Analysis of gene subtypes and molecular transmission characteristics of HIV-1 infected individuals in Shanghai from 2015 to 2018

Objective Analyze the molecular epidemiological characteristics and influencing factors of human immunodeficiency virus type 1 (HIV-1) infected individuals in Shanghai, and to provide a scientific basis for developing effective intervention measures. Method A total of 1 322 serum samples from newly reported HIV-1 infected individuals between 2015 and 2018 were collected. Nested PCR was employed to amplify the HIV-1 pol gene sequences. Virus subtype analysis was then conducted based on the pol gene sequences, and a molecular network was constructed using the optimal gene distance. The characteristics of the molecular network and its influencing factors were analyzed. Results A total of 1 241 HIV-1 pol gene sequences were obtained from 1 322 samples, and 12 HIV genotypes were identified. The dominant subtypes were with CRF01_AE and CRF07_BC subtypes, accounting for 50.93% and 34.0%. respectively. Among these, 530 sequences entered the molecular network, with a clustering rate of 42.71% (530/1241), A total of 95 transmission clusters were formed, with cluster sizes ranging from 2 to 219 nodes. One large cluster contained 219 nodes (41.32%, 219/530). The highest clustering rate was observed in the CRF07_BC subtype (59.48%, 251/422), followed by 01B (52.46%, 32/61) and CRF01_AE (34.55%, 218/631). Male-to-male sexual transmission was more likely to form networks compared to heterosexual transmission. Conclusions The HIV-1 gene subtypes were diverse, with CRF01_AE and CRF07BC subtypes as the main dominant strainsin Shanghai. during 2015-2018, The molecular network showed an clustered distribution, and MSM are infected with HIV-1 have a faster ability to transmit the virus, leading to higher infection rates and easier entry into the network as high-risk carriers. Strengthening HIV-1 molecular monitoring can timely understand the transmission dynamics of the virus strain in different populations and help public health departments take effective intervention measures to reduce new HIV infections and prevent the spread of the epidemic