Molecular epidemiology of HIV-1 subtypes in India

Origin and evolutionary history of the predominant subtype C

Ujjwal Neogi, Irene Bontell, Anita Shet, Ayesha de Costa, Soham Gupta, Vishal Diwan, Ranbir S. Laishram, Ajay Wanchu, Udaykumar Ranga, Akhil C. Banerjea, Anders Sönnerborg

Research output: Contribution to journalArticle

Abstract

Background: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C). However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA) of the predominant HIV-1C strains. Methodology/Principal Findings: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10%) of unique recombinant forms (BC and A1C) was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively). The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag) to 1974 (env). Pol-gene analysis was considered to provide the most reliable estimate [1971, (95% CI: 1965-1976)]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. Conclusions/Significance: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular surveillance to guide efficient disease intervention strategies.

Original languageEnglish (US)
Article numbere39819
JournalPLoS One
Volume7
Issue number6
DOIs
StatePublished - Jun 29 2012
Externally publishedYes

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molecular epidemiology
Molecular Epidemiology
Human immunodeficiency virus 1
HIV-1
India
Genes
pol Genes
Geographical distribution
Population Growth
genes
population growth
ancestry
Blood
gag Genes
env Genes
Viral Genes
Population Density
Sample Size
geographical distribution
population size

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Molecular epidemiology of HIV-1 subtypes in India : Origin and evolutionary history of the predominant subtype C. / Neogi, Ujjwal; Bontell, Irene; Shet, Anita; de Costa, Ayesha; Gupta, Soham; Diwan, Vishal; Laishram, Ranbir S.; Wanchu, Ajay; Ranga, Udaykumar; Banerjea, Akhil C.; Sönnerborg, Anders.

In: PLoS One, Vol. 7, No. 6, e39819, 29.06.2012.

Research output: Contribution to journalArticle

Neogi, U, Bontell, I, Shet, A, de Costa, A, Gupta, S, Diwan, V, Laishram, RS, Wanchu, A, Ranga, U, Banerjea, AC & Sönnerborg, A 2012, 'Molecular epidemiology of HIV-1 subtypes in India: Origin and evolutionary history of the predominant subtype C', PLoS One, vol. 7, no. 6, e39819. https://doi.org/10.1371/journal.pone.0039819
Neogi, Ujjwal ; Bontell, Irene ; Shet, Anita ; de Costa, Ayesha ; Gupta, Soham ; Diwan, Vishal ; Laishram, Ranbir S. ; Wanchu, Ajay ; Ranga, Udaykumar ; Banerjea, Akhil C. ; Sönnerborg, Anders. / Molecular epidemiology of HIV-1 subtypes in India : Origin and evolutionary history of the predominant subtype C. In: PLoS One. 2012 ; Vol. 7, No. 6.
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abstract = "Background: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C). However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA) of the predominant HIV-1C strains. Methodology/Principal Findings: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10{\%}) of unique recombinant forms (BC and A1C) was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively). The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag) to 1974 (env). Pol-gene analysis was considered to provide the most reliable estimate [1971, (95{\%} CI: 1965-1976)]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. Conclusions/Significance: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular surveillance to guide efficient disease intervention strategies.",
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AU - Neogi, Ujjwal

AU - Bontell, Irene

AU - Shet, Anita

AU - de Costa, Ayesha

AU - Gupta, Soham

AU - Diwan, Vishal

AU - Laishram, Ranbir S.

AU - Wanchu, Ajay

AU - Ranga, Udaykumar

AU - Banerjea, Akhil C.

AU - Sönnerborg, Anders

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N2 - Background: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C). However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA) of the predominant HIV-1C strains. Methodology/Principal Findings: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10%) of unique recombinant forms (BC and A1C) was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively). The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag) to 1974 (env). Pol-gene analysis was considered to provide the most reliable estimate [1971, (95% CI: 1965-1976)]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. Conclusions/Significance: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular surveillance to guide efficient disease intervention strategies.

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