Merge pull request #995 from ScilifelabDataCentre/update_calls

Update calls

content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -2,9 +2,11 @@
 title: Amount of SARS-CoV-2 in wastewater (SEEC-KTH)
 plotly: true
 aliases:
-    - /dashboards/wastewater/covid_quant_kth/
+  - /dashboards/wastewater/covid_quant_kth/
 ---
 
+<div class="alert alert-info">As of June 2023, the SARS-CoV-2 data will no longer be updated by SEEC-KTH. Data from after June 2023 is <a href="/dashboards/wastewater/covid_quantification/covid_quant_slu/">available from other research groups.</a></div>
+
 <div class="mt-3">
   <a href="/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard</a>
 </div>
@@ -99,9 +101,9 @@ Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali,
 
 ## Methods
 
- To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) 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)). SARS-like virus specific N3-primers ([Lu *et al.*, 2020](https://doi.org/10.3201/eid2608.201246)) with SYBR Green chemistry ([Perez-Zabaleta *et al.*, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)) are used to quantify SARS-CoV-2.
+To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) 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)). SARS-like virus specific N3-primers ([Lu _et al._, 2020](https://doi.org/10.3201/eid2608.201246)) with SYBR Green chemistry ([Perez-Zabaleta _et al._, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)) are used to quantify SARS-CoV-2.
 
-After concentration, filtering, and preparation, the samples are analysed using the qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema *et al.* (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). In some cases, raw wastewater samples were frozen at -20℃, and concentrated wastewater or purified RNA samples were sometimes stored at -80℃ before the next analysis step was carried out. The concentration method initially used by SEEC-KTH was based on one of their earlier studies ([Jafferali *et al.*, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), which compared four different concentration methods. This method was used until week 35 of 2021. After this time, the group began to instead use [the Promega kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) for the concentration step.
+After concentration, filtering, and preparation, the samples are analysed using the qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema _et al._ (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). In some cases, raw wastewater samples were frozen at -20℃, and concentrated wastewater or purified RNA samples were sometimes stored at -80℃ before the next analysis step was carried out. The concentration method initially used by SEEC-KTH was based on one of their earlier studies ([Jafferali _et al._, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), which compared four different concentration methods. This method was used until week 35 of 2021. After this time, the group began to instead use [the Promega kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) for the concentration step.
 
 ## Archived data
 

content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md

@@ -2,7 +2,7 @@
 title: Amount of SARS-CoV-2 in wastewater (SEEC-SLU)
 plotly: true
 aliases:
-    - /dashboards/wastewater/covid_quant_slu/
+  - /dashboards/wastewater/covid_quant_slu/
 ---
 
 <div class="mt-3">
@@ -18,7 +18,7 @@ The data and visualisation on this page are usually updated weekly, typically on
 
 ## Wastewater collection sites
 
-SLU-SEEC collect and analyse samples from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk next to the number of people indicates that the figure is preliminary.  
+SLU-SEEC collect and analyse samples from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk next to the number of people indicates that the figure is preliminary.
 
   <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="775px" >}}</div>
@@ -62,7 +62,7 @@ SLU-SEEC collect and analyse samples from multiple areas. The below table shows
 
 <div class="alert alert-info">Last updated: <span id="last_modified_uppsala"></span></div>
 
-<b>Important note:</b> Historical data for Knivsta, Vaxholm, and Österåker are available in the dataset (linked below). However, they are no longer included in the visualisation.
+<b>Important note:</b> Historical data for Ekerö, Enköping, Knivsta, Tierp, Vaxholm, Älvkarleby, and Österåker are available in the dataset (linked below). However, they are no longer included in the visualisation.
 
 Please note that although the same methods are used for all cities shown on this tab, differences in the wastewater collection systems and populations of different cities might bias direct comparisons between cities.
 
@@ -109,7 +109,7 @@ Please note that although the same methods are used for all cities shown on this
 
 ## Reports from the research group
 
-The group provide reports to summarise their latest findings. The latest report is available [here](https://blobserver.dc.scilifelab.se/blob/Latest_weekly_report_SEEC-SLU) (only available in Swedish).
+The group provide reports to summarise their latest findings. The latest report is available [here](https://blobserver.dc.scilifelab.se/blob/Latest_weekly_report_SEEC-SLU.pdf) (only available in Swedish).
 
 ## Dataset
 
@@ -123,13 +123,13 @@ Székely, A. J., Vargas, J., Mohamed, N., Dafalla, I., Malmberg, M. (2021). Data
 
 **How to cite the method:**
 
-Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. *Environments*, *9*, 39. [https://doi.org/10.3390/environments9030039](https://doi.org/10.3390/environments9030039).
+Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. _Environments_, _9_, 39. [https://doi.org/10.3390/environments9030039](https://doi.org/10.3390/environments9030039).
 
 ## Methods
 
 For most cities represented on this page, raw, untreated wastewater samples that are representative of a single day are collected by flow compensated samplers at the wastewater treatment plants (WWTP). Uppsala is the exception, with all measurements since week 16 of 2021 instead representing 1 week. In Uppsala, samples are collected daily, and then combined flow-proportionally into one composite weekly sample for the purpose of analyses.
 
-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 the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) 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 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 the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) 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 below graph and datafile represent the ratio of the copy numbers measured by the N1 and PMMoV-assays, multiplied by 10<sup>4</sup>. As N1 copy number is 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.
 

content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -2,17 +2,19 @@
 title: Mängd SARS-COV-2 i avloppsvatten (SEEC-KTH)
 plotly: true
 aliases:
-    - /sv/dashboards/wastewater/covid_quant_kth/
+  - /sv/dashboards/wastewater/covid_quant_kth/
 ---
 
+<div class="alert alert-info">Från juni 2023 kommer SARS-COV-2 data från SEEK-KTH inte längre uppdateras. SARS-COV-2 data efter juni 2023 <a href="/sv/dashboards/wastewater/covid_quantification/covid_quant_slu/">finns tillgängligt från andra forskargrupper.</a></div>
+
 <div class="mt-3">
   <a href="/sv/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Gå tillbaka till SARS-CoV-2-kvantifiering inom avloppsvattenbaserad epidemiologi-dashboarden</a>
 </div>
 <br>
 
 ## Introduktion
 
-Projektet leds av professor Zeynep Cetecioglu Gurol med hjälp av Mariel Perez-Zabaleta and Isaac Owusu-Agyeman verksamna vid Kungliga Tekniska högskolan (KTH). Bioinformatikanalyser av avloppsvattendata sker i samarbete med  professor Luisa Hugerth (Uppsala Universitet). Forskarsamarbetet utgör SEEC-KTH. SEEC-KTH är nu en del av [Institutionen för Industriell bioteknologi](https://www.kth.se/dib/department-of-industrial-biotechnology-1.783103) vid KTH. Projektet finansieras nu som en del av SciLifeLab Pandemic Laboratory Preparedness (PLP) program. Mer information om PLP-programmet finns i [resources section](/resources/).
+Projektet leds av professor Zeynep Cetecioglu Gurol med hjälp av Mariel Perez-Zabaleta and Isaac Owusu-Agyeman verksamna vid Kungliga Tekniska högskolan (KTH). Bioinformatikanalyser av avloppsvattendata sker i samarbete med professor Luisa Hugerth (Uppsala Universitet). Forskarsamarbetet utgör SEEC-KTH. SEEC-KTH är nu en del av [Institutionen för Industriell bioteknologi](https://www.kth.se/dib/department-of-industrial-biotechnology-1.783103) vid KTH. Projektet finansieras nu som en del av SciLifeLab Pandemic Laboratory Preparedness (PLP) program. Mer information om PLP-programmet finns i [resources section](/resources/).
 
 Data och visualiseringar på den här sidan uppdateras vanligtvis veckovis, oftast på fredagar. Data bakom dashboarden uppdateras kontinuerligt.
 
@@ -99,9 +101,9 @@ Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali,
 
 ## Metoder
 
-För att korrigera för variation i population och avloppsvattenflöde kvantifierar gruppen förekomsten av viruset Pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten, 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 avloppsvattenproverna ([Symonds *et al.*, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För att kvantifiera mängd SARS-CoV-2 används SARS-specifika N3-primers ([Lu *et al.*, 2020](https://doi.org/10.3201/eid2608.201246)) och mätningen görs med metoden RT-qPCR med SYBR Green-kemi ([Perez-Zabaleta *et al.*, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)).
+För att korrigera för variation i population och avloppsvattenflöde kvantifierar gruppen förekomsten av viruset Pepper mild mottle virus (PMMoV), ett växtvirus från peppar som människor får i sig via maten, 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 avloppsvattenproverna ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). För att kvantifiera mängd SARS-CoV-2 används SARS-specifika N3-primers ([Lu _et al._, 2020](https://doi.org/10.3201/eid2608.201246)) och mätningen görs med metoden RT-qPCR med SYBR Green-kemi ([Perez-Zabaleta _et al._, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)).
 
-Efter koncentration, filtrering och beredning analyseras proverna med RT-qPCR -teknik för att kvantifiera förekomsten av SARS-CoV-2 RNA. För att kvantifiera SARS-CoV-2 användes primers i nukleokapsid-(N)-genen (tidigare använt och verifierat av [Medema *et al.* (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). I vissa fall har det obehandlade avloppsvattnet frusits ​​vid –20 °C och koncentrerat avloppsvatten eller renat RNA har lagrats vid -80°C innan nästa analyssteg genomfördes. Koncentrationsmetoden som initialt användes av SEEC-KTH baseras på en av deras tidigare studier ([Jafferali *et al.*, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), där fyra olika koncentrationsmetoder jämfördes. Denna metod användes fram till vecka 35, 2021. Efter denna tidpunkt började gruppen istället använda [Promegas kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) för att koncentrera proverna.
+Efter koncentration, filtrering och beredning analyseras proverna med RT-qPCR -teknik för att kvantifiera förekomsten av SARS-CoV-2 RNA. För att kvantifiera SARS-CoV-2 användes primers i nukleokapsid-(N)-genen (tidigare använt och verifierat av [Medema _et al._ (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). I vissa fall har det obehandlade avloppsvattnet frusits ​​vid –20 °C och koncentrerat avloppsvatten eller renat RNA har lagrats vid -80°C innan nästa analyssteg genomfördes. Koncentrationsmetoden som initialt användes av SEEC-KTH baseras på en av deras tidigare studier ([Jafferali _et al._, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), där fyra olika koncentrationsmetoder jämfördes. Denna metod användes fram till vecka 35, 2021. Efter denna tidpunkt började gruppen istället använda [Promegas kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) för att koncentrera proverna.
 
 ## Arkiverade data