Polymorphism of HIV-1 gag (p17) gene from female sex workers in Calcutta, India

Sengupta, Satarupa; Khetawat, Dimple; Jana, Smarajit; Sarkar, Kamalesh; Bhattacharya, Sujit; Chakrabarti, Sekhar

doi:10.1007/s00705-005-0562-5

Cited by 8 publications

(5 citation statements)

References 17 publications

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“…All of the previous studies of the molecular epidemiology of the Indian HIV-1 epidemic have used a few geographically localized samples and a single viral gene [5]–[8], [21], [22]. A recent such study of global trends in the molecular epidemiology of HIV-1 identified 1.06% recombinant strains (CRFs and URFs) in India between 2000 and 2007 [9].…”

Section: Discussionmentioning

confidence: 99%

“…HIV-1 p17 region gag (HXB2 position 790–1190), RT region of pol (HXB2 position 2598–3254) and C2V4 region of env (HXB2 position 7050–7550), respectively, were amplified by nested polymerase chain reaction (PCR) using iNtRON Taq Polymerase (Intron Biotech, South Korea) as described previously [5], [21], [27]. The following amplification conditions were common for all three genes were: 1 cycle at 95°C for 2 min, 3 cycles at 94°C for 1 min, 55°C for 1 min and 72°C for 3 min, followed by 32 cycles at 94°C for 1 min, 60°C for 1 min and 72°C for 3 min with a final extension at 72°C for 10 min.…”

Section: Methodsmentioning

confidence: 99%

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Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

et al. 2012

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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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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

et al. 2012

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“…Six A1C recombinant viruses have been reported from India, out of which only two are characterized based on a fulllength genome sequence 5,6 and four based on partial genome data from Calcutta, 7 Bengaluru, 8 and Pune. 9 B/C recombinant viruses were reported from Manipur by Lakhashe et al 10,11 based on full-length genome sequencing and by Bhanja et al 12 based on partial gene sequencing.…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization of Unique Intersubtype HIV Type 1 A1/C Recombinant Strain Circulating in Pune, India

Pandey

Tripathy²,

Paranjape³

2013

AIDS Research and Human Retroviruses

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An increasing number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) all over the world has necessitated being vigilant about new recombinants. Since the first report of a recombinant virus with an A1/C mosaic in 1998 more and more B/C and A/C recombinant viruses are being reported from India. Here we report the identification and characterization of a unique HIV-1 A1/C recombinant circulating in Western India. Analysis of the full-length genome using RIP, SimPlot, and jpHMM@Gobics has confirmed its mosaic structure with insertion of subtype A1 in the backbone of subtype C at three positions: gag-pol (1973 -15-2617 -47), pol-vif (4879 -37-5582 -32), and gp41 (8437 -106-8811 -8); however, RIP and SimPlot showed one more small insertion in integrase (4343-4519). Phylogenetic analysis confirmed that the recombinant virus has an insertion of clade A1 in the backbone of subtype C, which has come from Indian subtype C.

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“…Phylogenetic analyses of partial or full-length genomes have shown that the great majority of HIV-1 subtype C strains from India group in a monophyletic clade [ 17 , 25 , 26 , 30 , 36 , 38 – 41 ], designated C IN [ 26 ], which, according to phylodynamic analyses, originated in the 1970s [ 41 – 43 ], although sporadic cases of subtype C viruses branching outside of the C IN clade have been reported [ 6 , 30 , 36 , 41 ]. Analyses of relationships with viruses from other countries indicate that the African viruses most closely related to C IN are from the southern part of the continent [ 36 , 41 ], and that subtype C strains circulating in China [ 36 , 42 , 44 ], Myanmar [ 42 ], Nepal [ 45 , 46 ] and Bangladesh [ 47 ] derive from the Indian clade.…”

Section: Discussionmentioning

confidence: 99%

Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India

Alampalli¹,

Thomson

Raghavan³

et al. 2017

PLoS ONE

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India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics. Here we describe the development and implementation of approaches for HIV-1 NGS analysis in a southern Indian cohort. Plasma samples (n = 20) were obtained from HIV-1-confirmed individuals living in and around the city of Bengaluru. Near full-length genome recovery was obtained for 9 Indian HIV-1 patients, with recovery of full-length gag and env genes for 10 and 2 additional subjects, respectively. Phylogenetic analyses indicate the majority of sequences to be represented by subtype C viruses branching within a monophyletic clade, comprising viruses from India, Nepal, Myanmar and China and closely related to a southern African cluster, with a low prevalence of the A1C recombinant form also present. Development of algorithms for bespoke recovery and analysis at a local level will further aid clinical management of HIV-1 infected Indian subjects and delineate the progress of the HIV-1 pandemic in this and other geographical regions.

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Polymorphism of HIV-1 gag (p17) gene from female sex workers in Calcutta, India

Cited by 8 publications

References 17 publications

Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

Molecular Characterization of Unique Intersubtype HIV Type 1 A1/C Recombinant Strain Circulating in Pune, India

Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India

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