Detection of novel GII.17 norovirus in Argentina, 2015

Degiuseppe, Juan Ignacio; Gomes, Karina A.; Hadad, María F.; Parra, Gabriel I.; Stupka, Juan Andrés

doi:10.1016/j.meegid.2016.11.026

Cited by 16 publications

(11 citation statements)

References 13 publications

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“…23 Until now, classifying noroviruses into P-types was based on a naming system that used P-type designation linked to the corresponding VP1 genotype of the strain and when no VP1 sequence was known, orphan P-types and/or P types with alphabet letters were assigned [19]. Since an increasing number of recombinant strains have been recognized in recent years [33,37,40,51], we propose an update for the norovirus classification system in which P-types and VP1 genotypes are assigned independently. We also propose designating dual types with the capsid genotype listed first followed by P-type (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Since all three P-types are historic types, especially GII.P4 strains, which are of epidemiological importance worldwide and the current P-typing classification is based on relatively short nucleotide sequence fragments (762 nucleotides), we decided that we will re-visit this issue in our next classification update, which is expected to be based on complete ORF1 sequences. [33,40].…”

Section: Discussionmentioning

confidence: 99%

“…Dual typing (ORF1-RdRp=P type, ORF2=genotype) is now used routinely in many laboratories worldwide and at least 14 GI P-types and 27 GII P-types as well as 9 GI capsid genotypes and 22 GII capsid genotypes have been described [2,19,27]. Inclusion of norovirus diagnostic testing by real-time quantitative reverse transcription PCR into clinical and public health routine in recent years [27,[37][38][39] has confirmed the importance of GI and GII noroviruses globally [13,31,33,35,37,[40][41][42][43][44]. The increasing use of pathogen genome sequencing to unravel modes of transmission, sources of outbreaks, or to study the burden of infections has led to identification of several new candidate norovirus genogroups and genotypes since the last norovirus classification update in 2013 [9,12,33,40,41,43,[45][46][47][48][49].…”

Section: Introductionmentioning

confidence: 99%

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Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

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626

611

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Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically, they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1, respectively. In recent years, several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 49 (9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1, GII.NA2 and GIV. NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region, noroviruses can be divided into 60 P-types (14 GI, 37 GII, 2 GIII, 1 GIV, 2 GV, 2 GVI, 1 GVII and 1 GX), 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

Self Cite

626

611

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show abstract

“…In addition, Lindesmith et al (2018) , reported a strategy of camouflaging antigenic sites to carbohydrate blocking antibodies, named “particle breathing.” Since 1995, many variants causing global epidemics have emerged, including US 1995/96 in 1996 ( Fankhauser et al, 1998 ), Farmington Hills in 2002 ( Lopman et al, 2004 ), Hunter in 2004 ( Bull et al, 2006 ), Den Haag in 2006 ( Eden et al, 2010 ), New Orleans in 2009 ( Yen et al, 2011 ), and Sydney in 2012 ( van Beek et al, 2013 ). However, in 2014, a non-GII.4 genotype, named GII.17_Kawasaki, was reported as the main cause of outbreaks in Asia ( Lu et al, 2015 ; Matsushima et al, 2015 ; Thanh et al, 2016 ), some countries of the Americas ( Parra and Green, 2015 ; Degiuseppe et al, 2017 ; Silva et al, 2017 ) and Europe ( De Graaf et al, 2015 ; Giammanco et al, 2017 ).…”

Section: Introductionmentioning

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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“…Although the origin of GII.17 strains is still largely unknown, the GII.17 Kawasaki_2014 variant caused large AGE outbreaks in China, Japan, and South Korea (6–9) and sporadic infections in Hong Kong, Taiwan (10), the United States (11), Italy (12), Romania (13), and Australia. In Latin America, this emergent strain was detected in AGE outbreaks and sporadic cases in Brazil (14, 15) and in sporadic cases in Argentina (16).…”

Section: Announcementmentioning

confidence: 99%