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

The investigation was designed as a cross-sectional study drawing participants from the provincial HIV-positive surveillance repository in Jiangxi, a province in southeastern China with a substantial population under long-term antiretroviral care. The researchers applied standardized sample submission criteria to assemble two distinct cohorts. The first comprised 104 treatment-naïve individuals whose baseline viral load had been measured before starting therapy or within 30 days of initiating antiretroviral treatment, allowing assessment of pretreatment drug resistance. The second comprised 307 treatment-experienced individuals who had received standardized antiretroviral therapy for at least six months and who met the definition of virological failure, operationalized as a viral load exceeding 400 copies per milliliter of plasma. By anchoring enrollment in the surveillance system rather than in convenience sampling from single clinics, the study sought to capture a province-wide snapshot of resistance rather than the picture at selected treatment centers alone.

Genotypic resistance testing focused on the pol gene, which encodes the viral enzymes reverse transcriptase and protease, and on the integrase gene, which encodes the enzyme that inserts viral DNA into the host genome. Resistance profiles were interpreted using the Stanford HIV Drug Resistance Database, a widely used algorithm that translates sequence mutations into predicted levels of susceptibility for individual antiretroviral drugs. This genotypic approach detects resistance-associated mutations in the viral genome, the molecular footprints left behind when imperfectly suppressed virus replicates under drug pressure. Because HIV-1 lacks proofreading capability in its reverse transcriptase and replicates prolifically, every untreated infection already carries a swarm of viral variants, and drug exposure selectively amplifies those variants fortunate enough to carry mutations that blunt drug binding or activity.

The headline numbers concern multidrug resistance. In the treatment-naïve group, representing the largely transmitted or pretreatment component of the resistance landscape, multidrug resistance stood at 10.58 percent. Among patients who had failed therapy, the figure reached 28.01 percent, a statistically significant increase reported at a p value below 0.001. This near tripling quantifies what the authors describe as a profound shift: once antiretroviral pressure is applied and virological control is lost, the virus does not merely accumulate resistance to one agent but frequently acquires mutations that compromise entire drug classes simultaneously. For clinicians, multidrug resistance is the form of resistance that matters most, because it constrains the options available for constructing an effective salvage regimen and foreshadows cumulative treatment failure at the population level.

Class-by-class analysis showed that mutations associated with non-nucleoside reverse transcriptase inhibitors predominated. The K103N and K103R mutations, classic signatures of resistance to nevirapine and efavirenz, were detected in 28.66 percent of the virological failure cohort, compared with 9.61 percent among treatment-naïve individuals. These substitutions alter the hydrophobic pocket to which non-nucleoside inhibitors bind, reducing drug affinity by orders of magnitude while leaving viral replicative capacity largely intact, which is precisely why they outcompete wild-type virus under non-nucleoside-based therapy. Alongside this, the M184V and M184I mutations were markedly enriched in the failure group at 25.73 percent. M184V/I confers resistance to lamivudine and emtricitabine, the nucleoside analogues that typically anchor first-line regimens, and its prevalence in failed therapy severely compromises the nucleoside reverse transcriptase inhibitor backbone on which those regimens depend.

Against this troubling backdrop, two drug classes remained notably durable. Susceptibility to protease inhibitors and to integrase strand transfer inhibitors exceeded 93 percent in the study population, indicating that these components of combination therapy retained activity in the overwhelming majority of patients even after treatment failure. This durability reflects both the genetic barrier and the usage patterns of these drugs in the region: protease inhibitors require multiple sequential mutations to lose potency, and integrase inhibitors, particularly the second-generation agents dolutegravir and bictegravir, impose a high fitness cost on resistant variants. The findings therefore support a clinical pivot toward robust salvage regimens built around integrase strand transfer inhibitors, which the authors advocate urgently, especially as Jiangxi and comparable high-burden settings transition toward dolutegravir-based first-line therapy as the new standard of care.

Yet the integrase picture was not entirely reassuring. The study detected the polymorphic accessory mutations L74I or L74M in 2.93 percent of the virological failure cohort. Accessory mutations of this kind do not usually cause outright resistance to first-generation integrase inhibitors such as raltegravir or elvitegravir on their own, but they can contribute to reduced susceptibility and may serve as stepping stones toward higher-level resistance when combined with other substitutions. Their presence at baseline, before patients have accumulated extensive integrase inhibitor exposure, underscores a gap in current surveillance practice: because integrase inhibitors have only recently been scaled up in many Chinese treatment programs, baseline integrase gene sequences have not been routinely collected. The authors argue that establishing integrase surveillance now, before widespread dolutegravir and bictegravir exposure reshapes the viral population, is essential for detecting emerging resistance pathways early.

The distinction between pretreatment drug resistance and acquired drug resistance frames the public health interpretation of these findings. Pretreatment resistance, at roughly one in ten treatment-naïve individuals, reflects resistance transmitted from person to person or acquired during prior, sometimes undocumented, drug exposure. Acquired resistance, by contrast, is generated de novo within patients whose replication is incompletely suppressed, often through adherence gaps, pharmacokinetic variability, or inadequate regimens. The Jiangxi data show that the second process is the dominant engine of the province’s multidrug resistance burden, nearly tripling its prevalence. Each case of virological failure left unmanaged does not merely harm the individual patient; it can seed transmitted resistance into the wider epidemic, so intensified molecular surveillance and prompt regimen switching upon failure are the twin strategies the findings support.

Operationally, the study argues for concrete changes in the region’s treatment architecture. Regular viral load monitoring must be strengthened so that failure, defined here as a viral load above 400 copies per milliliter, is detected and acted upon before extensive resistance accumulates. Resistance genotyping should be deployed at the point of confirmed failure rather than reserved for exceptional cases, and the tested gene panel should expand to include integrase as second-generation integrase inhibitors become first-line. Salvage regimens should be anchored in drugs retaining high susceptibility, with the >93 percent susceptibility to protease and integrase inhibitors in this cohort suggesting these classes are the most reliable foundations. As China consolidates dolutegravir-based therapy nationally, the Jiangxi experience offers a quantitative baseline: a population carrying 10.58 percent pretreatment multidrug resistance that, under prior regimens, climbed to 28.01 percent after treatment exposure. Sustaining the durability that integrase inhibitors currently provide will depend on surveillance that moves as fast as the virus does.

Subject of Research: Acquired multi-class HIV-1 drug resistance emerging after antiretroviral therapy exposure in Jiangxi Province, China

Article Title: Treatment exposure drives a profound shift toward complex multi-class HIV-1 drug resistance

Article References: Mao, Z. Q., Mao, J., Zheng, H., Hu, Y., Tang, X. M., & Zhang, Q. L. (2026). Treatment exposure drives a profound shift toward complex multi-class HIV-1 drug resistance. Virology Journal. https://doi.org/10.1186/s12985-026-03308-w

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03308-w

Keywords: HIV-1, drug resistance, antiretroviral therapy, virological failure, multidrug resistance, NNRTI, NRTI, integrase inhibitors, protease inhibitors, pretreatment drug resistance, acquired drug resistance, genotypic resistance testing