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Bhavanam S, Freedman SB, Lee BE, Zhuo R, Qiu Y, Chui L, Xie J, Ali S, Vanderkooi OG, Pang XL. Differences in Illness Severity among Circulating Norovirus Genotypes in a Large Pediatric Cohort with Acute Gastroenteritis. Microorganisms 2020; 8:E1873. [PMID: 33256234 PMCID: PMC7760397 DOI: 10.3390/microorganisms8121873] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Norovirus is a major pathogen identified in children with acute gastroenteritis (AGE), little is known about the strain's diversity and their clinical severity. Stool and/or rectal swabs were collected from children ≤18 years of age recruited at emergency departments (ED), and a provincial nursing advice phone line due to AGE symptoms in the province of Alberta, Canada between December 2014 and August 2018. Specimens were tested using a reverse transcription real time PCR and genotyped by Sanger sequencing. The Modified Vesikari Scale score (MVS) was used to evaluate the disease severity. The objectives are to identify the Genogroup and Genotype distribution and to compare illness severity between the GI and GII genogroups and to complete further analyses comparing the GII genotypes identified. GII.4 was the genotype most commonly identified. Children with GII.4 had higher MVS scores (12.0 (10.0, 14.0; p = 0.002)) and more prolonged diarrheal (5 days (3.0, 7.8)) and vomiting (3.2 days (1.7, 5.3; p < 0.001)) durations compared to other non GII.4 strains. The predominant strain varied by year with GII.4 Sydney[P31] predominant in 2014/15, GII.4 Sydney[P16] in 2015/16 and 2017/18, and GII.3[P12] in 2016/17. Genogroup II norovirus strains predominated in children with AGE with variance between years; clinical severity associated with different strains varied with episodes being most severe among GII.4 infected children.
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Affiliation(s)
- Sudha Bhavanam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (S.B.); (R.Z.); (Y.Q.); (L.C.)
| | - Stephen B. Freedman
- Divisions of Pediatric Emergency Medicine and Gastroenterology, Departments of Pediatrics and Emergency Medicine, Alberta Children’s Hospital, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada;
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine & Dentistry, Women and Children’s Health Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada; (B.E.L.); (S.A.)
| | - Ran Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (S.B.); (R.Z.); (Y.Q.); (L.C.)
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (S.B.); (R.Z.); (Y.Q.); (L.C.)
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (S.B.); (R.Z.); (Y.Q.); (L.C.)
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, AB T6G 2J2, Canada
| | - Jianling Xie
- Departments of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada;
| | - Samina Ali
- Department of Pediatrics, Faculty of Medicine & Dentistry, Women and Children’s Health Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 2R3, Canada; (B.E.L.); (S.A.)
| | - Otto G. Vanderkooi
- Departments of Pediatrics, Microbiology, Immunology and Infectious Diseases, Pathology & Laboratory Medicine and Community Health Sciences, Alberta Children’s Hospital, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada;
| | - Xiaoli L. Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (S.B.); (R.Z.); (Y.Q.); (L.C.)
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, AB T6G 2J2, Canada
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Burke RM, Shah MP, Wikswo ME, Barclay L, Kambhampati A, Marsh Z, Cannon JL, Parashar UD, Vinjé J, Hall AJ. The Norovirus Epidemiologic Triad: Predictors of Severe Outcomes in US Norovirus Outbreaks, 2009-2016. J Infect Dis 2020; 219:1364-1372. [PMID: 30445538 DOI: 10.1093/infdis/jiy569] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Noroviruses are the leading cause of acute gastroenteritis outbreaks worldwide. Clarifying the viral, host, and environmental factors (epidemiologic triad) associated with severe outcomes can help target public health interventions. METHODS Acute norovirus outbreaks reported to the National Outbreak Reporting System (NORS) in 2009-2016 were linked to laboratory-confirmed norovirus outbreaks reported to CaliciNet. Outbreaks were analyzed for differences in genotype (GII.4 vs non-GII.4), hospitalization, and mortality rates by timing, setting, transmission mode, demographics, clinical symptoms, and health outcomes. RESULTS A total of 3747 norovirus outbreaks were matched from NORS and CaliciNet. Multivariable models showed that GII.4 outbreaks (n = 2353) were associated with healthcare settings (odds ratio [OR], 3.94 [95% confidence interval {CI}, 2.99-5.23]), winter months (November-April; 1.55 [95% CI, 1.24-1.93]), and older age of cases (≥50% aged ≥75 years; 1.37 [95% CI, 1.04-1.79]). Severe outcomes were more likely among GII.4 outbreaks (hospitalization rate ratio [RR], 1.54 [95% CI, 1.23-1.96]; mortality RR, 2.77 [95% CI, 1.04-5.78]). Outbreaks in healthcare settings were also associated with higher hospitalization (RR, 3.22 [95% CI, 2.34-4.44]) and mortality rates (RR, 5.65 [95% CI, 1.92-18.70]). CONCLUSIONS Severe outcomes more frequently occurred in norovirus outbreaks caused by GII.4 and those in healthcare settings. These results should help guide preventive interventions for targeted populations, including vaccine development.
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Affiliation(s)
- Rachel M Burke
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Minesh P Shah
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary E Wikswo
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
| | - Leslie Barclay
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
| | - Anita Kambhampati
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia.,IHRC, Inc, Atlanta, Georgia
| | - Zachary Marsh
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia.,Oak Ridge Institute for Science and Education, Tennessee, Atlanta, Georgia
| | | | - Umesh D Parashar
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
| | - Aron J Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
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MacLean AR, Gunson R. Automation and standardisation of clinical molecular testing using PCR.Ai - A comparative performance study. J Clin Virol 2019; 120:51-56. [PMID: 31563652 PMCID: PMC7172212 DOI: 10.1016/j.jcv.2019.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/16/2019] [Accepted: 08/13/2019] [Indexed: 12/23/2022]
Abstract
PCR.Ai is an automated final interpretation/verification step for in-house qPCR tests. PCR.Ai was compared to our routine analysis method. PCR.Ai was accurate for respiratory virus and norovirus detection. There were significant savings with PCR.Ai. PCR.Ai is a highly accurate time-saving tool for qPCR analysis.
Background We undertook a prospective clinical study to evaluate PCR.Ai’s (www.pcr.ai) accuracy and impact when automating the manual data-analysis and quality control steps associated with routine clinical pathogen testing using real-time PCR (qPCR). Objectives We evaluated the impact of PCR.Ai when used as the final interpretation/verification step for routine in-house qPCR tests for respiratory pathogens and for norovirus for a total of 22,200 interpretations. Study Design We compared PCR.Ai to our existing manual interpretation, to determine accuracy and hands-on time savings. PCR.Ai was accurate. Results and Conclusions There was 100% concurrence between validated respiratory virus and norovirus detection by our manual routine analysis method and PCR.Ai. Furthermore, there were significant routine savings with PCR.Ai of 45 min/respiratory run and 32 min/norovirus run. Our conclusion is that PCR.Ai is a highly accurate time-saving tool that reduces complexity of qPCR analysis and hence the need for specialists and hands-on time. It demonstrated capabilities to enable us to get results out more quickly with lower costs and less risk of errors.
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Affiliation(s)
- A R MacLean
- West of Scotland Specialist Virology Centre, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow, G31 2ER, United Kingdom.
| | - R Gunson
- West of Scotland Specialist Virology Centre, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow, G31 2ER, United Kingdom
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Mathew S, Alansari K, K Smatti M, Zaraket H, Al Thani AA, Yassine HM. Epidemiological, Molecular, and Clinical Features of Norovirus Infections among Pediatric Patients in Qatar. Viruses 2019; 11:E400. [PMID: 31035642 PMCID: PMC6563317 DOI: 10.3390/v11050400] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 02/05/2023] Open
Abstract
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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Affiliation(s)
- Shilu Mathew
- Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Khalid Alansari
- Pediatric Emergency Center, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Maria K Smatti
- Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Hassan Zaraket
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.
| | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar.
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Molecular epidemiology of noroviruses in children in South Greece, 2013‐2015. J Med Virol 2018; 90:1703-1711. [DOI: 10.1002/jmv.25251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022]
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Biswas S, Jackson P, Shannon R, Dulwich K, Sukla S, Dixon RA. Molecular screening of blue mussels indicated high mid-summer prevalence of human genogroup II Noroviruses, including the pandemic "GII.4 2012" variants in UK coastal waters during 2013. Braz J Microbiol 2017; 49:279-284. [PMID: 29097140 PMCID: PMC5914202 DOI: 10.1016/j.bjm.2017.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/05/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022] Open
Abstract
This molecular study is the first report, to the best of our knowledge, on identification of norovirus, NoV GII.4 Sydney 2012 variants, from blue mussels collected from UK coastal waters. Blue mussels (three pooled samples from twelve mussels) collected during the 2013 summer months from UK coastal sites were screened by RT-PCR assays. PCR products of RdRP gene for noroviruses were purified, sequenced and subjected to phylogenetic analysis. All the samples tested positive for NoVs. Sequencing revealed that the NoV partial RdRP gene sequences from two pooled samples clustered with the pandemic "GII.4 Sydney variants" whilst the other pooled sample clustered with the NoV GII.2 variants. This molecular study indicated mussel contamination with pathogenic NoVs even during mid-summer in UK coastal waters which posed potential risk of NoV outbreaks irrespective of season. As the detection of Sydney 2012 NoV from our preliminary study of natural coastal mussels interestingly corroborated with NoV outbreaks in nearby areas during the same period, it emphasizes the importance of environmental surveillance work for forecast of high risk zones of NoV outbreaks.
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Affiliation(s)
- Subhajit Biswas
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom.
| | - Philippa Jackson
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Rebecca Shannon
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Katherine Dulwich
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Soumi Sukla
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Ronald A Dixon
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
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Zhang P, Chen L, Fu Y, Ji L, Wu X, Xu D, Han J. Clinical and molecular analyses of norovirus-associated sporadic acute gastroenteritis: the emergence of GII.17 over GII.4, Huzhou, China, 2015. BMC Infect Dis 2016; 16:717. [PMID: 27894272 PMCID: PMC5126990 DOI: 10.1186/s12879-016-2033-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/15/2016] [Indexed: 11/11/2022] Open
Abstract
Background Noroviruses (NoVs) are the most common cause of non-bacterial acute gastroenteritis (AGE) in all age groups worldwide. The NoVs circulating in Huzhou over the past 7 years were predominantly GII.4 genotypes. In the winter of 2014–2015, a novel variant of NoV GII.17 emerged and became predominant. We report the epidemiological patterns and genetic characteristics of NoV after the appearance of GII.17 in Huzhou City, Zhejiang, China. Methods Between January and December 2015, 746 stool specimens collected from patients with acute gastroenteritis were screened for NoV. Real-time RT-PCR (qPCR) was performed for NoV detection. RT-PCR was used for genomic amplification and sequencing. Genogroups and genotypes were assigned using an online NoV typing tool (http://www.rivm.nl/mpf/norovirus/typingtool). Phylogenetic analyses were conducted using MEGA (ver. 6.06). Results In total, 196 (26.3%) specimens were identified as NoV-positive. NoV infection was found in all age groups tested (≤5, 6–15, 16–40, 41–60, and ≥60 years), with the 16–40-year age group having the highest detection rate (117/196, 59.7%). Of the 196 NoV-positive specimens, 191 (97.5%) viruses belonged to GII, and 4 (2.0%) to GI; one sample showed GI and GII co-infection. Overall, 117 (59.7%) viruses were sequenced, and new GII.P17/GII.17 variants were the dominant genotype, accounting for 75.2%, followed by GII.Pe/GII.4 Sydney 2012 strains (11.11%). AGE patients infected with the GII.P17/GII.17 genotypes almost all had abdominal pain and watery stools. Conclusions We report the epidemiological patterns and genetic characteristics of the emergence GII.17 over the GII.4 in Huzhou between January and December 2015. After the emergence of GII.17 in October 2014, it steadily replaced the previously circulating GII.4 Sydney 2012 strain, and continued to be dominant in 2015. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2033-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Yun Fu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Jiankang Han
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China. .,Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
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He Y, Jin M, Chen K, Zhang H, Yang H, Zhuo F, Zhao D, Zeng H, Yao X, Zhang Z, Chen L, Zhou Y, Duan ZJ. Gastroenteritis Outbreaks Associated with the Emergence of the New GII.4 Sydney Norovirus Variant during the Epidemic of 2012/13 in Shenzhen City, China. PLoS One 2016; 11:e0165880. [PMID: 27829005 PMCID: PMC5102426 DOI: 10.1371/journal.pone.0165880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 10/19/2016] [Indexed: 12/19/2022] Open
Abstract
Noroviruses (NoVs) are the leading cause of gastroenteritis outbreaks in humans worldwide. Since late 2012, a new GII.4 variant Sydney 2012 has caused a significant increase in NoV epidemics in several countries. From November of 2012 to January of 2013, three gastroenteritis outbreaks occurred in two social welfare homes (Outbreaks A and B) and a factory (Outbreak C) in Shenzhen city of China. Feces and swabs were collected for laboratory tests for causative agents. While no bacterial pathogen was identified, all three outbreaks were caused by NoVs with detection rates of 26.2% (16/61) at Outbreak A, 35.2% (38/108) at Outbreak B), and 59.3% (16/27) at Outbreaks C. For Outbreak B, 25 of the 29 symptomatic individuals (86.2%) and 13 of the 79 asymptomatic individuals (16.5%) were found NoV-positive. For Outbreak C, an asymptomatic food handler was NoV-positive. All thirteen NoV sequences from the three outbreaks were classified into genogroup II and genotype 4 (GII.4), which we identified to be the GII.4 Sydney 2012 variant. The genome of two isolates from Outbreaks A and B were recombinant with the opening reading frame (ORF) 1 of GII.4 Osaka 2007 and ORF2 and 3 of the GII.4 New Orleans. Our study indicated that the GII.4 Sydney 2012 variant emerged and caused the outbreaks in China.
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Affiliation(s)
- Yaqing He
- Southern Medical University, Guangzhou, Guangdong, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Miao Jin
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Kena Chen
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Hailong Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Fei Zhuo
- Shenzhen Luohu Center for Disease Control and Prevention, Shenzhen, China
| | - Dejian Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Huatang Zeng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiangjie Yao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zhen Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Long Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yuanping Zhou
- Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (ZJD); (YPZ)
| | - Zhao-jun Duan
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
- * E-mail: (ZJD); (YPZ)
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Jarchow-Macdonald AA, Halley S, Chandler D, Gunson R, Shepherd SJ, Parcell BJ. First report of an astrovirus type 5 gastroenteritis outbreak in a residential elderly care home identified by sequencing. J Clin Virol 2015; 73:115-119. [PMID: 26590691 DOI: 10.1016/j.jcv.2015.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 10/30/2015] [Accepted: 11/01/2015] [Indexed: 12/01/2022]
Abstract
BACKGROUND This is the report of an outbreak of human astrovirus type 5 gastroenteritis that occurred in a residential care home for older people in June 2013 in Tayside, Scotland, and which involved seven staff members and thirteen residents. This type of astrovirus has not been found in Scotland before and is rarely described in the literature. OBJECTIVES Using molecular methods such as PCR and sequencing to detect the cause of this gastroenteritis outbreak and to contain the outbreak using Public Health measures. STUDY DESIGN Following an epidemiological investigation, stool samples were sent for routine virology and microbiology testing at the local microbiology and virology laboratory and were found to be negative. Further testing with real-time PCR and gene sequencing at the West of Scotland Specialist Virology Centre was performed. Data on the epidemiology and the response to the outbreak was collected. RESULTS All samples had a 99% match to human astrovirus type 5. The use of standard infection control precautions with the addition of transmission-based precautions most likely contained the spread of the virus in this situation. CONCLUSIONS This report illustrates the importance of using PCR and sequencing to identify pathogens such as astrovirus in outbreaks of vomiting and diarrhoea in older people particularly if routine virology and microbiology tests are negative.
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Affiliation(s)
- Anna A Jarchow-Macdonald
- Medical Microbiology, Ninewells Hospital and Medical School, NHS Tayside, Dundee, DD1 9SY Scotland, UK.
| | - Shona Halley
- NHS Tayside, Directorate of Public Health, Clepington Road, Dundee, DD3 8EA Scotland, UK
| | - Daniel Chandler
- NHS Tayside, Directorate of Public Health, Clepington Road, Dundee, DD3 8EA Scotland, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Samantha J Shepherd
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Benjamin J Parcell
- Medical Microbiology, Aberdeen Royal Infirmary, Foresterhill, Aberdeen AB25 2ZN, UK
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10
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Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak. J Med Virol 2015; 88:551-70. [PMID: 26387663 DOI: 10.1002/jmv.24387] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.
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Affiliation(s)
- Aksara Thongprachum
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Han J, Ji L, Shen Y, Wu X, Xu D, Chen L. Emergence and predominance of norovirus GII.17 in Huzhou, China, 2014-2015. Virol J 2015; 12:139. [PMID: 26362650 PMCID: PMC4566299 DOI: 10.1186/s12985-015-0370-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/01/2015] [Indexed: 12/01/2022] Open
Abstract
Background Norovirus (NoV) has been recognized as the leading cause of both outbreaks and sporadic cases of acute gastroenteritis in children and adults worldwide. Stool samples collected from outpatients with clinical symptoms of acute gastroenteritis in all age groups at the First People’s Hospital in Huzhou, Huzhou, China between March 2014 and February 2015 were analyzed to gain insight into the epidemiology and genetic variation in NoV strains circulating in China. Method Real-time RT-PCR (qPCR) was performed for Norovirus detection. RT-PCR were used for genomic amplification and sequencing. Genogroup and genotype were assigned using the NoV Noronet typing tool and the strains were named according to the time of isolation. The phylogenetic analysis was conducted using MEGA 5. Results Of the 809 specimens, 193 (23.9 %) were positive for NoV, with GII.4 and GII.17 the most commonly identified strains. Phylogenetic analysis confirmed the presence of five recombinant strains in Huzhou. Recombinants GII.P13/GII.17 and GII.P12/GII.4 were newly detected in China. The GII.P13/GII.17 recombinant was first identified in October 2014 and steadily replaced GII.Pe/GII.4 (GII.4 Sydney 2012) as the predominant circulating NoV genotype. Conclusion This is the first report of the detection of GII.17 in the Huzhou area and of a NoV genotype being detected in greater numbers than GII.4. Furthermore, our results indicated that following the emergence of GII.17 in October 2014, it steadily replaced the previous circulating GII.4 Sydney2012 strain, which was the dominant circulating genotype for the past 2 years. As norovirus are the important cause of nonbacterial gastroenteritis, continuous and comprehensive study of the norovirus strains involved in large and cost-effective acute gastroenteritis would help understanding the molecular epidemiology of norovirus infections and development of improved prevention and control measures.
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Affiliation(s)
- Jiankang Han
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Yuehua Shen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
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12
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Gao Z, Li X, Yan H, Li W, Jia L, Hu L, Hu H, Liu B, Li J, Wang Q. Human calicivirus occurrence among outpatients with diarrhea in Beijing, China, between April 2011 and March 2013. J Med Virol 2015; 87:2040-7. [PMID: 25982899 DOI: 10.1002/jmv.24265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 12/28/2022]
Abstract
Human caliciviruses (HuCVs), including noroviruses (NoVs) and sapoviruses (SaVs), are the most common cause of diarrhea in adults and the second most common cause of diarrhea in children. Between April 2011 and March 2013, 3,832 fecal specimens were collected from outpatients with diarrhea from 17 hospitals in Beijing, China, and 669 specimens (17.5%) were positive for HuCV. Of the 287 HuCV-positive specimens, 263 (91.6%) were identified to be NoV, 23 (8.0%) were identified to be SaV, and one (0.3%) was identified to be a mixed infection of NoV and SaV. Of the 263 NoV-positive specimens, 237 (90.1%) were NoV GII, 21 (8.0%) were NoV GI, and 5 (1.9%) were a combination of NoV GI and GII. Among the 216 sequenced GII-positive samples, GII.4 was the most common genotype (70.4%, 152/216), followed by GII.13 (9.3%, 20/216). GII.4 Sydney_2012 was first detected in August 2012 and replaced GII.4 Den Haag_2006b as the predominant variant between September 2012 and March 2013. With the emergence of the GII.4 Sydney_2012 variant, 44.6% more patients with diarrhea visited the 17 hospitals (9,931 cases) than in the previous year (6,866 cases) between October and December 2012.
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Affiliation(s)
- Zhiyong Gao
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xitai Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hanqiu Yan
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Weihong Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lei Jia
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Li Hu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hong Hu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Baiwei Liu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jie Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Quanyi Wang
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
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13
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Wu FT, Chen HC, Yen C, Wu CY, Katayama K, Park Y, Hall AJ, Vinjé J, Huang JC, Wu HS. Epidemiology and molecular characteristics of norovirus GII.4 Sydney outbreaks in Taiwan, January 2012-December 2013. J Med Virol 2015; 87:1462-70. [PMID: 25946552 DOI: 10.1002/jmv.24208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2015] [Indexed: 12/16/2022]
Abstract
In 2012, a new norovirus GII.4 variant (GII.4 Sydney) emerged and caused the majority of the acute gastroenteritis outbreaks in Australia, Asia, Europe, and North America. We examined the epidemiologic and molecular virologic characteristics of reported acute gastroenteritis outbreaks determined to be caused by norovirus in Taiwan from January 2012 to December 2013. A total of 253 (45.7%) of 552 reported acute gastroenteritis outbreaks tested positive for norovirus, of which 165 (65.5%) were typed as GII.4 Sydney. GII.4 Sydney outbreaks were reported from all geographic areas of Taiwan and occurred most frequently in schools (35.8%) and long-term care facilities (24.2%). Person-to-person transmission was identified in 116 (70.3%) of the outbreaks. Phylogenetic analyses of full-length ORF2 of eight specimens indicated that GII.4 Sydney strains detected in Taiwan were closely related to strains detected globally. Continued outbreak surveillance and strain typing are needed to provide information on epidemiologic and virologic trends of novel norovirus strains.
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Affiliation(s)
- Fang-Tzy Wu
- Centers for Disease Control, Taipei, Taiwan.,National Yang Ming University, Taipei, Taiwan
| | | | - Catherine Yen
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - YoungBin Park
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Aron J Hall
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Ho-Sheng Wu
- Centers for Disease Control, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
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14
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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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15
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Zheng QM, Zeng HT, Dai CW, Zhang SX, Zhang Z, Mei SJ, He YQ, Ma HW. Epidemiological Investigation of a Norovirus GII.4 Sydney Outbreak in a China Elder Care Facility. Jpn J Infect Dis 2015; 68:70-4. [DOI: 10.7883/yoken.jjid.2014.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Qing-ming Zheng
- Guangming District Center for Disease Control and Prevention
| | - Hua-tang Zeng
- Guangming District Center for Disease Control and Prevention
| | - Chuan-wen Dai
- Guangming District Center for Disease Control and Prevention
| | | | - Zhen Zhang
- Guangming District Center for Disease Control and Prevention
| | - Shu-jiang Mei
- Guangming District Center for Disease Control and Prevention
| | - Ya-qing He
- Guangming District Center for Disease Control and Prevention
| | - Han-wu Ma
- Guangming District Center for Disease Control and Prevention
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16
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Molecular epidemiology of norovirus from patients with acute gastroenteritis in northwestern Spain. Epidemiol Infect 2014; 143:316-24. [DOI: 10.1017/s0950268814000740] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYThe high incidence of norovirus (NoV) infections seems to be related to the emergence of new variants that evolved by genetic drift of the capsid gene. In this work, that represents a first effort to describe the molecular epidemiology of NoV in the northwest of Spain, a total of eight different NoV genotypes (GII.1, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13, GII.14) were detected. The major genotypes observed were GII.4 (45·42%) and GII.14 (34·9%), being detected in all age groups. In addition, and although most of GII.4 sequences belonged to 2006b (7·2%) and 2010 (50·35%) variants, the presence of new NoV variants was observed. Phylogenetic analysis revealed that a high number of GII.4 sequences (35·24%) could be assigned to the newly emerging Sydney 2012 variant, even during late 2010. The high prevalence of NoV GII.14 observed in this study may indicate the emergence of this genotype in Spain.
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17
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Temporal dynamics of norovirus GII.4 variants in Brazil between 2004 and 2012. PLoS One 2014; 9:e92988. [PMID: 24667283 PMCID: PMC3965504 DOI: 10.1371/journal.pone.0092988] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/27/2014] [Indexed: 01/01/2023] Open
Abstract
Noroviruses (NoVs) are the major cause of acute gastroenteritis outbreaks, and, despite a wide genetic diversity, genotype II.4 is the most prevalent strain worldwide. Mutations and homologous recombination have been proposed as mechanisms driving the epochal evolution of the GII.4, with the emergence of new variants in 1–3-year intervals causing global epidemics. There are no data reporting the dynamics of GII.4 variants along a specific period in Brazil. Therefore, to improve the understanding of the comportment of these variants in the country, the aim of this study was to evaluate the circulation of NoV GII.4 variants during a 9-year period in 3 out of 5 Brazilian regions. A total of 147 samples were sequenced, and a phylogenetic analysis of subdomain P2 demonstrated the circulation of six GII.4 variants, Asia_2003, Hunter_2004, Den Haag_2006b, Yerseke_2006a, New Orleans_2009, and Sydney_2012, during this period. The most prevalent variant was Den Haag_2006b, circulating in different Brazilian regions from 2006 to 2011. A Bayesian coalescent analysis was used to calculate the mean evolutionary rate of subdomain P2 as 7.3×10−3 (5.85×10−3–8.82×10−3) subst./site/year. These analyses also demonstrated that clade Den Haag_2006b experienced a rapid expansion in 2005 and another in 2008 after a period of decay. The evaluation of the temporal dynamics of NoV GII.4 in Brazil revealed a similar pattern, with few exceptions, to the worldwide observation. These data highlight the importance of surveillance for monitoring the emergence of new strains of NoV GII.4 and its impact on cases of acute gastroenteritis.
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18
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Bruggink L, Dunbar N, Marshall J. Emergence of GII.e as a major ORF 1 norovirus genotype and its associated ORF 2 GII.4 variant forms. INFECTION GENETICS AND EVOLUTION 2014; 22:157-63. [DOI: 10.1016/j.meegid.2014.01.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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19
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20
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Leshem E, Wikswo M, Barclay L, Brandt E, Storm W, Salehi E, DeSalvo T, Davis T, Saupe A, Dobbins G, Booth HA, Biggs C, Garman K, Woron AM, Parashar UD, Vinjé J, Hall AJ. Effects and clinical significance of GII.4 Sydney norovirus, United States, 2012-2013. Emerg Infect Dis 2014; 19:1231-8. [PMID: 23886013 PMCID: PMC3739516 DOI: 10.3201/eid1908.130458] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During 2012, global detection of a new norovirus (NoV) strain, GII.4 Sydney, raised concerns about its potential effect in the United States. We analyzed data from NoV outbreaks in 5 states and emergency department visits for gastrointestinal illness in 1 state during the 2012-13 season and compared the data with those of previous seasons. During August 2012-April 2013, a total of 637 NoV outbreaks were reported compared with 536 and 432 in 2011-2012 and 2010-2011 during the same period. The proportion of outbreaks attributed to GII.4 Sydney increased from 8% in September 2012 to 82% in March 2013. The increase in emergency department visits for gastrointestinal illness during the 2012-13 season was similar to that of previous seasons. GII.4 Sydney has become the predominant US NoV outbreak strain during the 2012-13 season, but its emergence did not cause outbreak activity to substantially increase from that of previous seasons.
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Affiliation(s)
- Eyal Leshem
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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21
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Thongprachum A, Chan-it W, Khamrin P, Saparpakorn P, Okitsu S, Takanashi S, Mizuguchi M, Hayakawa S, Maneekarn N, Ushijima H. Molecular epidemiology of norovirus associated with gastroenteritis and emergence of norovirus GII.4 variant 2012 in Japanese pediatric patients. INFECTION GENETICS AND EVOLUTION 2014; 23:65-73. [PMID: 24508246 DOI: 10.1016/j.meegid.2014.01.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/17/2014] [Accepted: 01/19/2014] [Indexed: 12/25/2022]
Abstract
In late 2012, an outbreak of acute gastroenteritis due to norovirus variant Sydney_2012 occurred and have been reported from many counties. In this study, we described surveillance study of the incidence of norovirus infections among Japanese pediatric patients in association with gastroenteritis and investigated the antigenic change of the new variant Sydney_2012 circulated in Japanese populations. A total of 2381 fecal specimens collected from children with acute gastroenteritis in Hokkaido, Tokyo, Shizuoka, Kyoto, Osaka, and Saga from 2009 to 2013 were examined for norovirus and further analyzed molecularly. A high proportion (39.3%) of norovirus positive samples and several genotypes were detected. Norovirus GII.4 dominated over other genotypes (71.4%). The Den_Haag_2006b (43.2%) was detected as the predominant variant and co-circulated with New_Orleans_2009 (17.8%) until March 2012. Subsequently, they were displaced by Sydney_2012. The Sydney_2012 variant has been responsible for the majority of norovirus infections in 2012-2013 (85.7%). Although Sydney_2012 variant has a common ancestor with New_Orleans_2009 variant, analysis of P2 sub-domain showed a high level of diversity in comparison with other variants in four amino acid changes at the antigenic sites. The change in particular residue 393 of new variant may affect HBGA recognition. Analysis of noroviruses circulating in the past 4years revealed a change of predominant variant of norovirus GII.4 in each epidemic season. The change of amino acid in putative epitopes may have led the virus escape from the existing herd immunity and explain the increase of new variant outbreaks.
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Affiliation(s)
- Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Wisoot Chan-it
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
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22
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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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23
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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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24
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Outbreak of gastroenteritis caused by norovirus GII.4 Sydney variant after a wedding reception at a resort/activity centre, Finland, August 2012. Epidemiol Infect 2013; 142:1877-83. [PMID: 24229743 DOI: 10.1017/s0950268813002847] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In August 2012, an outbreak of gastroenteritis occurred among 88 persons attending a wedding reception at a resort/activity centre in Ylöjärvi, Finland. Of 39 interviewed guests, 23 met the case definition. Two persons were hospitalized. Epidemiological, laboratory and environmental investigations were conducted to characterize the outbreak and to recommend control measures. Investigation confirmed the presence of a new strain of norovirus GII.4 Sydney variant in stool specimens obtained from two wedding guests and on several environmental surfaces in the centre. In the questionnaire study, none of the foods or beverages served during the reception were significantly associated with the illness. Additional cases of gastroenteritis that occurred at the centre before and after the wedding reception supported the hypothesis of environmental transmission of norovirus. After thorough cleansing and disinfection and 1 week's quarantine, no new cases with symptoms typical for norovirus infection were identified at the centre.
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25
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Wong THN, Dearlove BL, Hedge J, Giess AP, Piazza P, Trebes A, Paul J, Smit E, Smith EG, Sutton JK, Wilcox MH, Dingle KE, Peto TEA, Crook DW, Wilson DJ, Wyllie DH. Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virol J 2013; 10:335. [PMID: 24220146 PMCID: PMC3874643 DOI: 10.1186/1743-422x-10-335] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Norovirus is the commonest cause of epidemic gastroenteritis among people of all ages. Outbreaks frequently occur in hospitals and the community, costing the UK an estimated £110 m per annum. An evolutionary explanation for periodic increases in norovirus cases, despite some host-specific post immunity is currently limited to the identification of obvious recombinants. Our understanding could be significantly enhanced by full length genome sequences for large numbers of intensively sampled viruses, which would also assist control and vaccine design. Our objective is to develop rapid, high-throughput, end-to-end methods yielding complete norovirus genome sequences. We apply these methods to recent English outbreaks, placing them in the wider context of the international norovirus epidemic of winter 2012. METHOD Norovirus sequences were generated from 28 unique clinical samples by Illumina RNA sequencing (RNA-Seq) of total faecal RNA. A range of de novo sequence assemblers were attempted. The best assembler was identified by validation against three replicate samples and two norovirus qPCR negative samples, together with an additional 20 sequences determined by PCR and fractional capillary sequencing. Phylogenetic methods were used to reconstruct evolutionary relationships from the whole genome sequences. RESULTS Full length norovirus genomes were generated from 23/28 samples. 5/28 partial norovirus genomes were associated with low viral copy numbers. The de novo assembled sequences differed from sequences determined by capillary sequencing by <0.003%. Intra-host nucleotide sequence diversity was rare, but detectable by mapping short sequence reads onto its de novo assembled consensus. Genomes similar to the Sydney 2012 strain caused 78% (18/23) of cases, consistent with its previously documented association with the winter 2012 global outbreak. Interestingly, phylogenetic analysis and recombination detection analysis of the consensus sequences identified two related viruses as recombinants, containing sequences in prior circulation to Sydney 2012 in open reading frame (ORF) 2. CONCLUSION Our approach facilitates the rapid determination of complete norovirus genomes. This method provides high resolution of full norovirus genomes which, when coupled with detailed epidemiology, may improve the understanding of evolution and control of this important healthcare-associated pathogen.
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Affiliation(s)
- T H Nicholas Wong
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Bethany L Dearlove
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jessica Hedge
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Adam P Giess
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - John Paul
- Public Health Laboratory, Royal Sussex County Hospital, Brighton, UK
| | - Erasmus Smit
- Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham, UK
| | - E Grace Smith
- Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham, UK
| | - Julian K Sutton
- Public Health Laboratory, Southampton General Hospital, Southampton, UK
| | - Mark H Wilcox
- Public Health Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - David H Wyllie
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
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Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013. J Clin Microbiol 2013; 52:147-55. [PMID: 24172151 DOI: 10.1128/jcm.02680-13] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Noroviruses are the leading cause of epidemic acute gastroenteritis in the United States. From September 2009 through August 2013, 3,960 norovirus outbreaks were reported to CaliciNet. Of the 2,895 outbreaks with a known transmission route, person-to-person and food-borne transmissions were reported for 2,425 (83.7%) and 465 (16.1%) of the outbreaks, respectively. A total of 2,475 outbreaks (62.5%) occurred in long-term care facilities (LTCF), 389 (9.8%) in restaurants, and 227 (5.7%) in schools. A total of 435 outbreaks (11%) were typed as genogroup I (GI) and 3,525 (89%) as GII noroviruses. GII.4 viruses caused 2,853 (72%) of all outbreaks, of which 94% typed as either GII.4 New Orleans or GII.4 Sydney. In addition, three non-GII.4 viruses, i.e., GII.12, GII.1, and GI.6, caused 528 (13%) of all outbreaks. Several non-GII.4 genotypes (GI.3, GI.6, GI.7, GII.3, GII.6, and GII.12) were significantly more associated with food-borne transmission (odds ratio, 1.9 to 7.1; P < 0.05). Patients in LTCF and people ≥65 years of age were at higher risk for GII.4 infections than those in other settings and with other genotypes (P < 0.05). Phylogeographic analysis identified three major dispersions from two geographic locations that were responsible for the GI.6 outbreaks from 2011 to 2013. In conclusion, our data demonstrate the cyclic emergence of new (non-GII.4) norovirus strains, and several genotypes are more often associated with food-borne outbreaks. These surveillance data can be used to improve viral food-borne surveillance and to help guide studies to develop and evaluate targeted prevention methods such as norovirus vaccines, antivirals, and environmental decontamination methods.
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Chaimongkol N, Khamrin P, Malasao R, Thongprachum A, Kongsricharoern T, Ukarapol N, Ushijima H, Maneekarn N. Molecular characterization of norovirus variants and genetic diversity of noroviruses and sapoviruses in Thailand. J Med Virol 2013; 86:1210-8. [DOI: 10.1002/jmv.23781] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Natthawan Chaimongkol
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Pattara Khamrin
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Rungnapa Malasao
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences; Institute of International Health, Graduate School of Medicine, The University of Tokyo; Tokyo Japan
| | | | - Nuthapong Ukarapol
- Department of Pediatrics; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences; Institute of International Health, Graduate School of Medicine, The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University; Tokyo Japan
| | - Niwat Maneekarn
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
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Maritschnik S, Kanitz EE, Simons E, Höhne M, Neumann H, Allerberger F, Schmid D, Lederer I. A Food Handler-Associated, Foodborne Norovirus GII.4 Sydney 2012-Outbreak Following a Wedding Dinner, Austria, October 2012. FOOD AND ENVIRONMENTAL VIROLOGY 2013; 5:220-225. [PMID: 24026524 PMCID: PMC3825590 DOI: 10.1007/s12560-013-9127-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/30/2013] [Indexed: 05/26/2023]
Abstract
On October 12, 2012, the provincial public health directorate of Salzburg reported a suspected norovirus (NV) outbreak among guests of a wedding-reception. The investigation aimed to confirm the causative agent, to identify the mode of transmission and to implement appropriate preventive measures. A probable outbreak case was defined as a wedding guest with diarrhoea or vomiting with disease onset from 7 to 10 October 2012 and who consumed food at the wedding dinner prepared by a hotel in the province Salzburg on 6 October 2012. A confirmed outbreak case fulfilled the criteria of a probable outbreak case and had a laboratory-confirmed NV infection. We conducted a cohort-investigation among the wedding guests. The case definitions were fulfilled in 26 wedding guests (25 %) including 2 confirmed cases. Females were 3.2 times more likely to develop disease (95 % CI 1.4-7.2) as compared to males. A mushroom dish was found to be associated with disease risk among females (risk ratio 2.3, 95 % CI 1.2-4.3). Two of 2 tested case-patients and 6 of 14 kitchen workers tested were positive for NV GII.4 Sydney. One kitchen staff-member worked during the wedding dinner despite diarrhoea. No food safety training was documented for the employees and the kitchen staff's restroom was lacking operational facilities for hand hygiene. We report the first investigated outbreak due to GII.4 Sydney, which was likely due to a symptomatic kitchen worker. Gender-specific eating behaviour may have posed female guests at higher risk of NV infection.
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Affiliation(s)
- Sabine Maritschnik
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Tomtebodavägen 11A, 17165 Solna, Sweden
| | - Elisabeth Eva Kanitz
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
| | - Erica Simons
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
| | - Marina Höhne
- FG15 Molecular epidemiology of viral pathogens, National Consultant Laboratory for Norovirus, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Heidelinde Neumann
- Public Health Authority Salzburg, Sebastian-Stief-Gasse 2, 5010 Salzburg, Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
| | - Ingeborg Lederer
- Austrian Agency for Health and Food Safety (AGES), Währingerstraße 25a, 1096 Vienna, Austria
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29
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Mai H, Jin M, Guo X, Liu J, Liu N, Cong X, Gao Y, Wei L. Clinical and epidemiologic characteristics of norovirus GII.4 Sydney during winter 2012-13 in Beijing, China following its global emergence. PLoS One 2013; 8:e71483. [PMID: 23977050 PMCID: PMC3745450 DOI: 10.1371/journal.pone.0071483] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/30/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Limited information is available on the molecular epidemiology of GII.4 Sydney-associated diarrhea in China in the winter of 2012-13 during the global epidemic associated with the emergence of GII.4 Sydney. METHODS Fecal specimens collected from 171 diarrhea outpatients (one from each) between late October 2012 and the middle of March 2013 were examined for NoV by reverse transcription-polymerase chain reaction and sequences corresponding to both the NoV partial polymerase and partial capsid regions were analyzed phylogenetically. Clinical characteristics of GII.4 Sydney cases versus other NoV-positive cases detected in a previous study were compared statistically. RESULTS Twenty-six (15.2%, 26/171) outpatients with diarrhea were infected with NoV. Twenty-two of the 26 (84.6%) identified NoV strains clustered into GII.4 Sydney. There was a significant difference in symptoms of fever (χ(2), P<0.05 ), abdominal pain (χ(2), P<0.05 ) and diarrhea frequency (Mann-Whitney U test, P<0.05) between the GII.4 Sydney case group and other NoV-positive case group. CONCLUSIONS The new NoV variant, GII.4 Sydney, has been circulating in Beijing, China and became the predominant strain in the winter of 2012-13. GII.4 Sydney causes severe fever, abdominal pain and higher diarrhea frequency clinically compared to other NoV infections.
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Affiliation(s)
- Huan Mai
- Peking University People’s Hospital, Peking University Hepatology Institute, Department of Infectious Diseases, Beijing, China
| | - Miao Jin
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - XiaoLin Guo
- Peking University People’s Hospital, Peking University Hepatology Institute, Department of Infectious Diseases, Beijing, China
| | - Jian Liu
- Peking University People’s Hospital, Department of Clinical Laboratory, Beijing, China
| | - Ning Liu
- Peking University People’s Hospital, Department of Clinical Laboratory, Beijing, China
| | - Xu Cong
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing, China
| | - Yan Gao
- Peking University People’s Hospital, Peking University Hepatology Institute, Department of Infectious Diseases, Beijing, China
- * E-mail:
| | - Lai Wei
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing, China
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30
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Vicentini F, Denadai W, Gomes YM, Rose TL, Ferreira MSR, Le Moullac-Vaidye B, Le Pendu J, Leite JPG, Miagostovich MP, Spano LC. Molecular characterization of noroviruses and HBGA from infected Quilombola children in Espirito Santo State, Brazil. PLoS One 2013; 8:e69348. [PMID: 23894453 PMCID: PMC3718680 DOI: 10.1371/journal.pone.0069348] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/08/2013] [Indexed: 12/27/2022] Open
Abstract
Noroviruses (NoV) are the main etiological agents of gastroenteritis outbreaks worldwide and susceptibility to NoV infection has been related to the histo-blood group antigen (HBGA). This study aimed to determine the prevalence of NoV strains and to evaluate the HBGA phenotype and genotype of children from semi-isolated Quilombola communities, descendents of black slaves in Brazil. A total of 397 children up to eleven years old, with and without diarrhea, from Quilombola Communities in the Espirito Santo State, Brazil, were investigated for the presence of NoV from August 2007 to September 2009. Feces were collected from all the children, and blood from the NoV positive children. NoV was screened by reverse transcription-PCR with primers for the RNA-dependent RNA polymerase region; genogroup was determined by PCR with primers for the C and D regions and genotyped by sequencing. HBGA phenotype was performed by gel-spinning and FUT2 and FUT3 were analyzed by PCR or sequencing analysis. NoV were detected in 9.2% (12/131) of diarrheic and 1.5% (4/266) of non-diarrheic children (p<0.05, Fisher's exact test). GI and GII genogroups were present in 12.5% and 87.5% of the samples, respectively. The following genotypes were characterized: GII.4 (25%), GII.12 (25%), GII.6 (12.5%) and GI.1 (6.3%), GI.3 (12.5%) and GI.4 (6.3%). Children infected with NoV showed the A (n = 6), O (n = 6), and B (n = 2) HBGA phenotypes, and 13 of them were classified as secretors (Se) and one as a non secretor (se). Mutations of Se (40), (171,216,357,428,739,960) were found for the FUT2 gene and mutations of Le (59, 202, 314) for the FUT3 gene. The only se child was infected by NoV GI, whereas the Se children were indiscriminately infected by GI or GII. This study showed rates of NoV infection in symptomatic and asymptomatic Quilombola children consistent with other studies. However, children under 12 months were seven times more affected than those between 1 and 5 years old. GII.12 was as frequent as GII.4 and GI.1 and GI.4 were described for the first time in Brazil. Owing to the small number of cases studied, no clear pattern of susceptibility and/or HBGA resistance could be inferred.
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Affiliation(s)
- Fernando Vicentini
- Departamento de Ciências da Saúde, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo, Brazil.
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31
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Fonager J, Barzinci S, Fischer TK. Emergence of a new recombinant Sydney 2012 norovirus variant in Denmark, 26 December 2012 to 22 March 2013. ACTA ACUST UNITED AC 2013; 18. [PMID: 23806295 DOI: 10.2807/1560-7917.es2013.18.25.20506] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here new recombinants between the norovirus II.4 Sydney 2012 and the II.4 New Orleans 2009 variants. This demonstrates that the II.4 Sydney 2012 variant is undergoing further diversification and suggests a potential for rapid evolution. We also provide primers, which allow the amplification and sequencing of both the current New Orleans 2009 and Sydney 2012 variants and the new II.4 New Orleans 2009/II.4 Sydney 2012 recombinants for more accurate surveillance and transmission tracking.
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Affiliation(s)
- J Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
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