This study examined HIV-1 pol sequences from 7,538 newly diagnosed, treatment-naïve individuals in Shanghai collected between 2018 and 2024. The investigators integrated three primary approaches: genotypic resistance testing to identify transmitted drug resistance (TDR), molecular transmission network analysis to map linkage patterns among sequences, and time-scaled discrete phylogeographic inference to assess cross-population movement of TDR lineages. Individuals were classified by hukou and residence: those with Shanghai hukou were defined as Shanghai residents; those without Shanghai hukou but residing in Shanghai were termed resident migrants; and those without Shanghai hukou residing outside Shanghai were categorized as temporary migrants.
Across the cohort, the overall prevalence of transmitted drug resistance (TDR) was 5.1% (95% CI: 4.6%–5.6%). Prevalence was higher among individuals classified as having recent infection, where TDR reached 7.3% (95% CI: 5.6%–9.5%). The difference in TDR prevalence by recent infection status was statistically significant (P = 0.004), indicating that recently infected individuals had a greater likelihood of harboring drug-resistant viruses at diagnosis.
Resistance associated with non-nucleoside reverse transcriptase inhibitors (NNRTIs) increased significantly over the study period; this trend was statistically significant after adjustment (adjusted P = 0.009). The temporal rise in NNRTI-associated TDR was driven primarily by the K103N/S mutation. The abstract reports the aggregate signal of increasing NNRTI resistance and identifies K103N/S as the predominant driver, but further granular data on year-by-year changes or absolute counts by mutation were not reported in the source abstract.
In multivariable analysis, two factors were independently associated with higher odds of TDR. Recent infection was associated with an adjusted odds ratio (AOR) of 1.66. Resident migrant status (i.e., individuals without Shanghai hukou who resided in Shanghai) was associated with an AOR of 1.31. These findings indicate that both recency of infection and population mobility status were independent correlates of transmitted resistance in this cohort. The abstract does not provide the full set of covariates included in the multivariable model or additional model diagnostics; those details were not reported in the source abstract.
TDR sequences were not randomly distributed across inferred transmission networks. Statistical testing demonstrated significant non-random clustering of TDR sequences within networks (P < 0.001). Notably, 59.2% of the networked TDR sequences were concentrated within a small fraction of clusters—2.7% of all transmission clusters. This concentration suggests that a small number of clusters account for a large share of networked TDR, consistent with focalized transmission of resistant viruses within particular linkage groups.
Time-scaled discrete phylogeographic analyses indicated substantial cross-population linkages of lineages carrying TDR. Both temporary migrants (individuals residing outside Shanghai) and resident migrants contributed disproportionately to introductions of TDR-associated lineages into the Shanghai network. Resident migrants in particular demonstrated notable network characteristics: they participated in 44.1% of networked links, were overrepresented within TDR transmission clusters (78.9% of those clusters included resident migrants), and were disproportionately involved in TDR-to-TDR network edges (74.3%). These patterns suggest that resident migrants may serve as connective nodes bridging non-local and local transmission networks, thereby facilitating cross-population dissemination of resistant viruses.
The combined findings—moderate overall TDR prevalence (5.1%), higher TDR among recent infections, a rising trend in NNRTI resistance driven by K103N/S, and concentrated clustering with mobility-linked introductions—support a structured pattern of TDR dissemination in a large, mobile urban setting. The results underscore the influence of population mobility on cross-population TDR dynamics and point to potential benefits of targeted surveillance strategies. Specifically, enhanced genotypic resistance testing and network-informed monitoring among mobile subgroups (including resident and temporary migrants) and recently infected individuals may improve early detection of emergent resistant lineages.
The abstract emphasizes implications for surveillance but does not provide specific programmatic recommendations, cost-effectiveness data, or operational details for targeted interventions; such details were not reported in the source abstract.
Keywords included by the authors were: HIV-1; molecular transmission network; phylogeography; population mobility; transmitted drug resistance.