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

Abstract

Background: 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.

Methods: 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.

Results: 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.

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 to 1990, additional strains are likely circulating in DRC and possibly elsewhere.

FIGURE 1.

Coverage plot of NGS data for the CG-0018a-01 HIV-xGen library illustrates the average coverage depth of 47,783 across the length of the genome.

FIGURE 2.

Sequence analysis of the CG-0018a-01 complete genome. A, HIV-1 group M maximum likelihood phylogenetic tree (7578 bp) shows the sequence of CG-0018a-01 groups with the 2 putative subtype L sequences with a bootstrap of 100. B, SimPlot (Window: 500 bp, Step: 50 bp) and Bootscan (Window: 500 bp, Step 100 bp) show % identity is highest to the putative subtype L reference sequences except in the well-conserved pol region (approximate positions 3500–4600). C, Results of neighbor-joining phylogenetic analysis of positions 3500–4600 show that the sequence of CG-0018a-01 continues to group with the putative subtype L sequences with a bootstrap of 97.