Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan

Rashid A. Kang L. Yi F. Mir F. Getaneh Y. Shao Y. Abidi S.H.
2023 Frontiers Media SA

Frontiers in Cellular and Infection Microbiology
2023 #13

Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the pol gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into pol and vif regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into vpu, rev, tat and env regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks. Copyright

children , genetic recombination , HIV-1 , Larkana , Pakistan , phylogeny

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School of Medicine, Nankai University, Tianjin, China
State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
College of Life Sciences, Nankai University, Tianjin, China
Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
Ethiopian Public Health Institute, Addis Ababa, Ethiopia
Changping Laboratory, Beijing, China
Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan

School of Medicine
State Key Laboratory for Infectious Disease Prevention and Control
College of Life Sciences
Department of Pediatric and Child Health
Ethiopian Public Health Institute
Changping Laboratory
Department of Biological and Biomedical Sciences
Department of Biomedical Sciences

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