Publications using MicrobeTrace

HIV-1

Notes from the Field: HIV Diagnoses Among Persons Who Inject Drugs — Northeastern Massachusetts, 2015–2018

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

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

Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study

Phylogenetic Network Analyses Reveal the Influence of Transmission Clustering on the Spread of HIV Drug Resistance in Quebec from 2002 to 2022

Viral hepatitis

Looking back into the Hepatitis C Virus epidemic dynamics from Unnao, India through phylogenetic approach Genomic epidemiology of resurgent hepatitis A in Florida, 2018–2022

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

Viral Special pathogens

HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations

Bacterial and parasitic 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] (https://pubmed.ncbi.nlm.nih.gov/33729050/)

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

Incorporation of MicrobeTrace into TB workflows

https://www.youtube.com/watch?v=c1JL3Gkshig

SARS-CoV-2, Influenza virus and other respiratory viruses

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2 Multidisciplinary Community-Based Investigation of a COVID-19 Outbreak Among Marshallese and Hispanic/Latino Communities — Benton and Washington Counties, Arkansas, March–June 2020

Participation in Fraternity and Sorority Activities and the Spread of COVID-19 Among Residential University Communities - Arkansas, August 21-September 5, 2020.

Multiple COVID-19 Outbreaks Linked to a Wedding Reception in Rural Maine — August 7–September 14, 2020

Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break — Chicago, Illinois, March–May 2021

SARS-CoV-2 transmission in a Georgia school district — United States, December 2020–January 2021

Transmission Dynamics of COVID-19 Outbreaks Associated with Child Care Facilities — Salt Lake City, Utah, April–July 2020

Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona

COMMUNITY ASSESSMENT OF COVID-19 ELKHART COUNTY, IN

Predicting 4th wave of the COVID-19 Outbreak in Vietnam

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission

Other viruses

Miscellaneous topics

Investigating and forecasting infectious disease dynamics using epidemiological and molecular surveillance data

Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

Breast Cancer-the-State-of-the Art in the World and Islamic Development Banks Members Countries (IsDB-MCs)