Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A.
We studied the molecular evolution of the fusion protein (F) gene in the human respiratory syncytial virus subgroup A (HRSV-A). We performed time-scaled phylogenetic analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. We also conducted genetic distance (p-distance), positive/negative selection, and Bayesian skyline plot analyses. Furthermore, we mapped the amino acid substitutions of the protein. The MCMC-constructed tree indicated that the HRSV F gene diverged from the bovine RSV (BRSV) gene approximately 550years ago and had a relatively low substitution rate (7.59×10(-4) substitutions/site/year). Moreover, a common ancestor of HRSV-A and -B diverged approximately 280years ago, which has since formed four distinct clusters. The present HRSV-A strains were assigned six genotypes based on F gene sequences and attachment glycoprotein gene sequences. The present strains exhibited high F gene sequence similarity values and low genetic divergence. No positive selection sites were identified; however, 50 negative selection sites were identified. F protein amino acid substitutions at 17 sites were distributed in the F protein. The effective population size of the gene has remained relatively constant, but the population size of the prevalent genotype (GA2) has increased in the last 10years. These results suggest that the HRSV-AF gene has evolved independently and formed some genotypes.
Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan. Electronic address: kimhiro@nih.go.jp.
Hirokazu
H
Kimura
Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Pediatrics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan.
Koo
K
Nagasawa
Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamiokimachi, Maebashi-shi, Gunma 371-0052, Japan.
Hiroyuki
H
Tsukagoshi
Division of Virology, Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan.
Yuki
Y
Matsushima
School of Medical Technology, Faculty of Health Science, Gumma Paz College, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan.
Kiyotaka
K
Fujita
Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki-shi, Nagasaki 852-8523, Japan.
Lay Myint
LM
Yoshida
Department of Surgery, Kyorin University, School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan.
Ryota
R
Tanaka
Department of Respiratory Medicine, Kyorin University, School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan.
Haruyuki
H
Ishii
Department of Pediatrics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan.
Naoki
N
Shimojo
Pathogen Genomics Center, National institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
Makoto
M
Kuroda
Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
Akihide
A
Ryo
D019943:Amino Acid Substitution; D000818:Animals; D001499:Bayes Theorem; D002417:Cattle; D019143:Evolution, Molecular; D015870:Gene Expression; D014644:Genetic Variation; D005838:Genotype; D049669:History, 16th Century; D049671:History, 18th Century; D006801:Humans; D008390:Markov Chains; D008958:Models, Molecular; D017720:Molecular Epidemiology; D009010:Monte Carlo Method; D059645:Mutation Rate; D010802:Phylogeny; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology / Q000266:history* / Q000821:virology; D018113:Respiratory Syncytial Virus, Human / Q000145:classification / Q000235:genetics*; D014760:Viral Fusion Proteins / Q000235:genetics*
C526850:F protein, human respiratory syncytial virus; D014760:Viral Fusion Proteins
F gene; HRSV; Molecular evolution; Palivizumab