Characteristics of genotype, drug resistance, and molecular transmission network among newly diagnosed HIV‐1 infections in Shenzhen, China

Abstract The HIV‐1 pandemic has persisted for four decades, and poses a major challenge to global public health. Shenzhen, a city with large number of migrant populations in China, is suffering HIV‐1 epidemic. It is necessary to continuously conduct the molecular surveillance among newly diagnosed HIV‐1 patients in these migrant population. In this study, plasma samples of newly diagnosed and ART‐naive HIV‐1 infections were collected from Shenzhen city in China. The partial genes of HIV‐1 gag and pol were amplified and sequenced for the analysis of genotype, drug resistance, and molecular transmission network. Ninety‐one sequences of pol gene were obtained from newly diagnosed HIV‐1 infections in Shenzhen, and seven HIV‐1 subtypes were revealed in this investigation. Among them, the circulating recombinant form (CRF) 07_BC was the mostly frequent subtype (53.8%, 49/91), followed by CRF01_AE (20.9%, 19/91), CRF55_01B (9.9%, 9/91), unique recombinant forms (URFs) (8.8%, 8/91), B (3.3%, 3/91), CRF59_01B (2.2%, 2/91), and CRF08_BC (1.1%, 1/91). The overall prevalence of pretreatment drug resistance (PDR) was 23.1% (21/91), and 52.38% (11/21) of the PDR was specific for the nonnucleotide reverse transcriptase inhibitors (NNRTIs). Furthermore, a total of 3091 pol gene sequences were used to generate 19 molecular transmission clusters, and then one growing cluster, a new cluster, and a cluster with growth reactivation were identified. The result revealed that more sexual partner, CRF_07BC subtype, and seven amino acid deletions in gag p6 region might be the influencing factors associated with the high risk of transmission behavior. Compared with CRF01_AE subtype, CRF07_BC subtype strains were more likely to form clusters in molecular transmission network. This suggests that long‐term surveillance of the HIV‐1 molecular transmission should be a critical measure to achieve a precise intervention for controlling the spread of HIV‐1 in China.