ArticlePLoS computational biology2017
Estimating time of HIV-1 infection from next-generation sequence diversity.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 63 citations in OpenAlex.
- Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.PLoS pathogens · 2020Trial
- Estimating HIV-1 Viremic Time From Reservoir Sequence Diversity With Uncertainty Quantification.The Journal of infectious diseases · 2026Article
- Recent HIV infection among women and men enrolling to care in urban clinics in Ethiopia.BMC infectious diseases · 2026Article
- Prediction of recent HIV-1 infections using Shannon entropy analysis of HIV-1 group-specific antigen protein sequence.Virology journal · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
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- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
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- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Impact of Variable Sampling on Estimates of HIV-1 Reservoir Formation Dates.The Journal of infectious diseases · 2024Article
- Genetic Diversity From Proviral DNA as a Proxy for Time Since HIV-1 Infection.The Journal of infectious diseases · 2024Article
- Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen.PLoS pathogens · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Using viral sequence diversity to estimate time of HIV infection in infants.PLoS pathogens · 2023Article
- Multiple Infection and Human Immunodeficiency Virus Superinfection Among Persons who Inject Drugs in Indonesia and Ukraine.The Journal of infectious diseases · 2022Article
- Genotypic and Phenotypic Diversity of the Replication-Competent HIV Reservoir in Treated Patients.Microbiology spectrum · 2022Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 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
- SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity.Virus evolution · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Estimating the time since infection (TI) in newly diagnosed HIV-1 patients is challenging, but important to understand the epidemiology of the infection. Here we explore the utility of virus diversity estimated by next-generation sequencing (NGS) as novel biomarker by using a recent genome-wide longitudinal dataset obtained from 11 untreated HIV-1-infected patients with known dates of infection. The results were validated on a second dataset from 31 patients. Virus diversity increased linearly with time, particularly at 3rd codon positions, with little inter-patient variation. The precision of the TI estimate improved with increasing sequencing depth, showing that diversity in NGS data yields superior estimates to the number of ambiguous sites in Sanger sequences, which is one of the alternative biomarkers. The full advantage of deep NGS was utilized with continuous diversity measures such as average pairwise distance or site entropy, rather than the fraction of polymorphic sites. The precision depended on the genomic region and codon position and was highest when 3rd codon positions in the entire pol gene were used. For these data, TI estimates had a mean absolute error of around 1 year. The error increased only slightly from around 0.6 years at a TI of 6 months to around 1.1 years at 6 years. Our results show that virus diversity determined by NGS can be used to estimate time since HIV-1 infection many years after the infection, in contrast to most alternative biomarkers. We provide the regression coefficients as well as web tool for TI estimation.
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