ArticleAIDS research and human retroviruses2017
HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
Article in AIDS research and human retroviruses, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.Nature microbiology · 2024Article
- Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences.BMC bioinformatics · 2023Article
- Article
- Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana.BMC infectious diseases · 2022Article
- Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.The Journal of infectious diseases · 2022Article
- Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions.Virus evolution · 2021Article
- Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial.The Journal of infectious diseases · 2020Article
- Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters.Scientific reports · 2020Article
- A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings.Journal of clinical microbiology · 2020Article
- Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.The lancet. HIV · 2020Article
- Effect of HIV Subtype and Antiretroviral Therapy on HIV-Associated Neurocognitive Disorder Stage in Rakai, Uganda.Journal of acquired immune deficiency syndromes (1999) · 2019Article
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.Nature communications · 2019Article
- Next-generation sequencing of HIV-1 single genome amplicons.Biomolecular detection and quantification · 2019Article
- Designing & Conducting Trials To Reliably Evaluate HIV Prevention Interventions.Statistical communications in infectious diseases · 2019Article
- Genetic Cluster Analysis for HIV Prevention.Current HIV/AIDS reports · 2018Review
- A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.PloS one · 2018Article
- Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.Virus evolution · 2018Article
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32 authors.
Funding
Abstract
To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n=2,833; MRC/UVRI Uganda, n=701; Mochudi Prevention Project, n=359; Africa Health Research Institute Resistance Cohort, n=92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3' end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phylogeny reconstruction is expected.
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