Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing

Abstract

Objective To investigate the quasispecies variation characteristics of HBV in Tibetan population based on the third-generation sequencing. Methods An epidemiological investigation of hepatitis B virus was conducted by our department of infectious disease in southern Tibet from May 2016 to July 2017. A total of 24 HBsAg positive subjects were obtained in this investigation and were assignd into the plateau Tibetan group, and then another 24 cases subjected from our outpatient department were recruited and served as the plain Han control group. Their HBV DNA was extracted, and the full virus sequence was amplified to build a whole genome sequencing library, and then sequenced on the third-generation sequencing platform PacBio RSⅡ. Biological information tools such as ClustalW, MEGA and SimPlot were used to analyze the quasispecies characteristics. Results Totally 29 samples were successfully amplified and sequenced finally, including 9 cases from the Tibetan group with an average of 65 quasispecies sequences per sample, and 20 cases from the control group with an average of 124 quasispecies sequences per sample. After comparative analysis, 7 cases (7/9, 77.8%) of typeC/D1 HBV were found in the Tibetan group with recombining at 750 nt by type D4 and type C2 HBV, 1 case of type C/D2 HBV was recombined by type D3 and type C2 HBV at 1 500 nt, and the rest 1 was type C2. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C gen was highere in the Tibetan group than the control group. Variation spectrums of nucleic acid were different between the recombinant HBV and the control. The nucleic acid mutation of the C/D recombinant HBV was mainly in EnhⅡ, BCP, and preS regions, while the HBV sequences in the control group were dominated by mutations in preC, S, and X regions besides BCP and preS regions. Conclusion The C/D recombinant strain is the dominant strain of HBV in Tibetans, and C/D1 HBV is more common. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C in Tibetans are higher than those of the Han, While the variants of nucleotide mainly occur in the Enh Ⅱ, BCP, and preS regions

Keywords

• hepatitis virus b
• high-throughput sequencing
• third-generation
• quasispecies
• tibetan nationality