Molecular characterization and drug resistance pattern in pol gene of HIV-1 sub-subtypes circulating in Lahore, Pakistan.

Abstract

This study aimed to determine sub-subtypes and circulating recombinant forms (CRFs) in Pakistan using the pol gene, identification of amino acid substitutions, structural changes, and drug resistance evaluation in the p66 region of reverse transcriptase. A total of 50 HIV-positive blood samples were collected from Lahore Pakistan, confirmed by Real Time-Polymerase Chain Reaction. The samples were further processed for pol gene amplification followed by nucleotide sequencing through the Sanger method. Out of 50 samples, 26 samples were amplified, and 14 sequences were obtained. The sequences were aligned with reference sequences to determine subtyping and phylogenetic analysis. Moreover, amino acid substitutions and drug resistance patterns were also determined in the RTp66 region. Phylogenetic analysis showed that 8 sequences of our isolates were closely related to circulating recombinant form (CRF43_02 G), and 3 sequences were of CRF30_026 (CRF02_AG) subtypes while the remaining 3 sequences were related to CRF35_A1D, CRF95_02B (CRF02_AG) and Subtype G of HIV-1. Several amino acid substitutions were identified in our isolates which show no impact on the structure of protein. Furthermore, the isolate QAU-AZ2 (OR086936) proposes variable degree of resistance to nevirapine (NVP), etravirine (ETR), rilpivirine (RPV), efavirenz (EFV), Doravirine (DOR); while no resistance against NNTRI and NTRI was observed in the remaining isolates. Further studies are required to (i) examine the function of identified amino acid substitutions through molecular docking, and (ii) sequence the complete pol gene of the viral isolates from Pakistani patients to determine possible drug resistance associated with amino acid substitutions.