2026-06-30T03:03:29Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/66302024-09-27T20:55:16Zcom_20.500.12105_2052com_20.500.12105_2051col_20.500.12105_19609
Repisalud
author
Alampalli, Shuba Varshini
author
Thomson, Michael M
author
Sampathkumar, Raghavan
author
Sivaraman, Karthi
author
U K J, Anto Jesuraj
author
Dhar, Chirag
author
D Souza, George
author
Berry, Neil
author
Vyakarnam, Annapurna
funder
Unión Europea. Comisión Europea. 7 Programa Marco
2018-11-19T14:13:43Z
2018-11-19T14:13:43Z
2017
PLoS One. 2017 Dec 8;12(12):e0188603
10.1371/journal.pone.0188603
1932-6203
1932-6203
PloS one
29220350
http://hdl.handle.net/20.500.12105/6630
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.
eng
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
journal article
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URL
https://repisalud.isciii.es/bitstreams/19330b1d-152d-463f-9950-558c076d6908/download
File
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application/pdf
DeepSequencingOfNear_2017.pdf
URL
https://repisalud.isciii.es/bitstreams/552628ff-def4-4394-9ff8-109af324871b/download
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DeepSequencingOfNear_2017.pdf.txt