Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017

Lun, Jennifer H; Hewitt, Joanne; Yan, Grace J. H.; Tuipulotu, Daniel Enosi; Rawlinson, William D.; White, Peter A.

doi:10.3390/v10100548

Cited by 43 publications

(42 citation statements)

References 56 publications

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“…Although, its presence does not mean that the virus is active or infectious, we cannot exclude the hypothesis that this virus can also be present in the fish flesh that can be consumed raw or undercooked in several meals, possessing a potential risk to human health. Noroviruses are the leading cause of viral gastroenteritis worldwide, and are estimated to cause 677 million cases and ≈ 210,000 human deaths every year [45].…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, in the last decades, the GII.4 variant dominated NoV infections, being responsible for 60-80% of all NoV outbreaks. Therefore, in the last years, we observed the emergence of a novel GII.4 recombinant virus responsible for several outbreaks worldwide [45,46] that retained the Sydney 2012 capsid-coding sequence but acquired a new structural region (GII.P16/GII.4 Sydney 2012) [45,46].…”

Section: Discussionmentioning

confidence: 99%

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The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

Silva

Parreira

Martínez-Puchol

et al. 2020

Foods

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Much of the knowledge on viruses is focused on those that can be propagated using cell-cultures or that can cause disease in humans or in economically important animals and plants. However, this only reflects a small portion of the virosphere. Therefore, in this study, we explore by targeted next-generation sequencing, how the virome varies between Atlantic horse mackerels and gilthead seabreams from fisheries and aquaculture from the center and south regions of Portugal. Viral genomes potentially pathogenic to fish and crustaceans, as well as to humans, were identified, namely Astroviridae, Nodaviridae, Hepadnaviridae, Birnaviridae, Caliciviridae, and Picornaviridae families. Also bacteriophages sequences were identified corresponding to the majority of sequences detected, with Myoviridae, Podoviridae, and Siphoviridae, the most widespread families in both fish species. However, these findings can also be due to the presence of bacteria in fish tissues, or even to contamination. Overall, seabreams harbored viruses from a smaller number of families in comparison with mackerels. Therefore, the obtained data show that fish sold for consumption can harbor a high diversity of viruses, many of which are unknown, reflecting the overall uncharacterized virome of fish. While cross-species transmission of bonafide fish viruses to humans is unlikely, the finding of human pathogenic viruses in fish suggest that fish virome can be a potential threat regarding food safety.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

Silva

Parreira

Martínez-Puchol

et al. 2020

Foods

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“…The GII.P16 genotype has already been associated with several different capsid genotypes (GII.P16-GII.2, GII.P16-GII.3, GII.P16-GII.4, GII.P16-GII.1, GII.P16-GII.12, GII.P16-GII.10) (Ruis et al, 2017;Nagasawa et al, 2018;Barclay et al, 2019). Previous studies suggested that the GII.4_Sydney strain acquired GII.P16 from the GII.P16-GII.2 strains (Tohma et al, 2017;Lun et al, 2018). This hypothesis was supported in this study, since strains clustered closer in the temporal reconstruction tree, and the TMRCA of both strains emerged in 2010.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary and Molecular Analysis of Complete Genome Sequences of Norovirus From Brazil: Emerging Recombinant Strain GII.P16/GII.4

et al. 2020

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Noroviruses (NoVs) are enteric viruses that cause acute gastroenteritis, and the pandemic GII.4 genotype is spreading and evolving rapidly. The recombinant GII.P16/GII.4_Sydney strain emerged in 2016, replacing GII.P31/GII.4_Sydney (GII.P31 formerly known as GII.Pe) in some countries. We analyzed the complete genome of 20 NoV strains (17 GII.P31/GII.4_ Sydney and 3 GII.P16/GII.4_Sydney) from Belém and Manaus, Brazil, collected from 2012 to 2016. Phylogenetic trees were constructed by maximum likelihood method from 191 full NoV-VP1 sequences, demonstrated segregation of the Sydney lineage in two larger clades, suggesting that GII.4 strains associated with GII.P16 already have modifications compared with GII.P31/GII.4. Additionally, the Bayesian Markov Chain Monte Carlo method was used to reconstruct a time-scaled phylogenetic tree formed by GII.P16 ORF1 sequences (n = 117) and three complete GII.P16 sequences from Belém. The phylogenetic tree indicated the presence of six clades classified into different capsid genotypes and locations. Evolutionary rates of the ORF1 gene of GII.P16 strains was estimated at 2.01 × 10 −3 substitutions/site/year, and the most recent common ancestors were estimated in 2011 (2011-2012, 95% HPD). Comparing the amino acid (AA) sequence coding for ORF1 with the prototype strain GII.P16/GII.4, 36 AA changes were observed, mainly in the non-structural proteins p48, p22, and RdRp. GII.P16/GII.4 strains of this study presented changes in amino acids 310, 333, 373, and 393 of the antigenic sites in the P2 subdomain, and ML tree indicating the division within the Sydney lineage according to the GII.P16 and GII.P31 polymerases. Notably, as noroviruses have high recombination rates and the GII.4 genotype was prevalent for a long time in several locations, additional and continuous evolutionary analyses of this new genotype should be needed in the future.

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“…Circulating GII.4 strains shared homology with emergent recombinant strain GII.P16-GII.4/RUS/ 2017 (MG892929), GII.P16-GII.4 Sydney/2012 (KY887601) and GII.P4 New Orleans/2009/GII.4/Sydney 2012 (MG585810.1) (52). The Novosibirsk-2017 strain harbors several AA changes within the main epitope of the P2 capsid domain and shares a common ancestor with the NoV GII.4 variants Apeldoorn 2008 and New Orleans 2009 [51]. On the other hand, the Sydney-2012 strain was also isolated in the United States, Denmark, Japan, and Scotland [52,53,54,55].…”

Section: Discussionmentioning

confidence: 99%

Epidemiological, Molecular, and Clinical Features of Norovirus Infections among Pediatric Patients in Qatar

Mathew

Alansari

Smatti

et al. 2019

Viruses

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Background: Norovirus (NoV) is recognized as the second most important etiological agent leading to acute gastroenteritis globally. In order to determine the burden and characteristics of NoV infections in children in Qatar, profiling of circulating genotypes and their correlation with demographics and clinical manifestations were evaluated. Methods: A total of 177 NoV-positive fecal samples were collected from children suffering from acute gastroenteritis (AGE) during two-year period between June 2016 and June 2018. The age of the subjects ranged between 3 months and 12 years (median of 15 months). Genotyping was performed by amplifying and sequencing parts of viral VP1 and RNA-dependent RNA polymerase (RdRp) regions. Phylogenetic analysis and evolutionary relationships were performed using MEGA7.0. Fisher’s exact test was used to run statistical analysis for the clinical and demographical characteristics of circulating strains. Results: Overall, NoV infections were relatively higher in males than females with a ratio of 1.3:1 (p = 0.0073). Most of the NoV infections were reported in children between 1 and 3 years old (49.7%), followed by those <1 and >3 years of age (41.2% and 9.1%, respectively). NoV infections occurred throughout the year, with a noticeable increase in summer (36.6%) and drop in winter (25.4%). Nearly all (98.8%) NoV-infected children were positive for genogroup II (GII) compared to only two samples (1.2%) being positive for genogroup I (GI): GI.3 and GI.4. NoV genotype GII.4 (62.2%), GII.2 (15.8%), and GII.3 (13.5%) were predominant in our study. The detected strains shared >98% sequence homology with emerging recombinant strain of GII.P16-GII.4/RUS/Novosibirsk/2017 (MG892929), GII.P16-GII.4 Sydney/2012 (KY887601), GII.4 Sydney/2012, recombinant GII.P4 New Orleans /2009/GII.4 Sydney 2012 (MG585810.1), and the emerging strain GII.P16-GII.2 CHN/2017 (MH321823). Severe clinical illness (vesikari score >10) was reported in children infected with genotypes sharing homology with the above emerging strains. While GII.4 was reported in all age groups, NoV GII.3 infections were higher in children <1 year of age. Both genogroups (GII.4 and GII.3) in addition to GII.2 reported higher incidence in Qatari subjects compared to other nationalities (p = 0.034). Conclusion: This is the first report about NoV molecular epidemiology in Qatar. The most detected NoV strain was genogroup GII, which is the dominant genotype in the Middle East region. Further, we report GII.4, GII.2, and GII.3 as the most predominant NoV genotypes in our study. Moreover, disease severity scores were higher among children genotyped with genogroup GI (GI.4) and genogroup GII (GII.4, GII.2, GII.3, GII.6, and GII.7).

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Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017

Cited by 43 publications

References 56 publications

The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

Evolutionary and Molecular Analysis of Complete Genome Sequences of Norovirus From Brazil: Emerging Recombinant Strain GII.P16/GII.4

Epidemiological, Molecular, and Clinical Features of Norovirus Infections among Pediatric Patients in Qatar

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