HIV-1 genetic diversity and pretreatment resistance in Yunnan, a key endemic region of China

To formulate control strategies and understand the prevalence of HIV-1 pretreatment drug resistance (PDR), this study investigated the characteristics of viral genotype distribution and PDR prevalence and associated factors in Yunnan Province, China, a key HIV-endemic region. In 2022, 399 individuals initiating or re-initiating antiretroviral treatment in Yunnan Province were surveyed using the probability proportional to size (PPS) sampling method. Viral RNA was extracted, amplified, and sequenced in the pol gene region. The characteristics of the distribution of HIV-1 genotypes and drug-resistant mutations were analyzed. Of the 377 pol sequences obtained, 17 HIV-1 genotypes were identified. The most common strains were CRF08_BC (48.0%), CRF07_BC (21.8%), and CRF01_AE (12.7%). Multivariate analysis revealed that CRF08_BC was more prevalent among individuals aged 30 years and over (adjusted odds ratio (aOR) = 2.859), while CRF01_AE was more prevalent among ethnic minorities (aOR = 2.395) and individuals with a higher level of education levels (aOR = 5.606). The rate of nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations was 9.3%, highest in CRF01_AE (16.7%), with S68G/S68G mutations prevalent in CRF01_AE (8.3%). The non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation rate was 39.3%, significantly higher in CRF08_BC and rare genotypes, with V179D/V (11.7%) and E138A/Q/G (11.4%) as the predominant mutations. Protease inhibitor (PI) resistance mutation rates were lower (1.9% for primary mutations and 2.9% for accessory mutations), with the accessory mutation Q58E being most prevalent in CRF07_BC (6.1%). The core PDR rate (12 drugs according to WHO criteria) was 11.4%, including 10.3% resistance to EFV/NVP. Meanwhile, resistance to newer NNRTIs, such as RPV, was found in 16.2% of cases. A history of previous antiviral treatment (aOR = 6.675) and infection with the CRF08_BC strain (aOR = 4.682) were independent risk factors for drug resistance. HIV-1 exhibited extremely high genetic diversity in Yunnan Province, alongside a relatively high rate of PDRs to NNRTIs. The distribution of drug-resistant mutations demonstrated genotypic specificity. A first-line regimen based on EFV/NVP poses potential risks and requires enhanced monitoring of drug resistance, as well as optimization of treatment strategies, particularly for high-risk populations. Not applicable.