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Calduch EN, Cattaert T, Verstraeten T. Model estimates of hospitalization discharge rates for norovirus gastroenteritis in Europe, 2004-2015. BMC Infect Dis 2021; 21:757. [PMID: 34353287 PMCID: PMC8340375 DOI: 10.1186/s12879-021-06421-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2021] [Indexed: 01/10/2023] Open
Abstract
Background Norovirus is an important cause of acute gastroenteritis globally. However, norovirus is rarely laboratory confirmed or recorded explicitly as a cause of hospitalization. In recent years, there has been an interest in using medical databases and indirect modelling methods to estimate the incidence of norovirus gastroenteritis. The objective of this study was to estimate the incidence of hospitalizations for norovirus gastroenteritis in Europe (2004–2015) using nationwide in-patient discharge records from different European countries. Methods National hospital discharge registers in all 28 European Union countries (at that time) and all 4 European Free Trade Association countries were contacted and invited to participate in the study. Discharges with ICD9/ICD10 codes for acute gastroenteritis (AGE) as first-listed (principal) diagnosis were extracted to assess hospitalization rates for AGE and norovirus gastroenteritis (NGE), overall, by age group, country, month, and seasonal year. The number of cause-unspecified episodes was regressed against pathogen-specific AGE episodes: Rotavirus, Clostridium difficile, Other Bacterial, Other Viral and Parasitic separately. NGE hospital discharges were estimated for each month by calculating the difference between observed cause-unspecified and model-predicted counts, assuming that any remaining seasonality not otherwise captured in the model was due to norovirus, and adding those to the coded NGE episodes to get the total number of norovirus-associated episodes. Results Data were available from 15 countries, representing 68% of the total population in Europe. Only 24.4% of all AGE discharges were coded as cause-specified. We estimated that between 2004 and 2015, the overall rate of NGE hospital discharges in Europe was 3.9 per 10,000 person-years, ranging from 1.2 (Portugal) to 10.7 (Lithuania). Norovirus was predicted to be responsible for 17% of all AGE hospital discharges in Europe in this period. Norovirus affects individuals of all ages, but NGE discharge rates were highest in children < 5 years (24.8 per 10,000 person-years), and adults aged ≥80 years (10.7 per 10,000 person-years). Conclusion We estimated that 1 in 400 hospitalizations in Europe can be attributed to Norovirus. In the absence of routine norovirus testing and recording in hospital settings, modelling methods are useful resources to estimate the incidence of norovirus gastroenteritis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06421-z.
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Affiliation(s)
| | - Tom Cattaert
- P95 Pharmacovigilance and Epidemiology Services, Leuven, Belgium
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Farsi M, Roodbari F, Nejati B, Arashkia A, Jalilvand S, Nateghian A, Rahbarimanesh A, Marashi SM, Shoja Z. Prevalence and genetic diversity of norovirus genogroup II in children less than 5 years of age with acute gastroenteritis in Tehran, Iran. Med Microbiol Immunol 2018; 207:201-210. [PMID: 29619604 DOI: 10.1007/s00430-018-0541-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Viral gastroenteritis is a major public health problem worldwide. In Iran, very limited studies have been performed with regard to the epidemiology of noroviruses. This study aimed to evaluate the prevalence and molecular epidemiology of GII noroviruses in hospitalized children less than 5 years of age with acute gastroenteritis (AGE). A total of 210 stool specimens were collected from Ali Asghar Children's Hospital and Bahrami Children's Hospital in Tehran, from June 2015 to June 2016. The samples were screened by real-time RT-PCR for genogroup II (GII). Positive samples were genotyped by semi-nested PCR followed by Sanger sequencing and phylogenetic analysis. Norovirus was identified in 36 (17.1%) of 210 specimens. Based on genetic analysis of RdRp and capsid sequences, the strains were clustered into eight RdRp-capsid genotypes: GII.P4-GII.4 Sydney_2012 (41.7%), GII.Pe-GII.4 Sydney_2012 (30.6%), GII.P21-GII.3 (13.9%), GII.P16-GII.4 Sydney_2012 (2.8%), GII.P16-GII.12 (2.8%), GII.P2-GII.4 Sydney_2012 (2.8%), GII.P7-GII.7 (2.8%) and GII.P2-GII.2 (2.8%). We determined several different co-circulating norovirus genotypes in children < 5 years of age with AGE in our hospital in Tehran, Iran. Continued molecular surveillance of noroviruses, including typing of both RdRp and capsid genes, is important for monitoring emerging strains in our continued efforts to reduce the overall burden of norovirus disease.
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Affiliation(s)
- Mahsa Farsi
- Biology Department, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Fatemeh Roodbari
- Biology Department, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Behrooz Nejati
- Biology Department, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Arash Arashkia
- Virology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Somayeh Jalilvand
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Nateghian
- Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Aliakbar Rahbarimanesh
- Department of Pediatric Infectious Diseases, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sayed Mahdi Marashi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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3
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Kabue JP, Meader E, Hunter PR, Potgieter N. Genetic characterisation of Norovirus strains in outpatient children from rural communities of Vhembe district/South Africa, 2014-2015. J Clin Virol 2017; 94:100-106. [PMID: 28783578 DOI: 10.1016/j.jcv.2017.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/24/2017] [Accepted: 07/08/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Norovirus (NoV) is now the most common cause of both outbreaks and sporadic non-bacterial gastroenteritis worldwide. However, data supporting the role of NoV in diarrheal disease are limited in the African continent. OBJECTIVES This study investigates the distribution of NoV genotypes circulating in outpatient children from rural communities of Vhembe district/South Africa. STUDY DESIGN Stool specimens were collected from children under five years of age with diarrhea, and controls without diarrhea, between July 2014 and April 2015. NoV-positive samples, detected previously by Realtime PCR, were analysed using conventional RT-PCR targeting the partial capsid and polymerase genes. Nucleotide sequencing methods were performed to genotype the strains. RESULTS The sequence analyses demonstrated multiple NoV genotypes including GI.4 (13.8%), GI.5 (6.9%), GII.14 (6.9%), GII.4 (31%), GII.6 (3.4%), GII.P15 (3.4%), GII.P21 (3.4%) and GII.Pe (31%). The most prevalent NoV genotypes were GII.4 Sydney 2012 variants (n=7) among the capsid genotypes, GII.Pe (n=9) among the polymerase genotypes and GII.Pe/GII.4 Sydney 2012 (n=8) putative recombinants among the RdRp/Capsid genotypes. Two unassigned GII.4 variants were found. CONCLUSIONS The findings highlighted NoV genetic diversity and revealed continuous pandemic spread and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An unusual RdRp genotype GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe district/South Africa. NoV surveillance is warranted to help to inform investigations into NoV evolution and disease burden, and to support on-going vaccine development programmes.
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Affiliation(s)
- Jean Pierre Kabue
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa.
| | - Emma Meader
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK
| | - Paul R Hunter
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK; Department of Environmental Health, Tshwane University of Technology, Pretoria, South Africa
| | - Natasha Potgieter
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa; Dean, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
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4
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Fumian TM, da Silva Ribeiro de Andrade J, Leite JPG, Miagostovich MP. Norovirus Recombinant Strains Isolated from Gastroenteritis Outbreaks in Southern Brazil, 2004-2011. PLoS One 2016; 11:e0145391. [PMID: 27116353 PMCID: PMC4846083 DOI: 10.1371/journal.pone.0145391] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/03/2015] [Indexed: 12/02/2022] Open
Abstract
Noroviruses are recognized as one of the leading causes of viral acute gastroenteritis, responsible for almost 50% of acute gastroenteritis outbreaks worldwide. The positive single-strand RNA genome of noroviruses presents a high mutation rate and these viruses are constantly evolving by nucleotide mutation and genome recombination. Norovirus recombinant strains have been detected as causing acute gastroenteritis outbreaks in several countries. However, in Brazil, only one report of a norovirus recombinant strain (GII.P7/GII.20) has been described in the northern region so far. For this study, 38 norovirus strains representative of outbreaks, 11 GII.4 and 27 non-GII.4, were randomly selected and amplified at the ORF1/ORF2 junction. Genetic recombination was identified by constructing phylogenetic trees of the polymerase and capsid genes, and further SimPlot and Bootscan analysis of the ORF1/ORF2 overlap. Sequence analysis revealed that 23 out of 27 (85%) non-GII.4 noroviruses were recombinant strains, characterized as: GII.P7/GII.6 (n = 9); GIIP.g/GII.12 (n = 4); GII.P16/GII.3 (n = 4); GII.Pe/GII.17 (n = 2); GII.P7/GII.14 (n = 1); GII.P13/GII.17 (n = 1); GII.P21/GII.3 (n = 1); and GII.P21/GII.13 (n = 1). On the other hand, among the GII.4 variants analyzed (Den Haag_2006b and New Orleans_2009) no recombination was observed. These data revealed the great diversity of norovirus recombinant strains associated with outbreaks, and describe for the first time these recombinant types circulating in Brazil. Our results obtained in southern Brazil corroborate the previous report for the northern region, demonstrating that norovirus recombinant strains are circulating more frequently than we expected. In addition, these results emphasize the relevance of including ORF1/ORF2-based analysis in surveillance studies as well as the importance of characterizing strains from other Brazilian regions to obtain epidemiological data for norovirus recombinant strains circulating in the country.
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Affiliation(s)
- Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- * E-mail:
| | | | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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5
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Chan MCW, Lee N, Hung TN, Kwok K, Cheung K, Tin EKY, Lai RWM, Nelson EAS, Leung TF, Chan PKS. Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014. Nat Commun 2015; 6:10061. [PMID: 26625712 PMCID: PMC4686777 DOI: 10.1038/ncomms10061] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/29/2015] [Indexed: 12/11/2022] Open
Abstract
Norovirus genogroup II genotype 4 (GII.4) has been the predominant cause of viral gastroenteritis since 1996. Here we show that during the winter of 2014-2015, an emergent variant of a previously rare norovirus GII.17 genotype, Kawasaki 2014, predominated in Hong Kong and outcompeted contemporary GII.4 Sydney 2012 in hospitalized cases. GII.17 cases were significantly older than GII.4 cases. Root-to-tip and Bayesian BEAST analyses estimate GII.17 viral protein 1 (VP1) evolves one order of magnitude faster than GII.4 VP1. Residue substitutions and insertion occur in four of five inferred antigenic epitopes, suggesting immune evasion. Sequential GII.4-GII.17 infections are noted, implicating a lack of cross-protection. Virus bound to saliva of secretor histo-blood groups A, B and O, indicating broad susceptibility. This fast-evolving, broadly recognizing and probably immune-escaped emergent GII.17 variant causes severe gastroenteritis and hospitalization across all age groups, including populations who were previously less vulnerable to GII.4 variants; therefore, the global spread of GII.17 Kawasaki 2014 needs to be monitored.
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Affiliation(s)
- Martin C W Chan
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Nelson Lee
- Department of Medicine and Therapeutics, Faculty of Medicine, 9/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Tin-Nok Hung
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Kirsty Kwok
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Kelton Cheung
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Edith K Y Tin
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Raymond W M Lai
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - E Anthony S Nelson
- Department of Paediatrics, Faculty of Medicine, 6/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Ting F Leung
- Department of Paediatrics, Faculty of Medicine, 6/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
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An increasing prevalence of recombinant GII norovirus in pediatric patients with diarrhea during 2010–2013 in China. INFECTION GENETICS AND EVOLUTION 2015; 31:48-52. [DOI: 10.1016/j.meegid.2015.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/18/2014] [Accepted: 01/07/2015] [Indexed: 11/21/2022]
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7
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Silva LDD, Rodrigues EL, Lucena MSSD, Lima ICGD, Oliveira DDS, Soares LS, Mascarenhas JDP, Linhares ADC, Gabbay YB. Detection of the pandemic norovirus variant GII.4 Sydney 2012 in Rio Branco, state of Acre, northern Brazil. Mem Inst Oswaldo Cruz 2015; 108:1068-70. [PMID: 24141954 PMCID: PMC4005546 DOI: 10.1590/0074-0276130293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/16/2013] [Indexed: 11/22/2022] Open
Abstract
Noroviruses (NoVs) are important cause of gastroenteritis in humans worldwide.
Genotype GII.4 is responsible for the majority of outbreaks reported to date. This
study describes, for the first time in Brazil, the circulation of NoV GII.4 variant
Sydney 2012 in faecal samples collected from children aged less than or equal to
eight years in Rio Branco, state of Acre, northern Brazil, during July-September
2012.
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8
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Chan MCW, Leung TF, Kwok AK, Lee N, Chan PKS. Characteristics of patients infected with norovirus GII.4 Sydney 2012, Hong Kong, China. Emerg Infect Dis 2014; 20:658-61. [PMID: 24656073 DOI: 10.3201/eid2004.13457] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Norovirus GII.4 Sydney 2012 has spread globally since late 2012. We report hospitalization of patients infected with this strain skewed toward infants and young children among 174 cases during August 2012-July 2013 in Hong Kong, China. This group had higher fecal viral load (≈10-fold) than did older children and adults.
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9
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Mans J, Murray TY, Taylor MB. Novel norovirus recombinants detected in South Africa. Virol J 2014; 11:168. [PMID: 25228444 PMCID: PMC4181420 DOI: 10.1186/1743-422x-11-168] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/12/2014] [Indexed: 12/26/2022] Open
Abstract
Background Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA). Results Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x2 analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa. Conclusions Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses.
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Affiliation(s)
- Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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10
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Ruether IGA, Dimitriou TG, Tsakogiannis D, Kyriakopoulou Z, Amoutzias GD, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Characterization of novel intergenogroup and intergenotype recombinant noroviruses from central Greece. Mol Cell Probes 2014; 28:204-10. [PMID: 24751495 DOI: 10.1016/j.mcp.2014.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 01/14/2023]
Abstract
Noroviruses (NoVs) are a major causative agent of acute gastroenteritis in humans. They are members of the Caliciviridae family and based on the genetic analysis of the RdRp and capsid regions, human NoVs are divided into three genogroups (Gs), GI, GII, and GIV. The three genogroups further segregate into distinct lineages called genotypes. The NoV genus is genetically diverse and recombination of viral RNA is known to depend upon various immunological and intracellular constraints that may allow the emergence of viable recombinants. In this study, three Noroviral strains detected in clinical samples revealed two hitherto unobserved recombination events between GII.9/GII.4 and GII.9/GI.7 genogroups. To our knowledge, these intergenotype and intergenogroup recombination events of GII.9/GII.4 and GII.9/GI.7, in ORF1 and ORF2 genes respectively are reported for the first time and highlight the ongoing evolution of noroviruses.
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Affiliation(s)
- I G A Ruether
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - T G Dimitriou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - D Tsakogiannis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - Z Kyriakopoulou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - G D Amoutzias
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - C Gartzonika
- University of Ioannina, Medical School, Department of Microbiology, Ioannina, Greece
| | - S Levidiotou-Stefanou
- University of Ioannina, Medical School, Department of Microbiology, Ioannina, Greece
| | - P Markoulatos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece.
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11
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Chan MCW, Leung TF, Kwok AK, Lee N, Chan PKS. Characteristics of Patients Infected with Norovirus GII.4 Sydney 2012, Hong Kong, China. Emerg Infect Dis 2014. [PMID: 24656073 PMCID: PMC3966374 DOI: 10.3201/eid2004.131457] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Norovirus GII.4 Sydney 2012 has spread globally since late 2012. We report hospitalization of patients infected with this strain skewed toward infants and young children among 174 cases during August 2012–July 2013 in Hong Kong, China. This group had higher fecal viral load (≈10-fold) than did older children and adults.
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12
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Eden JS, Hewitt J, Lim KL, Boni MF, Merif J, Greening G, Ratcliff RM, Holmes EC, Tanaka MM, Rawlinson WD, White PA. The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology 2013; 450-451:106-13. [PMID: 24503072 DOI: 10.1016/j.virol.2013.12.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 12/15/2022]
Abstract
Norovirus is the leading cause of acute gastroenteritis with most infections caused by GII.4 variants. To understand the evolutionary processes that contribute to the emergence of GII.4 variants, we examined the molecular epidemiology of norovirus-associated acute gastroenteritis in Australia and New Zealand from 893 outbreaks between 2009 and 2012. Throughout the study GII.4 New Orleans 2009 was predominant; however, during 2012 it was replaced by an emergent GII.4 variant, Sydney 2012. An evolutionary analysis of capsid gene sequences was performed to determine the origins and selective pressures driving the emergence of these recently circulating GII.4 variants. This revealed that both New Orleans 2009 and Sydney 2012 share a common ancestor with GII.4 Apeldoorn 2007. Furthermore, pre-epidemic ancestral variants of each virus were identified up to two years before their pandemic emergence. Adaptive changes at known blockade epitopes in the viral capsid were also identified that likely contributed to their emergence.
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Affiliation(s)
- John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joanne Hewitt
- The Institute of Environmental Science and Research Ltd (ESR), Porirua, New Zealand
| | - Kun Lee Lim
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia; Molecular Laboratory, Department of Pathology, Singapore General Hospital, Singapore
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Juan Merif
- Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Gail Greening
- The Institute of Environmental Science and Research Ltd (ESR), Porirua, New Zealand
| | - Rodney M Ratcliff
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - William D Rawlinson
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia; Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, Randwick, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.
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13
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Ji L, Wu X, Yao W, Chen L, Xu D, Shen Y, Shen J, Han J. Rapid emergence of novel GII.4 sub-lineages noroviruses associated with outbreaks in Huzhou, China, 2008-2012. PLoS One 2013; 8:e82627. [PMID: 24324813 PMCID: PMC3853588 DOI: 10.1371/journal.pone.0082627] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 10/26/2013] [Indexed: 12/23/2022] Open
Abstract
Infection caused by noroviruses (NoVs) is one of the most important causes of acute gastroenteritis in humans worldwide. To gain insight into the epidemiology of and genetic variation in NoV strains, stool samples collected from 18 outbreaks of acute gastroenteritis in Huzhou, China, between January 2008 and December 2012 were analyzed. Samples were tested for NoVs by real-time RT-PCR. Partial sequences of the RNA- dependent RNA polymerase (RdRp) and capsid gene of the positive samples were amplified by RT-PCR, and the PCR products were sequenced and used for phylogenetic analysis. NoVs were found to be responsible of 88.8% of all nonbacterial acute gastroenteritis outbreaks in Huzhou over the last 5 years. Genogroup II outbreaks largely predominated and represented 93% of all outbreaks. A variety of genotypes were found among genogroups I and II, including GI.4, GI.8, GII.4, and GII.b. Moreover, phylogenetic analyses identified two recombinant genotypes (polymerase/capsid): GI.2/GI.6 and GII.e/GII.4 2012 Sydney. GII.4 was predominant and involved in 8/10 typed outbreaks. During the study period, GII.4 NoV variants 2006b, New Orleans 2009, and Sydney 2012 were identified. This is the first report of the detection of GII.4 New Orleans 2009 variant, GII.e/GII.4 Sydney 2012 recombinant in outbreaks of acute gastroenteritis in China.
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Affiliation(s)
- Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Wenting Yao
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Yuehua Shen
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Jiayu Shen
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
| | - Jiankang Han
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang Province, China
- * E-mail:
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Abstract
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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