Molecular Evolution of the Capsid Gene in Norovirus Genogroup I.
We studied the molecular evolution of the capsid gene in all genotypes (genotypes 1-9) of human norovirus (NoV) genogroup I. The evolutionary time scale and rate were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also performed selective pressure analysis and B-cell linear epitope prediction in the deduced NoV GI capsid protein. Furthermore, we analysed the effective population size of the virus using Bayesian skyline plot (BSP) analysis. A phylogenetic tree by MCMC showed that NoV GI diverged from the common ancestor of NoV GII, GIII, and GIV approximately 2,800 years ago with rapid evolution (about 10(-3) substitutions/site/year). Some positive selection sites and over 400 negative selection sites were estimated in the deduced capsid protein. Many epitopes were estimated in the deduced virus capsid proteins. An epitope of GI.1 may be associated with histo-blood group antigen binding sites (Ser377, Pro378, and Ser380). Moreover, BSP suggested that the adaptation of NoV GI strains to humans was affected by natural selection. The results suggested that NoV GI strains evolved rapidly and date back to many years ago. Additionally, the virus may have undergone locally affected natural selection in the host resulting in its adaptation to humans.
Gunma Prefectural Institute of Public Health and Environmental Science, Maebashi-shi, Gunma 371-0052, Japan.
Miho
M
Kobayashi
Hokkaido Institute of Public Health, Sapporo-shi, Hokkaido 060-0819, Japan.
Shima
S
Yoshizumi
Aomori Prefectural Public Health and Environment Center, Aomori-shi, Aomori 030-8566, Japan.
Sayaka
S
Kogawa
Iwate Prefectural Meat Inspection Center, Shiwa-cho, Iwate 020-3311, Japan.
Tomoko
T
Takahashi
Miyagi Prefectural Institute of Public Health and Environment, Sendai-shi, Miyagi 983-0836, Japan.
Yo
Y
Ueki
Saitama Institute of Public Health, Yoshimi-machi, Saitama 355-0133, Japan.
Michiyo
M
Shinohara
Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi, Tochigi 329-1196, Japan.
Fuminori
F
Mizukoshi
Gunma Prefectural Institute of Public Health and Environmental Science, Maebashi-shi, Gunma 371-0052, Japan.
Hiroyuki
H
Tsukagoshi
Gunma Prefectural Institute of Public Health and Environmental Science, Maebashi-shi, Gunma 371-0052, Japan.
Yoshiko
Y
Sasaki
Kanagawa Prefectural Institute of Public Health, Chigasaki-shi, Kanagawa 253-0087, Japan.
Rieko
R
Suzuki
Kawasaki City Institute for Public Health, Kawasaki-shi, Kanagawa 210-0821, Japan.
Hideaki
H
Shimizu
Miyazaki Prefecture Kobayashi Meat Inspection Center, Kobayashi-shi, Miyazaki 886-0004, Japan.
Akira
A
Iwakiri
Kawasaki City Institute for Public Health, Kawasaki-shi, Kanagawa 210-0821, Japan.
Nobuhiko
N
Okabe
Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-0821, Japan.
Komei
K
Shirabe
Ehime Prefectural Institute of Public Health and Environmental Science, Matsuyama-shi, Ehime 790-0003, Japan.
Hiroto
H
Shinomiya
Gunma Prefectural Institute of Public Health and Environmental Science, Maebashi-shi, Gunma 371-0052, Japan.
Kunihisa
K
Kozawa
Department of Safety Research on Blood and Biological Products, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan.
Hideki
H
Kusunoki
Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan.
Akihide
A
Ryo
Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
Makoto
M
Kuroda
Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.|Saitama Institute of Public Health, Yoshimi-machi, Saitama 355-0133, Japan.
Kazuhiko
K
Katayama
Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan.|Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
Hirokazu
H
Kimura
D000595:Amino Acid Sequence; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D005814:Genes, Viral / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D008969:Molecular Sequence Data; D029322:Norovirus / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics*
D036022:Capsid Proteins