Publications using MicrobeTrace

HIV-1

Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria

Human Immunodeficiency Virus (HIV) Outbreak Investigation Among Persons Who Inject Drugs in Massachusetts Enhanced by HIV Sequence Data

Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission

Opioid Use Fueling HIV Transmission in an Urban Setting: An Outbreak of HIV Infection Among People Who Inject Drugs—Massachusetts, 2015–2018

Increased HIV diagnoses in West Virginia counties highly vulnerable to rapid HIV dissemination through injection drug use: a cautionary tale

Identification of a Human Immunodeficiency Virus Type 1 and Neurosyphilis Cluster in Vermont

The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)

HIV-1 Outbreak Investigation Among Persons Who Inject Drugs in Massachusetts Enhanced by HIV Sequence Data

Integration with other pipelines

Viral hepatitis

GHOST: global hepatitis outbreak and surveillance technology

Next-generation sequencing studies on the E1-HVR1 region of hepatitis C virus (HCV) from non-high-risk HCV patients living in Punjab and Khyber Pakhtunkhwa, Pakistan

Bacterial diseases

Exploring and comparing the structure of sexual networks affected by Neisseria gonorrhoeae

Phylogenomic analysis of Neisseria gonorrhoeae transmission to assess sexual mixing and HIV transmission risk in England: a cross-sectional, observational, whole-genome sequencing study

Tuberculosis Outbreak Associated With Delayed Diagnosis and Long Infectious Periods in Rural Arkansas, 2010-2018

Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis

Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters

Genotyping Cyclospora cayetanensis from multiple outbreak clusters with an emphasis on a cluster linked to bagged salad mix - United States, 2020

SARS-CoV-2 and COVID-19

Multidisciplinary Community-Based Investigation of a COVID-19 Outbreak Among Marshallese and Hispanic/Latino Communities — Benton and Washington Counties, Arkansas, March–June 2020