Unassigned Complex Unique Recombinant Forms Related to CRF36_cpx in Children Identified in an HIV-1 Outbreak in Pakistan

Abstract

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 during the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. The 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 DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals of the 344 samples collected. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned unique recombinant forms in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.

Keywords: HIV-1; Pakistan; children; drug resistance; unique recombinant form.

Fig. 1. Phylogenetic analysis of unassigned URFs

(A) ML phylogenetic tree for 14 outbreak sequences represented by the gray box and the Cameroonian CRF02_36cpx recombinant sequence indicated by the black arrow. ML phylogenetic tree for 1 outbreak sequence (AKULO_387) constructed using MSAs (developed on the breakpoints predicted by jpHMM) spanning nucleotides (B) 2236–3192 and (C) 3193–3313 (with reference to the HXB2 position). The AKULO_387 sequence is shown by the black arrow. The node support values of the clusters of interest (A–C). The gray-colored branches represent the aLRT SH-like support values ‡0.80. aLRT, approximate likelihood ratio test; ML, maximum likelihood; SH, Shimodaira–Hasegawa; URF, unique recombinant form.

Figure 2. Phylogenetic analysis of unassigned URF in AKULO 248

Phylogenetic analysis of unassigned URF in AKULO 248: ML phylogenetic tree showing the AKULO_248 sequence (red color). The blue-colored branches represent the aLRT SH-like support values ‡0.80. The AKULO_248 sequence is shown by the black arrow.