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Complete genome sequence of CG-0018a-01 establishes HIV-1 subtype L

Yamaguchi, Julie BS1; McArthur, Carole MD2; Vallari, Ana MS1; Sthreshley, Larry PhD3; Cloherty, Gavin A. PhD1; Berg, Michael G. PhD1; Rodgers, Mary A. PhD1

JAIDS Journal of Acquired Immune Deficiency Syndromes: November 06, 2019 - Volume Publish Ahead of Print - Issue - p
doi: 10.1097/QAI.0000000000002246
Original Article: PDF Only
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Background: The full spectrum of HIV-1 diversity can be found in central Africa, including two divergent HIV-1 strains collected in 1983 and 1990 in Democratic Republic of Congo (DRC) that were preliminarily classified as group M subtype L. However, a third epidemiologically distinct subtype L genome must be identified to designate L as a true subtype.

Methods: Specimen CG-0018a-01 was collected in 2001 in DRC as part of an HIV prevention of mother to child transmission (PMTCT) study. Prior sub-genomic HIV-1 sequences from this specimen branched closely with proposed subtype L references. Metagenomic (mNGS) and HIV-specific target enriched (HIV-xGen) libraries were combined for next generation sequencing (NGS) to extend genome coverage. mNGS reads were analyzed for the presence of other co-infections with the SURPI bioinformatics pipeline.

Results: A complete HIV-1 genome was generated with an average coverage depth of 47,783x. After bioinformatic analysis also identified Hepatitis B virus (HBV) reads, a complete HBV genotype A genome was assembled with an average coverage depth of 73,830x. The CG-0018a-01 HIV-1 genome branched basal to the two previous putative subtype L strains with strong bootstrap support of 100. With no evidence of recombination present, the strain was classified as subtype L.

Conclusions: The CG-0018a-01 HIV-1 genome establishes subtype L and confirms ongoing transmission in DRC as recently as 2001. Since CG-0018a-01 is more closely related to an ancestral strain than to isolates from 1983 or 1990, additional strains are likely circulating in DRC and possibly elsewhere.

1Infectious Disease Research, Abbott Diagnostics, Abbott Park, Illinois, USA

2School of Dentistry, University of Missouri — Kansas City, Kansas City, Missouri, USA

3Presbyterian Church (USA), Kinshasa, Democratic Republic of the Congo

Corresponding author: Mary A Rodgers, 100 Abbott Park Rd, Abbott Park, IL 60064 Phone: 224-668-8936 Fax: 224-668-3271 e-mail: mary.rodgers@abbott.com

Conflicts of Interest and Sources of Funding: JY, AV, GAC, MGB, and MAR are employees and shareholders of Abbott Laboratories. The study was funded by Abbott Laboratories.

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