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Title: HIV-1 Transmission during Early Infection in Men Who Have Sex with Men: A Phylodynamic Analysis

Journal Article · · PLoS Medicine
 [1];  [2];  [3];  [4];  [4];  [2]
  1. Imperial College, London (United Kingdom)
  2. Univ. of Michigan, Ann Arbor, MI (United States)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Michigan Department of Community Health, Detroit, MI (United States)
+ Show Author Affiliations

Conventional epidemiological surveillance of infectious diseases is focused on characterization of incident infections and estimation of the number of prevalent infections. Advances in methods for the analysis of the population-level genetic variation of viruses can potentially provide information about donors, not just recipients, of infection. Genetic sequences from many viruses are increasingly abundant, especially HIV, which is routinely sequenced for surveillance of drug resistance mutations. In this study, we conducted a phylodynamic analysis of HIV genetic sequence data and surveillance data from a US population of men who have sex with men (MSM) and estimated incidence and transmission rates by stage of infection.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1321730
Report Number(s):
LA-UR-13-23215
Journal Information:
PLoS Medicine, Vol. 10, Issue 12; ISSN 1549-1676
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 88 works
Citation information provided by
Web of Science

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Cited By (40)

Sexually transmitted hepatitis C virus infections: current trends, and recent advances in understanding the spread in men who have sex with men journal August 2019
Challenges of HIV diagnosis and management in the context of pre‐exposure prophylaxis (PrEP), post‐exposure prophylaxis (PEP), test and start and acute HIV infection: a scoping review journal December 2019
Early HIV Infections Among Men Who Have Sex with Men in Five Cities in the United States journal February 2015
Characteristics of Persons Who Inject Drugs with Recent HIV Infection in the United States: National HIV Behavioral Surveillance, 2012 journal February 2019
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis journal March 2019
Natural selection favoring more transmissible HIV detected in United States molecular transmission network journal December 2019
Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California journal May 2016
Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control journal February 2018
Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)–Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1–Infected Individuals With Social Links journal April 2018
Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection journal April 2019
Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina journal April 2019
Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny journal May 2014
Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo journal April 2017
Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa journal July 2018
Sources of HIV infection among men having sex with men and implications for prevention journal January 2016
Spatiotemporal dynamics of HIV-1 transmission in France (1999–2014) and impact of targeted prevention strategies journal February 2017
Phylodynamic Inference for Structured Epidemiological Models journal April 2014
Bayesian phylodynamic inference with complex models journal November 2018
Reassessment of HIV-1 Acute Phase Infectivity: Accounting for Heterogeneity and Study Design with Simulated Cohorts journal March 2015
Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis journal November 2015
Viral Genetic Linkage Analysis in the Presence of Missing Data journal August 2015
Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic journal June 2016
Estimating epidemiological parameters of a stochastic differential model of HIV dynamics using hierarchical Bayesian statistics journal July 2018
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Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo posted_content December 2016
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Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa text January 2018
Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection text January 2019
Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina text January 2020
Clinical and public health implications of acute and early HIV detection and treatment: a scoping review text January 2017
Trends in the Mechanistic and Dynamic Modeling of Infectious Diseases journal July 2016
Strong influence of behavioral dynamics on the ability of testing and treating HIV to stop transmission journal April 2015
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Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing journal November 2019
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