Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jul 7:6:29400.
doi: 10.1038/srep29400.

Molecular evolution of the capsid gene in human norovirus genogroup II

Miho Kobayashi  1 , Yuki Matsushima  2 , Takumi Motoya  3 , Naomi Sakon  4 , Naoki Shigemoto  5 , Reiko Okamoto-Nakagawa  6 , Koichi Nishimura  7 , Yasutaka Yamashita  8 , Makoto Kuroda  9 , Nobuhiro Saruki  1 , Akihide Ryo  10 , Takeshi Saraya  11 , Yukio Morita  12 , Komei Shirabe  6 , Mariko Ishikawa  2 , Tomoko Takahashi  13 , Hiroto Shinomiya  8 , Nobuhiko Okabe  2 , Koo Nagasawa  14 , Yoshiyuki Suzuki  15 , Kazuhiko Katayama  16 , Hirokazu Kimura  10   14
Affiliations

Molecular evolution of the capsid gene in human norovirus genogroup II

Miho Kobayashi et al. Sci Rep. .

Abstract

Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10(-3) substitutions/site/year), resulting in three lineages. The GII capsid gene had large pairwise distances (maximum > 0.39). The effective population sizes of the present GII strains were large (>10(2)) for about 400 years. Positive (20) and negative (over 450) selection sites were estimated. Moreover, some linear and conformational B-cell epitopes were found in the deduced GII capsid protein. These results suggested that norovirus GII strains rapidly evolved with high divergence and adaptation to humans.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Phylogenetic tree of the capsid gene on NoV constructed by the Bayesian MCMC method.
203 strains of human GII, three strains of swine GII, nine strains of GI, one strain of GIII, and three strains of GIV were included in this tree. Grey bars show 95% HPDs. The scale bar represents actual time (year). The time of the most recent common ancestor of this tree was around 854 CE. GII strains were divided from GIV around 1630 CE. NoV GII was formed three lineages.
Figure 2
Figure 2
Bayesian skyline plots of all NoV GII (a) GII.2 (b) GII.3 (c) GII.4 (d) and GII.6 (e). The x-axis represents actual time (years) and starts at mean tree model root height. The y-axis represents the effective population size. Mean effective population size is shown as a black line. HPDs of 95% are shown as grey lines.
Figure 3
Figure 3. Location of positive selection sites on predicted structure of capsid protein in GII.4/Bristol/1993/UK.
To construct the model, we used five suitable templates of NoV capsid sequences (PDB ID: 1IHM, 3ONU, 4RLZ, 3PUM, and 4X07). Twenty positively selected sites on chains A and B are colored purple and orange, respectively. The HBGA binding sites are colored blue and pink. These sites were located within the surface of the protein.
Figure 4
Figure 4. Predicted linear B-cell epitopes mapping on the capsid protein of GII. 4.
The predicted structure of capsid protein is the same as in Fig. 3. Linear B-cell epitopes on chain A and B are shown in green and blue, respectively. Common locations among all genotypes are represented by deeper tones. These sites consist of 11 amino acids (DPTXXXPAPXG or similar sequence to this).
Figure 5
Figure 5. Predicted conformational B-cell epitopes mapping on the capsid protein of GII. 4.
The predicted structure of capsid protein is the same as in Fig. 3. These sites on chain A and B are shown in green and blue, respectively. Most of conformational epitopes were located in the P1 and P2 domains.
See this image and copyright information in PMC

References

    1. Green K. Y. In Fields Virology 6th edn, Vol. 1 (eds Knipe D. M. et al..) Ch. 20, 582–608 (Lippincott Williams & Wilkins, 2013).
    1. Hamano M. et al.. Epidemiology of acute gastroenteritis outbreaks caused by Noroviruses in Okayama, Japan. J. Med. Virol. 77, 282–289 (2005). - PubMed
    1. Chan-It W. et al.. Emergence of a new norovirus GII.6 variant in Japan, 2008–2009. J. Med. Virol. 84, 1089–1096 (2012). - PubMed
    1. Bernard H. et al.. Outbreak Investigation Team. Large multistate outbreak of norovirus gastroenteritis associated with frozen strawberries, Germany, 2012. Euro. Surveill. 19, 20719 (2014). - PubMed
    1. Zomer T. P. et al.. A foodborne norovirus outbreak at a manufacturing company. Epidemiol. Infect. 138, 501–506 (2010). - PubMed

Publication types

Substances