Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea.

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Abstract

Norovirus (NoV) genogroups I and II are frequently recognized as the main causes of acute gastroenteritis and outbreaks of non-bacterial foodborne diseases. Furthermore, variants and recombinant strains of this virus are continuously emerging worldwide. The aim of this study was to identify NoV strains and to investigate and characterize rare genotypes. Stool samples (n = 500) were collected from patients with symptoms of acute gastroenteritis in Korea between December 2004 and November 2007. For analysis of the samples, rapid genotype screening was performed using reverse transcriptase-polymerase chain reaction. Full sequencing, using a newly designed set of 12 primers, revealed GII-12/13 strain. The partial sequence of GII-12/13 strain was compared with published NoV (GII-1 - 14) sequences targeting RdRp and capsid regions using phylogenetic analysis with the SimPlot program, which could evaluate recombination breakpoints. SimPlot analysis was also performed with the strain GII-12/Gifu-96/JPN (AB045603) for the RdRp region and with GII-13/G5175B-83/AUS(DQ379714) for the capsid region. NoV was detected in 19 of the 500 stool samples (3.8%). Genogroup GII-4 was found most frequently (n = 9, 1.8%), followed by GII-3 (n = 4, 0.8%), GII-6 (n = 3, 0.6%), GI-6 (n = 2, 0.4%), and GII-12/13 (n = 1, 0.2%). Importantly, we identified a novel NoV recombinant strain, C9-439 (KF289337), indicating potential risks, which suggested that, recombination occurred in the region between open reading frames 1 and 2 of the GII-12/13 strain and that breakpoints occurred in the polymerase region.

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Most cited references 31

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Norovirus gastroenteritis.

Roger I. Glass, Umesh D Parashar, Mary Estes (2009)

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Recombination within the pandemic norovirus GII.4 lineage.

John-Sebastian Eden, Megumi M. Tanaka-Arakawa, Aaron P White … (2013)

Norovirus (NoV) is the leading cause of viral gastroenteritis globally. Since 1996, NoV variants of a single genetic lineage, GII.4, have been associated with at least six pandemics of acute gastroenteritis and caused between 62 and 80% of all NoV outbreaks. The emergence of these novel GII.4 variants has been attributed to rapid evolution and antigenic variation in response to herd immunity; however, the contribution of recombination as a mechanism facilitating emergence is increasingly evident. In this study, we sought to examine the role that intragenotype recombination has played in the emergence of GII.4 variants. Using a genome-wide approach including 25 complete genome sequences generated as part of this study, 11 breakpoints were identified within the NoV GII.4 lineage. The breakpoints were located at three recombination hot spots: near the open reading frame 1/2 (ORF1/2) and ORF2/3 overlaps, as well as within ORF2, which encodes the viral capsid, at the junction of the shell and protruding domains. Importantly, we show that recombination contributed to the emergence of the recent pandemic GII.4 variant, New Orleans 2009, and a newly identified GII.4 variant, termed Sydney 2012. Reconstructing the evolutionary history of the GII.4 lineage reveals the widespread impact of both inter- and intragenotype recombination on the emergence of many GII.4 variants. Lastly, this study highlights the many challenges in the identification of true recombination events and proposes that guidelines be applied for identifying NoV recombinants.

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Norovirus Recombination in ORF1/ORF2 Overlap

Rowena Bull, Grant S. Hansman, Leighton Clancy … (2005)

Norovirus (NoV) genogroups I and II (GI and GII) are now recognized as the predominant worldwide cause of outbreaks of acute gastroenteritis in humans. Three recombinant NoV GII isolates were identified and characterized, 2 of which are unrelated to any previously published recombinant NoV. Using data from the current study, published sequences, database searches, and molecular techniques, we identified 23 recombinant NoV GII and 1 recombinant NoV GI isolates. Analysis of the genetic relationships among the recombinant NoV GII isolates identified 9 independent recombinant sequences; the other 14 strains were close relatives. Two of the 9 independent recombinant NoV were closely related to other recombinants only in the polymerase region, and in a similar fashion 1 recombinant NoV was closely related to another only in the capsid region. Breakpoint analysis of recombinant NoV showed that recombination occurred in the open reading frame (ORF)1/ORF2 overlap. We provide evidence to support the theory of the role of subgenomic RNA promoters as recombination hotspots and describe a simple mechanism of how recombination might occur in NoV.