ArticleMolecular biology and evolution2010
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 66 citations in OpenAlex.
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- The importance of epistasis in the evolution of viral pathogens.Virus evolution · 2025Review
- A road map for in vivo evolution experiments with blood-borne parasitic microbes.Molecular ecology resources · 2022Review
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure.Current opinion in HIV and AIDS · 2019Review
- Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.Virus evolution · 2018Article
- Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity.Virus evolution · 2018Article
- Patterns of coevolving amino acids unveil structural and dynamical domains.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men.Journal of virology · 2017Article
- Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations.Scientific reports · 2017Article
- Identifying wrong assemblies in de novo short read primary sequence assembly contigs.Journal of biosciences · 2016Article
- Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients.International journal of molecular sciences · 2016Article
- Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.Viruses · 2016Article
- HIV-1 Promoter Single Nucleotide Polymorphisms Are Associated with Clinical Disease Severity.PloS one · 2016Article
- Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease.PLoS computational biology · 2015Article
- Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies.Computers in biology and medicine · 2015Article
- Article
- The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations.PLoS computational biology · 2014Article
- Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform.Journal of virological methods · 2014Article
- Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use?Current infectious disease reports · 2014Article
- Genetic attributes of blood-derived subtype-C HIV-1 tat and env in India and neurocognitive function.Journal of medical virology · 2014Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 3 countries.
Funding
Abstract
Rapidly evolving viruses such as HIV-1 display extensive sequence variation in response to host-specific selection, while simultaneously maintaining functions that are critical to replication and infectivity. This apparent conflict between diversifying and purifying selection may be resolved by an abundance of epistatic interactions such that the same functional requirements can be met by highly divergent sequences. We investigate this hypothesis by conducting an extensive characterization of sequence variation in the HIV-1 nef gene that encodes a highly variable multifunctional protein. Population-based sequences were obtained from 686 patients enrolled in the HOMER cohort in British Columbia, Canada, from which the distribution of nonsynonymous substitutions in the phylogeny was reconstructed by maximum likelihood. We used a phylogenetic comparative method on these data to identify putative epistatic interactions between residues. Two interactions (Y120/Q125 and N157/S169) were chosen to further investigate within-host evolution using HIV-1 RNA extractions from plasma samples from eight patients. Clonal sequencing confirmed strong linkage between polymorphisms at these sites in every case. We used massively parallel pyrosequencing (MPP) to reconstruct within-host evolution in these patients. Experimental error associated with MPP was quantified by performing replicates at two different stages of the protocol, which were pooled prior to analysis to reduce this source of variation. Phylogenetic reconstruction from these data revealed correlated substitutions at Y120/Q125 or N157/S169 repeated across multiple lineages in every host, indicating convergent within-host evolution shaped by epistatic interactions.
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Registered trials
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