Journal of virology 2017 01 11() pii 10.1128/JVI.01841-16
As the epidemiological epicentre of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43.02%), but 7 other subtypes (33.14%), 20 circulating recombinant forms (CRFs: 11.63%), and 20 unclassified (11.63%) sequences were also found. Of the rare and unclassified subtypes, 18 specimens were selected for next generation sequencing (NGS) by a modified HIV-SMART method to obtain full genome sequences. NGS produced 14 new complete genomes, which included pure subtypes C (n=2), D (n=1), F1 (n=1), H (n=3), and J (n=1). The two Cs and one of the H genomes branched basal to their respective subtype branches but had no evidence of recombination. The remaining 6 genomes were complex recombinants of 2 or more subtypes, including A1, F, G, H, J, K, and unclassified fragments, including one CRF25 isolate, which branched basal to all CRF25 references. Notably, all recombinant H fragments branched basal to the H clade. Spatial-geographical analysis indicated that the diverse sequences identified here did not expand globally. The full- and sub-genomic sequences identified in our study population significantly increase the documented diversity of the continually evolving HIV-1 pandemic.
Very little is known about the ancestral HIV-1 strains that founded the global pandemic, and very few complete genome sequences are available from patients in the Congo Basin where HIV-1 expanded early in the global pandemic. By sequencing a sub-genomic fragment of the HIV-1 envelope from study participants in the DRC, we identified rare variants for complete genome sequencing. The basal branching of some of the complete genome sequences we recovered suggests that these strains are more closely related to ancestral HIV-1 sequences than to previously reported strains and is evidence that the local diversification of HIV in the DRC continues to outpace the diversity of global strains decades after the emergence of the pandemic.