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Sun Z, Niu P, Jin M, Zhang R, Gao Q, Wang H, Ma X, Wang J. Genotyping and traceability analysis of norovirus in Yantai between 2017 and 2019. J Med Virol 2023; 95:e29220. [PMID: 37947460 DOI: 10.1002/jmv.29220] [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: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
To investigate the diversity and evolution of noroviruses in Yantai in recent years, this study focused on the coat protein regions of norovirus-positive samples with nucleic acid detection (cycle threshold) values below 30 between 2017 and 2019. A total of 81 sequences were obtained for genotyping. Initially, a high-throughput sequencing approach was established to perform the whole-genome sequencing of multiple typical diarrheal strains. Using bioinformatics software such as BEAST, recombinant variant analysis was performed for each genotype of the norovirus strains, and genetic evolutionary analysis was conducted for the dominant strain GII.4, as well as the rare variant GII.21. The results showed that there were multiple genotypes such as GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.13, GII.17, GII.21, and GIX.1 in the positive samples of norovirus from 2017 to 2019. GII.4 is characterized by diverse genotypes, with new changes in antigenic epitopes occurring during the course of the epidemic. This may have led to the emergence of a new pandemic. This suggests a need to strengthen surveillance. The results of this study suggest that attention should be paid to the predominant genotypes prevalent in neighboring countries and regions, and the safety supervision of imported food should be strengthened to aid in the prevention and control of related viruses.
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Affiliation(s)
- Zhenlu Sun
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Peihua Niu
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Miao Jin
- Department of Viral Diarrhea, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Qiao Gao
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Hongtao Wang
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Xuejun Ma
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Ji Wang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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Gutierrez MB, de Figueiredo MR, Fialho AM, Cantelli CP, Miagostovich MP, Fumian TM. Nosocomial acute gastroenteritis outbreak caused by an equine-like G3P[8] DS-1-like rotavirus and GII.4 Sydney[P16] norovirus at a pediatric hospital in Rio de Janeiro, Brazil, 2019. Hum Vaccin Immunother 2021; 17:4654-4660. [PMID: 34402714 DOI: 10.1080/21645515.2021.1963169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Worldwide, rotavirus (RVA) and norovirus are considered major etiological agents of acute gastroenteritis (AGE) in pediatric population admitted to hospitals. This study describes the investigation of nosocomial infections caused by emergent RVA and norovirus strains reported at a pediatric hospital in southern Brazil in May 2019. This outbreak affected 30 people among children and adults. Nine stool samples (eight children and one nurse) were obtained and analyzed by RT-qPCR to detect and quantify RVA and norovirus. Positive samples were genotyped by sequencing and subjected to phylogenetic analysis. We detected RVA in 44.4% (4/9) and norovirus in 55.5% (5/9) at high viral loads, ranging from 3.5 × 107 to 6.1 × 107 and 3.2 × 102 to 3.2 × 109 genome copies/g of stool, respectively. Co-infections were not observed. RVA VP4 and VP7 gene sequencing in combination with polyacrylamide gel electrophoresis identified the circulation of equine-like G3P[8] DS-1-like, and the partial sequencing of the other nine genes revealed that strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background. The emergent recombinant norovirus variant, GII.4 Sydney[P16], was identified by ORF1-2 sequencing. Active surveillance and effective prevention measures should be constantly reinforced to avoid the spread of nosocomial viral infections into hospitals, which could severely affect pediatric patients admitted with underlying health conditions.
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Affiliation(s)
- Meylin B Gutierrez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Mirza Rocha de Figueiredo
- Department of Hospital Epidemiology and Surveillance Centre, The National Institute of Women, Children and Adolescents Health Fernandes Figueira (IFF), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
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Degiuseppe JI, Stupka JA. Genotype distribution of Group A rotavirus in children before and after massive vaccination in Latin America and the Caribbean: Systematic review. Vaccine 2019; 38:733-740. [PMID: 31771863 DOI: 10.1016/j.vaccine.2019.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND During the last decade, most of Latin American and the Caribbean (LAC) countries have implemented oral live rotavirus vaccines in their national vaccination programs with remarkable results. However, it has been suggested that massive vaccination could lead to the replacement of circulating genotypes or the emergence of new variants or neutralizing antibodies escape mutants, which may reduce the effectiveness of the vaccine. The objective was to analyze the genetic diversity of Group A rotavirus before and after the introduction of universal vaccination in LAC. METHODS We conducted a systematic review of studies published in PubMed, Scielo and LILACS. There were considered only LAC countries with rotavirus massive vaccination strategy which had described circulating genotypes data in children under 5 years of age, either for surveillance or vaccine effectiveness purposes, from 2001 to 2017. Systematic review stages were carried out following the recommendations of PRISMA. RESULTS Of the 18 countries that included any of the two licensed rotavirus vaccines in their national schedules since 2006, only 7 (~39%) presented studies of RVA genetic diversity before and after implementation, and met the inclusion criteria. Four of them (Argentina, Brazil, Colombia and Nicaragua) experienced a rapid switch from Wa-like to DS-1-like strains. Also, G1P[8] association, considered the most predominant worldwide in the pre-vaccination era, decreased significantly and was only frequently detected in Venezuela and Nicaragua. No defined pattern of emergence at high frequencies of unusual associations was observed in the post vaccination period, except for some evidence of G9P[4] in Colombia, G3P[6] and G1P[4] in Nicaragua. CONCLUSIONS Even though the evidence shows a DS-1-like change trend, data from studies conducted in Latin America and the Caribbean are diverse and still not sufficient to assess the impact of vaccines on viral ecology or if genetic diversity is influenced by natural mechanisms of fluctuation.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratory of Viral Gastroenteritis, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina.
| | - Juan Andrés Stupka
- Laboratory of Viral Gastroenteritis, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
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Paula FLD, Sardi SI, Tigre DM, Fernandes FMDC, Campos GS. ACUTE GASTROENTERITIS ASSOCIATED WITH NOROVIRUS GII.4 VARIANTS. ARQUIVOS DE GASTROENTEROLOGIA 2019; 55:264-266. [PMID: 30540089 DOI: 10.1590/s0004-2803.201800000-67] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Norovirus (NoV) is an important etiologic agent of acute gastroenteritis and infects individuals of all ages, especially children in Brazil and worldwide. NoV GII.4 was the most prevalent genotype worldwide because of your extensive genetic diversity. In Brazil, especially in the Northeast, few studies have been developed for identify and molecularly characterize NoV. OBJECTIVE The present study aimed to detect and describe the molecular epidemiology of NoV associated with acute gastroenteritis. METHODS The viral RNA extracted from stool samples were subjected to Nested RT-PCR and the genotypes were determined by nucleotide sequences analysis. In total, 278 stool samples assisted at Aliança Hospital in the city of Salvador, with acute gastroenteritis were examined, between March 2009 and July 2012. RESULTS A high NoV rate (54.2%) was identified in children under 5 years of age. We detected the circulation of different NoV GII.4 variants in Salvador, during the study period as Den Haag 2006b, New Orleans 2009 and Sydney 2012. CONCLUSION These findings reinforce the need to study the molecular epidemiology of NoV infections in acute gastroenteritis.
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Affiliation(s)
- Fabiana Lopes de Paula
- Universidade Federal da Bahia (UFBA), Instituto de Ciências da Saúde, Laboratório de Virologia, Salvador, BA, Brasil.,Universidade Federal do Recôncavo da Bahia (UFRB), Centro de Ciências da Saúde, Santo Antônio de Jesus, BA, Brasil
| | - Silvia Inês Sardi
- Universidade Federal da Bahia (UFBA), Instituto de Ciências da Saúde, Laboratório de Virologia, Salvador, BA, Brasil
| | - Dellane Martins Tigre
- Universidade Federal da Bahia (UFBA), Instituto de Ciências da Saúde, Laboratório de Virologia, Salvador, BA, Brasil.,Universidade Estadual do Sudoeste da Bahia (UESB), Departamento de Ciências Biológicas, Jequié, BA, Brasil
| | - Flora Maria de Campos Fernandes
- Universidade Federal da Bahia (UFBA), Instituto de Biologia, Laboratório de Genética de Populações e Evolução Molecular, Salvador, BA, Brasil
| | - Gúbio Soares Campos
- Universidade Federal da Bahia (UFBA), Instituto de Ciências da Saúde, Laboratório de Virologia, Salvador, BA, Brasil
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Ludwig-Begall LF, Mauroy A, Thiry E. Norovirus recombinants: recurrent in the field, recalcitrant in the lab - a scoping review of recombination and recombinant types of noroviruses. J Gen Virol 2018; 99:970-988. [PMID: 29906257 DOI: 10.1099/jgv.0.001103] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are recognized as the major global cause of sporadic and epidemic non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Intragenotypic recombination has long been postulated to be a driving force of GII.4 noroviruses, the predominant genotype circulating in humans for over two decades. Increasingly, emergence and re-emergence of different intragenotype recombinants have been reported. The number and types of norovirus recombinants remained undefined until the 2007 Journal of General Virology research article 'Norovirus recombination' reported an assembly of 20 hitherto unclassified intergenotypic norovirus recombinant types. In the intervening decade, a host of novel recombinants has been analysed. New recombination breakpoints have been described, in vitro and in vivo studies supplement in silico analyses, and advances have been made in analysing factors driving norovirus recombination. This work presents a timely overview of these data and focuses on important aspects of norovirus recombination and its role in norovirus molecular evolution. An overview of intergenogroup, intergenotype, intragenotype and 'obligatory' norovirus recombinants as detected via in silico methods in the field is provided, enlarging the scope of intergenotypic recombinant types to 80 in total, and notably including three intergenogroup recombinants. A recap of advances made studying norovirus recombination in the laboratory is given. Putative drivers and constraints of norovirus recombination are discussed and the potential link between recombination and norovirus zoonosis risk is examined.
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Affiliation(s)
- Louisa F Ludwig-Begall
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
| | - Axel Mauroy
- 2Staff direction for risk assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Blv du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Etienne Thiry
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
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Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea. Epidemiol Infect 2017; 145:2231-2240. [PMID: 28651680 DOI: 10.1017/s0950268817001273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses (NoVs) are major causal agents of acute gastroenteritis in humans. NoV GII.4 is the predominant genotype globally. However, uncommon and minor types of NoVs are consistently detected and some have been shown to dominate over GII.4. Therefore, the prevalence of dominant and uncommon NoVs makes the identification of these viruses important for the prediction and prevention of pandemics. In this study, the full-genome sequence of a NoV (strain JW) detected in Korea was extensively characterized. The full-length genome was 7510 nucleotides long, and phylogenetic analysis based on the whole-genome sequences, including open reading frame (ORF)1, ORF2, and ORF3, indicated that it belonged to the GII.21 genotype. Strain JW showed maximum identity with strain YO284; however, comparison of the amino acid sequence of ORF2, which functions as an antigen, showed substitutions in several amino acids. GII.21 is not a prevalent epidemiological agent of acute gastroenteritis in humans, but it is consistently found in gastroenteritis patients from several countries. The present study provides the first full-genome sequence analysis of NoV GII.21 isolated from a patient in Korea. Our findings provide not only valuable genome information but also data for epidemiology studies, epidemic prevention, and vaccine development strategies.
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Portal TM, Siqueira JAM, Costa LCPDN, Lima ICGD, Lucena MSSD, Bandeira RDS, Linhares ADC, Luz CRNED, Gabbay YB, Resque HR. Caliciviruses in hospitalized children, São Luís, Maranhão, 1997-1999: detection of norovirus GII.12. Braz J Microbiol 2016; 47:724-30. [PMID: 27161199 PMCID: PMC4927645 DOI: 10.1016/j.bjm.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 01/04/2016] [Indexed: 01/12/2023] Open
Abstract
Gastroenteritis is one of the most common diseases during childhood, with norovirus (NoV) and sapovirus (SaV) being two of its main causes. This study reports for the first time the incidence of these viruses in hospitalized children with and without gastroenteritis in São Luís, Maranhão. A total of 136 fecal samples were tested by enzyme immunoassays (EIA) for the detection of NoV and by reverse transcription-polymerase chain reaction (RT-PCR) for detection of both NoV and SaV. Positive samples for both agents were subjected to sequencing. The overall frequency of NoV as detected by EIA and RT-PCR was 17.6% (24/136) and 32.6% (15/46), respectively in diarrheic patients and 10.0% (9/90) in non-diarrheic patients (p<0.01). Of the diarrheic patients, 17% had fever, vomiting and anorexia, and 13% developed fever, vomiting and abdominal pain. Of the 24 NoV-positive samples, 50% (12/24) were sequenced and classified as genotypes GII.3 (n=1), GII.4 (6), GII.5 (1), GII.7 (2), GII.12 (1) and GII.16 (1). SaV frequency was 9.8% (11/112), with 22.6% (7/31) in diarrheic patients and 4.9% (4/81) in nondiarrheic (p=0.04) ones. In diarrheic cases, 27.3% had fever, vomiting and anorexia, whereas 18.2% had fever, anorexia and abdominal pain. One SaV-positive sample was sequenced and classified as GII.1. These results show a high genetic diversity of NoV and higher prevalence of NoV compared to SaV. Our data highlight the importance of NoV and SaV as enteropathogens in São Luís, Maranhão.
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Affiliation(s)
- Thayara Morais Portal
- Programa de Pós-Graduação em Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém, Pará, Brazil
| | | | | | | | | | | | | | | | | | - Hugo Reis Resque
- Seção de Virologia, Instituto Evandro Chagas/SVS/MS, Ananindeua, Pará, Brazil.
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da Silva Poló T, Peiró JR, Mendes LCN, Ludwig LF, de Oliveira-Filho EF, Bucardo F, Huynen P, Melin P, Thiry E, Mauroy A. Human norovirus infection in Latin America. J Clin Virol 2016; 78:111-9. [DOI: 10.1016/j.jcv.2016.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
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Amaral MSC, Estevam GK, Penatti M, Lafontaine R, Lima ICG, Spada PKP, Gabbay YB, Matos NB. The prevalence of norovirus, astrovirus and adenovirus infections among hospitalised children with acute gastroenteritis in Porto Velho, state of Rondônia, western Brazilian Amazon. Mem Inst Oswaldo Cruz 2015; 110:215-21. [PMID: 25946245 PMCID: PMC4489452 DOI: 10.1590/0074-02760140381] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/12/2015] [Indexed: 01/10/2023] Open
Abstract
Although viruses are well-established causes of acute gastroenteritis, few data on the circulation of these pathogens in Porto Velho, state of Rondônia, Brazil, are available. Thus, faecal samples from hospitalised diarrhoeic children, under six years of age, were collected and tested for the presence of norovirus (NoV), adenovirus (AdV) and astrovirus (AstV) from February 2010-February 2012. Specimens were screened by reverse-transcription polymerase chain reaction and viruses were found in 10.7% (63/591) of the cases. NoV, AdV and AstV were detected in 7.8%, 2% and 0.8% of the samples, respectively. NoV infection was observed at all ages and was most prevalent in zero-18-month-old children (84.7%; p = 0.002). A higher incidence of NoV was detected from February-April 2010, when it was found in 52.2% of the cases. Co-infections involving these viruses, rotavirus and enteropathogenic bacteria were detected in 44.4% (28/63) of the children with viral diarrhoea. Nosocomial infections were demonstrated in 28.6% (18/63) of the cases in which viruses were detected. The present paper reports, for the first time, the circulation of NoV and AstV among the paediatric population of Porto Velho and it contributes to our understanding of the roles of these pathogens in gastrointestinal infections.
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Affiliation(s)
| | | | - Marilene Penatti
- Hospital Infantil Cosme e Damião, Secretaria de Estado da Saúde, Porto Velho, RO, Brasil
| | - Roger Lafontaine
- Centro de Pesquisa em Medicina Tropical, Porto Velho, RO, Brasil
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Genetic diversity of norovirus in hospitalised diarrhoeic children and asymptomatic controls in Dar es Salaam, Tanzania. INFECTION GENETICS AND EVOLUTION 2014; 26:340-7. [DOI: 10.1016/j.meegid.2014.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 01/26/2023]
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Bruggink L, Marshall J. Altered patterns of norovirus GII.b recombinant forms in gastroenteritis outbreaks in victoria, Australia, 2002-2005 compared to 2006-2011. J Med Virol 2013; 85:1433-43. [DOI: 10.1002/jmv.23633] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 01/18/2023]
Affiliation(s)
- L.D. Bruggink
- Victorian Infectious Diseases Reference Laboratory; North Melbourne Victoria Australia
| | - J.A. Marshall
- Victorian Infectious Diseases Reference Laboratory; North Melbourne Victoria Australia
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