Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

Abstract

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan.

Circulation of multiple subtypes (A, G and CRFs 02_AG) of human immunodeficiency virus type 1 (HIV-1) in selected districts of Punjab province, Pakistan

“…In another study, population density and frequent migration of HIV-infected individuals have been suggested to influence the emergence of novel subtypes or inter-subtype recombinants and circulating recombinant forms [37,38]. The findings of the current study are in agreement with a previous study conducted in Sindh province, Pakistan, in which multiple HIV-1 subtypes and inter-subtype recombinants were identified [15,[39][40][41]. Furthermore, according to the Los Alamos HIV Database, subtype A (74.2%) is the most frequently reported HIV-1 subtype in Pakistan, while subtype B, C, G, A1/G, 02_AG, 35_AD, 02A1, 01_AE and others account for 5.7%, 4.3%, 1.6% and 1.7%, 4.3%, 1.4%, 2.7%, 2.9% and 1.3%, respectively (www.hiv.lanl.gov).…”

Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines

“…CRF01_AE has spread widely through sexual transmission among MSMs. The significantly higher percentage of recombinants in this study than those previously reported [4,8,9] demonstrates that the proportion of recombinants in a region can be significantly underestimated using only partial genome sequences [31][32][33][34]. An accurate distribution of HIV-1 subtypes, CRFs and unique recombinants can only be reliably estimated by NFLG sequences.…”

HIV-1 phylodynamic analysis among people who inject drugs in Pakistan correlates with trends in illicit opioid trade

“…Recently, Chen et al . [ 10 ] reported on unique CRF02_AG/A1 recombinants, indicating ongoing recombination between locally transmitted CRF02_AG and A1 strains, suggesting that these unique recombinants may become major epidemic strains in Pakistan. It is likely that we underestimated the proportion of recombinant HIV-1 sequences in our population given we only sequenced a portion of the HIV-1 pol gene.…”

“…The observed 20-30% amplification failure was likely due to nucleic acid degradation during storage [8] and/or low viral loads (≦ 1,000 copies/mL) [9]. Even though our HIV-1 genotyping primers have been validated in-house as part of the Canadian HIV-1 Strain and Drug Resistance Surveillance program, we cannot rule out the possibility of amplification failure attributed to poor primer annealing efficiency to sequences from unique HIV-1 circulating recombinant forms (CRFs) recently reported in Pakistan [10].…”