Drug-Resistant HIV Strains Circulate Widely in Yunnan Transmission Networks, Study Finds

A detailed genomic surveillance study from Qujing, a prefecture in northeastern Yunnan Province, China, has revealed that drug-resistant HIV-1 strains are not only common among people whose therapy has failed but are also circulating within active local transmission networks that include newly diagnosed, treatment-naive individuals. The research, led by Fangchuan Wei and colleagues at Yunnan Infectious Disease Hospital and published in BMC Infectious Diseases, combined genotypic resistance testing, molecular transmission network analysis, and Bayesian phylogenetics to map how resistance emerges and spreads in a regional epidemic. The findings carry direct implications for how antiretroviral therapy is monitored and how transmission clusters are targeted for intervention.

The study addressed two distinct but connected forms of drug resistance. Pretreatment drug resistance, abbreviated PDR, refers to resistance mutations detected in people who have never yet received antiretroviral therapy, whether acquired at the moment of infection from a partner carrying resistant virus or developed during earlier, sometimes unrecorded, exposure to antiretroviral drugs. Acquired drug resistance, or ADR, by contrast, arises in people receiving treatment, typically when the virus replicates in the presence of suboptimal drug pressure, allowing mutations that compromise drug efficacy to accumulate. Both forms threaten the long-term effectiveness of first-line therapy regimens, and their relative prevalence in a given region shapes treatment policy.

To quantify these phenomena, the team collected blood samples from two groups: individuals experiencing antiretroviral therapy failure between 2023 and 2024, and treatment-naive individuals diagnosed in 2024. From these samples, the researchers used nested reverse transcription polymerase chain reaction to amplify two critical regions of the HIV-1 pol gene, which encodes the viral protease and reverse transcriptase enzymes. These enzymes are the principal targets of the most widely used antiretroviral drug classes, so mutations in the corresponding gene segments translate directly into clinical resistance. The purified amplicons were then sequenced by the Sanger method, and the resulting mutation profiles were interpreted against the Stanford HIV Drug Resistance Database, a widely used reference tool that scores which mutations confer resistance to which drugs.

The results revealed a striking asymmetry between the two populations. Among 341 treatment-naive individuals, the prevalence of pretreatment drug resistance was 10.85 percent, meaning 37 people carried at least one resistance-associated mutation before ever starting therapy. Resistance to non-nucleoside reverse transcriptase inhibitors, or NNRTIs, dominated this picture, accounting for 7.62 percent of the cohort. The specific mutations most frequently observed were at positions E138, found in 7.33 percent of samples, V179 at 4.99 percent, and K103 at 4.40 percent. Resistance to protease inhibitors stood at 2.93 percent, while resistance to nucleoside reverse transcriptase inhibitors, or NRTIs, was comparatively rare at 0.88 percent. This pattern matters clinically because NNRTIs remain components of standard first-line regimens in many settings, and elevated pretreatment resistance to this class can undermine treatment from the outset.

Among the 743 individuals who had experienced treatment failure, the picture was considerably more severe. Acquired drug resistance was detected in 41.45 percent of these samples, with NNRTI resistance again the most prevalent category at 37.55 percent. The mutation landscape mirrored that seen in the naive group: K103 mutations appeared in 24.76 percent of samples, E138 in 11.04 percent, and V179 in 10.77 percent. NRTI resistance affected 17.23 percent of the treatment-failure cohort, with the M184 mutation, which compromises the widely used drugs lamivudine and emtricitabine, predominant at 15.61 percent. Protease inhibitor resistance remained relatively uncommon at 2.56 percent. The overlap in dominant mutations between the two groups suggested to the researchers that resistant viruses generated during failed therapy may be passing into new infections rather than arising independently in each newly diagnosed person.

To test that hypothesis, the team turned to molecular transmission network analysis, a technique that compares viral genetic sequences across individuals and links those whose viruses are sufficiently similar, typically within a small genetic distance threshold, into clusters that represent recent or ongoing chains of transmission. The analysis identified CRF08_BC, a circulating recombinant form that combines subtype C and subtype B ancestry and is well established in parts of western China, as the predominant HIV-1 subtype in Qujing and as the major genetic background underlying local transmission clusters. Within these clusters, the E138 and K103 resistance mutations appeared frequently, indicating that NNRTI-resistant viruses were embedded in the very networks driving new infections.

The network analysis also yielded insights into who is most likely to be drawn into transmission clusters. Among treatment-naive individuals, those aged 50 years or older had markedly higher odds of being included in a network, with an adjusted odds ratio of 7.499. HIV-1 subtype and drug resistance status were also independently associated with network membership. This finding points to older adults as a population in which clustered, and potentially rapid, transmission is occurring, a demographic that public health programs have not always prioritized for intensive prevention efforts. The association between resistance status and network inclusion further suggests that resistant viruses are not isolated curiosities but active participants in the local epidemic.

Perhaps the most consequential finding emerged when the researchers constructed a combined network including both treatment-naive and treatment-failure individuals. Of the 16 pretreatment drug resistance cases that fell within the network, 13, or 81.25 percent, were located in mixed clusters that also contained individuals with acquired drug resistance. This co-clustering provides strong molecular evidence that resistance generated under the selective pressure of failing therapy is being transmitted onward to newly infected people, rather than each resistant case in a newly diagnosed individual arising de novo. In other words, the treatment clinic and the transmission network are connected: unmanaged virological failure today becomes pretreatment resistance in tomorrow’s newly diagnosed patients.

Bayesian phylogenetic analysis reinforced this conclusion. By modeling the evolutionary relationships and estimated timing of viral lineages, the analysis supported sustained local circulation of CRF08_BC drug-resistant strains within Qujing itself, rather than repeated introductions of resistant viruses from elsewhere. This distinction is epidemiologically important. Sustained local circulation means that resistant lineages have taken root in the regional epidemic and will continue to propagate unless the chains of transmission are interrupted and virological failure is detected and managed promptly. Imported resistance, by contrast, might be addressed through screening at entry points into the care system; locally entrenched resistance demands sustained surveillance within the community.

The authors conclude that the dominance of NNRTI resistance in both pretreatment and acquired settings, the central role of CRF08_BC in local transmission clusters, the co-clustering of resistant newly diagnosed and treatment-failing individuals, and the sustained local circulation of drug-resistant strains together argue for strengthened drug resistance surveillance, timely detection and management of virological failure, and targeted interventions aimed at highly clustered populations, particularly older adults. The study was approved by the Ethics Review Committee of Yunnan Infectious Disease Hospital and was conducted as a secondary analysis of anonymized surveillance and laboratory data, with the informed consent requirement formally waived. Funded by Yunnan provincial science and technology programs and a national special project on major infectious disease prevention and control, the work illustrates how integrating genotypic resistance testing with molecular epidemiology can transform routine surveillance data into actionable maps of where resistance is born, where it travels, and whom public health programs must reach to stop it.

Subject of Research: HIV-1 drug resistance and molecular transmission networks in Qujing, Yunnan, China

Article Title: HIV-1 genotypic drug resistance and molecular transmission network characteristics in Qujing, Northeastern Yunnan, China

Article References: Wei, F., Li, J., Fan, H., Li, Y., Li, X., Lao, Y., Lou, J., Dong, X., & Liu, J. (2026). HIV-1 genotypic drug resistance and molecular transmission network characteristics in Qujing, Northeastern Yunnan, China. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14544-4

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14544-4

Keywords: HIV-1, drug resistance, pretreatment drug resistance, acquired drug resistance, NNRTI, molecular transmission network, CRF08_BC, Bayesian phylogenetics, antiretroviral therapy, Yunnan, China, genotypic resistance testing