Unassigned complex unique recombinant forms related to CRF36_cpx in children identified in an HIV-1 outbreak in Pakistan

In 2019, an outbreak of HIV infection predominantly affecting children occurred in Larkana district, Pakistan. This is the largest outbreak ever reported in this age group in Pakistan. In this study, we report two HIV-1 unique recombinant forms identified within the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. Pol gene was sequenced and used to detect HIV subtype/recombinant forms using subtype, recombination, and phylogenetic analyses. Drug resistance mutation (DRM) analysis was performed to characterize the drug DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals out of 344 samples. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned URFs in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.