Objective: To study the sequence diversity of the hypervariable region 1(HVR1) in the putative envelope protein E2/NS1 of HCV in Beijing and its neighbouring regions.
Methods: The cDNAs (nt1119-1258) derived from plasma of 46 patients infected with genotype II/1b HCV were amplified, purified and directly sequenced by using RT-nested polymerase chain reaction(PCR) and dideoxynucleotide chain termination method.
Results: The HVR1 was found in aa384-408 positions of E2 protein, which had some differences with other report. Compared with HCV-J, HCV-TW, HCV-HB and HCV-HB11, the nucleotide sequence homological rates of these HVR1 were 44.0%-66.7%(57.7%), 48.0%-72.0%(60.0%), 60.0%-85.3%(69.8%), and 56.0%-81.3%(68.2%) respectively, and the amino acid sequence homological rates were 20.0%-56.0%(38.2%), 32.0%-64.0%(45.7%), 36.0%-76.0%(49.8%) and 40.0%-76.0%(55.6%) respectively. There were 6 conserved amino acids in HVR1: AA385(Thr), AA389, 390, 406(Gly), AA401(Ser) and AA403(Phe). Two highly conserved amino acids were only found in this paper.
Conclusion: The further study of the diversity of HVR1 and its biological significance will be beneficial to the development of HCV vaccine.