COVID-19: cytokine storm, Kawasaki-like syndrome, multisystem inflammatory syndrome in children (MIS-C), and paediatric inflammatory multisystem syndrome (PIMS). -In England, the [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) has [defined](https://www.nice.org.uk/guidance/ng188/chapter/context) *Post-COVID-19 syndrome* as "...signs and symptoms that develop during or after an infection consistent with COVID‑19, continue for more than 12 weeks, and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body...". NICE states that *Post‑COVID‑19 syndrome* can be considered as a diagnosis during the first three months after the acute infection phase of COVID-19 while healthcare assessments are completed to determine whether the symptoms could be explained by an alternative disease. Further, NICE [defines](https://www.nice.org.uk/guidance/ng188/chapter/context) the term *Long COVID* as "...signs and symptoms that continue or develop after acute COVID‑19. It includes both ongoing symptomatic COVID‑19 (from 4 to 12 weeks) and post‑COVID‑19 syndrome (12 weeks or more)...”. In December 2020, NICE, in partnership with the Scottish Intercollegiate Guidelines Network and the Royal College of General Practitioners, published a [guideline for health and care practitioners](https://www.nice.org.uk/guidance/NG188) (NG188) on identifying, assessing, and managing the long-term effects of COVID-19. +In England, the [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) has [defined](https://www.nice.org.uk/guidance/ng188/chapter/context) _Post-COVID-19 syndrome_ as "...signs and symptoms that develop during or after an infection consistent with COVID‑19, continue for more than 12 weeks, and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body...". NICE states that _Post‑COVID‑19 syndrome_ can be considered as a diagnosis during the first three months after the acute infection phase of COVID-19 while healthcare assessments are completed to determine whether the symptoms could be explained by an alternative disease. Further, NICE [defines](https://www.nice.org.uk/guidance/ng188/chapter/context) the term _Long COVID_ as "...signs and symptoms that continue or develop after acute COVID‑19. It includes both ongoing symptomatic COVID‑19 (from 4 to 12 weeks) and post‑COVID‑19 syndrome (12 weeks or more)...”. In December 2020, NICE, in partnership with the Scottish Intercollegiate Guidelines Network and the Royal College of General Practitioners, published a [guideline for health and care practitioners](https://www.nice.org.uk/guidance/NG188) (NG188) on identifying, assessing, and managing the long-term effects of COVID-19. -In the USA, The [Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) defines *Post-COVID conditions* as "...a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19...". The CDC distinguishes between *Long COVID*, *Multiorgan Effects of COVID-19*, and *Effects of COVID-19 Treatment or Hospitalisation*. For example, they define *Long COVID* as "a range of symptoms that can last weeks or months after first being infected with the virus that causes COVID-19 or can appear weeks after infection.". For information on *Post-COVID conditions* from the CDC, [see this page](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). The [National Institutes of Health (NIH)](https://www.nih.gov) in the USA uses the term *Post-Acute Sequelae of SARS-CoV-2 infection* (PASC) to refer to the effects of COVID-19 after the initial stages of infection. In February 2021, The NIH [launched a research initiative](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) to identify the causes of PASC and, ultimately, to find methods for prevention and treatments for individuals that don’t recover fully over a period of a few weeks following the acute infection phase of COVID-19. +In the USA, The [Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) defines _Post-COVID conditions_ as "...a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19...". The CDC distinguishes between _Long COVID_, _Multiorgan Effects of COVID-19_, and _Effects of COVID-19 Treatment or Hospitalisation_. For example, they define _Long COVID_ as "a range of symptoms that can last weeks or months after first being infected with the virus that causes COVID-19 or can appear weeks after infection.". For information on _Post-COVID conditions_ from the CDC, [see this page](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). The [National Institutes of Health (NIH)](https://www.nih.gov) in the USA uses the term _Post-Acute Sequelae of SARS-CoV-2 infection_ (PASC) to refer to the effects of COVID-19 after the initial stages of infection. In February 2021, The NIH [launched a research initiative](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) to identify the causes of PASC and, ultimately, to find methods for prevention and treatments for individuals that don’t recover fully over a period of a few weeks following the acute infection phase of COVID-19. -The [Swedish Board of Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/) describes patients with *Postcovid* as individuals exhibiting prolonged symptoms, or experiencing new relevant symptoms after the acute phase of COVID-19 infection. While the severity of symptoms will diminish over time for most individuals (such individuals do not need assistance from healthcare during the recovery), some individuals experience symptoms that are debilitating and need treatment, rehabilitation, and other follow-up medical care. In April 2021, Socialstyrelsen [published a report dedicated to Postcovid](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf) that defines the condition and provides recommendations. +The [Swedish Board of Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/) describes patients with _Postcovid_ as individuals exhibiting prolonged symptoms, or experiencing new relevant symptoms after the acute phase of COVID-19 infection. While the severity of symptoms will diminish over time for most individuals (such individuals do not need assistance from healthcare during the recovery), some individuals experience symptoms that are debilitating and need treatment, rehabilitation, and other follow-up medical care. In April 2021, Socialstyrelsen [published a report dedicated to Postcovid](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf) that defines the condition and provides recommendations. ### Research efforts -A large number of research articles, case reports, and reviews focused on *Post COVID-19 condition* have been published over the last year (e.g. [Dani *et al.* (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre *et al.* (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil *et al.* (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin *et al.* (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). The primary aims of these studies are to identify factors that could be used to predict when *Post COVID-19 condition* is more likely to develop, the underlying causes of the condition, and potential treatments. A recently published study by [Sudre and colleagues](https://doi.org/10.1038/s41591-021-01292-y) proposed a prediction model to identify individuals at risk of *Post COVID-19 condition* using data from the [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/), where participants self-reported their symptoms in an app on their mobile devices. The results indicated that individuals experiencing more than five symptoms during the first week of illness were more likely to develop *Post COVID-19 condition* (odds ratio = 3.53 (2.76–4.50)). In addition, the study showed that the development of *Post COVID-19 condition* was more likely in females, and that the risk also rose with increasing age and body mass index. The researchers behind the study propose that their model could be used to identify individuals at risk of developing *Post COVID-19 condition*. This could inform trials of preventative or treatment methods, and aid in the planning of education and rehabilitation services. +A large number of research articles, case reports, and reviews focused on _Post COVID-19 condition_ have been published over the last year (e.g. [Dani _et al._ (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre _et al._ (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil _et al._ (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin _et al._ (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). The primary aims of these studies are to identify factors that could be used to predict when _Post COVID-19 condition_ is more likely to develop, the underlying causes of the condition, and potential treatments. A recently published study by [Sudre and colleagues](https://doi.org/10.1038/s41591-021-01292-y) proposed a prediction model to identify individuals at risk of _Post COVID-19 condition_ using data from the [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/), where participants self-reported their symptoms in an app on their mobile devices. The results indicated that individuals experiencing more than five symptoms during the first week of illness were more likely to develop _Post COVID-19 condition_ (odds ratio = 3.53 (2.76–4.50)). In addition, the study showed that the development of _Post COVID-19 condition_ was more likely in females, and that the risk also rose with increasing age and body mass index. The researchers behind the study propose that their model could be used to identify individuals at risk of developing _Post COVID-19 condition_. This could inform trials of preventative or treatment methods, and aid in the planning of education and rehabilitation services. diff --git a/content/english/dashboards/vaccines.md b/content/english/dashboards/vaccines.md index 843fffe63..9a7125dfc 100644 --- a/content/english/dashboards/vaccines.md +++ b/content/english/dashboards/vaccines.md @@ -5,11 +5,11 @@ banner: /dashboard_thumbs/vaccines.jpg toc: true plotly: true menu: - dashboard_menu: - identifier: vaccines - name: "Vaccine administration: COVID-19" + dashboard_menu: + identifier: vaccines + name: "Vaccine administration: COVID-19" aliases: - - /data_types/health_data/vaccines/ + - /data_types/health_data/vaccines/ dashboards_topics: [COVID-19, Infectious diseases] --- @@ -77,7 +77,7 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/ **Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). -To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. +To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. ### Administration of vaccinations over time diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md index daa082294..3bab5ba33 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md @@ -2,7 +2,7 @@ title: Amount of SARS-CoV-2 in wastewater (GU) plotly: true aliases: - - /dashboards/wastewater/covid_quant_gu/ + - /dashboards/wastewater/covid_quant_gu/ ---
@@ -18,13 +18,13 @@ The data and visualisation on this page are usually updated weekly. ## Wastewater collection sites -Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/). +Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/). ## Visualisations
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-*The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023).* +_The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023)._ +
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}
@@ -72,7 +76,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p **Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\ **Contact:** -**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501). +**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501). **How to cite method:** Saguti, F., Magnil, E., Enache, L., Churqui, M.P., Johansson, A., Lumley, D., Davidsson, F., Dotevall, L., Mattsson, A., Trybala, E., Lagging, M., Lindh, M., Gisslen, M., Brezicka, T., Nystrom, K. and Norder, H. (2021). Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. [https://doi.org/10.1016/j.watres.2020.116620](https://doi.org/10.1016/j.watres.2020.116620). @@ -83,7 +87,7 @@ Wang, H., Churqui, M.P., Tunovic, T., Enache, L., Johansson, A., Karmander, A., Samples of wastewater were collected using a fixed-site sampler that collected 30ml per 10,000m3 of the incoming wastewater. For the purposes of analysis, seven samples (each representing a 24 hour period) were pooled to create a weekly sample. The weekly sample, which consisted of 1.5-15l of wastewater (depending on the flow) was sent to the Clinical Microbiology Laboratory at Sahlgrenska University Hospital for analysis. Analyses were conducted on the Monday after the sample was collected. -At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti *et al.*, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti *et al.* (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome. +At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti _et al._, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti _et al._ (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome.
diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md index 7efec25d3..dd9f04558 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md @@ -65,6 +65,10 @@ Please also note that although the same methods are used for all cities shown on
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_stockholm.json" height="550px" >}}
@@ -76,7 +80,7 @@ Please also note that although the same methods are used for all cities shown on
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- Scroll the plot sideways to view all data. + Rotating your phone may improve graph layout
diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index 2bdc3b4eb..dafa5969f 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -65,6 +65,10 @@ Please note that although the same methods are used for all cities shown on this
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}
@@ -101,7 +105,7 @@ For most cities represented on this page, raw, untreated wastewater samples that The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega). -Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39). +Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson *et al.* (2022)](https://www.mdpi.com/2076-3298/9/3/39). The data in the graph and datafile represent the ratio of the copy numbers measured by the Flu SC2 Multiplex Assay and PMMoV-assays, multiplied by 1000. As the Flu SC2 Multiplex Assay provides a proxy for SARS-CoV-2 virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of COVID-19 infections in the population of the wastewater catchment area. To align the data generated by the current method with the data generated by methods and quantification assays used earlier, older data has been transformed using conversion factors. The conversion factors are estimated based on common alignment periods when old and new methods are used in parallel. diff --git a/content/english/dashboards/wastewater/enteric_quantification/_index.md b/content/english/dashboards/wastewater/enteric_quantification/_index.md index 675acff03..bc188685c 100644 --- a/content/english/dashboards/wastewater/enteric_quantification/_index.md +++ b/content/english/dashboards/wastewater/enteric_quantification/_index.md @@ -34,6 +34,10 @@ The wastewater samples for virus analysis are collected at Ryaverket's wastewate Please see [the section with summary information about the viruses](#basic-virus-information) for more information on each of the viruses for which data is being collected. +
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/enteric_graph_gu.json" height="550px" >}}
diff --git a/content/english/dashboards/wastewater/influenza_quantification/_index.md b/content/english/dashboards/wastewater/influenza_quantification/_index.md index 8197bd8ae..7cce7c7c6 100644 --- a/content/english/dashboards/wastewater/influenza_quantification/_index.md +++ b/content/english/dashboards/wastewater/influenza_quantification/_index.md @@ -32,6 +32,10 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip ### Influenza A +
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infA.json" height="600px" >}}
@@ -40,6 +44,10 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip ### Influenza B +
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infB.json" height="600px" >}}
diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md index 08452dd7f..3e065f5fc 100644 --- a/content/svenska/dashboards/post_covid.md +++ b/content/svenska/dashboards/post_covid.md @@ -5,22 +5,22 @@ banner: /dashboard_thumbs/postcovid.jpg toc: true plotly: true menu: - dashboard_menu: - identifier: post_covid - name: Postcovid + dashboard_menu: + identifier: post_covid + name: Postcovid aliases: - - /sv/data_types/health_data/post_covid/ + - /sv/data_types/health_data/post_covid/ ---
Vänligen notera att graferna endast har engelska figurtexter.
Sedan början av 2020 har covid-19 pandemin utmanat hälso- och sjukvården och förändrat samhällen runt om i världen. Forskning och empiri har visat att covid-19 under den akuta infektionen kan ha olika svårighetsgrad, från mild till moderat till svår. De flesta individer som insjuknar i Covid-19, oavsett sjukdomens svårighetsgrad under den akuta infektionen, återhämtar sig och uppvisar inga kvarstående symptom efter återhämtningen. Vissa patienter uppvisar dock, efter den akuta infektionen, kvarstående eller sena symptom efter covid-19. Besvär och symtom som rapporterats är exempelvis svår trötthet, sämre hälsa, ledvärk, hjärntrötthet (svårighet att koncentrera sig på vissa uppgifter under längre tid) och hjärtklappning ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8), [Marx, 2021](https://doi.org/10.1038/s41592-021-01145-z)). -I vetenskaplig litteratur och media används ett flertal olika begrepp för att beskriva kvarstående eller sena symtom efter en akut covid-19 infektion exempelvis långtidscovid, post-akut covid-19, långtidssjuka vid covid-19 och postcovid. I enlighet med Socialstyrelsen så använder vi på denna sida definitionen *postcovid* för kvarstående eller sena symptom efter covid-19. Se *[bakgrundsinformationen](#background)* nedan för mer information om klassificering och den forskning som bedrivs inom ämnet. +I vetenskaplig litteratur och media används ett flertal olika begrepp för att beskriva kvarstående eller sena symtom efter en akut covid-19 infektion exempelvis långtidscovid, post-akut covid-19, långtidssjuka vid covid-19 och postcovid. I enlighet med Socialstyrelsen så använder vi på denna sida definitionen _postcovid_ för kvarstående eller sena symptom efter covid-19. Se _[bakgrundsinformationen](#background)_ nedan för mer information om klassificering och den forskning som bedrivs inom ämnet. -Kön (kvinna), hög ålder och nedsatt allmän hälsa är exempel på faktorer som har visat sig vara förknippade med långvariga symtom efter en Covid-19-infektion ([Sudre *et al.*, 2021](https://www.nature.com/articles/s41591-021-01292-y)). Även om listan över symtom förknippade med postcovid är relativt allmän, påverkar symtomen ofta patienternas livskvalitet. Medan de flesta studier hittills har varit beskrivande, undersöker flera nya studier t.ex. samsjukligheter mellan postcovid och annan kronisk sjukdom respektive med daglig medicinering. Studier tyder på att samsjukligheter kan förutsäga risken för postcovid ([Važgėlienė *et al.*, 2022](https://www.mdpi.com/2077-0383/11/21/6278)). +Kön (kvinna), hög ålder och nedsatt allmän hälsa är exempel på faktorer som har visat sig vara förknippade med långvariga symtom efter en Covid-19-infektion ([Sudre _et al._, 2021](https://www.nature.com/articles/s41591-021-01292-y)). Även om listan över symtom förknippade med postcovid är relativt allmän, påverkar symtomen ofta patienternas livskvalitet. Medan de flesta studier hittills har varit beskrivande, undersöker flera nya studier t.ex. samsjukligheter mellan postcovid och annan kronisk sjukdom respektive med daglig medicinering. Studier tyder på att samsjukligheter kan förutsäga risken för postcovid ([Važgėlienė _et al._, 2022](https://www.mdpi.com/2077-0383/11/21/6278)). -På denna sida kan du hitta visualiseringar av statistik relaterade till *postcovid* baserat på data från [Socialstyrelsen](https://www.socialstyrelsen.se), en översikt över forskningsprojekt inom området postcovid som för närvarande genomförs i Sverige och vetenskapliga publikationer. +På denna sida kan du hitta visualiseringar av statistik relaterade till _postcovid_ baserat på data från [Socialstyrelsen](https://www.socialstyrelsen.se), en översikt över forskningsprojekt inom området postcovid som för närvarande genomförs i Sverige och vetenskapliga publikationer. För mer information om postcovid i Sverige, se följande [avsnitt](https://www.socialstyrelsen.se/coronavirus-covid-19/socialstyrelsens-roll-och-uppdrag/postcovid/) på Socialstyrelsens webbplats och rapporten Postcovid– kvarstående eller sena symtom efter covid-19. Stöd till [beslutsfattare och personal i hälso- och sjukvården (del 2) (publicerad april 2021)](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf). @@ -38,11 +38,11 @@ All källkod som används för att göra visualiseringarna på denna sidan finns ## Statistik om postcovid i Sverige -De första patienterna som uppvisade kvarstående långvariga symptom efter covid-19-infektion kom i kontakt med sjukvården våren 2020. Flera diagnoser och diagnoskoder har sedan dess använts inom sjukvården. Den 1 juni 2020 började Socialstyrelsen använda diagnosen *Z86.1A (Covid-19 i den egna sjukhistorien)*. *Diagnoskoden U09.9 (ICD-10-SE) Postinfektiöst tillstånd efter covid-19*, infördes 16 oktober 2020 och kompletterade och ersatte delvis koden *Z86.1A*. Från 1 januari 2021 upphörde diagnoskoden *Z86.1A* att gälla och ersattes med diagnoskoden *U08.9*, Covid-19 i den egna sjukhistorien, enligt [WHO (Världshälsoorganisationens)](https://www.who.int) riktlinjer. +De första patienterna som uppvisade kvarstående långvariga symptom efter covid-19-infektion kom i kontakt med sjukvården våren 2020. Flera diagnoser och diagnoskoder har sedan dess använts inom sjukvården. Den 1 juni 2020 började Socialstyrelsen använda diagnosen _Z86.1A (Covid-19 i den egna sjukhistorien)_. _Diagnoskoden U09.9 (ICD-10-SE) Postinfektiöst tillstånd efter covid-19_, infördes 16 oktober 2020 och kompletterade och ersatte delvis koden _Z86.1A_. Från 1 januari 2021 upphörde diagnoskoden _Z86.1A_ att gälla och ersattes med diagnoskoden _U08.9_, Covid-19 i den egna sjukhistorien, enligt [WHO (Världshälsoorganisationens)](https://www.who.int) riktlinjer. -Den senare diagnosen *U08.9* rekommenderas för en person som får vård av en annan sjukdom eller skada men där det anses vara relevant (av viss betydelse) att denna person tidigare har haft covid-19. Denna diagnos bör endast ges efter att personen inte längre anses ha covid-19. Denna diagnos är bara en ytterligare diagnos (bidiagnos) och bör endast tilldelas vid sidan av en huvuddiagnos, det kan inte vara själva huvuddiagnosen. +Den senare diagnosen _U08.9_ rekommenderas för en person som får vård av en annan sjukdom eller skada men där det anses vara relevant (av viss betydelse) att denna person tidigare har haft covid-19. Denna diagnos bör endast ges efter att personen inte längre anses ha covid-19. Denna diagnos är bara en ytterligare diagnos (bidiagnos) och bör endast tilldelas vid sidan av en huvuddiagnos, det kan inte vara själva huvuddiagnosen. -Diagnosen för *postcovid* som Socialstyrelsen rekommenderar är *U09.9 (ICD-10-SE)-Postinfektiöst tillstånd efter covid-19*. Denna diagnos bör endast ges efter att personen inte längre anses ha en pågående covid-19 infektion. Koden används för tillstånd som kvarstående eller sena besvär efter den akuta infektionen har gått över. Genom att använda termen *postcovid* skiljer sjukvården på en pågående infektion (covid-19) och ett efterföljande hälsotillstånd utan infektion (*postcovid*). +Diagnosen för _postcovid_ som Socialstyrelsen rekommenderar är _U09.9 (ICD-10-SE)-Postinfektiöst tillstånd efter covid-19_. Denna diagnos bör endast ges efter att personen inte längre anses ha en pågående covid-19 infektion. Koden används för tillstånd som kvarstående eller sena besvär efter den akuta infektionen har gått över. Genom att använda termen _postcovid_ skiljer sjukvården på en pågående infektion (covid-19) och ett efterföljande hälsotillstånd utan infektion (_postcovid_). För mer information och aktuella riktlinjer för diagnoser som används för tillstånd relaterade till covid-19, se [denna sida](https://www.socialstyrelsen.se/utveckla-verksamhet/e-halsa/klassificering-och-koder/icd-10/) på Socialstyrelsens webbplats. @@ -116,23 +116,19 @@ Kartorna nedan visar antal individer som fått diagnoskoderna av intresse per l #### Diagnoskod U09.9 -Denna tabell visar de vanligaste diagnosgrupper som har rapporterats tillsammans med diagnoskoden *U09.9 (ICD-10-SE)-Post-infektiöst tillstånd efter covid-19 (Postcovid)*. Siffrorna och procentsatserna nedan visar hur många individer som fått diagnosen U09.9 och samtidigt har diagnoser från nedanstående diagnosgrupper. Data nedan återspeglar perioden från och med den 16 oktober 2020 och fram till den senaste uppdateringen (se ovan). +Denna tabell visar de vanligaste diagnosgrupper som har rapporterats tillsammans med diagnoskoden _U09.9 (ICD-10-SE)-Post-infektiöst tillstånd efter covid-19 (Postcovid)_. Siffrorna och procentsatserna nedan visar hur många individer som fått diagnosen U09.9 och samtidigt har diagnoser från nedanstående diagnosgrupper. Data nedan återspeglar perioden från och med den 16 oktober 2020 och fram till den senaste uppdateringen (se ovan).
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/accompdiag_table_swe.json" height="500px" >}}
-*Observera att en individ kan ha mer än en diagnosgrupp som rapporteras tillsammans med U09.9 Postinfektiöst tillstånd efter covid-19 (Postcovid). Om en individ har samma besvär vid flera vårdtillfällen/läkarbesök räknas diagnosen bara en gång.* +_Observera att en individ kan ha mer än en diagnosgrupp som rapporteras tillsammans med U09.9 Postinfektiöst tillstånd efter covid-19 (Postcovid). Om en individ har samma besvär vid flera vårdtillfällen/läkarbesök räknas diagnosen bara en gång._ **Källkod som används för att skapa tabellen:** [Källkod som används för att skapa tabellen (engelska)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Källkod som används för att skapa tabellen (svenska)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). ### Vårdkontakter -Denna graf visar antal vårdkontakter för patienter med de av de tre diagnoskoderna. Observera att grafen börjar från vecka 22 2020, men att diagnoskoderna *U08.9* och *U09.9* börjar användas först vid senare tillfälle (se information ovan). Varje vårdkontakt efter det att patienten fått diagnosen räknas in i dessa data. Data visas per vecka. Observera att dessa uppgifter inte är fullständiga eftersom information om antalet vårdkontakter från vissa veckor inte är tillgängliga på grund av patientsekretessen. Notera att uppgifterna inte är fullständiga, eftersom data från vissa vårdgivare (t.ex. husläkare) inte rapporteras in till Patientregistret på grund av patientsekretessen. Inrapporterade data från de senaste veckorna är preliminära, eftersom uppgifterna inte uppdateras direkt. Fördröjningen att rapportera in uppgifter kan vara längre under traditionella semesterperioder, som under sommaren. - -
- Skrolla grafen horisontellt för att se alla data -
+Denna graf visar antal vårdkontakter för patienter med de av de tre diagnoskoderna. Observera att grafen börjar från vecka 22 2020, men att diagnoskoderna _U08.9_ och _U09.9_ börjar användas först vid senare tillfälle (se information ovan). Varje vårdkontakt efter det att patienten fått diagnosen räknas in i dessa data. Data visas per vecka. Observera att dessa uppgifter inte är fullständiga eftersom information om antalet vårdkontakter från vissa veckor inte är tillgängliga på grund av patientsekretessen. Notera att uppgifterna inte är fullständiga, eftersom data från vissa vårdgivare (t.ex. husläkare) inte rapporteras in till Patientregistret på grund av patientsekretessen. Inrapporterade data från de senaste veckorna är preliminära, eftersom uppgifterna inte uppdateras direkt. Fördröjningen att rapportera in uppgifter kan vara längre under traditionella semesterperioder, som under sommaren.
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}
@@ -146,10 +142,6 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e #### Diagnoskod U09.9 -
- Skrolla grafen horisontellt för att se alla data -
-
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}
@@ -158,10 +150,6 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e #### Diagnoskod Z86.1A/U08.9 -
- Skrolla grafen horisontellt för att se alla data -
-
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}
@@ -188,23 +176,23 @@ Det här avsnittet presenterar en lista över publicerade vetenskapliga artiklar ### Postcovid -I enlighet med Socialstyrelsen så använder vi på denna sida definitionen postcovid för kvarstående eller sena symptom efter covid-19. Patienter med postcovid uppvisar kvarvarande eller sena besvär som varar minst två månader efter den akuta fasen av COVID-19-infektion ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). Besvären och symptomen som patienterna uppvisar varierar, liksom symtomens varaktighet och svårighetsgrad (även om symtomen ofta ger sämre hälsa): svår trötthet, myalgi (muskelsmärta och smärtor) och autonom dysregulering. Vissa personer med postcovid har kvarvarande symptom från det akuta infektionsstadiet, medan andra med postcovid uppvisar nya symptom efter den inledande akuta infektionen ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis *et al.*, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido *et al.*, 2020](https://doi.org/10.1016/j.cmi.2020.07.028)). +I enlighet med Socialstyrelsen så använder vi på denna sida definitionen postcovid för kvarstående eller sena symptom efter covid-19. Patienter med postcovid uppvisar kvarvarande eller sena besvär som varar minst två månader efter den akuta fasen av COVID-19-infektion ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). Besvären och symptomen som patienterna uppvisar varierar, liksom symtomens varaktighet och svårighetsgrad (även om symtomen ofta ger sämre hälsa): svår trötthet, myalgi (muskelsmärta och smärtor) och autonom dysregulering. Vissa personer med postcovid har kvarvarande symptom från det akuta infektionsstadiet, medan andra med postcovid uppvisar nya symptom efter den inledande akuta infektionen ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis _et al._, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido _et al._, 2020](https://doi.org/10.1016/j.cmi.2020.07.028)). ### Definition saknas -I september 2020, inrättade WHO [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) koden för *Post COVID-19 condition - U09.9 - Post COVID-19 condition, unspecified*. En [WHO rapport från april 2021](https://www.who.int/publications/i/item/9789240025035)  beskriver att det finns ett behov av att karakterisera och tidigare definiera tillståndet efter COVID-19 för att öka förståelsen för tillståndet och underlätta diagnosticering. Idag har postcovid ännu inte en universell definition med avseende symptom och sjukdomsvaraktighet vilket behövs för diagnos. Myndigheter och institut i olika länder använder egna definitioner och termer. Relaterade diagnoskoder som upprättats av WHO är *U08.9 - Personal history of COVID-19, unspecified and U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified*. Diagnoskoden *U08.9* används för att beskriva en tidigare covid-19 infektion (bekräftad eller sannolik) som kan påverka individens hälsostatus, även om den akuta infektionen är över. Diagnoskoden *U10.9* används för att beskriva ”...a temporal association with COVID-19: Cytokine storm; Kawasaki-like syndrome; Multisystem Inflammatory Syndrome in Children (MIS-C); Paediatric Inflammatory Multisystem Syndrome (PIMS)...”. +I september 2020, inrättade WHO [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) koden för _Post COVID-19 condition - U09.9 - Post COVID-19 condition, unspecified_. En [WHO rapport från april 2021](https://www.who.int/publications/i/item/9789240025035)  beskriver att det finns ett behov av att karakterisera och tidigare definiera tillståndet efter COVID-19 för att öka förståelsen för tillståndet och underlätta diagnosticering. Idag har postcovid ännu inte en universell definition med avseende symptom och sjukdomsvaraktighet vilket behövs för diagnos. Myndigheter och institut i olika länder använder egna definitioner och termer. Relaterade diagnoskoder som upprättats av WHO är *U08.9 - Personal history of COVID-19, unspecified and U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified*. Diagnoskoden *U08.9* används för att beskriva en tidigare covid-19 infektion (bekräftad eller sannolik) som kan påverka individens hälsostatus, även om den akuta infektionen är över. Diagnoskoden *U10.9* används för att beskriva ”...a temporal association with COVID-19: Cytokine storm; Kawasaki-like syndrome; Multisystem Inflammatory Syndrome in Children (MIS-C); Paediatric Inflammatory Multisystem Syndrome (PIMS)...”. -I England har [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) [definierat](https://www.nice.org.uk/guidance/ng188/chapter/context) *Post-COVID-19 syndrom* som ”…Signs and symptoms that develop during or after an infection consistent with COVID-19, continue for more than 12 weeks and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body…”. NICE säger att Post COVID 19 -syndrom kan betraktas som en diagnos under de tre första månaderna efter akut infektion, medan sjukvården bedömer om patienten kan ha en alternativ underliggande sjukdom som kan förklara symptomen. +I England har [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) [definierat](https://www.nice.org.uk/guidance/ng188/chapter/context) _Post-COVID-19 syndrom_ som ”…Signs and symptoms that develop during or after an infection consistent with COVID-19, continue for more than 12 weeks and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body…”. NICE säger att Post COVID 19 -syndrom kan betraktas som en diagnos under de tre första månaderna efter akut infektion, medan sjukvården bedömer om patienten kan ha en alternativ underliggande sjukdom som kan förklara symptomen. Vidare [definierar](https://www.nice.org.uk/guidance/ng188/chapter/context) NICE termen Long COVID som "... signs and symptoms that continue or develop after acute COVID-19. It includes both ongoing symptomatic COVID-19 (from 4 to 12 weeks) and post-COVID-19 syndrome (12 weeks or more)…". I december 2020 publicerade NICE, i samarbete med Scottish Intercollegiate Guidelines Network och Royal College of General Practitioners, [riktlinjer för vård- och omsorgspersonal](https://www.nice.org.uk/guidance/ng188/chapter/context) (NG188) för att identifiera, bedöma och hantera de långsiktiga effekterna av COVID-19. -[Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) beskriver *Post-COVID conditions* som ”…a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19…”. CDC skiljer mellan Long COVID, Multiorgan Effects of COVID-19 och Effects of COVID-19 Treatment or Hospitalization…”. Ett antal olika termer används för att beskriva olika typer av Post-COVID conditions som long COVID, long-haul COVID, post-acute COVID-19, long-term effects of COVID, eller chronic COVID. För mer information om Post-COVID conditions från CDC, se denna [sida](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). [National Institutes of Health (NIH)](https://www.nih.gov) i USA använder termen Post-Acute Sequelae of SARS-CoV-2-infection (PASC) för att hänvisa till effekterna av COVID-19 efter de första stadierna av infektion. I februari 2021 [lancerade NIH ett forskningsinitiativ](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) för att identifiera orsakerna till PASC och identifiera metoder för förebyggande och behandlingar för individer som inte återhämtar sig helt inom några veckor efter den akuta infektionsfasen. +[Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) beskriver _Post-COVID conditions_ som ”…a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19…”. CDC skiljer mellan Long COVID, Multiorgan Effects of COVID-19 och Effects of COVID-19 Treatment or Hospitalization…”. Ett antal olika termer används för att beskriva olika typer av Post-COVID conditions som long COVID, long-haul COVID, post-acute COVID-19, long-term effects of COVID, eller chronic COVID. För mer information om Post-COVID conditions från CDC, se denna [sida](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). [National Institutes of Health (NIH)](https://www.nih.gov) i USA använder termen Post-Acute Sequelae of SARS-CoV-2-infection (PASC) för att hänvisa till effekterna av COVID-19 efter de första stadierna av infektion. I februari 2021 [lancerade NIH ett forskningsinitiativ](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) för att identifiera orsakerna till PASC och identifiera metoder för förebyggande och behandlingar för individer som inte återhämtar sig helt inom några veckor efter den akuta infektionsfasen. I vetenskapliga publikationer och medias rapportering används flera olika begrepp för att beskriva kvarstående eller sena symtom efter covid-19: långtidscovid, post-akut covid-19, långtidssjuka vid covid-19 och sena effekter av covid-19 är några exempel. Ingen av dessa begrepp har emellertid haft en entydig klinisk definition. I Sverige beskriver Socialstyrelsen postcovid som kvarstående eller sena symptom efter covid-19. Medan besvärens svårighetsgrad minskar över tid för de flesta individer (dessa individer behöver inte hjälp från sjukvården under återhämtningen), upplever vissa individer kvarstående besvär som påverkar deras hälsa och behöver behandling, rehabilitering och uppföljande medicinsk vård. I april 2021 [publicerade Socialstyrelsen en rapport om Postcovid](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf) som definierar tillståndet och ger rekommendationer. ### Aktuell forskning -Ett stort antal vetenskapliga artiklar, fallrapporter och reviews med fokus på postcovid har publicerats under det senaste året (jmfr. [[Dani *et al.* (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre *et al.* (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil *et al.* (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin *et al.* (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). De flesta vetenskapliga artiklar har haft som syfte att identifiera riskfaktorer och faktorer som kan användas för att prediktera individer som kan utveckla postcovid efter den akuta covid-19 infektionen. En nyligen publicerad studie av [Sudre och kollegor](https://doi.org/10.1038/s41591-021-01292-y) har lagt fram en modell för att prediktera individer som riskerar utveckla postcovid utifrån data från [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/). I denna studie självrapporterar deltagarna sina symtom i en app på sin mobiltelefon. Resultaten indikerade att individer som upplevde fler än fem symtom under den första sjukdomsveckan hade högre risk att utveckla kvarstående symptom efter covid-19 (oddskvot = 3,53 (2,76–4,50)). Dessutom visade studien att postcovid var mer sannolikt hos kvinnor och att risken också ökade med ökande ålder och högre BMI. Forskarna bakom studien föreslår att deras prediktionsmodell kan användas för att identifiera individer som riskerar att utveckla postcovid. Dessa resultat kan användas för förebyggande vård och för att utveckla behandlingsmetoder och stöd vid planering av utbildning och rehabilitering. +Ett stort antal vetenskapliga artiklar, fallrapporter och reviews med fokus på postcovid har publicerats under det senaste året (jmfr. [[Dani _et al._ (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre _et al._ (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil _et al._ (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin _et al._ (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). De flesta vetenskapliga artiklar har haft som syfte att identifiera riskfaktorer och faktorer som kan användas för att prediktera individer som kan utveckla postcovid efter den akuta covid-19 infektionen. En nyligen publicerad studie av [Sudre och kollegor](https://doi.org/10.1038/s41591-021-01292-y) har lagt fram en modell för att prediktera individer som riskerar utveckla postcovid utifrån data från [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/). I denna studie självrapporterar deltagarna sina symtom i en app på sin mobiltelefon. Resultaten indikerade att individer som upplevde fler än fem symtom under den första sjukdomsveckan hade högre risk att utveckla kvarstående symptom efter covid-19 (oddskvot = 3,53 (2,76–4,50)). Dessutom visade studien att postcovid var mer sannolikt hos kvinnor och att risken också ökade med ökande ålder och högre BMI. Forskarna bakom studien föreslår att deras prediktionsmodell kan användas för att identifiera individer som riskerar att utveckla postcovid. Dessa resultat kan användas för förebyggande vård och för att utveckla behandlingsmetoder och stöd vid planering av utbildning och rehabilitering. diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md index 4e21a5951..38d26ed96 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md @@ -2,7 +2,7 @@ title: Mängd SARS-COV-2 i avloppsvatten (GU) plotly: true aliases: - - /sv/dashboards/wastewater/covid_quant_gu/ + - /sv/dashboards/wastewater/covid_quant_gu/ ---
@@ -12,13 +12,13 @@ aliases: ## Introduktion -Detta projekt leds av professor Helene Norder (Göteborgs universitet, GU), i samarbete med anställda vid Göteborgs universitet och Sahlgrenska Universitetssjukhuset (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti och Kristina Nyström). Avloppsvattenprover insamlas av Lucica Enache vid Ryaverkets avloppsreningsverk, Gryaab AB, Göteborg. +Detta projekt leds av professor Helene Norder (Göteborgs universitet, GU), i samarbete med anställda vid Göteborgs universitet och Sahlgrenska Universitetssjukhuset (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti och Kristina Nyström). Avloppsvattenprover insamlas av Lucica Enache vid Ryaverkets avloppsreningsverk, Gryaab AB, Göteborg. Data och visualiseringar på denna sida uppdateras veckovis. ## Insamlingsplatser för avloppsvatten -Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. waste water plant WWTP) i Göteborg. Insamling av avloppsvattenprov startade 10 februari 2020 (vecka 7). Ryaverkets avloppsreningsverk samlar in avloppsvatten från mer än 790,000 invånare samt även från närliggande industrier. Avloppsvatten samlas även in från invånare och industrier inom närliggande områden som exempelvis Ale, Härryda, Kungälv, Lerum, Mölndal och Partille, samt från smältvatten från äldre delar av Göteborg. Mängd avloppsvatten från hushåll ligger på samma nivå över året, men den totala mängden avloppsvatten kan variera över året beroende på väderlek (högre luftfuktighet ger större mängd avloppsvatten). För mer information om uppsamling av avloppsvatten, veckor, volym avloppsvatten och flöde se [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/). +Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. waste water plant WWTP) i Göteborg. Insamling av avloppsvattenprov startade 10 februari 2020 (vecka 7). Ryaverkets avloppsreningsverk samlar in avloppsvatten från mer än 790,000 invånare samt även från närliggande industrier. Avloppsvatten samlas även in från invånare och industrier inom närliggande områden som exempelvis Ale, Härryda, Kungälv, Lerum, Mölndal och Partille, samt från smältvatten från äldre delar av Göteborg. Mängd avloppsvatten från hushåll ligger på samma nivå över året, men den totala mängden avloppsvatten kan variera över året beroende på väderlek (högre luftfuktighet ger större mängd avloppsvatten). För mer information om uppsamling av avloppsvatten, veckor, volym avloppsvatten och flöde se [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/). ## Visualiseringar @@ -53,6 +53,10 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng.
--> +
+ Skrolla grafen horisontellt för att se alla data. +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}
@@ -69,9 +73,9 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. **Kontakt:** -**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\ +**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\ -**För att citera datasetet:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501). +**För att citera datasetet:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501). **För att citera metoden som används:** Saguti, F., Magnil, E., Enache, L., Churqui, M.P., Johansson, A., Lumley, D., Davidsson, F., Dotevall, L., Mattsson, A., Trybala, E., Lagging, M., Lindh, M., Gisslen, M., Brezicka, T., Nystrom, K. and Norder, H. (2021). Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. [https://doi.org/10.1016/j.watres.2020.116620](https://doi.org/10.1016/j.watres.2020.116620). @@ -80,9 +84,9 @@ Wang, H., Churqui, M.P., Tunovic, T., Enache, L., Johansson, A., Karmander, A., ## Metoder -Insamling av avloppsvatten sker genom en fast insamlare som samlar in 30ml avlopps vatten per 10,000m3  av inkommande avloppsvatten. För analys veckovis poolas sju prover (varje avloppsvatten prov representerar insamling under ett dygn). Veckoprovet består av 1.5-15l avloppsvatten (beroende av flödet) som skickas till Klinisk Mikrobiologi vid Sahlgrenska Universitetssjukhuset för analys. Analys sker på måndagen i veckan efter provinsamling. +Insamling av avloppsvatten sker genom en fast insamlare som samlar in 30ml avlopps vatten per 10,000m3  av inkommande avloppsvatten. För analys veckovis poolas sju prover (varje avloppsvatten prov representerar insamling under ett dygn). Veckoprovet består av 1.5-15l avloppsvatten (beroende av flödet) som skickas till Klinisk Mikrobiologi vid Sahlgrenska Universitetssjukhuset för analys. Analys sker på måndagen i veckan efter provinsamling. -På Klinisk Mikrobiologi, koncentreras virusmängd genom en metod utvecklad på laboratoriet till en volym av 2.5ml. Denna metod använder NanoCeram electropositive filter (Argonide, Florida, USA) för att koncentrera prover, följt av ultracentrifugering som sekundär metod för att koncentrera prover ([Saguti *et al.*, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nukleinsyror extraherades därefter från ett 1ml koncentrerat prov med hjälp av QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Realtids-PCR (RT-qPCR) användes för att detektera den RNA-beroende RNA polymerase (RdRP) regionen på SARS-CoV-2. Alla körningar innehöll en positiv kontroll bestående av en seriellt utspädd plasmid (Eurofins Genomics, Ebersberg, Germany). Nukleasfritt vatten används som negativ kontroll. Ct-värden från qPCR användes för att kvantifiera mängd SARS-CoV-2 genom i provet. En detaljerad beskrivning av hur mängd SARS-CoV-2 beräknas finns i [Saguti *et al.* (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). Den relativa virusmängden i avloppsvatten beräknades genom att dela mängd viralt genom i prover med mängd SARS-CoV-2 genom i ingående mängd avloppsvatten vecka 11 (mitten av mars) 2020. Prover från alla följande veckor har innehållit detekterbara SARS-CoV-2 genom. +På Klinisk Mikrobiologi, koncentreras virusmängd genom en metod utvecklad på laboratoriet till en volym av 2.5ml. Denna metod använder NanoCeram electropositive filter (Argonide, Florida, USA) för att koncentrera prover, följt av ultracentrifugering som sekundär metod för att koncentrera prover ([Saguti _et al._, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nukleinsyror extraherades därefter från ett 1ml koncentrerat prov med hjälp av QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Realtids-PCR (RT-qPCR) användes för att detektera den RNA-beroende RNA polymerase (RdRP) regionen på SARS-CoV-2. Alla körningar innehöll en positiv kontroll bestående av en seriellt utspädd plasmid (Eurofins Genomics, Ebersberg, Germany). Nukleasfritt vatten används som negativ kontroll. Ct-värden från qPCR användes för att kvantifiera mängd SARS-CoV-2 genom i provet. En detaljerad beskrivning av hur mängd SARS-CoV-2 beräknas finns i [Saguti _et al._ (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). Den relativa virusmängden i avloppsvatten beräknades genom att dela mängd viralt genom i prover med mängd SARS-CoV-2 genom i ingående mängd avloppsvatten vecka 11 (mitten av mars) 2020. Prover från alla följande veckor har innehållit detekterbara SARS-CoV-2 genom.
From b8b922325b3352bd67ab688b7d0efc9b3ac74c1c Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Fri, 29 Sep 2023 14:44:46 +0200 Subject: [PATCH 2/5] Add notes about phone rotation to Swedish version dashboards --- content/english/dashboards/covid_publications.md | 2 +- content/svenska/dashboards/RECOVAC.md | 8 ++++++++ content/svenska/dashboards/covid_publications.md | 15 ++++++++++----- content/svenska/dashboards/post_covid.md | 12 ++++++++++++ content/svenska/dashboards/vaccines.md | 11 ++++++----- .../covid_quantification/covid_quant_GU.md | 2 +- .../covid_quantification/covid_quant_KTH.md | 6 +++++- .../covid_quantification/covid_quant_SLU.md | 6 +++++- .../wastewater/enteric_quantification/_index.md | 4 ++++ .../wastewater/influenza_quantification/_index.md | 8 ++++++++ 10 files changed, 60 insertions(+), 14 deletions(-) diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md index c322727aa..f07f3acea 100644 --- a/content/english/dashboards/covid_publications.md +++ b/content/english/dashboards/covid_publications.md @@ -19,7 +19,7 @@ The code used to produce the visulations on this page can be found on [GitHub](h ## Number of new publications -This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not. +This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated weekly, though the publications database is not.
Rotating your phone may improve graph layout diff --git a/content/svenska/dashboards/RECOVAC.md b/content/svenska/dashboards/RECOVAC.md index 910bc25b0..b0b203f95 100644 --- a/content/svenska/dashboards/RECOVAC.md +++ b/content/svenska/dashboards/RECOVAC.md @@ -93,6 +93,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the
+
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}
@@ -143,6 +147,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the
+
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}
diff --git a/content/svenska/dashboards/covid_publications.md b/content/svenska/dashboards/covid_publications.md index 3293deaea..3caacd26b 100644 --- a/content/svenska/dashboards/covid_publications.md +++ b/content/svenska/dashboards/covid_publications.md @@ -5,12 +5,13 @@ banner: /dashboard_thumbs/publications.jpg toc: false plotly: true menu: - dashboard_menu: - identifier: covid_19_publications_vis - name: Översikt över COVID-19 publikationer + dashboard_menu: + identifier: covid_19_publications_vis + name: Översikt över COVID-19 publikationer aliases: - - /projects/dashboard/ + - /projects/dashboard/ --- +
En svensk översättning av denna sida kommer inom kort. @@ -22,7 +23,11 @@ The code used to produce the visulations on this page can be found on [GitHub](h ## Number of new publications -This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not. +This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated weekly, though the publications database is not. + +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
{{< publications_per_month >}} diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md index 3e065f5fc..8a7e176b6 100644 --- a/content/svenska/dashboards/post_covid.md +++ b/content/svenska/dashboards/post_covid.md @@ -130,6 +130,10 @@ Denna tabell visar de vanligaste diagnosgrupper som har rapporterats tillsammans Denna graf visar antal vårdkontakter för patienter med de av de tre diagnoskoderna. Observera att grafen börjar från vecka 22 2020, men att diagnoskoderna _U08.9_ och _U09.9_ börjar användas först vid senare tillfälle (se information ovan). Varje vårdkontakt efter det att patienten fått diagnosen räknas in i dessa data. Data visas per vecka. Observera att dessa uppgifter inte är fullständiga eftersom information om antalet vårdkontakter från vissa veckor inte är tillgängliga på grund av patientsekretessen. Notera att uppgifterna inte är fullständiga, eftersom data från vissa vårdgivare (t.ex. husläkare) inte rapporteras in till Patientregistret på grund av patientsekretessen. Inrapporterade data från de senaste veckorna är preliminära, eftersom uppgifterna inte uppdateras direkt. Fördröjningen att rapportera in uppgifter kan vara längre under traditionella semesterperioder, som under sommaren. +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}
@@ -142,6 +146,10 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e #### Diagnoskod U09.9 +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}
@@ -150,6 +158,10 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e #### Diagnoskod Z86.1A/U08.9 +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}
diff --git a/content/svenska/dashboards/vaccines.md b/content/svenska/dashboards/vaccines.md index b1ade3c1d..2d73ed204 100644 --- a/content/svenska/dashboards/vaccines.md +++ b/content/svenska/dashboards/vaccines.md @@ -5,12 +5,13 @@ banner: /dashboard_thumbs/vaccines.jpg toc: true plotly: true menu: - dashboard_menu: - identifier: vaccines - name: Administrering av covid-19 vaccin + dashboard_menu: + identifier: vaccines + name: Administrering av covid-19 vaccin aliases: - - /sv/data_types/health_data/vaccines/ + - /sv/data_types/health_data/vaccines/ --- +
    Uppgifterna på den här sidan uppdateras inte längre vid datakällan. Vi utvärderar för närvarande användningen av andra datakällor för vaccindata. Se vår RECOVAC dashboard för mer information om vaccin effektivitet och säkerhet (denna dashboard är endast tillgänglig på engelska). @@ -75,7 +76,7 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/ **Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). -To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. +To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. ### Administration of vaccinations over time diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md index 38d26ed96..9eb83ba55 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md @@ -54,7 +54,7 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng.
-->
- Skrolla grafen horisontellt för att se alla data. + Att rotera mobiltelefonen kan förbättra grafens layout
diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md index 9dcd6f2aa..c20872a57 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md @@ -64,6 +64,10 @@ Notera också att även om samma metoder används för alla städer som visas p
+
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_stockholm.json" height="550px" >}}
@@ -75,7 +79,7 @@ Notera också att även om samma metoder används för alla städer som visas p
Senast uppdaterad:
- Skrolla grafen horisontellt för att se alla data. + Att rotera mobiltelefonen kan förbättra grafens layout
diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index b6ef33c51..3d053b40a 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -64,6 +64,10 @@ Notera också att även om samma metoder används för alla städer som visas p
+
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}
@@ -100,7 +104,7 @@ För de flesta städer som representeras på den här sidan används flödeskomp Proverna bearbetas enligt standardmetoder. För prover som samlats in fram till och med vecka 18 2021 koncentrerades virala partiklar med hjälp av elektronegativ filtrering ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Från vecka 19 2021 har det virala genomiska materialet istället koncentrerats och extraherats med hjälp av en metod som använder Maxwell RSC Enviro TNA-kitet (Promega). -Absolut kvantifiering av antalet kopior av SARS-CoV-2-genomet utförs med ett One-Step RT-qPCR. Till och med vecka 31 2023 kvantifierades virusgenom med ett [SARS-CoV-2 specifikt N1-test från Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). För att korrigera för variation i population och avloppsvattenflöde kvantifieras förekomsten av pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten. PMMoV kvantifieras med hjälp av en modifierad version av testet i [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV är det vanligaste RNA-viruset i avföring från människa och används för att uppskatta mängden avföring från människa i avloppsvattenprover ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För mer information om hur normaliseringsmetoden utvärderats se [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39). +Absolut kvantifiering av antalet kopior av SARS-CoV-2-genomet utförs med ett One-Step RT-qPCR. Till och med vecka 31 2023 kvantifierades virusgenom med ett [SARS-CoV-2 specifikt N1-test från Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). För att korrigera för variation i population och avloppsvattenflöde kvantifieras förekomsten av pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten. PMMoV kvantifieras med hjälp av en modifierad version av testet i [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV är det vanligaste RNA-viruset i avföring från människa och används för att uppskatta mängden avföring från människa i avloppsvattenprover ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För mer information om hur normaliseringsmetoden utvärderats se [Isaksson *et al.* (2022)](https://www.mdpi.com/2076-3298/9/3/39). Data som presenteras i grafen visar förhållandet mellan det kopieantal som uppmätts med Flu SC2 Multiplex-testet och PMMoV-testet, multiplicerat med 1000. Resultat från Flu SC2 Multiplex-testet är en proxy för mängden SARS-CoV-2 i avloppsvattnet och PMMoV är en proxy för mängden avföring från människa i avloppsvattnet. Detta förhållande kan i sin tur anses vara en proxy för andelen infekterade individer i populationen i avloppsvattnets upptagningsområde. För att kunna jämföra den data som genereras med den nuvarande metoden med data som genererats med tidigare metoder och kvantifieringsanalyser, har äldre data omvandlats med hjälp av omvandlingsfaktorer. Omvandlingsfaktorerna beräknas baserat på jämförelseperioder när gamla och nya metoder använts parallellt. diff --git a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md index 8994099f1..192e8c617 100644 --- a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md +++ b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md @@ -32,6 +32,10 @@ Avloppsvattenprover för virusanalys samlas in vid Ryaverkets avloppsreningsverk Vänligen se [avsnittet med sammanfattande information om virusen](#grundläggande-virusinformation) för mer information om vart och ett av de virus som data samlas in för. +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/enteric_graph_gu.json" height="550px" >}}
diff --git a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md index b8dcd00a3..419c52b7a 100644 --- a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md +++ b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md @@ -32,6 +32,10 @@ SLU-SEEC samlar in och analyserar prover för kvantifiering av nivåerna av infl ### Influensa A +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infA.json" height="600px" >}}
@@ -40,6 +44,10 @@ SLU-SEEC samlar in och analyserar prover för kvantifiering av nivåerna av infl ### Influensa B +
+ Att rotera mobiltelefonen kan förbättra grafens layout +
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infB.json" height="600px" >}}
From 34745ff44c340b1ab180c4402df06441e9569d0e Mon Sep 17 00:00:00 2001 From: LianeHughes Date: Mon, 2 Oct 2023 12:56:00 +0200 Subject: [PATCH 3/5] Update content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md --- .../wastewater/covid_quantification/covid_quant_SLU.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index dafa5969f..30cb7e79a 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -105,7 +105,7 @@ For most cities represented on this page, raw, untreated wastewater samples that The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega). -Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson *et al.* (2022)](https://www.mdpi.com/2076-3298/9/3/39). +Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39). The data in the graph and datafile represent the ratio of the copy numbers measured by the Flu SC2 Multiplex Assay and PMMoV-assays, multiplied by 1000. As the Flu SC2 Multiplex Assay provides a proxy for SARS-CoV-2 virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of COVID-19 infections in the population of the wastewater catchment area. To align the data generated by the current method with the data generated by methods and quantification assays used earlier, older data has been transformed using conversion factors. The conversion factors are estimated based on common alignment periods when old and new methods are used in parallel. From 5f9ee28811875962873c7c16f6faa9111e85bdf6 Mon Sep 17 00:00:00 2001 From: LianeHughes Date: Mon, 2 Oct 2023 12:56:08 +0200 Subject: [PATCH 4/5] Update content/svenska/dashboards/post_covid.md --- content/svenska/dashboards/post_covid.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md index 8a7e176b6..5e71b31dd 100644 --- a/content/svenska/dashboards/post_covid.md +++ b/content/svenska/dashboards/post_covid.md @@ -192,7 +192,7 @@ I enlighet med Socialstyrelsen så använder vi på denna sida definitionen post ### Definition saknas -I september 2020, inrättade WHO [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) koden för _Post COVID-19 condition - U09.9 - Post COVID-19 condition, unspecified_. En [WHO rapport från april 2021](https://www.who.int/publications/i/item/9789240025035)  beskriver att det finns ett behov av att karakterisera och tidigare definiera tillståndet efter COVID-19 för att öka förståelsen för tillståndet och underlätta diagnosticering. Idag har postcovid ännu inte en universell definition med avseende symptom och sjukdomsvaraktighet vilket behövs för diagnos. Myndigheter och institut i olika länder använder egna definitioner och termer. Relaterade diagnoskoder som upprättats av WHO är *U08.9 - Personal history of COVID-19, unspecified and U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified*. Diagnoskoden *U08.9* används för att beskriva en tidigare covid-19 infektion (bekräftad eller sannolik) som kan påverka individens hälsostatus, även om den akuta infektionen är över. Diagnoskoden *U10.9* används för att beskriva ”...a temporal association with COVID-19: Cytokine storm; Kawasaki-like syndrome; Multisystem Inflammatory Syndrome in Children (MIS-C); Paediatric Inflammatory Multisystem Syndrome (PIMS)...”. +I september 2020, inrättade WHO [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) koden för _Post COVID-19 condition - U09.9 - Post COVID-19 condition, unspecified_. En [WHO rapport från april 2021](https://www.who.int/publications/i/item/9789240025035)  beskriver att det finns ett behov av att karakterisera och tidigare definiera tillståndet efter COVID-19 för att öka förståelsen för tillståndet och underlätta diagnosticering. Idag har postcovid ännu inte en universell definition med avseende symptom och sjukdomsvaraktighet vilket behövs för diagnos. Myndigheter och institut i olika länder använder egna definitioner och termer. Relaterade diagnoskoder som upprättats av WHO är _U08.9 - Personal history of COVID-19, unspecified and U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified. Diagnoskoden _U08.9_ används för att beskriva en tidigare covid-19 infektion (bekräftad eller sannolik) som kan påverka individens hälsostatus, även om den akuta infektionen är över. Diagnoskoden _U10.9_ används för att beskriva ”...a temporal association with COVID-19: Cytokine storm; Kawasaki-like syndrome; Multisystem Inflammatory Syndrome in Children (MIS-C); Paediatric Inflammatory Multisystem Syndrome (PIMS)...”. I England har [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) [definierat](https://www.nice.org.uk/guidance/ng188/chapter/context) _Post-COVID-19 syndrom_ som ”…Signs and symptoms that develop during or after an infection consistent with COVID-19, continue for more than 12 weeks and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body…”. NICE säger att Post COVID 19 -syndrom kan betraktas som en diagnos under de tre första månaderna efter akut infektion, medan sjukvården bedömer om patienten kan ha en alternativ underliggande sjukdom som kan förklara symptomen. From 5278121a18c119efc5a5e4978b3683464d3a6170 Mon Sep 17 00:00:00 2001 From: LianeHughes Date: Mon, 2 Oct 2023 12:56:15 +0200 Subject: [PATCH 5/5] Update content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md --- .../wastewater/covid_quantification/covid_quant_SLU.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index 3d053b40a..a086e7c1b 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -104,7 +104,7 @@ För de flesta städer som representeras på den här sidan används flödeskomp Proverna bearbetas enligt standardmetoder. För prover som samlats in fram till och med vecka 18 2021 koncentrerades virala partiklar med hjälp av elektronegativ filtrering ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Från vecka 19 2021 har det virala genomiska materialet istället koncentrerats och extraherats med hjälp av en metod som använder Maxwell RSC Enviro TNA-kitet (Promega). -Absolut kvantifiering av antalet kopior av SARS-CoV-2-genomet utförs med ett One-Step RT-qPCR. Till och med vecka 31 2023 kvantifierades virusgenom med ett [SARS-CoV-2 specifikt N1-test från Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). För att korrigera för variation i population och avloppsvattenflöde kvantifieras förekomsten av pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten. PMMoV kvantifieras med hjälp av en modifierad version av testet i [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV är det vanligaste RNA-viruset i avföring från människa och används för att uppskatta mängden avföring från människa i avloppsvattenprover ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För mer information om hur normaliseringsmetoden utvärderats se [Isaksson *et al.* (2022)](https://www.mdpi.com/2076-3298/9/3/39). +Absolut kvantifiering av antalet kopior av SARS-CoV-2-genomet utförs med ett One-Step RT-qPCR. Till och med vecka 31 2023 kvantifierades virusgenom med ett [SARS-CoV-2 specifikt N1-test från Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). För att korrigera för variation i population och avloppsvattenflöde kvantifieras förekomsten av pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten. PMMoV kvantifieras med hjälp av en modifierad version av testet i [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV är det vanligaste RNA-viruset i avföring från människa och används för att uppskatta mängden avföring från människa i avloppsvattenprover ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För mer information om hur normaliseringsmetoden utvärderats se [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39). Data som presenteras i grafen visar förhållandet mellan det kopieantal som uppmätts med Flu SC2 Multiplex-testet och PMMoV-testet, multiplicerat med 1000. Resultat från Flu SC2 Multiplex-testet är en proxy för mängden SARS-CoV-2 i avloppsvattnet och PMMoV är en proxy för mängden avföring från människa i avloppsvattnet. Detta förhållande kan i sin tur anses vara en proxy för andelen infekterade individer i populationen i avloppsvattnets upptagningsområde. För att kunna jämföra den data som genereras med den nuvarande metoden med data som genererats med tidigare metoder och kvantifieringsanalyser, har äldre data omvandlats med hjälp av omvandlingsfaktorer. Omvandlingsfaktorerna beräknas baserat på jämförelseperioder när gamla och nya metoder använts parallellt.