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J Virol. 2017 Feb 28;91(6). pii: e01841-16. doi: 10.1128/JVI.01841-16. Print 2017 Mar 15.

Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo.

Author information

1
Infectious Disease Research, Abbott Diagnostics, Abbott Park, Illinois, USA mary.rodgers@abbott.com.
2
Wellcome Trust-Africa Centre for Population Health, University of KwaZulu-Natal, Durban, Republic of South Africa.
3
College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa.
4
Infectious Disease Research, Abbott Diagnostics, Abbott Park, Illinois, USA.
5
School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA.
6
Presbyterian Church (USA), Kinshasa, Democratic Republic of the Congo.
7
Research Department of Infection, University College London, London, United Kingdom.

Abstract

As the epidemiological epicenter 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-switching mechanism at the 5' end of the RNA template (SMART) method to obtain full-genome sequences. NGS produced 14 new complete genomes, which included pure subtype C (n = 2), D (n = 1), F1 (n = 1), H (n = 3), and J (n = 1) genomes. The two subtype C genomes and one of the subtype 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 subtypes A1, F, G, H, J, and K and unclassified fragments, including one subtype CRF25 isolate, which branched basal to all CRF25 references. Notably, all recombinant subtype H fragments branched basal to the H clade. Spatial-geographical analysis indicated that the diverse sequences identified here did not expand globally. The full-genome and subgenomic sequences identified in our study population significantly increase the documented diversity of the strains involved in the continually evolving HIV-1 pandemic.IMPORTANCE 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 subgenomic 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 that we recovered suggests that these strains are more closely related to ancestral HIV-1 strains 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.

KEYWORDS:

HIV-1 surveillance; full-length genome; genetic diversity; next-generation sequencing; phylogenetic analysis; recombination

PMID:
28077647
PMCID:
PMC5331799
DOI:
10.1128/JVI.01841-16
[Indexed for MEDLINE]
Free PMC Article

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