Genetic analysis of the capsid gene of genotype GII.2 noroviruses.
Noroviruses (NoVs) are considered to be a major cause of acute nonbacterial gastroenteritis in humans. The NoV genus is genetically diverse, and genotype GII.4 has been most commonly identified worldwide in recent years. In this study we analyzed the complete capsid gene of NoV strains belonging to the less prevalent genotype GII.2. We compared a total of 36 complete capsid sequences of GII.2 sequences obtained from the GenBank (n = 5) and from outbreaks or sporadic cases that occurred in The Netherlands (n = 10) and in Osaka City, Japan (n = 21), between 1976 and 2005. Alignment of all capsid sequences did not show fixation of amino acid substitutions over time as an indication for genetic drift. In contrast, when strains previously recognized as recombinants were excluded from the alignment, genetic drift was observed. Substitutions were found at five informative sites (two in the P1 subdomain and three in the P2 subdomain), segregating strains into five genetic groups (1994 to 1997, 1999 to 2000, 2001 to 2003, 2004, and 2005). Only one amino acid position changed consistently between each group (position 345). Homology modeling of the GII.2 capsid protein showed that the five amino acids were located on the surface of the capsid and close to each other at the interface of two monomers. The data suggest that these changes were induced by selective pressure, driving virus evolution. Remarkably, this was observed only for nonrecombinant genomes, suggesting differences in behavior with recombinant strains.
Iritani
Nobuhiro
N
Laboratory for Infectious Diseases and Perinatal Screening, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands. n-iritani@city.osaka.lg.jp
Vennema
Harry
H
Siebenga
J Joukje
JJ
Siezen
Roland J
RJ
Renckens
Bernadet
B
Seto
Yoshiyuki
Y
Kaida
Atsushi
A
Koopmans
Marion
M
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D017250:Caliciviridae Infections / Q000453:epidemiology / Q000821:virology*; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics*; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D005838:Genotype; D006801:Humans; D007564:Japan / Q000453:epidemiology; D008565:Membrane Proteins / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D009426:Netherlands / Q000453:epidemiology; D029322:Norovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011487:Protein Conformation; D012641:Selection, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
D036022:Capsid Proteins; D008565:Membrane Proteins