Inter-seasonal diversity of norovirus genotypes: Emergence and selection of virus variants

Abstract

This study describes a method used to determine the diversity of NoVs co-circulating in the community that consisted of the analysis of a limited number of strains collected from outbreaks occurring at different times of the NoV season. The diversity of twenty NoV strains collected from outbreaks occurring at the beginning of each NoV season (September) was compared to the diversity found in the middle (December) and at the end of the season (March). The method was validated through the characterisation of greater numbers of strains at times when novel genotypes or variants were detected. A total of 864 strains from outbreaks of gastroenteritis from the 2003/04, 2004/05 and 2005/06 seasons were genotyped, with the majority of outbreaks occurring in the UK. There was a greater diversity of NoV genotypes at the beginning of two of the three seasons, 2003/04 and 2005/06, when compared to strains circulating at the end of the seasons, and GII-4 NoV strains predominated (>90%) at the end of each season. Data from this study also identified the co-circulation and differentiation of three major GII-4 variants (v2, v3, and v4). Detailed analysis of a larger number of strains throughout each season confirmed that variants emerged, became the predominant circulating strain and were ultimately replaced with another variant selected from a pool of variants. By June 2006, GII-4 v4 (Hu/NoV/Rhyl440/2005/UK) emerged as the predominant GII-4 strain, usurping the previous GII-4 v3 strain [Hu/NoV/Hunter284E/040/AU] to become the commonest co-circulating strain, in the UK in 2006.

Prevalence and characteristics of asymptomatic norovirus infection in the community in England

“…Second, it has been suggested that the at Library on April 12, 2010 http://aje.oxfordjournals.org marked winter-time increase in hospital admissions for respiratory infections may drive the strong seasonality of norovirus outbreaks in this setting, and that there are distinct norovirus strains circulating in hospital populations and in the community that may have different transmission characteristics (29); therefore, the incidence of community disease or general practitioner consultations would not necessarily show the marked seasonality seen in health careassociated outbreaks. However, detailed characterization of the molecular epidemiology of norovirus infections in the community is needed, for comparison with the extensive data that already exist for hospital-acquired infections (30,31), to understand better the factors driving the different seasonality of health-care outbreaks and community disease. Finally, it is also possible that there was more outof-season norovirus transmission during this study because of the emergence of a new norovirus variant, as described above (32).…”

Transmission Events within Outbreaks of Gastroenteritis Determined through Analysis of Nucleotide Sequences of the P2 Domain of Genogroup II Noroviruses

“…Small batches of fecal specimens were prepared as described previously using the guanidinium thiocyanate-silica method (10) or in larger batches using a Roche total nucleic acid extraction kit (Roche Diagnostics Ltd., Burgess Hill, United Kingdom) according to manufacturer's instructions and a Roche MagNAPure automated extractor (7). Briefly, for the guanidinium thiocyanate-silica procedure, a 200-ul fecal extract in phosphate-buffered saline was added to 1 ml of L6 buffer (Severn Biotech, United Kingdom) and 20 l of silica, and the silica pellet was then washed with L2 buffer (Severn Biotech, United Kingdom)-70% ethanol-acetone.…”

Emerging GII.4 norovirus variants affect children with diarrhea in Palermo, Italy in 2006

“…Different genome fragments, such as region A (part of the RdRp gene), region C (part of the capsid gene), or the region spanning the ORF1 and ORF2, have been used to demonstrate the evolution of GII.4 variants [Gallimore et al, 2007;Siebenga et al, 2007b;Buesa et al, 2008]. In this study, sequence analysis of the region A allowed us to demonstrate that three GII.4 variants, 2004GII.4 variants, , 2006aGII.4 variants, , and 2006b phylogenetic tree confirming their close evolutionary relationships [Siebenga et al, 2007b;Buesa et al, 2008] [Gallimore et al, 2007;Buesa et al, 2008;Reuter et al, 2008;Siebenga et al, 2008].…”

“…ORF2 sequences representative of the six GII.4 variants recovered in Europe in the last 15 years. The characteristic motifs reported by Gallimore et al [2007], based on the amino acids at position 6, 9, and 15, were taken into consideration for determination of the variant. This allowed the identification of four NoV variants, 2002NoV variants, , 2004NoV variants, , 2006aNoV variants, , and 2006b, in agreement with the results obtained by RdRp sequence analysis (Fig.…”

“…The high incidence of NoV infections seems to be related to the sequential appearance and rapid spread of new variants and/or of recombinant NoV strains. Key mutations of the capsid protein VP1 are associated with GII.4 NoV variants emerging consecutively worldwide and named, based on the first year of detection, as: <1996, 1996, 2002, 2004, 2006a, and 2006b [Vinje and Koopmans, 1996;Vinje et al, 1997;Kroneman et al, 2004;Lopman et al, 2004;Gallimore et al, 2007;Siebenga et al, 2007b].…”