HIV drug resistance and HIV transmission risk factors among newly diagnosed individuals in Southwest China

Guangxi is located in Southwest China, adjacent to Vietnam and the Yunnan and Guangdong provinces. It is one of the areas in China that is most heavily affected by the human immunodeficiency virus 1 (HIV-1) in China [1]. Since the identification of the first individual infected with HIV in Guangxi in 1996 [2], the number of infected individuals has increased. By the end of 2017, Guangxi has the second highest number of reported HIV cases (113,500) in the country [3]. The Free Antiretroviral Treatment Program was launched in 2003 in China, and the “Treat for All” policy was implemented in 2016, and under which HIV-positive individuals were treated after being diagnosis of HIV regardless of their CD4+ cell count [4].

The widespread use and increased coverage of ART has reduced significantly reduced the risk of HIV transmission and decreased HIV-related morbidity and mortality [5]. Meanwhile, the increase in ART access corresponds to an increase in HIV drug resistance, which can be transmitted to newly infected individuals. TDR in HIV has become a major concern as it may lead to the failure of first-line ART [6]. Certain studies have suggested that significant large variations in the prevalence of TDR can be expected in different areas worldwide based on the differences in the availability of treatments and variances in socioeconomic development [7‐9]. The prevalence is relatively high in high-income countries; for e.g., it is 11.2% in the United States [10], 14.7% in Romania [11] and 9.9% in Spain [12]. In middle- and low-income countries, lower estimates of TDR the prevalence have been reported; for e.g., it is 6.3% in Latin America [8], 5.7% in India, and < 5.0% in African countries [13]. A nationwide cross-sectional survey conducted in 2015 revealed 3.6% overall prevalence of drug resistance to be in China [14]. However, more recently, the prevalence of TDR been reported to increase to 12.2% in Tianjin [15], 17.4% in Shanghai [16], and 6.12% in Beijing [17].

As the HIV epidemic continues to spread, it is essential to investigate the changing trends in HIV-1 genetics as well as the prevalence and transmission of TDR in individual locations. Here, we performed an extensive cross-sectional study on individuals newly diagnosed with HIV between 2016 and 2018 in Guangxi.

We aimed to reveal the genetic characteristics and prevalence of transmitted HIV TDR among the newly diagnosed individuals in Guangxi, China. Our study revealed that the major epidemic HIV-1 subtypes detected in Guagnxi were CRF01_AE (42.14%), CRF07_BC (30.93%), CRF08_BC (15.9%) and CRF55_01B (6.86%). The distribution of HIV-1 subtypes has changed in the last two decades. Subtypes B and E were the major prevalent strains before 2000 [2]. In 2013, Liu et al. found that CRF01_AE (77.6%), CRF08_BC (10.7%), and CRF07_BC (7.4%) were the major strains in Guangxi [21]. In 2015, Zhang et al. observed that CRF01_AE (62.0%), CRF07_BC (25.0%), and CRF08_BC (6.5%) were the major strains [22]. However, the proportion of individuals infected with CRF01_AE gradually declined, whereas the proportion of individuals infected with CRF07_BC increased [21, 22]. CRF07_BC was first detected in intravenous-drug users in Guangxi in 2002 [23]. To our knowledge, in this study, we observed the first incidence of CRF68_01B, CRF85_BC, and unconfirmed unique recombinant strains in Guangxi. Their routes of transmission warrant further study. These findings indicated the existence of high genetic heterogeneity and subtype/CRF diversity in HIV-1 in Guangxi, and showed that the new CRFs had spread to provinces with population movement. Furthermore, the continuation of HIV recombination led to the production of new CRFs and URF, which made the HIV subtypes more diverse and complex. Additionally, the introduction of the new CRFs had a profound impact on the local HIV epidemic, and made the spread across a floating population easier. Therefore, the surveillance of HIV subtype should be strengthened further.

According to the categorisation method established by WHO [24], the overall prevalence of TDR in Guangxi was at a moderate level (5–15%). It was higher than the prevalence determined in the region in a previous study [25] as well as in other regions of China [17, 26, 27]. As the increase in TDR will affect the antiviral treatment and the spread of drug resistance, the surveillance of TDR should be strengthened, and measures to curb the increase of TDR should be adopted. A significant difference was observed between the prevalence of TDR and marital status and subtype, which contradicted from the results of a previous study [17, 28]. When marital status was used as a categorisation parameter, unmarried individuals were most likely to develop drug resistance. When categorised based on subtype, patients with the CRF08_BC subtype were the most likely to develop drug resistance. Therefore, these two high-risk factors should be considered in clinical settings. We found a significantly higher prevalence of mutations related to NNRTI resistance than of those associated with resistance to PIs or NRTIs. Mutations related to NNRTI resistance were common, especially V179E (7.21%) and V179D (3.21%). Most V179E mutations were detected in CRF55_01B, and most V179D mutations were detected in CRF01_AE, CRF07_BC, and CRF08_BC subtypes. In case of NNRTIs, the mutation V106I, which can cause low-level resistance to doravirine, was a major cause of drug resistance. High-level resistance to efavirenz and nevirapine primarily resulted from the mutations K103N, L100I, and P225H. In case of NRTIs, 0.86% of the individuals were predicted to be resistant to zidovudine, stavudine, and didanosine. In case of PIs, 1.74% of the individuals were predicted to be resistant to nelfinavir and tipranavir. Combinatorial therapy with lamivudine, efavirenz, and nevirapine has been prescribed as the first-line ART regimen in China, and the total drug resistance rate to these three drugs found to be 2.61% in our study. Therefore, the emergence of these mutations might be related to the use of this first-line regimen. The higher prevalence of TDR may be caused by prolonged ART, as noted in other studies [29, 30].

To further understand the transmission of drug resistance, we constructed transmission clusters based on HIV-1 sequences. Our cluster analysis revealed that 585 individuals could be segregated into 119 clusters, including MSM, heterosexual men, heterosexual women, and intravenous-drug users; this indicated that the transmission characteristics were complicated. In the largest cluster, which comprised 146 individuals (1 woman, 145 men), MSM was the major route of transmission. Analysis of this super cluster suggested that MSM were strongly associated with the local epidemic. Additionally, 43.4% (36/83) of the individuals infected by drug-resistant strains were included in 19 clusters, in which drug resistance was mostly associated with heterosexuality (88.89%). Three clusters were identified that included drug-resistant individuals sharing a transmission relationship with each other, which counted for 44.4% (16/36). The result indicated that the spread of TDR may have occurred in the transmission network. The major infection route in the three clusters was heterosexual transmission (83.3%), and there were five women carrying TDR included in the TDR transmission network. This shows that drug-resistant individuals, especially women should be studied further, because they may act as a potential source of TDR. Logistic regression analysis revealed that being unmarried, having educational level of junior high school or lower, and subtype CRF08_BC may be related to TDR to transmit in the clusters. The reasons for the association of these parameters with TDR to transmit should be investigated further.

The present study revealed a diverse, complex distribution of HIV-1 subtypes in Guangxi, and a moderate prevalence of TDR. However, there are several limitations in the study including the number of intravenous-drug users. Additionally, 13% of the samples could not be sequenced successfully, the major causes may include sample quality, low viral load in patients, or low sensitivity of reagents. The lack of data on contact between study participants was also another limitation. Future studies conducted on a larger, more diverse group with contact information available is necessary to design effective strategies for intervention in high-risk populations. Regardless, the risk of TDR was pronounced and must be factored into the treatment and prevention policies. Our findings will be helpful in determining the optimal primary ART and implementing effective interventions that target the major populations at risk in the area.