ArticleBioinformatics (Oxford, England)2016
SPMM: estimating infection duration of multivariant HIV-1 infections.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.Scientific reports · 2017Pooled it
- HIV-1 genetic diversity to estimate time of infection and infer adherence to preexposure prophylaxis.AIDS (London, England) · 2019Trial
- Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects.PloS one · 2020Article
- Article
- An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model.Theoretical population biology · 2019Article
- HIITE: HIV-1 incidence and infection time estimator.Bioinformatics (Oxford, England) · 2018Article
- Enhancement of viral escape in HIV-1 Nef by STEP vaccination.AIDS (London, England) · 2016Article
- Molecular clock of HIV-1 envelope genes under early immune selection.Retrovirology · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationIllustrating how HIV-1 is transmitted and how it evolves in the following weeks is an important step for developing effective vaccination and prevention strategies. It is currently possible through DNA sequencing to account for the diverse array of viral strains within an infected individual. This provides an unprecedented opportunity to pinpoint when each patient was infected and which viruses were transmitted.
resultsHere we develop a mathematical tool for early HIV-1 evolution within a subject whose infection originates either from a single or multiple viral variants. The shifted Poisson mixture model (SPMM) provides a quantitative guideline for segregating viral lineages, which in turn enables us to assess when a subject was infected. The infection duration estimated by SPMM showed a statistically significant linear relationship with that by Fiebig laboratory staging (P = 0.00059) among 37 acutely infected subjects. Our tool provides a functional approach to understanding early genetic diversity, one of the most important parameters for deciphering HIV-1 transmission and predicting the rate of disease progression. AVAILABILITY AND IMPLEMENTATION: SPMM, webserver, is available at http://www.hayounlee.org/web-tools.html. CONTACT: hayoun@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.