Analysis of the history and spread of HIV-1 in Uganda using phylodynamics

The Journal of General Virology
Gonzalo YebraAndrew J Leigh Brown

Abstract

HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct the history and spread of HIV subtypes A1 and D in Uganda and explore the transmission dynamics in high-risk populations. We analysed HIV pol sequences from female sex workers in Kampala (n = 42), Lake Victoria fisher-folk (n = 46) and a rural clinical cohort (n = 74), together with publicly available sequences from adjacent regions in Uganda (n = 412) and newly generated sequences from samples taken in Kampala in 1986 (n = 12). Of the sequences from the three Ugandan populations, 60 (37.1 %) were classified as subtype D, 54 (33.3 %) as subtype A1, 31 (19.1 %) as A1/D recombinants, six (3.7 %) as subtype C, one (0.6 %) as subtype G and 10 (6.2 %) as other recombinants. Among the A1/D recombinants we identified a new candidate circulating recombinant form. Phylodynamic and phylogeographic analyses using BEAST indicated that the Ugandan epidemics originated in 1960 (1950-1968) for subtype A1 and 1973 (1970-1977) for D, in rural south-western Uganda with subsequent spread to Kampala. They also showed extensive interconnection with adjacent countries. The sequence analysis shows both epidemics grew exponenti...Continue Reading

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Citations

Apr 12, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Gonzalo YebraAndrew J Leigh Brown
Jun 6, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Tetyana I VasylyevaGkikas Magiorkinis
Jun 10, 2016·PloS One·Sana EybpooshAli Akbar Haghdoost
Apr 1, 2017·The Brazilian Journal of Infectious Diseases : an Official Publication of the Brazilian Society of Infectious Diseases·Antonio Walter de Oliveira Filho, Carlos Brites
Mar 30, 2017·AIDS·Amin S HassanJoakim Esbjörnsson
Feb 21, 2018·Current HIV/AIDS Reports·Mary Kate GrabowskiArt F Y Poon
Feb 2, 2018·Journal of Acquired Immune Deficiency Syndromes : JAIDS·M Kumi SmithVivian L Go
May 13, 2020·Virus Evolution·Heather E GrantAndrew J Leigh Brown
Nov 27, 2019·Virus Evolution·Pedro M M AraújoNuno S Osório
Jan 28, 2021·AIDS Research and Human Retroviruses·Ronald Moses GaliwangoDavid Serwadda

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Methods Mentioned

BETA
ELISA

Software Mentioned

RAxML
PhyML
Path
ClusterPicker
ViroBLAST
Gen
SCUEAL
Google Earth
SPREAD
TreeAnnotator

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