Phylogenetic Analysis of the Complete Genome of 18 Norwalk-like Viruses

Abstract

"Norwalk-like viruses" (NLV), a member of the family Caliciviridae, are the major causative agents of acute gastroenteritis and are genetically divided into two groups, genogroup I (GI) and genogroup II (GII). We have determined the complete nucleotide sequences of 10 new NLV strains. Using this information together with eight known NLV sequences, the criteria to further classify genotypes of NLV were investigated. Validation of the topological error based on the bootstrap value and the branch length (distance) allowed us to identify two potential subgenomic regions suitable for the genotyping. They were the putative 3D-like RNA-dependent RNA polymerase (polymerase) and the capsid N-terminal/Shell domains (capsid N/S domain). When the distance distribution analysis was performed, the polymerase-based classification did not separate the strains into internal clusters within the genogroup. Furthermore, a diversity plot analysis of the complete nucleotide sequences of WUG1, a NLV GI strain, and Saitama U1, a NLV GII strain, indicated that the genotype was different between the polymerase and capsid N/S domain, suggesting that these strains are the genetic recombinants. Therefore, polymerase is not suitable for genotyping. On the other hand, the clustering based on the capsid N/S domain successfully distinguished the NLV as well as the grouping based on the antigenicity, as determined by both antigen and antibody ELISAs with recombinant virus-like particles. As the nucleotide sequences of the primers for the capsid N/S domain are highly conserved among the NLV, the amplification of the unknown genotype can be easily performed. This method will facilitate global surveying as well as epidemiologic study on NLV.

Porcine enteric caliciviruses: Genetic and antigenic relatedness to human caliciviruses, diagnosis and epidemiology

“…Genetic classification of these viruses based on phylogenetic analysis of the complete capsid sequences is the generally accepted method [46,48,49]. Katayama et al [48] investigated which region of the genome was most suitable to classify the genotypes and genogroups of NoVs based on similarity plot analysis, bootstrap value and pairwise distances of the entire genomes of 18 strains, the complete sequences of ORF1, ORF2 and ORF3, and segments of ORF1 and ORF2. They found that the full-length genome, the complete ORF1 or ORF2, and the capsid Nterminal/S domain could segregate viruses into genus, genogroup and genotypes (also called genetic clusters).…”

“…The RdRp-capsid junction region of caliciviruses contains a highly conserved ~20 nucleotide (nt) motif in genomic and subgenomic RNA molecules that is suggested to be a transcription start signal [1,48]. This conserved nucleotide motif is almost identical within each genogroup of NoVs and SaVs, probably facilitating homologous recombination during co-infection of a cell by different genotypes of NoVs or SaVs within the same genogroup.…”

“…This conserved nucleotide motif is almost identical within each genogroup of NoVs and SaVs, probably facilitating homologous recombination during co-infection of a cell by different genotypes of NoVs or SaVs within the same genogroup. In fact, recombinant NoVs having a recombination site at the RdRp-capsid junction region were identified in humans, calves and pigs [15,48,[59][60][61][62][63]. Two porcine NoVs, QW170 and QW218 strains, which share 99% nt identity at the 3'-end 3kb sequence of the genome, were reported as potential recombinants [15].…”

“…Low infectious doses [1], prolonged asymptomatic shedding [80], environmental stability [121] and great strain diversity [47,51] increase the risk of infections by this virus family. Moreover, the identification of closely related animal enteric caliciviruses in pigs and cattle, and the existence of recombinants within human NoVs [48,60], porcine NoVs [15], bovine NoVs [63,122], and also within the human and the porcine SaVs [43,50] raises concerns for possible infections or co-infections of humans with animal or with human and animal enteric caliciviruses, respectively. One possible source for mixed occurrence of both animal and human enteric caliciviruses is via human consumption of contaminated raw shellfish.…”

Molecular characterization of norovirus GII strains identified in Albania

“…A large selection of primers are available currently and these are able to amplify the most of genetic variants arising from the accumulation of point mutations associated with genetic recombination events. Most of the investigators have chosen primers for conserved regions, such the RdRp gene, in order to detect the greatest number of different strains [Jiang et al, 1990[Jiang et al, , 1993Ando et al, 2000;Katayama et al, 2002;Vinjé et al, 2004] but not all sequences can be accurately classified into the proper clusters by phylogenetic analyses [Zheng et al, 2006]; however, GII.4 variants were observed after the molecular analysis of the ORF1 region [Marshall and Bruggink, 2011]. During the last years it highlights a lack of reported data about sequence analyses of RdRp region that could suggest the use of this approach in addition to the VP1 capsid protein study chosen by the major networks of NoV surveillance [Park et al, 2011].…”