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Brief Report: Complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L.

Authors
  • Yamaguchi, Julie1
  • Vallari, Ana1
  • McArthur, Carole2
  • Sthreshley, Larry3
  • Cloherty, Gavin A1
  • Berg, Michael G1
  • Rodgers, Mary A1
  • 1 Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL.
  • 2 School of Dentistry, University of Missouri-Kansas City, Kansas City, MO; and.
  • 3 Presbyterian Church (USA), Kinshasa, Democratic Republic of the Congo. , (Congo - Kinshasa)
Type
Published Article
Journal
Journal of acquired immune deficiency syndromes (1999)
Publication Date
Mar 01, 2020
Volume
83
Issue
3
Pages
319–322
Identifiers
DOI: 10.1097/QAI.0000000000002246
PMID: 31693506
Source
Medline
Language
English
License
Unknown

Abstract

The full spectrum of HIV-1 diversity can be found in Central Africa, including 2 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. Specimen CG-0018a-01 was collected in 2001 in DRC as part of an HIV diversity study. Previous subgenomic HIV-1 sequences from this specimen branched closely with proposed subtype L references. Metagenomic next-generation sequencing (mNGS) and HIV-specific target-enriched (HIV-xGen) libraries were combined for NGS to extend genome coverage. mNGS reads were analyzed for the presence of other coinfections with the sequence-based ultrarapid pathogen identification bioinformatics pipeline. A complete HIV-1 genome was generated with an average coverage depth of 47,783×. After bioinformatic analysis also identified hepatitis B virus reads, a complete hepatitis B virus genotype A genome was assembled with an average coverage depth of 73,830×. The CG-0018a-01 HIV-1 genome branched basal to the 2 previous putative subtype L strains with strong bootstrap support of 100. With no evidence of recombination present, the strain was classified as subtype L. 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 to 1990, additional strains are likely circulating in DRC and possibly elsewhere.

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