Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes

Rousseau, Christine; Birditt, Brian; McKay, A.; Stoddard, Julia N.; Lee, Tsan Chun; McLaughlin, Sherry; Moore, Sarah; Shindo, Nice; Learn, Gerald H.; Korber, Bette T.; Berthou, Christian; Goulder, Philip; Kiepiela, Photini; Walker, Bruce D.; Mullins, James I.

doi:10.1016/j.jviromet.2006.04.009

Cited by 87 publications

(86 citation statements)

References 34 publications

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“…HIV strains IIIB and Bal are X4 and R5 viruses, respectively, grown in PBL cultures. ADA, LAI and NDK (Joliot et al, 2001;Rousseau et al, 2006;Schwartz et al, 1994) HeLa cell lines were kindly provided by Dr M. Alizon and Dr U. Hazan (Institut Cochin, Paris, France). VSV-G env and the HIV-1 env and rev sequences of the HIV-1 subtype B strains QH0692.42, AC10, 6535.5 and pRHPA4259.7 and subtype D strain NDK were obtained through the MRC CFAR NIBSC programme.…”

Section: Discussionmentioning

confidence: 99%

HLA-C is necessary for optimal human immunodeficiency virus type 1 infection of human peripheral blood CD4 lymphocytes

Baroni

Matucci

Scarlatti

et al. 2009

Journal of General Virology

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The hypothesis that open conformers of HLA-C on target cells might directly exert an effect on their infectability by human immunodeficiency virus (HIV) has been suggested previously. This was tested by exploiting the peculiar specificity of monoclonal antibody (mAb) L31 for HLA-C open conformers to show that normal levels of Env-driven fusion were restored in HLA-C transfectants of a major histocompatibility complex-deleted (fusion-incompetent) cell line. The physiological relevance of this finding is now confirmed in this report, where small interfering RNA (siRNA) technology was used to silence HLA-C expression in peripheral blood lymphocytes (PBLs) from 11 healthy donors. Infectability by HIV (strains IIIB and Bal and primary isolates) was significantly reduced (P50.016) in silenced cells compared with cells that maintained HLA-C expression in 10 of the 11 PBL donors. Normal infectability was resumed, together with HLA-C expression, when the effect of siRNA interference waned after several days in culture. Additional confirmation of the HLA-C effect was obtained in several assays employing HLA-C-positive and -negative cell lines, a number of HIV strains and also pseudoviruses. In particular, viruses pseudotyped with env genes from HIV strains AC10 and QH0692.42 were assayed on siRNA-silenced lymphocytes from three healthy donors: the differences in infection with pseudoviruses were even higher than those observed in infections with normal viruses. INTRODUCTIONThree recent whole-genome association studies have demonstrated and confirmed that minor allele variants of singlenucleotide polymorphisms in the major histocompatibility complex (MHC; in particular HLA-C) gene regions are associated with a lower viral load at the set point and additionally with delayed human immunodeficiency virus type 1 (HIV-1) disease progression (Fellay et al., 2007;Limou et al., 2009;van Manen et al., 2009). These findings, which echo a previous report on the association between HLA-C alleles and rapid progression to AIDS (Carrington et al., 1999), have prompted wide speculations on the role of HLA (and HLA-C in particular) in HIV biology and immunology. HLA-C differs from HLA-A and -B because HIV-1 selectively downregulates HLA-A and -B, but does not significantly affect HLA-C (or HLA-E). Therefore, infected cells display reduced detection by both cytotoxic lymphocytes and natural killer (NK) cells (Cohen et al., 1999). The hypothesis that HLA-C might exert an effect directly on HIV infectivity was originally suggested by De Santis et al. (1996), exploiting the peculiar specificity of monoclonal antibody (mAb) L31 to show that normal levels of Env-driven fusion were restored in HLA-C transfectants (Grassi et al., 1991;Setini et al., 1996) of an MHC-deleted (fusion-incompetent) cell line. The physiological relevance of this finding is confirmed in this report, where small interfering RNA (siRNA) technology was used to silence HLA-C expression in peripheral blood lymphocytes (PBLs), the natural target of HIV-1. Two different kinds o...

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Section: Discussionmentioning

confidence: 99%

HLA-C is necessary for optimal human immunodeficiency virus type 1 infection of human peripheral blood CD4 lymphocytes

Baroni

Matucci

Scarlatti

et al. 2009

Journal of General Virology

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“…Viral RNA extraction from plasma samples, cDNA synthesis, genome (ϳ9.1 kb) amplification, cloning, and sequencing were performed as described previously (59). We amplified viral genomes from single viral RNA templates.…”

Section: Methodsmentioning

confidence: 99%

Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes

Herbeck

Rolland

Liu

et al. 2011

J Virol

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HIV-1 transmission and viral evolution in the first year of infection were studied in 11 individuals representing four transmitter-recipient pairs and three independent seroconverters. Nine of these individuals were enrolled during acute infection; all were men who have sex with men (MSM) infected with HIV-1 subtype B. A total of 475 nearly full-length HIV-1 genome sequences were generated, representing on average 10 genomes per specimen at 2 to 12 visits over the first year of infection. Single founding variants with nearly homogeneous viral populations were detected in eight of the nine individuals who were enrolled during acute HIV-1 infection. Restriction to a single founder variant was not due to a lack of diversity in the transmitter as homogeneous populations were found in recipients from transmitters with chronic infection. Mutational patterns indicative of rapid viral population growth dominated during the first 5 weeks of infection and included a slight contraction of viral genetic diversity over the first 20 to 40 days. Subsequently, selection dominated, most markedly in env and nef. Mutants were detected in the first week and became consensus as early as day 21 after the onset of symptoms of primary HIV infection. We found multiple indications of cytotoxic T lymphocyte (CTL) escape mutations while reversions appeared limited. Putative escape mutations were often rapidly replaced with mutually exclusive mutations nearby, indicating the existence of a maturational escape process, possibly in adaptation to viral fitness constraints or to immune responses against new variants. We showed that establishment of HIV-1 infection is likely due to a biological mechanism that restricts transmission rather than to early adaptive evolution during acute infection. Furthermore, the diversity of HIV strains coupled with complex and individual-specific patterns of CTL escape did not reveal shared sequence characteristics of acute infection that could be harnessed for vaccine design.

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“…Sequences were selected from the Los Alamos HIV-1 sequence database (http://hiv-web.lanl.gov/content/hiv-db/mainpage.html) in August 2005 (n ϭ 118) and from sequences obtained as part of our studies of South African subjects (n ϭ 152) from KwaZulu-Natal Province, South Africa (42). The South African sequences we obtained were collected as part of a study approved by the University of Washington and University of KwaZulu-Natal internal review boards, and all subjects gave informed consent.…”

Section: Methodsmentioning

confidence: 99%

Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections

Rousseau

Learn

Bhattacharya

et al. 2007

J Virol

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Recombinant human immunodeficiency virus type 1 (HIV-1) strains containing sequences from different viral genetic subtypes (intersubtype) and different lineages from within the same subtype (intrasubtype) have been observed. A consequence of recombination can be the distortion of the phylogenetic signal. Several intersubtype recombinants have been identified; however, less is known about the frequency of intrasubtype recombination. For this study, near-full-length HIV-1 subtype C genomes from 270 individuals were evaluated for the presence of intrasubtype recombination. A sliding window schema (window, 2 kb; step, 385 bp) was used to partition the aligned sequences. The Shimodaira-Hasegawa test detected significant topological incongruence in 99.6% of the comparisons of the maximum-likelihood trees generated from each sequence partition, a result that could be explained by recombination. Using RECOMBINE, we detected significant levels of recombination using five random subsets of the sequences. With a set of 23 topologically consistent sequences used as references, bootscanning followed by the interactive informative site test defined recombination breakpoints. Using two multiple-comparison correction methods, 47% of the sequences showed significant evidence of recombination in both analyses. Estimated evolutionary rates were revised from 0.51%/year (95% confidence interval [CI], 0.39 to 0.53%) with all sequences to 0.46%/year (95% CI, 0.38 to 0.48%) with the putative recombinants removed. The timing of the subtype C epidemic origin was revised from 1961 (95% CI, 1947 to 1962) with all sequences to 1958 (95% CI, 1949 to 1960) with the putative recombinants removed. Thus, intrasubtype recombinants are common within the subtype C epidemic and these impact analyses of HIV-1 evolution.Human immunodeficiency virus type 1 (HIV-1) genetic diversity is generated during viral replication and is caused by error-prone reverse transcription, host-mediated hypermutation, and recombination. Recombination has been estimated to occur approximately 2.8 times per genome per viral replication cycle (61). Detectable recombination requires simultaneous infection with more than one virus at the cellular level. In a previous report, an average of three to four distinct proviral genomes were found in infected spleen cells (21), indicating that conditions do exist for extensive recombination between different viral genomes. Indeed, numerous intersubtype recombinants resulting in both unique forms found in single individuals and circulating forms have been observed (http://hiv-web.lanl.gov/content/hiv-db /CRFs/CRFs.html). Furthermore, recombination among sequences from the same subtype, or intrasubtype recombination, has also been observed within individual patients (36,47,59).Recombination can distort the phylogenetic signal. In phylogenetic analyses, the variant sites in the recombinant portions of the genome will appear as parallel evolution (homoplasy) instead of a single lineage. This can cause longer branch lengths, overestimate th...

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Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes

Cited by 87 publications

References 34 publications

HLA-C is necessary for optimal human immunodeficiency virus type 1 infection of human peripheral blood CD4 lymphocytes

HLA-C is necessary for optimal human immunodeficiency virus type 1 infection of human peripheral blood CD4 lymphocytes

Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes

Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections

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