Molecular Diversity of HIV-1 among Long Term Non-progressors attending MJAP-ISS clinic, Mulago

Abstract

Background: To date efforts are still being made to develop an efficacious and safe vaccine to stop the spread of Human Immunodeficiency Virus. Long term non-progressors (LTNPs); who harbour the virus but clinically show some control over it, present clues for development of prophylactic and therapeutic development to abrogate disease or prevent infection. Studies to determine mechanisms of natural HIV control in the absence of ART have proposed a number of host and viral mechanisms involved, albeit only explain approximately 50% of LTNP status meaning that the other half remains unaccounted for. Further studies need to continue to be done to unmask more mechanisms of disease non-progression. This study sought to investigate virological factors associated with disease non-progression in a Ugandan cohort of LTNPs attending MJAP ISS clinic, Mulago. We determined the proportions of HIV-1 subtypes among LTNPs and the prevalence of known drug resistant mutations in the pol gene of their virus. Methods: We conducted a cross-sectional HIV sequence analysis on 43 LTNPs and 12 progressors in a parent study (ELITE Study). Plasma viral loads were determined with Roche Cobas HIV-1 Monitor test kit and RNA extraction with Qiagen Viral RNA Mini-kit from samples with >1,000RNA copies/ml. Hi-Fidelity Superscript III kit was used for cDNA synthesis and a nested PCR with Choice Taq to PCR amplify fragments. Sanger sequencing (Big Dye Terminator) with an automated ABI 3730XL was used to obtain sequences. Sequences were edited in Bio-Edit software and mutations in sequences determined by uploading into the Stanford HIV Drug resistance database. Results: Thirteen (13) LTNPs samples have been studied, amplified and sequenced for structural genes with varying success; Pol (11 of PR-RT and 5 of Integrase), Gag (7) and Env (5). Based on pol sequences, 4 of the viruses were subtype A and 9 of subtype D. Three patients had accessory Protease inhibitor drug resistance mutations; L33F and Q58E. One of the three had major Nucleoside Reverse transcriptase mutations i.e. D67DG, K70KT, T215TNSY & K219N. Another 1 of the 3 had major Non-Nucleoside Reverse Transcriptase mutation. Conclusion. Subtype D was the most predominant subtype among LTNPs and drug resistance mutations were found in females with HIV-1 subtype A.