In this study, 18 different HIV-1 genotype were found which the prevalence of non-B subtypes was predominant in Chongqing over the last seven years, accounting for 97.4%. Among non-B subtypes, CRF07_BC was the dominate genotype, followed by CRF01_AE and CRF08_BC, which consistent with the result of previous study [8, 9]. The higher proportion of CRF07-BC in Chongqing may be related to its proximity to Yunnan Province. CRF07_BC was originated from Dehong, Yunnan in the early 1990s and consisted of a large number of recombinant strains of the BC subtype, which then spread throughout the country [10, 11]. However, PLWH with CRF01_AE subtype had the highest incidence of drug resistance, which was higher than CRF07_BC, CRF08_BC and B + C subtype. Therefore, a question was raised that whether the differences among subtypes could have an effect on viral drug resistance. Several studies reported that the resistance mutation profiles of different subtypes of strains may differ under drug selection pressure, thus having an effect on viral resistance [12,13,14].

A previous study showed that the rate of the pretreatment HIV-1 drug resistance in Chongqing was 24.14%, which lower than the percentage observed in Yunnan province with the most severe HIV epidemic in China (34.2%) [8, 15]. However, in this study, we focused the analysis on the drug resistance in PLWH with viral load rebound and clinical suspicion of drug resistance. Therefore, among 3105 participants, the drug-resistance rate was up to 46.6%. There were two reasons accounted for this result. First of all, the site of this research was located in the relatively economically disadvantaged western region of China and PLWH received the first-line free ART medications including two NRTIs combined with one NNRTI. Secondly, the various side effects of free ART drugs led to irregularity and poor adherence with medication, and PLWH were more likely to develop resistance.

Among 1405 drug-resistance participants, the frequency of NNRTI resistance (43.8%) was higher than that of NRTI resistance (29.5%) and PI resistance (3.4%). And the drugs with the most serious HIV-1 resistance in Chongqing consist of three NNRTI class drugs (NVP, EFV, DLV) and two NRTI class drugs (3TC, FTC). Since free ART program recommended two NRTIs in combination with one NNRTI as the first-line ART regimen in which NNRTIs mainly included NVP and EFV. Therefore, in this study, the medium/high resistance level to NVP and EFV were higher than 30%. The high proportion of NNRTI-resistance was primarily attributed to the low genetic barrier to resistance and a long plasmatic half-life [15, 16]. Additionally, TDF and ETR are the representative varieties of new generation NRTI and NNRTI class drugs. Although the prevlance of TDF- and ETR-resistance were significantly lower than that of older generation varieties, the resistance rate of about 10% still has warning significance.

The analysis of drug resistance mutation loci in this study revealed that the most common NRTI-associated mutation loci were M184V/I and K65R/N, with mutation frequencies of 26.1% and 13.1%, respectively. M184V/I mutations resulted in high resistance to 3TC and FTC, and the incidence of M184V/I mutations was significantly higher in those who received 3TC and TDF regimens than in those who received FTC and TDF regimens [17,18,19]. The thymidine analogue mutation (TAM) group was detected in 373 samples in this study, including M41L, D67N, K70R, K219Q/E, L210W and T215Y/F [20]. The most common mutations in TAMs consisted of K70R (6.5%), D67N (5.9%) and K219QE (4.3%). As revealed by the statistics, PLWH carrying TAMs had the resistance rates of 52.3%, 74.3%, 83.9% and 84.2% to TDF, 3TC, EFV and NVP, respectively. The rates of resistance to TDF, 3TC, EFV and NVP in PLWH without carrying TAMs reached 12.7%, 21.3%, 36.2% and 34.3%, respectively. PLWH carrying TAMs (compared with non-carriers) had significantly more resistance mutations to TDF and NNRTIs (NVP, EFV) and cytidine analogs (lamivudine), and the differences achieved statistical significance (P < 0.05). Although accumulation of TAMs loci could cause more widespread resistance, TAMs were transmitted to uninfected individuals, and the above individuals were subsequently at higher risk of ART failure [21]. Common mutation loci in NNRTIs consisted of V179D/E, K103N//S and V106M/A. The frequency of all three mutations was nearly 10-20%. Other major drug-resistant mutant loci consisted of Y181CIV, K101PE, F227L, V108I, L100I, G190ACS, M230L, P225H, E138KAGQ, as well as A98G. The presence of multiple mutant loci alone or in combination can lead to a moderately high level of viral resistance to NVP, DLV, and EFV [22, 23], which could explain the high rate of resistance to NNRTI class drugs in our group of cases. The main resistance loci for PIs included A71IVT and L10FIV mutations. Resistance to PIs was rare, which was correlated with the late introduction of PIs into southwest China, the short duration of clinical application and the high resistance barrier. It is noteworthy that drug resistance is the main cause of virologic failure in PLWH. Drug resistance is dynamic and mutates over time, especially those introduced at later time points, in the form of natural polymorphisms. Drug-resistant strains should be continuously monitored to understand and update the prevalence of major drug-resistant genes in our region.

Additionally, CD4 T-cell counts have commonly served as an indicator of the immune status of PLWH. In this study, the incidence of drug-resistant mutations was significantly lower in PLWH with CD4 T-cell counts ≥ 200/µL than in the < 200/µL group since PLWH with high CD4 T-cell counts. A better immune status, adequate disease awareness, and good adherence with medication may be accounted for this result. Therefore, the rate of drug-resistance mutations was lower in PLWH with high CD4 T-cell counts.

There are some limitations in this study. Firstly, some of the cases in this group contained incomplete clinical data, which did not affect the analysis of the main results, whereas it was still the limitation of this study as a retrospective study. secondly, this research focused on the situation of patients who received ART treatment based on The National Free Antiretroviral Treatment Program of China. Therefore, our study did not analyze the drug resistance for integrase inhibitors.

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