Identification of a Novel Second-Generation HIV-1 Circulating Recombinant Form (CRF174_0708) Arising from CRF07_BC and CRF08_BC in Yunnan, China

Extraordinary HIV-1 recombination is occurring in China. Here, a novel second-generation circulating recombinant form (CRF174_0708) was found in Yunnan Province, China. First, Bootscanning revealed a mosaic structure with three subtype B segments inserted into a subtype C backbone. However, phylogenetic analysis showed that subregions 2B (2978-3267) and 4B (6023-6196) were related to CRF07_BC, whereas subregion 6B (8846-8997) was related to CRF08_BC, suggesting that the sequences could be recombined from CRF07_BC and CRF08_BC. Furthermore, Bootscanning-guided partitioning with subregion-specific phylogenetic analysis confirmed that subregions I (790-1902), III (2636-3746), V (4327-5825), VII (6023-6196) and IX (6379-6782) from CRF07_BC, and subregions II (1903-2635), IV (3747-4326), VI (5826-6022), VIII (6197-6378) and XI (7463-9512) from CRF08_BC. Bayesian dating traced the emergence to 2005-2007, consistent with the expansion of the parental strains. This discovery advanced our understanding of HIV-1 evolution.