A novel HIV-1 circulating recombinant form (CRF161_0107) from CRF01_AE-C5 lineage among men who have sex with men in southwestern China

Samples were collected from three men who have sex with men (MSM) infected with HIV-1 (19KMM070, 18KMM039 and 20M100) in Yunnan Province in 2018, 2019 and 2020, respectively. Near-full-length genome (NFLG) sequences were amplified using nested PCR and Sanger sequencing. The NFLGs spanned from the 5' long terminal repeat (LTR) to the 3' LTR, with lengths of 8,415 bp (660–9,068 bp on HXB2), 8,759 bp (638–9,368 bp on HXB2) and 8,730 bp (760–9,513 bp on HXB2), respectively. These NFLGs had a consistent mosaic architecture comprising alternating CRF01_AE and CRF07_BC segments. Five breakpoints partitioned the genome into six subregions (HXB2 coordinates): ICRF01_AE (760–3959), IICRF07_BC (3960–6120), IIICRF01_AE (6121–6347), IVCRF07_BC (6348–8231), VCRF01_AE (8232–8484) and VICRF07_BC (8485–9513). This recombinant form was designated a novel CRF: CRF161_0107.