HIV-1 transmitted drug resistance in Shanghai, 2018–2024: population mobility shapes cross-population TDR transmission dynamics

We analyzed HIV-1 <i>pol</i> sequences from 7,538 newly diagnosed, treatment-naïve individuals in Shanghai (2018–2024), integrating genotypic resistance testing, molecular transmission network analysis, and time-scaled discrete phylogeographic inference. Individuals with Shanghai hukou were classified as Shanghai residents, whereas those without Shanghai hukou were categorized by residence as resident migrants (residing in Shanghai) or temporary migrants (residing outside Shanghai).

Overall TDR prevalence was 5.1% (95% CI: 4.6%–5.6%), and was higher among individuals with recent infections (7.3%, 95% CI: 5.6%–9.5%; <i>P</i> = 0.004). Non-nucleoside reverse transcriptase inhibitors (NNRTIs)-associated resistance increased significantly over the study period (adjusted <i>P</i> = 0.009) driven primarily by K103N/S. In multivariable analysis, TDR was independently associated with recent infection (AOR = 1.66) and resident migrant status (AOR = 1.31).