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Bonura F, Filizzolo C, Pizzo M, Sanfilippo GL, Cacioppo F, Palazzotto E, Di Bernardo F, Collura A, Martella V, De Grazia S, Giammanco GM. Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology. Viruses 2023; 15:2303. [PMID: 38140544 PMCID: PMC10747129 DOI: 10.3390/v15122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Chiara Filizzolo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Mariangela Pizzo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giuseppa L. Sanfilippo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Federica Cacioppo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Emilia Palazzotto
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Antonina Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Vito Martella
- Dipartimento di Sanità Pubblica e Zootecnia, Università Aldo Moro di Bari, 70010 Valenzano, Italy;
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giovanni M. Giammanco
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
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Hughes SL, Greer AL, Elliot AJ, McEwen SA, Young I, Papadopoulos A. Epidemiology of norovirus and viral gastroenteritis in Ontario, Canada, 2009-2014. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2021; 47:397-404. [PMID: 34737671 PMCID: PMC8525908 DOI: 10.14745/ccdr.v47i10a01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Norovirus is the most common cause of acute gastroenteritis in Canada. The illness causes great morbidity and high societal costs. The objective of this article is to describe the epidemiology of norovirus in the province of Ontario, Canada from 2009 to 2014. METHODS To assess activity of norovirus and viral gastroenteritis (VGE) in Ontario, three datasets were acquired from the provincial government: two traditional surveillance datasets (outbreak and laboratory) and syndromic surveillance data (telehealth), all spanning 2009-2014. All outbreaks, laboratory submissions and telehealth calls were first assessed for total VGE. Norovirus and norovirus-like illness totals were calculated as a proportion of VGE to estimate agent-specific activity levels. Affected institution types, sexes and age groups were also analyzed. RESULTS Between 2009 and 2014, 41.5% of VGE outbreaks, 63.4% of VGE laboratory submissions and 36.6% of all acute gastroenteritis-related (not restricted to viral causes) telehealth calls were attributed to norovirus and norovirus-like illness in Ontario. The most commonly affected institution type was long-term care homes and the most commonly affected age groups were younger (younger than five years) and older (older than 65 years) individuals. Females were slightly more frequently affected than males. CONCLUSION Norovirus and norovirus-like illnesses were the leading cause of VGE in Ontario between 2009 and 2014. They comprised the greatest percentage of VGE when compared with all other VGE-associated viruses. Additional work is needed to determine all component costs and necessary public health actions to reduce the burden of disease.
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Affiliation(s)
| | - Amy L Greer
- Department of Population Medicine, University of Guelph, Guelph, ON
| | - Alex J Elliot
- Real-time Syndromic Surveillance Team, Field Service, National Infection Service, Public Health England, Birmingham, UK
| | - Scott A McEwen
- Department of Population Medicine, University of Guelph, Guelph, ON
| | - Ian Young
- School of Occupational and Public Health, Ryerson University, Toronto, ON
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Bonura F, Urone N, Bonura C, Mangiaracina L, Filizzolo C, Sciortino G, Sanfilippo GL, Martella V, Giammanco GM, De Grazia S. Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome. J Infect 2021; 83:69-75. [PMID: 33887286 DOI: 10.1016/j.jinf.2021.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/21/2021] [Accepted: 04/10/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene. METHODS Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016-2019 from children hospitalized with acute gastroenteritis. RESULTS The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively. CONCLUSIONS The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Noemi Urone
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Giuseppa Sciortino
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Giuseppa L Sanfilippo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy.
| | - Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
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De Grazia S, Bonura F, Cappa V, Li Muli S, Pepe A, Urone N, Giammanco GM. Performance evaluation of a newly developed molecular assay for the accurate diagnosis of gastroenteritis associated with norovirus of genogroup II. Arch Virol 2018; 163:3377-3381. [PMID: 30191373 DOI: 10.1007/s00705-018-4010-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/20/2018] [Indexed: 11/26/2022]
Abstract
The performance of a newly proposed fully automated cassette-based sample-to-results solution for norovirus (NoV) detection, InGenius Norovirus ELITe MGB®, was evaluated. A total of 120 selected archival stool samples from children hospitalized for acute gastroenteritis were used to compare the results to a reference real-time RT-PCR. The InGenius NoV assay showed optimal diagnostic accuracy (sensitivity, 100%; specificity, 95.7%) and was able to correctly detect the entire wide panel of epidemiologically relevant genotypes tested. These preliminary results suggest that the InGenius NoV assay can be recommended as a valuable method for accurate diagnosis of NoV GII infection in epidemic and sporadic gastroenteritis.
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Affiliation(s)
- Simona De Grazia
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy.
| | - Floriana Bonura
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
| | - Vincenzo Cappa
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
| | - Sara Li Muli
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
| | - Arcangelo Pepe
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
| | - Noemi Urone
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
| | - Giovanni M Giammanco
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Via del Vespro, 133, 90127, Palermo, Italy
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Xue C, Pan L, Zhu W, Wang Y, Fu H, Cui C, Lu L, Qiao S, Xu B. Molecular epidemiology of genogroup II norovirus infections in acute gastroenteritis patients during 2014-2016 in Pudong New Area, Shanghai, China. Gut Pathog 2018; 10:7. [PMID: 29483945 PMCID: PMC5824483 DOI: 10.1186/s13099-018-0233-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norovirus (NoV), a member of the Caliciviridae, is now recognized as the leading cause of acute gastroenteritis (AGE) worldwide. Globally, the GII.4 Sydney_2012 variant has predominated in NoV-related AGE since 2012, although the novel variant GII.17 has also been reported as responsible for gastroenteritis outbreaks in East Asia since 2014. This study aimed to disclose the recent genotype patterns of NoV genogroup II (GII) presenting in AGE patients in Pudong New Area of Shanghai through a laboratory-based syndromic surveillance system. The study further aimed to delineate the predominant strains circulating in the population. METHODS Pudong New Area is located in eastern Shanghai and covers 20.89% of the Shanghai population. The laboratory-based syndromic surveillance system is composed of 12 sentinel hospitals among the 68 general hospitals in this area. AGE patients who sought medical care were sampled following an AGE surveillance protocol. Stool samples were collected from participating patients, and a standardized questionnaire was given to each patient by trained nurses to gain information on the disease profiles and demographics of the patients. Real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to screen the GI nd GII NoV and RT-PCR was used to amplify NoV GII partial capsid protein open reading frame 2 (ORF2). NoV Genotyping Tool (version 1.0, RIVM, MA Bilthoven, Netherlands) was used for genotyping, and a phylogenetic analysis was conducted by MEGA 7.0. RESULTS During 2014-2016, among the 2069 virus-infected AGE cases, 65.88% were caused by NoV. NoV-AGE occurred most frequently in the periods from October to March. The patients with more severe diarrheal symptoms and vomiting were more likely to be infected by NoV. The main genotypes were GII.17 (44.69%) and GII.4 (39.26%), which dominated the NoV-AGE epidemics jointly or in turn, whereas a slight increase in GII.2 was observed beginning in May 2016. The GII.17 strains tended to cluster more with the Hu/JP/2014/GII.P17_GII.17/Kawasaki323 variants, representing novel prevalent strains. Among the GII.4 strains, the GII.4 Sydney_2012 variant was still the predominant strain. CONCLUSIONS NoV GII has become the main cause of virus-infected AGE in Pudong New Area, Shanghai. The predominant genotypes of NoV GII were GII.17 and GII.4. Comprehensive laboratory-based surveillance is important for clinical diagnosis and treatment. Identification of emerging new genotypes is also crucial for the prevention and control of NoV-infected AGE.
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Affiliation(s)
- Caoyi Xue
- School of Public Health, Fudan University, Shanghai, 200032 China
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Lifeng Pan
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Weiping Zhu
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Yuanping Wang
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Huiqin Fu
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Chang Cui
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Lan Lu
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Sun Qiao
- Shanghai Pudong New Area Center for Disease Control and Prevention, 3039 Zhangyang Road, Shanghai, 200136 China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136 China
| | - Biao Xu
- School of Public Health, Fudan University, Shanghai, 200032 China
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Melhem NM, Zaraket H, Kreidieh K, Ali Z, Hammadi M, Ghanem S, Hajar F, Haidar A, Inati A, Rajab M, Fakhouri H, Ghanem B, Baasiri G, Dbaibo G. Clinical and epidemiological characteristics of norovirus gastroenteritis among hospitalized children in Lebanon. World J Gastroenterol 2016; 22:10557-10565. [PMID: 28082807 PMCID: PMC5192266 DOI: 10.3748/wjg.v22.i48.10557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/27/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To assess the burden of norovirus (NoV) and to determine the diversity of circulating strains among hospitalized children in Lebanon.
METHODS Stool samples were collected from children presenting with acute gastroenteritis to six major hospitals in Lebanon. A total of 739 eligible stool samples, testing negative for diarrhea caused by rotavirus as a possible viral pathogen, were collected between January 2011 and June 2013. A standardized questionnaire including demographic, epidemiological and clinical observations was used at the time of hospitalization of children presenting with diarrhea. Viral RNA was extracted from stool samples followed by reverse transcription polymerase chain reaction and nucleotide sequencing of a fragment of the viral protein 1 capsid gene. Multiple sequence alignments were carried out and phylogenetic trees were constructed using the MEGA 6 software.
RESULTS Overall, 11.2% of stool samples collected from children aged < 5 years tested positive for NoV genogroups I (GI) and II (GII). GII accounted for 10.6% of the gastroenteritis cases with only five samples being positive for GI (0.7%). The majority of hospitalized children showed symptoms of diarrhea, dehydration, vomiting and fever. Upon sequencing of positive samples and based on their clustering in the phylogenetic tree, 4/5 of GI gastroenteritis cases were designated GI.3 and one case as GI.4. GII.4 was predominantly detected in stool of our study participants (68%). We report a JB-15/KOR/2008 GII.4 Apeldoorn 2008-like variant strain circulating in 2011; this strain was replaced between 2012 and 2013 by a variant sharing homology with the Sydney/NSW0514/2012/AUS GII.4 Sydney 2012 and Sydney 2012/FRA GII.4 strains. We also report the co-circulation of non-GII.4 genotypes among hospitalized children. Our data show that NoV gastroenteritis can occur throughout the year with the highest number of cases detected during the hot months.
CONCLUSION The majority of NoV-associated viral gastroenteritis cases among our participants are attributable to GII.4, which is compatible with results reported worldwide.
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Kulkarni R, Patel A, Bhalla S, Chhabra P, Cherian S, Chitambar SD. Characterization of GII.4 noroviruses circulating among children with acute gastroenteritis in Pune, India: 2005-2013. INFECTION GENETICS AND EVOLUTION 2015; 37:163-73. [PMID: 26611824 DOI: 10.1016/j.meegid.2015.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022]
Abstract
Genogroup II genotype 4 noroviruses (GII.4 NoVs), an important cause of sporadic childhood gastroenteritis worldwide, undergo continuous evolution leading to the periodic emergence of novel variants. The present study was undertaken for surveillance of GII.4 NoVs and identification and characterization of GII.4 variants circulating among children with sporadic gastroenteritis in Pune, India during 2005-2013. Among the 12 GII genotypes detected in the study, GII.4 was predominant. Sequencing and phylogenetic analysis of ORF2 (major capsid protein VP1 gene) of the GII.4 NoVs revealed circulation of seven GII.4 variants, Hunter_2004 (2005-2007), Yerseke_2006a (2006), DenHaag_2006b (2007), Osaka_2007 (2007-2009), Apeldoorn_2007 (2008), New Orleans_2009 (2008-2012) and Sydney_2012 (2013), with the Pune strains grouping with the contemporary global reference strains. The Hunter_2004, Osaka_2007 and New Orleans_2009 variants showed prolonged circulation, with the Hunter_2004 and New Orleans_2009 variants differentiating into temporally separated sub-clusters. Analysis of VP1 sequences and predicted structures of the GII.4 variants identified variant specific amino acid positions, particularly in and near (within 8A(°)) the epitopes A-E, displaying differences in the sequence and physicochemical characteristics of the different variants. Comparison with the reference strains of each of the GII.4 variants revealed up to 11 amino acid substitutions at the variant specific positions in the GII.4 strains from Pune. Amino acid variations were also noted among the strains of the same GII.4 variant in Pune. The strains of different sub-clusters identified in the Hunter_2004 and New Orleans_2009 variants showed differences in sequence and physicochemical properties of either or all of the epitopes A, C and E. The study thus describes the temporal variations and diversity of the GII.4 strains in Pune and emphasizes continuous monitoring and analysis of the GII.4 variants.
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Affiliation(s)
- Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Amit Patel
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Shilpa Bhalla
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Preeti Chhabra
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Sarah Cherian
- Bioinformatics Group, National Institute of Virology, Pune, India
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