Analysis of HIV Type 1 Subtype C Full-Length gag Gene Sequences from India: Novel Observations and Plausible Implications

Gupta, R.M.; Prasad, V.V.S.P.; Rai, Arvind; Seth, Pradeep

doi:10.1089/aid.2005.21.1066

Cited by 16 publications

(8 citation statements)

References 17 publications

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“…3). It may be pertinent to mention that a distinct Indian subclade was also recognized by our group earlier based on the full-length gag gene sequences form 25 Indian isolates of subtype C. 8 These findings imply that both structural as well as regulatory genes can be used for virus subtyping.…”

mentioning

confidence: 52%

“…Substantial data are available on the genomic diversity of structural genes (env/gag) of almost all the important subtypes of HIV-1 [5][6][7] including our own recent report on full-length gag gene sequences from India. 8 In recent years, however, due emphasis has been given to the regulatory nef gene that plays a crucial and multiple role in HIV infection. 9,10 The nef gene was first identified as an open reading frame (ORF), which partially overlaps with the 3Ј-long terminal repeat (LTR) of HIV-1, and was reported to have a negative effect on viral replication, hence the name "negative factor" or "nef."…”

Section: Introductionmentioning

confidence: 99%

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Genomic Diversity in the RegulatorynefGene Sequences in Indian Isolates of HIV Type 1: Emergence of a Distinct Subclade and Predicted Implications

Kumar

Jain

Pasha

et al. 2006

AIDS Research and Human Retroviruses

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The regulatory functional nef gene is known to mediate a cascade of events during pathogenesis in HIV infection. Variability in the nef gene sequences of HIV-1 A and B subtypes has been well documented. Reasonable data are also available on the pattern of genomic changes in the nef gene of African strains of HIV-1 subtype C, but very little is known about heterogeneity in the nef gene of Indian strains of HIV-1 subtype C, which accounts for 90% of the estimated 5.2 million cases of HIV infection in India. This is a huge number and, therefore, it is important to reveal the extent of sequence variability in the nef gene of HIV-1 subtypes circulating in different parts of India. We carried out full-length nef gene (approximately 620 bp) sequencing on a large number of clinical isolates of HIV-1 circulating in different geographic regions of India. Comparative and phylogenetic analysis revealed 88% (38/43) of cases was HIV-1 subtype C; four cases were diagnosed as subtype A and only one as subtype B. Although most of the crucial functional motifs of the nef gene were conserved, we did observe a few important variations in juxtapositions to functional domains. Interestingly, analyzed nef sequences showed an evolving pattern of segregation away from those reported from other parts of the world, to form a distinct Indian subclade. Deduced amino acid (aa) sequences used to predict HLA binding epitopes for consensus nef gene sequences of Indian strains of HIV-1 revealed two HLA subtype binding domains, GAFDLSFFL (at aa 83) and LTFGWCFKL (at aa 136), in high frequency. The findings from the present study may encourage use of nef gene in molecular diagnostics/genotyping, keeping track of the evolutionary trend and pinpointing the emergence of recombinant strains, and in the future, designing a multiepitope HIV vaccine suitable for the Indian population.

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confidence: 52%

Section: Introductionmentioning

confidence: 99%

Genomic Diversity in the RegulatorynefGene Sequences in Indian Isolates of HIV Type 1: Emergence of a Distinct Subclade and Predicted Implications

Kumar

Jain

Pasha

et al. 2006

AIDS Research and Human Retroviruses

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“…Subtype A strains were found to be related to Central and East African subtype and subtype B strains obtained from Manipur were related to subtype B sequences circulating in Thailand [13]. However, recent studies have clearly shown that subtype C strains have displaced subtype B in the IV drug users in that part of India [7,15].…”

Section: The Indian Scenariomentioning

confidence: 98%

Evolution of HIV-1 in India

Seth¹

2010

Indian J. Virol.

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Nearly 25 years after the discovery of the human immunodeficiency virus type 1 (HIV-1) effective control of the AIDS pandemic remains elusive. At the root of this challenge is the evolution of this virus to elude immune control. Error-prone nature of replication and retro-transcription is the hallmark of this virus. This fidelity of replication in HIV-1 is due to the absence of proof-reading/repair and post-replicative error correction mechanisms that normally operate during replication of DNA viruses. Advances in sequencing technology and expanded disease surveillance have allowed researchers to characterize the variation in HIV-1 around the world and within individual patient overtime. Although HIV-1 has been classified into distinct subtypes, the classification does not reflect dynamic genetic evolution of HIV-1 through which new strains are constantly emerging. The resultant viral diversity has implications for differential rates of disease progression in different geographical areas, differential responses to antiretroviral therapy (including the development of resistance), and vaccine development. In this review evolution of HIV-1 in India is discussed.

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“…Amino acid signature sequences were identified using VESPA. 14 We assessed whether CRF07_BC sequences from Beijing had amino acid substitutions characteristic of their origin. We found that the CRF07_BC Beijing sequence differed at five amino acids from that of other CRF07_BC sequences.…”

Section: Analysis Of Gag-pol Gene Of Beijing Bmentioning

confidence: 99%

Sequence Analysis of the gag–pol Gene of Human Immunodeficiency Virus Type 1 of Intersubtype (B′/C) Recombinant Strain in Beijing, China

Xin

Bai

et al. 2011

AIDS Research and Human Retroviruses

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Little is known about the molecular and biological properties of HIV-1 intersubtype B 0 /C in Beijing. To fill the gap, we sequenced and analyzed the gag-pol genes from 39 HIV-1 B 0 /C recombinant infectors in Beijing, China during 2007. The results show that 36 CRF07_BC and 2 CRF08_BC isolates have a structural profile identical or nearly identical to CRF07_BC or CRF08_BC according to sequences in the gag-pol regions. The CRF07_BC circulating in injecting drug users (IDUs) and heterosexuals forms a diverse phylogenetic tree and most isolates from homosexuals cluster together. However, all the B 0 /C recombinant strains were remarkable for their low interpatient diversity in gag-pol genes (3.1, 3.0, and 2.2% for isolates from IDUs, heterosexuals, and homosexuals, respectively). We identified I7V, E91G, N242T, and K361R in the gag gene and R290I (HXB2 positions) in the pol gene as signature amino acid substitutions characteristic of HIV-1 CRF07_BC from the Beijing lineage. In addition, one new B 0 /C recombinant was detected. These results may contribute to an understanding of HIV-1 in Beijing.

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Analysis of HIV Type 1 Subtype C Full-Length gag Gene Sequences from India: Novel Observations and Plausible Implications

Cited by 16 publications

References 17 publications

Genomic Diversity in the RegulatorynefGene Sequences in Indian Isolates of HIV Type 1: Emergence of a Distinct Subclade and Predicted Implications

Genomic Diversity in the RegulatorynefGene Sequences in Indian Isolates of HIV Type 1: Emergence of a Distinct Subclade and Predicted Implications

Evolution of HIV-1 in India

Sequence Analysis of the gag–pol Gene of Human Immunodeficiency Virus Type 1 of Intersubtype (B′/C) Recombinant Strain in Beijing, China

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