Human norovirus infection: surveillance and source tracking

Genome characterization of a GII.6 norovirus strain identified in China

Noroviruses (NoVs) are the primary cause of non-bacterial acute gastroenteritis worldwide. Most NoV infections are caused by GII.4, but GII.6 is also an important genotype with a long-term persistence in human populations. In this study, the complete genome sequence of a NoV strain GZ2010-L96 isolated in China was identified and analyzed phylogenetically. The viral genome comprised 7550 nucleotides, and its phylogenetic analysis revealed that the strain belonged to GII.6 genotype. All reported GII.6 NoV capsid protein sequences were also collected for comparative analysis, and GZ2010-L96 was clustered into GII.6-b with other 8 strains. Meanwhile, it was found that 53 spots on viral capsid showed subcluster specificity according to multiple alignments. Moreover, homologous modeling of GZ2010-L96 based on comparison with GII.4 VA387 strain showed a different antigen distribution pattern. In summary, the genome of the GII.6 strain GZ2010-L96 detected in China was extensively characterized, and phylogenetic analyses of GII.6 NoVs based on the capsid proteins may reveal a different evolution process from the predominant genotype GII.4.

Emerging and re-emerging enteric viruses causing multinational foodborne disease outbreaks

ABSTRACT: 

The development of molecular detection methods has led to recognition of viruses as important foodborne pathogens. The most common foodborne virus is norovirus, which together with HAV are transmitted via food consumed raw, such as shellfish, fresh produce and soft fruit. HEV is increasingly being recognized as an emerging foodborne virus in developed countries. The transmission route of HEV includes zoonotic transmission in association with pork products. Ongoing changes in food commerce and production from national to internationally-distributed foodstuffs are leading to widespread infections and multinational outbreaks. Recent large viral outbreaks have been linked to oysters, frozen berries and semidried tomatoes.

Complete genome analysis of a novel norovirus GII.4 variant identified in China

The complete genome sequence of a novel norovirus strain GZ2010-L87 identified in Guangzhou was analyzed phylogenetically in this study. The RNA genome of the GZ2010-L87 strain is composed of 7,559 nucleotides. The phylogenetic analysis based on open reading frame (ORF) 2 revealed that the strain belongs to the GII.4 genotype, forming the new cluster GII.4-2009 which was also identified in Asia and the USA since 2009. Furthermore, phylogenetic analyses of the full genome and the different open reading frame sequences of GZ2010-L87 and other representative strains suggested that the novel strain did not undergo recombination. Comparative analysis with the consensus sequence of 31 completely sequenced norovirus GII.4-2009 genomes showed 86 mismatched nucleotides (56 in ORF1, 16 in ORF2, and 14 in ORF3), resulting in 19 amino acid changes (9 in ORF1, 3 in ORF2, and 7 in ORF3). Furthermore, 12 variable sites were found on the capsid protein of norovirus GII.4-2009, and most were located at the P2 domain. Meanwhile, based on comparison with other GII.4 clusters, 14 sites were shown specific to the novel cluster. In summary, the genome of the new GII.4-2009 variant GZ2010-L87, which was first identified in China, was extensively characterized with a large panel of genetically diverse noroviruses. The genomic information obtained from the novel variant can be used not only as a full-length norovirus sequence standard in China but also as reference data for future evolution research.

A simple and novel method for GII norovirus genome clone with generic primers

AIMS

This study aims to establish a novel method for cloning GII norovirus genome using generic primers rationally designed based on multiple alignments of 96 GII norovirus genome sequences.

METHODS AND RESULTS

Based on conservative analysis of 96 GII norovirus genome sequences available in GenBank, three fragments encompassing the full-length genome were rationally designed. Fragments A, B and C were amplified by primers N1F/N2819R, N2689F/COG2R and COG2F/adaptor, respectively. Meanwhile, the sensitivity of the novel primers was evaluated, which could achieve 10(1) RTPCRU, as determined by the common detection primer pair JV12/JV13. The availability of the novel protocol was verified by sequencing two norovirus strains with different genotypes.

CONCLUSIONS

Primers for GII norovirus genome clone were rationally designed, and a novel GII genome clone method was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

The three-fragment cloning method can be used as a universal tool to collect information on the genome of norovirus strains for future evolution and antivirus studies.