Multiple Introduction and Naturally Occuring Drug Resistance of HCV among HIV-Infected Intravenous Drug Users in Yunnan: An Origin of China's HIV/HCV Epidemics

Abstract

Background: The human immunodeficiency virus 1 (HIV-1) epidemic in China historically stemmed from intravenous drug users (IDUs) in Yunnan. Due to a shared transmission route, hepatitis C virus (HCV)/HIV-1 co-infection is common. Here, we investigated HCV genetic characteristics and baseline drug resistance among HIV-infected IDUs in Yunnan.

Methods: Blood samples of 432 HIV-1/HCV co-infected IDUs were collected from January to June 2014 in six prefectures of Yunnan Province. Partial E1E2 and NS5B genes were sequenced. Phylogenetic, evolutionary and genotypic drug resistance analyses were performed.

Results: Among the 293 specimens successfully genotyped, seven subtypes were identified, including subtypes 3b (37.9%, 111/293), 3a (21.8%, 64/293), 6n (14.0%, 41/293), 1b (10.6%, 31/293), 1a (8.2%, 24/293), 6a (5.1%, 15/293) and 6u (2.4%, 7/293). The distribution of HCV subtypes was mostly related to geographic location. Subtypes 3b, 3a, and 6n were detected in all six prefectures, however, the other four subtypes were detected only in parts of the six prefectures. Phylogeographic analyses indicated that 6n, 1a and 6u originated in the western prefecture (Dehong) and spread eastward and showed genetic relatedness with those detected in Burmese. However, 6a originated in the southeast prefectures (Honghe and Wenshan) bordering Vietnam and was transmitted westward. These subtypes exhibited different evolutionary rates (between 4.35×10-4 and 2.38×10-3 substitutions site-1 year-1) and times of most recent common ancestor (tMRCA, between 1790.3 and 1994.6), suggesting that HCV was multiply introduced into Yunnan. Naturally occurring resistance-associated mutations (C316N, A421V, C445F, I482L, V494A, and V499A) to NS5B polymerase inhibitors were detected in direct-acting antivirals (DAAs)-naïve IDUs.

Conclusion: This work reveals the temporal-spatial distribution of HCV subtypes and baseline HCV drug resistance among HIV-infected IDUs in Yunnan. The findings enhance our understanding of the characteristics and evolution of HCV in IDUs and are valuable for developing HCV prevention and management strategies for this population.

Fig 1. Neighbor-joining phylogenetic tree of partial E1E2 gene from HIV/HCV co-infected IUDs in Yunnan.

Neighbor-joining phylogenetic tree for 265 E1E2 sequences and relative reference sequences. The scale bar indicates 10% nucleotide sequence divergence. Values on the branches represent the percentage of 1000 bootstrap replicates and bootstrap values over 70% are shown in the tree.

Fig 2. Neighbor-joining phylogenetic tree of partial NS5B gene from HIV/HCV coinfected IUDs in Yunnan.

Neighbor-joining phylogenetic tree for 240 NS5B sequences and relative reference sequences. The scale bar indicates 5% nucleotide sequence divergence. Values on the branches represent the percentage of 1000 bootstrap replicates and bootstrap values over 70% are shown in the tree.

Fig 3. Geographic distribution of the HCV subtypes in Yunnan.

Dot Density Map for 1a, 1b, 3a, 3b, 6a, 6n and 6u, respectively, which showed the constituent ratio of each subtype in each prefecture. One dot represents 0.025% of the subjects in each prefecture.

Fig 4. The Distribution of HCV subtypes for six prefectures in Yunnan.

The constitution of HCV subtypes for each prefecture was showed.

Fig 5. Maximum clade credibility (MCC) tree representing the rooted genealogy of HCV sutypes 1a, 6a, 6n and 6u among HIV/HCV coinfected IDUs in Yunnan.

(A) The MCC tree for subtype 1a strains. (B) The MCC tree for subtype 6a strains. (C) The MCC tree for subtype 6n strains. (D) The MCC tree for subtype 6u strains. The MCC trees were obtained by Bayesian MCMC analysis based on partial NS5B gene (H77: 8340–9233) implemented in BEAST v 1.7.4. The uncorrelated exponential relaxed molecular clock method was used in combination with the Bayesian Skyline coalescent tree prior under GTR+I+G4 nucleotide substitution model. The branch lengths in the MCC trees reflect time and the corresponding time-scale is shown at the bottom of the trees. The posterior probabilities of the key nodes and the tMRCA medians for the interested nodes are indicated.