High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

Li Yin, Li Liu, Yijun Sun, Wei Hou, Amanda C. Lowe, Brent P. Gardner, Marco Salemi, Wilton B. Williams, William G. Farmerie, John W. Sleasman, Maureen M. Goodenow

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Background: Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children.Results: Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later.Conclusions: Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

Original languageEnglish (US)
Article number108
JournalRetrovirology
Volume9
DOIs
StatePublished - Dec 17 2012
Externally publishedYes

Fingerprint

High-Throughput Nucleotide Sequencing
Biodiversity
Ecosystem
HIV-1
Population
Population Genetics
Viruses
Viral Structures
Microbiota
Computational Biology
Blood Cells
Infection

Keywords

  • Biodiversity
  • Fitness
  • Founder virus persistence
  • HIV-1 envelope V3
  • Most recent common ancestor
  • Population structure
  • Pyrosequencing
  • Quasispecies

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. / Yin, Li; Liu, Li; Sun, Yijun; Hou, Wei; Lowe, Amanda C.; Gardner, Brent P.; Salemi, Marco; Williams, Wilton B.; Farmerie, William G.; Sleasman, John W.; Goodenow, Maureen M.

In: Retrovirology, Vol. 9, 108, 17.12.2012.

Research output: Contribution to journalArticle

Yin, L, Liu, L, Sun, Y, Hou, W, Lowe, AC, Gardner, BP, Salemi, M, Williams, WB, Farmerie, WG, Sleasman, JW & Goodenow, MM 2012, 'High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems', Retrovirology, vol. 9, 108. https://doi.org/10.1186/1742-4690-9-108
Yin, Li ; Liu, Li ; Sun, Yijun ; Hou, Wei ; Lowe, Amanda C. ; Gardner, Brent P. ; Salemi, Marco ; Williams, Wilton B. ; Farmerie, William G. ; Sleasman, John W. ; Goodenow, Maureen M. / High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. In: Retrovirology. 2012 ; Vol. 9.
@article{e6e6bf5bbf0540578c530655d38bc05d,
title = "High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems",
abstract = "Background: Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-na{\"i}ve children.Results: Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later.Conclusions: Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.",
keywords = "Biodiversity, Fitness, Founder virus persistence, HIV-1 envelope V3, Most recent common ancestor, Population structure, Pyrosequencing, Quasispecies",
author = "Li Yin and Li Liu and Yijun Sun and Wei Hou and Lowe, {Amanda C.} and Gardner, {Brent P.} and Marco Salemi and Williams, {Wilton B.} and Farmerie, {William G.} and Sleasman, {John W.} and Goodenow, {Maureen M.}",
year = "2012",
month = "12",
day = "17",
doi = "10.1186/1742-4690-9-108",
language = "English (US)",
volume = "9",
journal = "Retrovirology",
issn = "1742-4690",
publisher = "BioMed Central",

}

TY - JOUR

T1 - High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

AU - Yin, Li

AU - Liu, Li

AU - Sun, Yijun

AU - Hou, Wei

AU - Lowe, Amanda C.

AU - Gardner, Brent P.

AU - Salemi, Marco

AU - Williams, Wilton B.

AU - Farmerie, William G.

AU - Sleasman, John W.

AU - Goodenow, Maureen M.

PY - 2012/12/17

Y1 - 2012/12/17

N2 - Background: Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children.Results: Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later.Conclusions: Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

AB - Background: Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children.Results: Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later.Conclusions: Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

KW - Biodiversity

KW - Fitness

KW - Founder virus persistence

KW - HIV-1 envelope V3

KW - Most recent common ancestor

KW - Population structure

KW - Pyrosequencing

KW - Quasispecies

UR - http://www.scopus.com/inward/record.url?scp=84870976695&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84870976695&partnerID=8YFLogxK

U2 - 10.1186/1742-4690-9-108

DO - 10.1186/1742-4690-9-108

M3 - Article

C2 - 23244298

AN - SCOPUS:84870976695

VL - 9

JO - Retrovirology

JF - Retrovirology

SN - 1742-4690

M1 - 108

ER -