ArticlePLoS pathogens2018
Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.
Article in PLoS pathogens, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 30 citations in OpenAlex.
- Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.medRxiv : the preprint server for health sciences · 2024Article
- Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.Virus evolution · 2024Article
- Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing.Frontiers in cellular and infection microbiology · 2024Article
- Broadly neutralizing antibodies targeting HIV: Progress and challenges.Clinical immunology (Orlando, Fla.) · 2023Review
- Accelerating antiviral drug discovery: lessons from COVID-19.Nature reviews. Drug discovery · 2023Review
- Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates.Virus evolution · 2023Article
- Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains.PLoS pathogens · 2022Article
- Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS.Virus evolution · 2022Article
- Article
- SARS-CoV-2 within-host diversity and transmission.Science (New York, N.Y.) · 2021Article
- Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on.Scientific reports · 2020Article
- Persistence of HIV transmission clusters among people who inject drugs.AIDS (London, England) · 2020Article
- HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification.Virus evolution · 2020Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- HIV-1 Subtype Distribution and Diversity Over 18 Years in Rakai, Uganda.AIDS research and human retroviruses · 2020Article
- Linking influenza virus evolution within and between human hosts.Virus evolution · 2020Article
- Ethical challenges in pathogen sequencing: a systematic scoping review.Wellcome open research · 2020Article
- Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.PLoS pathogens · 2019Article
- Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV.PLoS pathogens · 2019Article
- Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2019Article
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 3 countries.
Funding
Abstract
HIV-1 undergoes multiple rounds of error-prone replication between transmission events, resulting in diverse viral populations within and among individuals. In addition, the virus experiences different selective pressures at multiple levels: during the course of infection, at transmission, and among individuals. Disentangling how these evolutionary forces shape the evolution of the virus at the population scale is important for understanding pathogenesis, how drug- and immune-escape variants are likely to spread in populations, and the development of preventive vaccines. To address this, we deep-sequenced two regions of the HIV-1 genome (p24 and gp41) from 34 longitudinally-sampled untreated individuals from Rakai District in Uganda, infected with subtypes A, D, and inter-subtype recombinants. This dataset substantially increases the availability of HIV-1 sequence data that spans multiple years of untreated infection, in particular for different geographical regions and viral subtypes. In line with previous studies, we estimated an approximately five-fold faster rate of evolution at the within-host compared to the population scale for both synonymous and nonsynonymous substitutions, and for all subtypes. We determined the extent to which this mismatch in evolutionary rates can be explained by the evolution of the virus towards population-level consensus, or the transmission of viruses similar to those that establish infection within individuals. Our findings indicate that both processes are likely to be important.
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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.