Full-Genomic Analysis of a Human Norovirus Recombinant GII.12/13 Novel Strain Isolated from South Korea

Won, Yu-Jung; Park, Jeong-Woong; Han, Sung-Hyun; Cho, Han-Gil; Kang, Lae Hyung; Lee, Sung-Geun; Ryu, Sangryeol; Paik, Soon-Young

doi:10.1371/journal.pone.0085063

Cited by 25 publications

(16 citation statements)

References 36 publications

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“…Since then, several recombinant strains have been sporadically reported around the globe. Between 2004 and 2007, 21 NoV recombinant types were identified; the NoV recombinant type GII.12/GII.13 was the first isolate identified in South Korea during this period [39] – [41] . In our current phylogenetic analysis of the RdRp/capsid regions, we identified 39 recombinant strains, which were then divided into seven different subtypes: GII.2/GII.10 (n = 1), GII.b/GII.3 (n = 3), GII.4/GII.2 (n = 1), GII.4/GII.3 (n = 8), GII.4/GII.6 (n = 12), GII.4/GII.12 (n = 12), and GII.16/GII.2 (n = 2).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

2014

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Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university hospitals in South Korea. We also analyzed the genetic diversity of the viruses and identified novel recombination events among the identified viral strains. Of 502 children with acute gastroenteritis admitted to our three hospitals between January 2011 and March 2012, genotyping of human noroviruses was performed in 171 (34%) norovirus-positive samples. Of these samples, 170 (99.5%) were in genogroup II (GII), while only one (0.5%) was in genogroup I (GI). The most common GII strain was the GII.4-2006b variant (n = 96, 56.5%), followed by GII.6 (n = 23, 13.5%), GII.12 (n = 22, 12.9%), GII.3 (n = 20, 11.8%), GII.2 (n = 6, 3.5%), GII.b (n = 2, 1.2%), and GII.10 (n = 1, 0.6%). Potential recombination events (polymerase/capsid) were detected in 39 GII strains (22.9%), and the most frequent genotypes were GII.4/GII.12 (n = 12, 30.8%), GII.4/GII.6 (n = 12, 30.8%), GII.4/GII.3 (n = 8, 20.5%), GII.b/GII.3 (n = 3, 7.7%), GII.16/GII.2 (n = 2, 5.1%), GII.4/GII.2 (n = 1, 2.6%), and GII.2/GII.10 (n = 1, 2.6%). For the first time, a novel GII.2/GII.10 recombination was detected; we also identified the GII.16/GII.2 strain for the first time in South Korea. Our data provided important insights into new recombination events, which may prove valuable for predicting the emergence of circulating norovirus strains with global epidemic potential.

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Section: Discussionmentioning

confidence: 99%

Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

2014

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“…To date, norovirus sequencing from clinical material has been achieved by two methods, namely, sequencing of overlapping PCR fragments (9)(10)(11)(12) and direct sequencing of total RNA (13)(14)(15)(16). The former generates a pure viral template, which improves the quality of sequencing but requires multiple PCR amplifications; the latter necessitates great depth of sequencing to generate the target norovirus genome.…”

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confidence: 99%

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

et al. 2016

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cNorovirus full-genome sequencing is challenging due to sequence heterogeneity among genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and transcriptome sequencing (RNA-Seq), which nonspecifically sequences all RNA, including host and bacterial RNA, in stool specimens. Target enrichment uses a panel of custom-designed 120-mer RNA baits that are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, which overcomes the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimize the sequencing of nontarget RNA. SureSelect target enrichment and Illumina sequencing were used to sequence full genomes from 507 norovirus-positive stool samples with reverse transcription-real-time PCR cycle threshold (C T ) values of 10 to 43. Sequencing on an Illumina MiSeq system in batches of 48 generated, on average, 81% on-target reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, and GII.17. When outliers were accounted for, we generated >80% genome coverage for all positive samples, regardless of C T values. A total of 164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain; 164/164 samples were successfully sequenced, compared to 158/164 samples that were amplified by PCR. Four of the samples that failed capsid PCR analysis had low titers, which suggests that target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity among norovirus genomes. N orovirus is a leading cause of outbreaks of acute gastroenteritis (1, 2), with an estimated prevalence of 20% in cases of acute gastroenteritis in developed countries (3) and a large financial burden, associated with ward and hospital closures, in health care settings (4). In countries in which rotavirus vaccine has been introduced, norovirus is now the leading cause of medically attended gastroenteritis in children (5, 6).Norovirus has a 7.5-kb single-stranded RNA genome organized into 3 open reading frames (ORFs), i.e., ORF1, ORF2, and ORF3. ORF1 encodes a nonstructural polyprotein that is cleaved posttranslationally and includes the RNA-dependent RNA polymerase. ORF2 encodes the major structural capsid protein, which is divided into shell (S) and protruding (P) domains. The P domain has two subdomains, P1 and P2. P2 is the most exposed antigenic site and contains immunogenic epitopes; consequently, it has the greatest sequence variation. ORF3 codes for a minor capsid protein.Comparison of viral genetic sequences allows linking of previously unrecognized transmission events or exclusion of cases from an outbreak. Traditionally, norovirus genotyping has involved PCR amplification and capillary sequencing of part...

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“…This region was very conservative for almost all GII NoVs (Won et al . ; Cotten et al . ), but for special NoV strains, other methods are still recommended for obtaining the complete genome sequences, such as 5′ RACE.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, it should be mentioned that the 5 0 end of the NoV genome could be hardly sequenced based on these amplification methods, since the sequence of this region only came from the relevant primer used for PCR amplification. This region was very conservative for almost all GII NoVs (Won et al 2013;Cotten et al 2014), but for special NoV strains, other methods are still recommended for obtaining the complete genome sequences, such as 5 0 RACE.…”

Section: Discussionmentioning

confidence: 99%

Direct sequencing and analysis of the genomes of newly emerging GII.17 norovirus strains in South China

Xue

Cai

et al. 2016

J Appl Microbiol

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Full-Genomic Analysis of a Human Norovirus Recombinant GII.12/13 Novel Strain Isolated from South Korea

Cited by 25 publications

References 36 publications

Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

Direct sequencing and analysis of the genomes of newly emerging GII.17 norovirus strains in South China

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