scholarly journals 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

PLoS ONE ◽  
2017 ◽  
Vol 12 (12) ◽  
pp. e0188603 ◽  
Author(s):  
Shuba Varshini Alampalli ◽  
Michael M. Thomson ◽  
Raghavan Sampathkumar ◽  
Karthi Sivaraman ◽  
Anto Jesuraj U. K. J. ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Full Length ◽  
Southern India ◽  
Recombinant Form ◽  
Subtype C ◽  
Hiv 1

scholarly journals Near Full-Length Genome Identification of a Novel HIV-1 Recombinant Form (CRF01_AE/B′/C) Among Heterosexuals in Jilin, China

2014 ◽  
Vol 30 (7) ◽  
pp. 695-700 ◽  
Author(s):  
Xingguang Li ◽  
Chuanyi Ning ◽  
Yanli Chen ◽  
Yi Feng ◽  
Min Wei ◽  
...  
Keyword(s):  
Full Length ◽  
Recombinant Form ◽  
Full Length Genome ◽  
Hiv 1

Full-Length Genome Analysis of HIV-1 Subtype C Utilizing CXCR4 and Intersubtype Recombinants Isolated in South Africa

2002 ◽  
Vol 18 (12) ◽  
pp. 879-886 ◽  
Author(s):  
Maria A. Papathanasopoulos ◽  
Tonie Cilliers ◽  
Lynn Morris ◽  
John L. Mokili ◽  
William Dowling ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Analysis ◽  
Full Length ◽  
Subtype C ◽  
Full Length Genome ◽  
Hiv 1

scholarly journals A Recent Outbreak of Human Immunodeficiency Virus Type 1 Infection in Southern China Was Initiated by Two Highly Homogeneous, Geographically Separated Strains, Circulating Recombinant Form AE and a Novel BC Recombinant

2000 ◽  
Vol 74 (23) ◽  
pp. 11286-11295 ◽  
Author(s):  
Sucheep Piyasirisilp ◽  
Francine E. McCutchan ◽  
Jean K. Carr ◽  
Eric Sanders-Buell ◽  
Wei Liu ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Southern China ◽  
Recombinant Form ◽  
Subtype C ◽  
Subtype B ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT New outbreaks of human immunodeficiency virus type 1 (HIV-1) among injecting drug users (IDUs) are spreading in China along heroin trafficking routes. Recently, two separate HIV-1 epidemics among IDUs were reported in Guangxi, Southern China, where partial sequencing of the env gene showed subtype C and circulating recombinant form (CRF) AE. We evaluated five virtually full-length HIV-1 genome sequences from IDUs in Guangxi to determine the genetic diversity and the presence of intersubtype recombinants. Sequence analysis showed two geographically separated, highly homogeneous HIV-1 strains. B/C intersubtype recombinants were found in three IDUs from Baise City, in a mountainous region near the Yunnan-Guangxi border. These were mostly subtype C, with portions of the capsid and reverse transcriptase (RT) genes from subtype B. The subtype B portion of the capsid was located in the N-terminal domain, which has been shown to influence virus core maturation, virus infectivity, and binding to cyclophilin A, whereas the subtype B portion of RT was located in the palm subdomain, which is the active site of the enzyme. These BC recombinants differed from a BC recombinant found in Xinjiang Province in northwestern China. CRF AE strains were found in IDUs from Nanning, the capital of Guangxi, and in IDUs from Pingxiang City near the China-Vietnam border. The AE and BC recombinants were both remarkable for their low interpatient diversity, less than 1% for the full genome. Rapid spread of HIV-1 among IDUs may foster the emergence of highly homogeneous strains, including novel recombinants in regions with multiple subtypes.

Full-Length Sequence of an Ethiopian Human Immunodeficiency Virus Type 1 (HIV-1) Isolate of Genetic Subtype C

1996 ◽  
Vol 12 (14) ◽  
pp. 1329-1339 ◽  
Author(s):  
MIKA O. SALMINEN ◽  
BO JOHANSSON ◽  
ANDERS SÖNNERBORG ◽  
SEYOUM AYEHUNIE ◽  
DEANNA GOTTE ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Full Length ◽  
Subtype C ◽  
Genetic Subtype ◽  
Immunodeficiency Virus ◽  
Full Length Sequence ◽  
Hiv 1

scholarly journals Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages

2021 ◽  
Author(s):  
Paballo Nkone ◽  
Shayne Loubser ◽  
Thomas C. Quinn ◽  
Andrew D. Redd ◽  
Arshad Ismail ◽  
...  
Keyword(s):  
T Lymphocyte ◽  
Deep Sequencing ◽  
Sanger Sequencing ◽  
Cytotoxic T Lymphocyte ◽  
Sequencing Data ◽  
Subtype C ◽  
Ctl Epitopes ◽  
Significant Difference ◽  
Minority Variant ◽  
Hiv 1

Abstract Background Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. In this study, deep sequencing was employed for characterisation of HIV-1 Pol CTL epitopes in mostly paired samples obtained during early and chronic stages of infection. Deep sequencing data was then compared to Sanger sequencing data only in samples obtained at baseline. Results Fifty-two participants were enrolled in the study. Their median age was 28 years (interquartile range: 24–32 years) and the majority of participants (92.3%) were female. Illumina minority variant analysis identified a significantly higher number of CTL epitopes (n = 65) compared to epitopes (n = 8) identified through Sanger sequencing. Most of the identified epitopes mapped to reverse transcriptase (RT) and integrase (IN) regardless of the method of sequencing. There was a significantly higher proportion of minority variant epitopes in RT (n = 39, 60.0%) compared to IN (n = 17, 26.2%) and PR (n = 9, 13.8%), p = 0.002 and < 0.0001, respectively. However, no significant difference was observed between the proportion of minority variant epitopes in IN versus PR, p = 0.06. Some epitopes were detected in either early or chronic HIV-1 infection whereas others were detected in both stages. Different distribution patterns of minority variant epitopes were observed in sample pairs; with some increasing or decreasing over time, while others remained constant. Some of the identified epitopes have not been previously reported for HIV-1 subtype C. There were also variants that could not be mapped to reported CTL epitopes in the Los Alamos HIV database. Conclusion Deep sequencing revealed many Pol CTL epitopes, including some not previously reported for HIV-1 subtype C. The findings of this study support the inclusion of RT and IN epitopes in HIV-1 vaccine candidates as these proteins harbour many CTL epitopes. Variants that were not mapped within CTL epitopes could represent new epitopes.

scholarly journals A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

2020 ◽  
Vol 117 (22) ◽  
pp. 12222-12229 ◽  
Author(s):  
Sophie Gryseels ◽  
Thomas D. Watts ◽  
Jean-Marie Kabongo Mpolesha ◽  
Brendan B. Larsen ◽  
Philippe Lemey ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Biological Data ◽  
Full Length ◽  
Subtype C ◽  
Divergence Time Estimates ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Hiv 1 ◽  
Formalin Fixed

With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 (“DRC66”)—a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.

scholarly journals Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes among chronically infected blood donors at four blood centers in Brazil

2014 ◽  
Vol 14 (S2) ◽  
Author(s):  
Rodrigo Pessôa ◽  
Jaqueline Tomoko Watanabe ◽  
Paula Loureiro ◽  
Maria Esther Lopes ◽  
Anna Barbara Carneiro-Proietti ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Blood Donors ◽  
Full Length ◽  
Infected Blood ◽  
Hiv 1
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