Journal of General Virology (1990), 71, 3027-3033. Printed in Great Britain 3027 The putative nucleocapsid and envelope protein genes of hepatitis C virus determined by comparison of the nucleotide sequences of two isolates derived from an experimentally infected chimpanzee and healthy human carriers Kenji Takeuchi, I Yoshihiro Kubo,lt Sumalee Boonmar, l~ Yushiro Watanabe, ~,2 Tohru Katayama, 3 Qui-Lim Choo,4 George Kuo, 4 Michael Houghton,4 Izumu Saito 1 and Tatsuo Miyamura 1. 1Laboratory of Hepatitis Viruses II, Department of Enteroviruses, National Institute of Health, Shinagawa-ku, Tokyo 141, 2 Second Department of Internal Medicine, St Marianna University School of Medicine, M iyamae-ku, Kawasaki-shi 213, 3Department of Surgery, National Tokyo Chest Hospital, Takegaoka, Kiyose-shi, Tokyo204, Japan and 4Chiton Corporation, Emeryville, California 94608, U.S.A. cDNA fragments of a 5'-terminal region of the hepatitis C virus (HCV) genome were isolated by the reverse polymerase chain reaction from RNA extracted from plasma samples of healthy Japanese carriers. Their nucleotide sequence was compared with that of the original isolate which had been passaged twice in chimpanzees. No deletions or insertions were observed between the two sequences in the regions examined. Both the 5' untranslated and putative nucleocapsid (core) protein regions were highly conserved (99 % and 91% nucleotide identities, respectively). In contrast, the region immediately downstream which encodes a putative envelope glycoprotein(s) showed only 74% nucleotide identity between the two isolates. At the polypeptide level, the core and envelope domains showed 97% and 75% amino acid identities, respec- tively. This envelope variation may reflect the adapta- tion of HCV to the different hosts and/or the result of immunological selection. The highly conserved nucleo- tide sequence of the 5' untranslated and core regions may play an important regulatory role in the life cycle of HCV. Hepatitis C virus (HCV) is the major cause of post- transfusion hepatitis throughout the world (Kuo et al., 1989; Alter et al., 1989; Miyamura et al., 1990). Over 50% of the chronic cases of sporadic non-A, non-B hepatitis without obvious percutaneous exposure are also considered to be associated with HCV infection (Kuo et al., 1989). The possible causative virus has recently been identified by cDNA cloning techniques using plasma from an experimentally-infected chimpanzee (Choo et al., 1989). The virus contains a positive stranded RNA genome of about 10000 nucleotides (Choo et al., 1989) which encodes a large polyprotein precursor of about 3000 amino acids (aa) (Q.-L. Choo et al., unpublished results). Although lacking extensive homology with any tPresent address: Department of Neurophysiology, Tokyo Metro- politan Institute for Neurosciences, Musashidai, Fuchu-shi, Tokyo 183, Japan. ~:Presentaddress: Department of Medical Sciences, Virus Research Institute, National Institute of Health, Nonthaburi 11000, Thailand. other known viruses, HCV appears to be distantly related to the flaviviruses and pestiviruses with the structural proteins being located at the N terminus of the polyprotein (Q.-L. Choo et al., unpublished results). The original HCV cDNA clones were derived from a virus which was isolated from a contaminated batch of human facter VIII concentrate from the U.S.A. follow- ing serial passage in two chimpanzees (Choo et al., 1989) (denoted as HCV UC for U.S.A. and chimpanzee in this study). Subsequently, we isolated HCV cDNA clones derived from the plasma of a healthy HCV carrier in Japan (denoted as HCV JH for Japan and human) and observed that the extent of aa identity between the U.S.A. clone and Japanese clone varied considerably from one region to another; about 90~o of aa were identical in the two non-structural regions examined, whereas only 74% were identical in (or near) the putative structural region (Kubo et al., 1989; Takeuchi et al., 1990a). In this report, we extended this analysis to the 0000-9773 © 1990 SGM