Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1
Restricted accessResearch articleFirst published online May, 2016
Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1
Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
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References
1.
TsuchieH, ManiarJK, YoshiharaN, ImaiM, KurimuraT, KitamuraT: Sequence analysis of V3 loop region of HIV-1 strains prevalent in India. Jpn J Med Sci Biol, 1993; 46:95–100.
2.
HemelaarJ, GouwsE, GhysPD, OsmanovS; WHO-UNAIDS Network for HIV Isolation and Characterisation: Global trends in molecular epidemiology of HIV-1 during 2000–2007. AIDS, 2011; 25:679–689.
3.
SenS, TripathySP, SahniAK, et al.: Human immunodeficiency virus type 1 gp 41 mutations in proviral DNA among antiretroviral treatment-naive individuals from India. AIDS Res Hum Retroviruses, 2009; 25:521–523.
4.
NeogiU, SoodV, ChowdhuryA, et al.: Genetic analysis of HIV-1 Circulating Recombinant Form 02_AG, B and C subtype-specific envelope sequences from Northern India and their predicted co-receptor usage. AIDS Res Ther, 2009; 6:28.
5.
LoleKS, BollingerRC, ParanjapeRS, et al.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol, 1999; 73:152–160.
6.
PandeyS, TripathyS, ParanjapeR: Molecular characterization of unique intersubtype HIV type 1 A1/C recombinant strain circulating in Pune, India. AIDS Res Hum Retroviruses, 2013; 29:1245–1253.
7.
DeshpandeA, Recordon-PinsonP, DeshmukhR, et al.: Molecular characterization of HIV type 1 isolates from untreated patients of Mumbai (Bombay), India, and detection of rare resistance mutations. AIDS Res Hum Retroviruses, 2004; 20:1032–1035.
8.
SenS, TripathySP, ChimanpureVM, PatilAA, BagulRD, ParanjapeRS: Human immunodeficiency virus type 1 drug resistance mutations in peripheral blood mononuclear cell proviral DNA among antiretroviral treatment-naive and treatment-experienced patients from Pune, India. AIDS Res Hum Retroviruses, 2007; 23:489–497.
9.
LallM, GuptaRM, SenS, KapilaK, TripathySP, ParanjapeRS: Profile of primary resistance in HIV-1-infected treatment-naive individuals from Western India. AIDS Res Hum Retroviruses, 2008; 24:987–990.
10.
DeshpandeA, JauvinV, PinsonP, JeannotAC, FleuryHJ: Phylogenetic analysis of HIV-1 reverse transcriptase sequences from 382 patients recruited in JJ Hospital of Mumbai, India, between 2002 and 2008. AIDS Res Hum Retroviruses, 2009; 25:633–635.
11.
PatilRT, GuptaRM, SenS, et al.: Emergence of drug resistance in human immunodeficiency virus type 1 infected patients from pune, India, at the end of 12 months of first line antiretroviral therapy initiation. ISRN AIDS, 2014; 2014:674906.
12.
DeshpandeA, KarkiS, Recordon-PinsonP, FleuryHJ: Drug resistance mutations in HIV type 1 isolates from naive patients eligible for first line antiretroviral therapy in JJ Hospital, Mumbai, India. AIDS Res Hum Retroviruses, 2011; 27:1345–1347.
13.
KumarM, SenS, GuptaRK, ChaturbhujD, TripathySP, ParanjapeRS: Prevalence of drug resistance in human immunodeficiency virus type 1-infected treatment-naive children in Pune, India. AIDS Res Hum Retroviruses, 2014; 30:294–298.
14.
AcharyaA, VaniawalaS, ShahP, MisraRN, WaniM, MukhopadhyayaPN: Development, validation and clinical evaluation of a low cost in-house HIV-1 drug resistance genotyping assay for Indian patients. PLoS One, 2014; 9:e105790.
15.
AzamM, MalikA, RizviM, SinghS, GuptaP, RaiA: Emergence of drug resistance-associated mutations in HIV-1 subtype C protease gene in north India. Virus Genes, 2013; 47:422–428.
16.
AzamM, MalikA, RizviM, RaiA: Zero prevalence of primary drug resistance-associated mutations to protease inhibitors in HIV-1 drug-naive patients in and around Aligarh, India. J Infect Dev Ctries, 2014; 8:79–85.
17.
MaitraA, SinghB, BanuS, et al.: Subtypes of HIV type 1 circulating in India: Partial envelope sequences. AIDS Res Hum Retroviruses, 1999; 15:941–944.
18.
AndrabiR, KumarR, BalaM, et al.: Envelope diversity, characteristics of V3 region and predicted co-receptor usage of human immunodeficiency viruses infecting north Indians. J Microbiol, 2012; 50:869–873.
19.
GuptaP, HusainM, HansC, et al.: Sequence heterogeneity in human immunodeficiency virus type 1 nef in patients presenting with rapid progression and delayed progression to AIDS. Arch Virol, 2014; 159:2303–2320.
20.
ShankarappaR, ChatterjeeR, LearnGH, et al.: Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: Identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virol, 2001; 75:10479–10487.
21.
KaradeS, PandeyS, GianchandaniS, et al.: Near full-length genomic characterization of a novel CRF 01_AE/C recombinant from Western India. AIDS Res Hum Retroviruses, 2015; 31:1269–1273.
22.
PandeySS, ThakarM, ParanjapeR: Characterization of novel HIV-1 intersubtype CRF01_AE/C and A1/C recombinants from India. Genome Announc, 2015; 3.
23.
LakhasheS, TripathyS, ParanjapeR, BhattacharyaJ: Evidence of a novel B/C recombinant exhibiting unique breakpoints of near full-length HIV type 1 genome from Northeastern India. AIDS Res Hum Retroviruses, 2008; 24:229–234.
24.
SalminenMO, KochC, Sanders-BuellE, et al.: Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology, 1995; 213:80–86.
25.
DashPK, SiddappaNB, MangaiarkarasiA, et al.: Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection. Retrovirology, 2008; 5:25.
26.
NadaiY, EyzaguirreLM, ConstantineNT, et al.: Protocol for nearly full-length sequencing of HIV-1 RNA from plasma. PLoS One, 2008; 3:e1420.
27.
KondoE, GottlingerHG: A conserved LXXLF sequence is the major determinant in p6gag required for the incorporation of human immunodeficiency virus type 1 Vpr. J Virol, 1996; 70:159–164.
28.
LuYL, BennettRP, WillsJW, GorelickR, RatnerL: A leucine triplet repeat sequence (LXX)4 in p6gag is important for Vpr incorporation into human immunodeficiency virus type 1 particles. J Virol, 1995; 69:6873–6879.
29.
ZhuH, JianH, ZhaoLJ: Identification of the 15FRFG domain in HIV-1 Gag p6 essential for Vpr packaging into the virion. Retrovirology, 2004; 1:26.
30.
FreedEO: The HIV-TSG101 interface: Recent advances in a budding field. Trends Microbiol, 2003; 11:56–59.
31.
FujiiK, MunshiUM, AblanSD, et al.: Functional role of Alix in HIV-1 replication. Virology, 2009; 391:284–292.
32.
LastereS, DalbanC, CollinG, et al.: Impact of insertions in the HIV-1 p6 PTAPP region on the virological response to amprenavir. Antivir Ther, 2004; 9:221–227.
33.
WadekarK, PandeyS, JainP, RoyVC, AsthanaA, ParanjapeR: Frequency of P/S(XX)P duplication and FRFE, absence of LYP in P6Gag of Indian human immunodeficiency virus-1 subtype C isolates. Am Med J, 2010; 1:140–147.
34.
PatilA, BhattacharyaJ: Natural deletion of L35Y36 in p6 gag eliminate LYPXnL/ALIX auxiliary virus release pathway in HIV-1 subtype C. Virus Res, 2012; 170:154–158.
35.
DybowskiJN, HeiderD, HoffmannD: Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput Biol, 2010; 6:e1000743.
36.
Lopez de VictoriaA, KieslichCA, RizosAK, KrambovitisE, MorikisD: Clustering of HIV-1 subtypes based on gp120 V3 loop electrostatic properties. BMC Biophys, 2012; 5:3.
37.
JensenMA, CoetzerM, van ’t WoutAB, MorrisL, MullinsJI: A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. J Virol, 2006; 80:4698–4704.
38.
CilliersT, NhlapoJ, CoetzerM, et al.: The CCR5 and CXCR4 coreceptors are both used by human immunodeficiency virus type 1 primary isolates from subtype C. J Virol, 2003; 77:4449–4456.
39.
KumarR, TuenM, LiH, TseDB, HioeCE: Improving immunogenicity of HIV-1 envelope gp120 by glycan removal and immune complex formation. Vaccine, 2011; 29:9064–9074.
40.
HuangX, JinW, HuK, et al.: Highly conserved HIV-1 gp120 glycans proximal to CD4-binding region affect viral infectivity and neutralizing antibody induction. Virology, 2012; 423:97–106.
41.
ZhangM, GaschenB, BlayW, et al.: Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology, 2004; 14:1229–1246.
42.
WyattR, KwongPD, DesjardinsE, et al.: The antigenic structure of the HIV gp120 envelope glycoprotein. Nature, 1998; 393:705–711.
43.
OgertRA, LeeMK, RossW, Buckler-WhiteA, MartinMA, ChoMW: N-linked glycosylation sites adjacent to and within the V1/V2 and the V3 loops of dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect coreceptor usage and cellular tropism. J Virol, 2001; 75:5998–6006.
44.
RodriguezMA, ShenC, RatnerD, et al.: Genetic and functional characterization of the LTR of HIV-1 subtypes A and C circulating in India. AIDS Res Hum Retroviruses, 2007; 23:1428–1433.
45.
NovitskyVA, MontanoMA, McLaneMF, et al.: Molecular cloning and phylogenetic analysis of human immunodeficiency virus type 1 subtype C: A set of 23 full-length clones from Botswana. J Virol, 1999; 73:4427–4432.
46.
NeogiU, BontellI, ShetA, et al.: Molecular epidemiology of HIV-1 subtypes in India: Origin and evolutionary history of the predominant subtype C. PLoS One, 2012; 7:e39819.
47.
ShenC, CraigoJ, DingM, ChenY, GuptaP: Origin and dynamics of HIV-1 subtype C infection in India. PLoS One, 2011; 6:e25956.
48.
KumarM, JainSK, PashaST, ChattopadhayaD, LalS, RaiA: Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: Emergence of a distinct subclade and predicted implications. AIDS Res Hum Retroviruses, 2006; 22:1206–1219.
49.
SinhaS, AhmadH, ShekharRC, et al.: Prevalence of HIV drug resistance mutations in HIV type 1 isolates in antiretroviral therapy naive population from Northern India. AIDS Res Treat, 2012; 2012:905823.
50.
CassolS, WenigerBG, BabuPG, et al.: Detection of HIV type 1 env subtypes A, B, C, and E in Asia using dried blood spots: A new surveillance tool for molecular epidemiology. AIDS Res Hum Retroviruses, 1996; 12:1435–1441.
51.
RajeshL, KarunaiananthamR, NarayananPR, SwaminathanS: Antiretroviral drug-resistant mutations at baseline and at time of failure of antiretroviral therapy in HIV type 1-coinfected TB patients. AIDS Res Hum Retroviruses, 2009; 25:1179–1185.
52.
SaravananS, MadhavanV, BalakrishnanP, et al.: Darunavir is a good third-line antiretroviral agent for HIV type 1-infected patients failing second-line protease inhibitor-based regimens in South India. AIDS Res Hum Retroviruses, 2013; 29:630–632.
53.
SiddappaNB, DashPK, MahadevanA, et al.: Identification of unique B/C recombinant strains of HIV-1 in the southern state of Karnataka, India. AIDS, 2005; 19:1426–1429.
