Objective To investigate the molecular epidemiological characteristics and drug resistance of HIV-1 among newly diagnosed antiretroviral therapy (ART)-naive infected individuals aged < 50 years in Pudong New Area, Shanghai, 2019–2021, and to provide evidence to refine local HIV prevention and control strategies.

Methods Blood samples (n=374) were collected from individuals newly diagnosed with HIV infection between 2019 and 2021. Inclusion criteria were as follows: (1) confirmed first-time HIV-positive diagnosis by Western blot and without prior ART, (2) age less than 50 years, (3) voluntary participation, and (4) current residence or employment in Pudong New Area. Exclusion criteria were: (1) unsuccessful RNA extraction or sequencing, (2) mixed bases in the HIV-pol region sequence ≥5%, and (3) sequences shorter than 1 000 base pairs. The HIV-1 pol gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) for both pretreatment drug resistance genotyping and HIV-1 subtype determination, with subsequent analysis using the Stanford University HIV Drug Resistance Database for 302 successfully sequenced samples. Demographic and epidemiologic data were collected through structured in-person interviews.

Results A total of 13 HIV-1 subtypes and unique recombinant forms (URFs) were identified among the 302 sequenced samples, of which 72.52% were from homosexual and 27.48% from heterosexual infections. The predominant strains were CRF07_BC (40.40%), CRF01_AE (36.09%) and CRF55_01B (8.28%). A significant variance in the distribution of viral subtypes was observed among individuals infected by different sexual transmission routes (χ²=22.161, P=0.003). However, the distribution of the prevalent strains CRF01_AE, CRF07_BC and CRF55_01B did not differ significantly between homosexual and heterosexual transmission (χ²=4.854, P=0.088), nor among the three age groups 15–24, 25–34 and 35–49 years (χ²=1.383, P=0.847). Resistance analysis showed a resistance rate of 5.96% in this population, with resistance levels ranging from low to intermediate to high. Non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs) and protein inhibitors (PIs) accounted for 4.97%, 0.66% and 0.33% of resistance, respectively. The difference in resistance rates between subtypes was statistically significant (χ²=10.511, P=0.037). All cases (n=25) of the recombinant subtype CRF55_01BC had mutations at the resistance locus, resulting in an 88.00% incidence of mutations at potential resistance loci and a 12.00% incidence of resistance associated with moderate to high levels of resistance.

Conclusions From 2019 to 2021, among the newly diagnosed HIV-1 infected individuals of young and middle-aged population in Pudong New Area, Shanghai, the genetic subtypes were predominantly CRF07_BC, CRF01_AE and CRF55_01B. However, new recombinant strains have emerged, indicating a trend toward diversification. In addition, varying degrees of pre-treatment drug resistance were observed in several subtypes.