Identification of a New HCV Subtype 6xg Among Injection Drug Users in Kachin, Myanmar

Abstract

Characterizing hepatitis C virus (HCV) genetic diversity not only allows us to trace its origin and evolutionary history, but also provides valuable insights into diagnosis, prevention and therapy of HCV infection. Although eight HCV genotypes and 86 subtypes have been classified, there are still some HCV variants that need to be assigned. The genotype 6 is the most diverse HCV genotype and mainly prevalent in Southeast Asia. In this study, we identified a new HCV subtype 6xg from injection drug users (IDUs) in Kachin, Myanmar. A distinctive feature of 6xg from other subtypes of the genotype 6 was a Lys insertion in NS5A gene, which changes the RRKR/K motif into RRKKR/K. Bayesian analyses showed that HCV 6xg originated during 1984-1988, and experienced a rapid population expansion during 2005-2009. We characterized HCV subtype profile among IDUs in this region, and detected six HCV subtypes, including 1a (12.0%), 3a (12.0%), 3b (24.0%), 6n (16.0%), 6xa (20.0%), and 6xg (12.0%). Importantly, we found that HCV subtype distribution in Kachin was very similar to that in Dehong prefecture of Yunnan, but very distinct from those in other regions of Myanmar and Yunnan, indicating that the China-Myanmar border region shared a unique HCV subtype pattern. The appearance of 6xg and the unique HCV subtype profile among IDUs in the China-Myanmar border region have significant epidemiological and public health implications.

Keywords: HCV 6xg; Myanmar; Yunnan; hepatitis C virus; injection drug users; subtype.

FIGURE 1

Geographical location and HCV subtype distribution among IDUs in Kachin, Myanmar. The data on HCV subtype profiles in Dehong, Kunming, Honghe and Wenshan, and Yangon were retrieved from previous studies (Shinji et al., 2004; Zhang et al., 2013; Chen et al., 2015; Wan et al., 2016).

FIGURE 2

Maximum likelihood trees of C/E2 (A) and NS5B (B) fragments of HCV strains in Kachin, Myanmar. The trees were constructed using MEGA 7.0 with ML method under the “GTR+I+G” model. The reliability of interior branches in the trees was evaluated by the bootstrap method with 1000 replications. Only bootstrap values over 75% are shown. The clade of the potential new HCV subtype is highlighted by an arrow.

FIGURE 3

Identification of the new HCV subtype 6xg. (A) ML tree of 3 representative full-length genomic sequences. (B) NS5A sequence feature of HCV subtype 6xg.

FIGURE 4

ML trees of E1/E2 (A) and NS5B (B) sequences using hit sequences. The hit sequences were obtained by HCV BLAST with HCV 6xg strains as query set. The clades of subtypes 6xg, 6xe, and 6n are highlighted by green, yellow, and red shadows, respectively. The sequences from the Burmese IDUs staying in Yunnan are highlighted by blue stars, and the strain isolated in 2002 is highlighted by a blue triangle. NA indicates that the nationality of IDUs is not available.

FIGURE 5

The maximum clade credibility trees of E1/E2 (A) and NS5B (B) fragments. The MCC trees were obtained by Bayesian MCMC analysis based on partial E1/E2 and NS5B sequences. The nodes of HCV subtype 6n, 6xe, and 6xg clades are shown using black dots. The node ages with 95% confidence interval are shown beside the nodes.

FIGURE 6

Bayesian skyline plot estimated the past population dynamics of HCV 6xg among IDUs. The y-axis represents the estimates of the effective number of HCV 6xg strains and the x-axis represents time. The solid line represents the median estimate and the shaded area represents the 95% confidence intervals.