Norovirus recombination

Abstract

RNA recombination is a significant driving force in viral evolution. Increased awareness of recombination within the genus Norovirus of the family Calicivirus has led to a rise in the identification of norovirus (NoV) recombinants and they are now reported at high frequency. Currently, there is no classification system for recombinant NoVs and a widely accepted recombinant genotyping system is still needed. Consequently, there is duplication in reporting of novel recombinants. This has led to difficulties in defining the number and types of recombinants in circulation. In this study, 120 NoV nucleotide sequences were compiled from the current GenBank database and published literature. NoV recombinants and their recombination breakpoints were identified using three methods: phylogenetic analysis, SimPlot analysis and the maximum χ 2 method. A total of 20 NoV recombinant types were identified in circulation worldwide. The recombination point is the ORF1/2 overlap in all isolates except one, which demonstrated a double recombination event within the polymerase region.

Lineage diversification and recombination in type-4 human astroviruses

“…By Simplot analysis, the cross over site was mapped upstream the conserved ORF1b/ ORF2 junction region. The exchange of genome fragments via recombination is common in single-stranded RNA viruses and appears to occur at higher frequency in highly conserved genomic regions among genetically related strains (Bull et al, 2007). Molecular recombination of genomic RNA can affect phylogenetic groupings, increase the virulence of the virus, confuse molecular epidemiological studies and have major implications in vaccine design (Bull et al, 2007).…”

“…The exchange of genome fragments via recombination is common in single-stranded RNA viruses and appears to occur at higher frequency in highly conserved genomic regions among genetically related strains (Bull et al, 2007). Molecular recombination of genomic RNA can affect phylogenetic groupings, increase the virulence of the virus, confuse molecular epidemiological studies and have major implications in vaccine design (Bull et al, 2007). As seen in noroviruses, the highly conserved junction region connecting the non-structural and structural genes of HAstVs seems to be a recombination hot spot (De Grazia et al, 2012;Wolfaardt et al, 2011).…”

Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection

“…While Lindesmith and coworkers have identified a recombination breakpoint at residue 265 located near the P1-1/P2 domain interface of NoV GII.4 strains (Lindesmith et al, 2008), this recombination break point was not found in this study. The absence of detected recombinants might be due to the fact that we did not have access to ORF1/ORF2 overlap sequences, previously found associated with NoV recombination break points (Bull et al, 2005(Bull et al, , 2007Phan et al, 2007). Thus, we cannot rule out that recombination occurred at the ORF1/ORF2 junction.…”

“…Since RNA recombination is believed to be one of the major driving forces in viral evolution (Worobey & Holmes, 1999), including NoV (Bull et al, 2005(Bull et al, , 2007Phan et al, 2007), we searched the 134 full-length (P1-1 and P2 capsid domains) NoV capsid nudeotide sequences for recombination events. The sequences were first aligned using CLUSTAL W-multialign with default settings on the Mobyle portal (Pasteur Institute), and then analysed by the RDP2 software to search for possible recombinants using different conventional recombination detection methods such as GENECONV, SIMPLOT, BOOTSCAN, MAXIMUM x 2 and CHIMAERA (Martin et al, 2005).…”

“…Since RNA recombination is believed to be one of the major driving forces in viral evolution, (Worobey & Holmes, 1999) including NoV (Bull et al, 2005(Bull et al, , 2007Phan et al, 2007), we searched the 134 full-length NoV capsid sequences (597 nt from the P1-1and P2 capsid domains) for recombination events. Some possible recombination events were located (e.g.…”