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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

Alampalli, Shuba Varshini ; Thomson, Michael M ; Sampathkumar, Raghavan ; Sivaraman, Karthi ; U K J, Anto Jesuraj ; Dhar, Chirag ; D Souza, George ; Berry, Neil ; Vyakarnam, Annapurna Paxton, William A.

PloS one, 2017-12, Vol.12 (12), p.e0188603-e0188603 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
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
Autor: Alampalli, Shuba Varshini ; Thomson, Michael M ; Sampathkumar, Raghavan ; Sivaraman, Karthi ; U K J, Anto Jesuraj ; Dhar, Chirag ; D Souza, George ; Berry, Neil ; Vyakarnam, Annapurna
Paxton, William A.
Assuntos: Acquired immune deficiency syndrome ; AIDS ; Algorithms ; Analysis ; Biology and Life Sciences ; Computer and Information Sciences ; Distribution ; DNA sequencing ; Drug resistance ; Gag protein ; Gene sequencing ; Genetic aspects ; Genomes ; Genomics ; Geography ; HIV ; HIV (Viruses) ; Human immunodeficiency virus ; Medicine and Health Sciences ; Nucleotide sequencing ; Pandemics ; Phylogeny ; Recovery ; Research and Analysis Methods ; Tuberculosis ; Viruses
É parte de: PloS one, 2017-12, Vol.12 (12), p.e0188603-e0188603
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Competing Interests: The authors have declared that no competing interests exist.
These authors also contributed equally to this work.
Descrição: 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.
Editor: United States: Public Library of Science
Idioma: Inglês

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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

Alampalli, Shuba Varshini ; Thomson, Michael M ; Sampathkumar, Raghavan ; Sivaraman, Karthi ; U K J, Anto Jesuraj ; Dhar, Chirag ; D Souza, George ; Berry, Neil ; Vyakarnam, Annapurna Paxton, William A.

United States: Public Library of Science

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