Defining HIV-1 transmission clusters based on sequence data

AS Hassan, OG Pybus, EJ Sanders, J Albert… - Aids, 2017 - journals.lww.com
Understanding HIV-1 transmission dynamics is relevant to both screening and intervention
strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based …

Sexual activity without condoms and risk of HIV transmission in serodifferent couples when the HIV-positive partner is using suppressive antiretroviral therapy

AJ Rodger, V Cambiano, T Bruun, P Vernazza… - Jama, 2016 - jamanetwork.com
Importance A key factor in assessing the effectiveness and cost-effectiveness of antiretroviral
therapy (ART) as a prevention strategy is the absolute risk of HIV transmission through …

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management

MEJ Woolhouse, A Rambaut, P Kellam - Science translational medicine, 2015 - science.org
The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings
in national and international capacity to detect, monitor, and respond to infectious disease …

[HTML][HTML] TreeCluster: Clustering biological sequences using phylogenetic trees

M Balaban, N Moshiri, U Mai, X Jia, S Mirarab - PloS one, 2019 - journals.plos.org
Clustering homologous sequences based on their similarity is a problem that appears in
many bioinformatics applications. The fact that sequences cluster is ultimately the result of …

Using molecular HIV surveillance data to understand transmission between subpopulations in the United States

AM Oster, JO Wertheim, AL Hernandez… - JAIDS Journal of …, 2015 - journals.lww.com
Background: Studying HIV transmission networks provides insight into the spread of HIV and
opportunities for intervention. We identified transmission dynamics among risk groups and …

Nationwide trends in molecular epidemiology of HIV-1 in China

X Li, W Li, P Zhong, K Fang, K Zhu… - AIDS research and …, 2016 - liebertpub.com
To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past
three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 …

Growth of HIV-1 molecular transmission clusters in New York City

JO Wertheim, B Murrell, SR Mehta… - The Journal of …, 2018 - academic.oup.com
Background HIV-1 genetic sequences can be used to infer viral transmission history and
dynamics. Throughout the United States, HIV-1 sequences from drug resistance testing are …

HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data

M Ragonnet-Cronin, YW Hu, SR Morris, Z Sheng… - The Lancet …, 2019 - thelancet.com
Background Transgender women are among the groups at highest risk for HIV infection, with
a prevalence of 27· 7% in the USA; and despite this known high risk, undiagnosed infection …

[HTML][HTML] Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

D Kühnert, R Kouyos, G Shirreff, J Pečerska… - PLoS …, 2018 - journals.plos.org
Drug resistant HIV is a major threat to the long-term efficacy of antiretroviral treatment.
Around 10% of ART-naïve patients in Europe are infected with drug-resistant HIV type 1 …

2016 United Kingdom national guideline on the sexual health care of men who have sex with men

D Clutterbuck, D Asboe, T Barber… - … journal of STD & …, 2018 - journals.sagepub.com
This guideline is intended for use in UK Genitourinary medicine clinics and sexual health
services but is likely to be of relevance in all sexual health settings, including general …