1
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Boxman ILA, Molin R, Persson S, Juréus A, Jansen CCC, Sosef NP, Le Guyader SF, Ollivier J, Summa M, Hautaniemi M, Suffredini E, Di Pasquale S, Myrmel M, Khatri M, Jamnikar-Ciglenecki U, Kusar D, Moor D, Butticaz L, Lowther JA, Walker DI, Stapleton T, Simonsson M, Dirks RAM. An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue. Food Microbiol 2024; 120:104478. [PMID: 38431324 DOI: 10.1016/j.fm.2024.104478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.
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Affiliation(s)
- Ingeborg L A Boxman
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Ramia Molin
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Sofia Persson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Anna Juréus
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Claudia C C Jansen
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Nils P Sosef
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Soizick F Le Guyader
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | - Joanna Ollivier
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | | | | | - Elisabetta Suffredini
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Simona Di Pasquale
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Mette Myrmel
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Mamata Khatri
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Urska Jamnikar-Ciglenecki
- University of Ljubljana Veterinary Faculty, Institute of Food Safety, Feed and Environment, Ljubljana, Slovenia.
| | - Darja Kusar
- University of Ljubljana Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia.
| | - Dominik Moor
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - Lisa Butticaz
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Tina Stapleton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - René A M Dirks
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
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2
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He X, Jiang N, Li Y. Saccharomyces cerevisiae cells that display norovirus P induce both systemic and mucosal neutralizing antibodies. Virology 2024; 594:110034. [PMID: 38460411 DOI: 10.1016/j.virol.2024.110034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/11/2024]
Abstract
The human norovirus (HuNov) is the leading cause of acute gastroenteritis (AGE) worldwide. Mucosal secretory IgA (sIgA) in the gastrointestinal tract interrupts the interaction between host cells and HuNov, thus inhibiting viral infection. In this study, we constructed a recombinant Saccharomyces cerevisiae (S. cerevisiae) expressing the HuNov P protein (GII. 4) and evaluated its immunogenicity in mice after oral delivery. First, the recombinant S. cerevisiae (EBY100/pYD1-P) efficiently expressed P, as evidenced by western blotting and indirect fluorescent assay. Second, after oral administration, EBY100/pYD1-P, especially the high-dose group (5 × 109 clone formation units), elicited systemic and mucosal immune responses characterized by significant sera IgG, IgA, and mucosal sIgA. More importantly, these antibodies showed a substantial neutralization effect against P. Lastly, EBY100/pYD1-P induced significant P-specific IFN-γ-secreting T cells and IL4-secreting T cells. Collectively, the recombinant S. cerevisiae expressing HuNov P is a promising mucosal vaccine candidate against HuNov.
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Affiliation(s)
- Xin He
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary, Huazhong Agricultural University, Wuhan, China
| | - Nianzhu Jiang
- School of Biological Engineering and Food, Hubei University of Technology, Wuhan, China
| | - Yaoming Li
- Department of Biology of Mucosal Pathogen, College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China; Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, China.
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3
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Li H, He F, Lv Z, Yi L, Zhang Z, Li H, Fu S. Tailored wastewater surveillance framework uncovered the epidemics of key pathogens in a Northwestern city of China. Sci Total Environ 2024; 926:171833. [PMID: 38522539 DOI: 10.1016/j.scitotenv.2024.171833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/03/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Wastewater surveillance enables rapid pathogen monitoring and community prevalence estimation. However, how to design an integrated and tailored wastewater surveillance framework to monitor major health threats in metropolises remains a major challenge. In this study, we first analyzed the historical clinical data of Xi'an city and designed a wastewater surveillance framework covering five key endemic viruses, namely, SARS-CoV-2, norovirus, influenza A virus (IAV), influenza B virus (IBV), respiratory syncytial virus (RSV), and hantavirus. Amplicon sequencing of SARS-CoV-2, norovirus and hantavirus was conducted biweekly to determine the prevalent community genotypes circulating in this region. The results showed that from April 2023 to August 2023, Xi'an experienced two waves of SARS-CoV-2 infection, which peaked in the middle of May-2023 and late August-2023. The sewage concentrations of IAV and RSV peaked in early March and early May 2023, respectively, while the sewage concentrations of norovirus fluctuated throughout the study period and peaked in late August. The dynamics of the sewage concentrations of SARS-CoV-2, norovirus, IAV, RSV, and hantavirus were in line with the trends in the sentinel hospital percent positivity data, indicating the role of wastewater surveillance in enhancing the understanding of epidemic trends. Amplicon sequencing of SARS-CoV-2 revealed a transition in the predominant genotype, which changed from DY.1 and FR.1.4 to the XBB and EG.5 subvariants. Amplicon sequencing also revealed that there was only one predominant hantavirus genotype in the local population, while highly diverse genotypes of norovirus GI and GII were found in the wastewater. In conclusion, this study provided valuable insights into the dynamics of infection trends and predominant genotypes of key pathogens in a city without sufficient clinical surveillance, highlighting the role of a tailored wastewater surveillance framework in addressing public health priorities. More importantly, our study provides the first evidence demonstrating the applicability of wastewater surveillance for hantavirus, which is a major health threat locally.
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Affiliation(s)
- Haifeng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Liu Yi
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Hui Li
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China.
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China; The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China.
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4
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Trudel-Ferland M, Collard MÈ, Goulet-Beaulieu V, Jubinville E, Hamon F, Jean J. Evaluation of a new automated viral RNA extraction platform for hepatitis A virus and human norovirus in testing of berries, lettuce, and oysters. Int J Food Microbiol 2024; 416:110664. [PMID: 38492524 DOI: 10.1016/j.ijfoodmicro.2024.110664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Fruits, vegetables, and shellfish are often associated with outbreaks of illness caused particularly by human norovirus (HuNoV) and hepatitis A virus (HAV), the leading causative agents of foodborne illness worldwide. The aim of this study was to evaluate a new automated nucleic acid extraction platform (EGENE-UP EASYPREP) for enteric viruses in several at-risk food matrices and to test its limit of detection in comparison to a semi-automated method (EGENE-UP) using Boom methodology for nucleic acid extraction as suggested in the reference method ISO 15216-2:2019. Fresh and frozen raspberries, frozen blackberries, romaine lettuce and oyster digestive glands were artificially contaminated with HAV, HuNoV GII.4 or HuNoV GI.7 at 102, 103 or 104 genome copies/sample. Virus was then recovered from the food matrix using the ISO method. Viral RNA extracted from frozen berry samples by the automated system was purified on a column for additional removal of RT-qPCR inhibitors. For fresh raspberry, oysters, and romaine lettuce, the two extraction platforms were deemed equivalent. For frozen raspberry, the automated platform appeared to be more efficient for viral recovery, particularly for HAV and HuNoV GI at lower concentrations. With frozen blackberries, the two platforms may be considered equivalent for all targeted viruses. However, the automated method led to less sample-associated inhibition of the PCR, 56.5 % of samples versus 95.0 % for the semi-automated. We thus found that the automated extraction can be performed easily by users while obtaining equivalent or even superior results to the ISO 15216-2:2019 method, and therefore appears to be suitable for routine sanitary monitoring in food processing and for tracing outbreaks of illness.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Marie-Ève Collard
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Valérie Goulet-Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | | | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada.
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5
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Trudel-Ferland M, Levasseur M, Goulet-Beaulieu V, Jubinville E, Hamon F, Jean J. Concentration of foodborne viruses eluted from fresh and frozen produce: Applicability of ultrafiltration. Int J Food Microbiol 2024; 416:110687. [PMID: 38554558 DOI: 10.1016/j.ijfoodmicro.2024.110687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Foodborne illnesses involving raw and minimally processed foods are often caused by human noroviruses (HuNoV) and hepatitis A virus (HAV). Since food is contaminated usually with small numbers of virions, these must be eluted from the food surface and then concentrated for detection. The objective of this study was to optimize an ultrafiltration (UF) concentration method for HAV and HuNoVs present on various fresh and frozen produce. The detection range of the optimized method and its applicability to different food matrices was compared to the reference method ISO 15216-1:2017. Strawberry, raspberry, blackberry, lettuce, and green onion (25 g) were contaminated with HAV, HuNoV GI.7 and HuNoV GII.4 and then recovered therefrom by elution. A commercial benchtop UF device was used for the concentration step. Viral RNA was extracted and detected by RT-qPCR. From fresh strawberries, recovery of HAV loaded at 104 genome copies per sample was 30 ± 13 %, elution time had no significant impact, and UF membrane with an 80-100 kDa cut-off in combination with Tris-glycine elution buffer at pH 9.5 was found optimal. At lower copy numbers on fresh strawberry, at least 1 log lower numbers of HuNoV were detectable by the UF method (103 vs 104 GII.4 copies/sample and 101 vs 103 GI.7 copies/sample), while HAV was detected at 101 genome copies/sample by both methods. Except on raspberry, the UF method was usually equivalent to the ISO method regardless of the virus tested. The UF method makes rapid viral concentration possible, while supporting the filtration of large volume of sample. With fewer steps and shorter analysis time than the ISO method, this method could be suitable for routine analysis of viruses throughout the food production and surveillance chain.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Marianne Levasseur
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Valérie Goulet-Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | | | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada.
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6
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Yang Y, An R, Lyu C, Wang D. Interactions between human norovirus and intestinal microbiota/microbes: A scoping review. Food Microbiol 2024; 119:104456. [PMID: 38225056 DOI: 10.1016/j.fm.2023.104456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Human norovirus (HuNoV) is an important foodborne virus, which causes non-bacterial acute gastroenteritis and is associated with a high disease burden. Recently, researchers have focus on the interaction between HuNoV and intestinal microbiota/microbes and engaged in studies investigating the implications of this interaction on HuNoV infection. However, the interaction mechanism and the implication of this interaction on host remain obscure. Current scoping review aimed to systematically investigate the interaction between HuNoV and intestinal microbiota, as well as their implication on HuNoV or HuNoV related symptoms. We found that HuNoV could bind to intestinal microbes and affect the intestinal microbial composition, diversity, and microbial gene expression. In reverse, intestinal microbes could affect HuNoV infectivity, although demonstrating contradictory effects (i.e., promote or inhibit HuNoV replication). These contradictory effects existed among microbes, in part, could be attributed to the differences among microbes (histo-blood group antigens and/or other small molecule substances). Results of current scoping review could assist in the selection and isolation of potential microbial candidates to prevent and/or alleviate HuNoV related symptoms.
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Affiliation(s)
- Yaqi Yang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ran An
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chenang Lyu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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7
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Costa JND, Siqueira JAM, Teixeira DM, Lobo PDS, Guerra SDFDS, Souza IM, Cardoso BTM, Farias LSS, Resque HR, Gabbay YB, Silva LDD. Epidemiological and molecular surveillance of norovirus in the Brazilian Amazon: description of recombinant genotypes and improvement of evolutionary analysis. Rev Inst Med Trop Sao Paulo 2024; 66:e22. [PMID: 38656038 DOI: 10.1590/s1678-9946202466022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/12/2024] [Indexed: 04/26/2024] Open
Abstract
Noroviruses are highly infectious, genetically diverse viruses. Global outbreaks occur frequently, making molecular surveillance important for infection monitoring. This cross-sectional descriptive study aimed to monitor cases of norovirus gastroenteritis in the Brazilian Amazon. Fecal samples were tested by immunoenzymatic assay, RT-PCR and genetic sequencing for the ORF1/ORF2 and protease regions. Bayesian inference with a molecular clock was employed to construct the phylogeny. The norovirus prevalence was 25.8%, with a higher positivity rate among children aged 0-24 months. Genogroup GII accounted for 98.1% of the sequenced samples, while GI accounted for 1.9% of them. The GII.P16/GII.4 genotype was the most prevalent, with an evolution rate of 2.87x10-3 and TMRCA estimated in 2012. This study demonstrates that norovirus is a primary causative agent of gastroenteritis and provides data on viral genetic diversity that may facilitate infection surveillance and vaccine development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hugo Reis Resque
- Instituto Evandro Chagas, Seção de Virologia, Ananindeua, Pará, Brazil
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8
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Hotta C, Fujinuma Y, Ogawa T, Akita M, Ogawa T. Surveillance of Wastewater to Monitor the Prevalence of Gastroenteritis Viruses in Chiba Prefecture (2014-2019). J Epidemiol 2024; 34:195-202. [PMID: 37211397 PMCID: PMC10918334 DOI: 10.2188/jea.je20220305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND In Japan, sentinel surveillance is used to monitor the trend of infectious gastroenteritis. Another method of pathogen surveillance, wastewater-based epidemiology, has been used recently because it can help to monitor infectious disease without relying on patient data. Here, we aimed to determine the viral trends reflected in the number of reported patients and number of gastroenteritis virus-positive samples. We focused on gastroenteritis viruses present in wastewater and investigated the usefulness of wastewater surveillance for the surveillance of infectious gastroenteritis. METHODS Real-time polymerase chain reaction was used for viral gene detection in wastewater. The number of reported patients per pediatric sentinel site and number of viral genome copies were compared for correlation potential. The number of gastroenteritis virus-positive samples reported by National Epidemiological Surveillance of Infectious Disease (NESID) and the status of gastroenteritis viruses detected in wastewater were also evaluated. RESULTS Genes of norovirus genotype I, norovirus genotype II, sapovirus, astrovirus, rotavirus group A, and rotavirus group C were detected in wastewater samples. Viruses were detected in wastewater during periods when no gastroenteritis virus-positive samples were reported to NESID. CONCLUSION Norovirus genotype II and other gastroenteritis viruses were detected in wastewater even during periods when no gastroenteritis virus-positive samples were found. Therefore, surveillance using wastewater can complement sentinel surveillance and is an effective tool for the surveillance of infectious gastroenteritis.
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Affiliation(s)
- Chiemi Hotta
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health
| | - Yuki Fujinuma
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health
| | - Takashi Ogawa
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health
| | - Mamiko Akita
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health
| | - Tomoko Ogawa
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health
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9
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Sekiya S, Masuoka H, Mizuno Y, Kibe M, Kosaka S, Natsuhara K, Hirayama K, Inthavong N, Kounnavong S, Tomita S, Takayasu L, Suda W, Yagyu F, Umezaki M. Asymptomatic Enteric Virus Infections and Association with the Gut Microbiome in Rural Residents of Northern Laos. Am J Trop Med Hyg 2024; 110:759-767. [PMID: 38471149 PMCID: PMC10993851 DOI: 10.4269/ajtmh.23-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 12/03/2023] [Indexed: 03/14/2024] Open
Abstract
Viral gastrointestinal infections are an important public health concern, and the occurrence of asymptomatic enteric virus infections makes it difficult to prevent and control their spread. This study aimed to determine the prevalence of and factors associated with asymptomatic enteric virus infection in adults in northern Laos. Fecal samples were collected from apparently healthy participants who did not report diarrhea or high fever at the time of the survey in northern Laos, and enteric viruses were detected using polymerase chain reaction (PCR) and reverse transcription (RT)-PCR. Individual characteristics, including the gut microbiome, were compared between asymptomatic carriers and noncarriers of each enteric virus. Of the participants (N = 255), 12 (4.7%) were positive for norovirus genogroup I (GI), 8 (3.1%) for human adenovirus, and 1 (0.4%) for norovirus GII; prevalence tended to be higher in less-modernized villages. Gut microbial diversity (evaluated by the number of operational taxonomic units) was higher in asymptomatic carriers of norovirus GI or human adenovirus than in their noncarriers. Gut microbiome compositions differed significantly between asymptomatic carriers and noncarriers of norovirus GI or human adenovirus (permutational analysis of variance, P <0.05). These findings imply an association between asymptomatic enteric virus infection and modernization and/or the gut microbiome in northern Laos.
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Affiliation(s)
- Sae Sekiya
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Masuoka
- Laboratory for Microbiome Science, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Mizuno
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Kibe
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoko Kosaka
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Kazuhiro Hirayama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nouhak Inthavong
- Ministry of Health, Lao Tropical and Public Health Institute, Vientiane, Laos
| | | | - Shinsuke Tomita
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | - Lena Takayasu
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wataru Suda
- Laboratory for Microbiome Science, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Fumihiro Yagyu
- Graduate School of International Development and Cooperation, Kibi International University, Hyogo, Japan
| | - Masahiro Umezaki
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Ushijima H, Hoque SA, Akari Y, Pham NTK, Phan T, Nishimura S, Kobayashi M, Sugita K, Okitsu S, Komoto S, Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. Int J Mol Sci 2024; 25:3619. [PMID: 38612429 PMCID: PMC11011564 DOI: 10.3390/ijms25073619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Norovirus (NoV) genogroup II, polymerase type P31, capsid genotype 4, Sydney_2012 variant (GII.P31/GII.4_Sydney_2012) has been circulating at high levels for over a decade, raising the question of whether this strain is undergoing molecular alterations without demonstrating a substantial phylogenetic difference. Here, we applied next-generation sequencing to learn more about the genetic diversity of 14 GII.P31/GII.4_Sydney_2012 strains that caused epidemics in a specific region of Japan, with 12 from Kyoto and 2 from Shizuoka, between 2012 and 2022, with an emphasis on amino acid (aa) differences in all three ORFs. We found numerous notable aa alterations in antigenic locations in the capsid region (ORF2) as well as in other ORFs. In all three ORFs, earlier strains (2013-2016) remained phylogenetically distinct from later strains (2019-2022). This research is expected to shed light on the evolutionary properties of dominating GII.P31/GII.4_Sydney_2012 strains, which could provide useful information for viral diarrhea prevention and treatment.
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Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka 1000, Bangladesh
| | - Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ngan Thi Kim Pham
- College of Industrial Technology, Nihon University, Narashino, Chiba 275-8575, Japan;
| | - Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | | | - Kumiko Sugita
- Sugita Children Clinic, Ibaraki, Osaka 567-0035, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
- Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita 879-5593, Japan
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
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11
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Wang Y, Gao Y, Shi C, Shen Y, Lu M, Sha D, Chen Y, Zhu D, Shi P. Prevalence, Clinical Features, and Genotypes of Norovirus-Associated Diarrhea in Wuxi, China, 2013-2020. Am J Trop Med Hyg 2024; 110:569-575. [PMID: 38266292 PMCID: PMC10919189 DOI: 10.4269/ajtmh.23-0490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/30/2023] [Indexed: 01/26/2024] Open
Abstract
Norovirus (NoV) is a common pathogen that can cause infectious diarrhea. This study aimed to determine the prevalence, clinical features, and genotypes of NoV-associated diarrhea in Wuxi, China. A total of 4,416 stool samples were collected from patients with diarrhea at enteric disease clinics of sentinel hospitals in Wuxi from February 1, 2013 to December 31, 2020. Univariate and Akaike information criterion stepwise logistic regression were used to identify differences as integrated within a clinical setting (NoV positive [+] versus NoV negative [-], NoV+ versus rotavirus [RV]+, NoV+ versus bacteria+, genogroup [G] I and GII genotypes). Norovirus was detected in 9.85% of stool samples, which was greater than other tested pathogens. Excluding coinfection of NoV and other viruses or bacteria, patients infected with NoV had a lower chance of acquiring the virus in summer (P < 0.001; odds ratio [OR], 0.257; 95% CI, 0.189-0.36) when compared with patients without NoV. Patients with diarrhea infected with NoV featured nausea and vomiting (P < 0.001; OR, 2.297, 95% CI, 1.85-2.86) and loose stools (P = 0.006; OR, 2.247; 95% CI, 1.30-4.10), but less abdominal cramping (P = 0.001; OR, 0.676; 95% CI, 0.54-0.84). Patients infected with RV (P < 0.001; OR, 0.413; 95% CI, 0.25-0.68) or bacteria (P < 0.001; OR, 0.422; 95% CI, 0.26-0.67) were more vulnerable to fever than those infected with NoV. A total of 379 GII strains were detected concomitant with 48 GI strains, and there was a seasonal difference between the GI and GII genotypes. Strengthening pathogen detection for infectious diarrhea was helpful for understanding the epidemiological characteristics of infections with NoV and, potentially, for preventing disease outbreaks.
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Affiliation(s)
- Yan Wang
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Yumeng Gao
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Chao Shi
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Yuan Shen
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Mingyan Lu
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Dan Sha
- Microbiological Laboratory, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Yujun Chen
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Ding Zhu
- Department of Disinfection and Vector Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Ping Shi
- Department of Acute Infectious Disease Prevention and Control, The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
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12
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Miotti C, Signorini ML, Oteiza JM, Prez VE, Barril PA. Meta-analysis of the prevalence of norovirus and hepatitis a virus in berries. Int J Food Microbiol 2024; 413:110577. [PMID: 38262124 DOI: 10.1016/j.ijfoodmicro.2024.110577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/25/2024]
Abstract
Norovirus (NoV) and hepatitis A virus (HAV) stand as the predominant agents associated with viral foodborne infections. Outbreaks have been documented to be caused by various types of food items, including fresh and/or frozen berries. Comprehensive data concerning crucial viral pathogens in berries remain limited and are not currently available in aggregate form. Consequently, the present study aimed to compile the existing information regarding the prevalence of NoV and HAV in this matrix. Records of foodborne viruses were systematically extracted from database repositories up to December 2022, adhering to PRISMA standards and were subjected to a multilevel random effect meta-analysis model to determine the mean occurrence rate of NoV and HAV. A high heterogeneity across studies was observed (I2 = 82 %), reflecting variations in the prevalence of sampling locations, years, berry types, and sample conditions, among other potential contributing factors. The prevalence of NoV and HAV in berries was calculated at 2.12 % (95 % CI 1.74-2.59 %), and no statistically differences were observed among the viral types or genogroup categories. However, it is important to clarify that this estimate should be taken with caution given the high heterogeneity. There was no discernible correlation between viral prevalence and any particular berry type. However, there was a temporal correlation observed with the year of sampling, revealing a significantly decreasing trend throughout the study period. A significant influence of the sample condition (fresh or frozen) was observed in relation to the prevalence of NoV GII and HAV. Overall higher viral prevalences were identified in berries originating from African countries as compared to those sourced from other continents. It was also noted that the prevalence of NoV GI was significantly higher in samples collected directly from farms compared to those obtained from retailers. The outcomes of this comprehensive meta-analysis propose that while viral contamination of berries is diminishing in more recent times, the prevalence remains substantial in certain African countries, having a significant risk for foodborne infections. It is imperative to implement intervention strategies in these regions to enhance product safety.
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Affiliation(s)
- Camila Miotti
- IDICAL - Instituto de Investigación de la Cadena Láctea (INTA - CONICET SANTA FE), Rafaela, Santa Fe, Argentina
| | - Marcelo Lisandro Signorini
- IDICAL - Instituto de Investigación de la Cadena Láctea (INTA - CONICET SANTA FE), Rafaela, Santa Fe, Argentina
| | - Juan Martín Oteiza
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Centenario, Neuquén, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Verónica Emilse Prez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Gastroenteritis Virales, Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Patricia Angélica Barril
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Centenario, Neuquén, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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13
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Gao J, Xue L, Li Y, Zhang J, Dai J, Ye Q, Wu S, Gu Q, Zhang Y, Wei X, Wu Q. A systematic review and meta-analysis indicates a high risk of human noroviruses contamination in vegetable worldwide, with GI being the predominant genogroup. Int J Food Microbiol 2024; 413:110603. [PMID: 38306773 DOI: 10.1016/j.ijfoodmicro.2024.110603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/30/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024]
Abstract
Human noroviruses (HuNoVs) are the most predominant viral agents of acute gastroenteritis. Vegetables are important vehicles of HuNoVs transmission. This study aimed to assess the HuNoVs prevalence in vegetables. We searched the Web of Science, Excerpta Medica Database, PubMed, and Cochrane databases until June 1, 2023. A total of 27 studies were included for the meta-analysis. Statistical analysis was conducted using Stata 14.0 software. This analysis showed that the pooled HuNoVs prevalence in vegetables was 7 % (95 % confidence interval (CI): 3-13) worldwide. The continent with largest number of studies was Europe, and the highest number of samples was lettuce. As revealed by the results of the subgroup meta-analysis, the prevalence of GI genogroup was the highest (3 %, 95 % CI: 1-7). A higher prevalence was seen in vegetables from farms (18 %, 95 % CI: 5-37), while only 4 % (95 % CI: 1-8) in retail. The HuNoVs prevalence of ready-to-eat vegetables and non-ready-to-eat vegetables was 2 % (95 % CI: 0-8) and 9 % (95 % CI: 3-16), respectively. The prevalence by quantitative real time RT-PCR was 8 % (95 % CI: 3-15) compared to 3 % (95 % CI: 0-13) by conventional RT-PCR. Furthermore, the HuNoVs prevalence in vegetables was 6 % (95 % CI: 1-14) in ISO pretreatment method and 8 % (95 % CI: 1-19) in non-ISO method, respectively. This study is helpful in comprehensively understanding the prevalence of HuNoVs contamination in vegetables worldwide.
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Affiliation(s)
- Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China.
| | - Yijing Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Jingsha Dai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangzhou, Guangdong 510070, China.
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14
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Jacobsen S, Faber M, Altmann B, Mas Marques A, Bock CT, Niendorf S. Impact of the COVID-19 pandemic on norovirus circulation in Germany. Int J Med Microbiol 2024; 314:151600. [PMID: 38246091 DOI: 10.1016/j.ijmm.2024.151600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/14/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Human norovirus is a major cause of viral gastroenteritis in all age groups. The virus is constantly and rapidly changing, allowing mutations and recombination events to create great diversity of circulating viruses. With the start of the COVID-19 pandemic in 2020, a wide range of public health measures were introduced worldwide to control human-to-human transmission of SARS-CoV-2. In Germany, control measures such as distance rules, contact restrictions, personal protection equipment as well as intensive hand hygiene were introduced. To better understand the effect of the measures to control the COVID-19 pandemic on incidence and the molecular epidemiological dynamics of norovirus outbreaks in Germany, we analyzed national notification data between July 2017 and December 2022 and characterized norovirus sequences circulating between January 2018 and December 2022. Compared to a reference period before the pandemic, the incidence of notified norovirus gastroenteritis decreased by 89.7% to 9.6 per 100,000 during the 2020/2021 norovirus season, corresponding to an incidence rate ratio (IRR) of 0.10. Samples from 539 outbreaks were genotyped in two regions of the viral genome from pre-pandemic (January 2018 to February 2020) and samples from 208 outbreaks during pandemic time period (March 2020 to December 2022). As expected, norovirus outbreaks were mainly found in child care facilities and nursing homes. In total, 36 genotypes were detected in the study period. A high proportion of recombinant strains (86%) was found in patients, the proportion of detected recombinant viruses did not vary between the pre-pandemic and pandemic phase. The proportion of the predominant recombinant strain GII.4 Sydney[P16] was unchanged before pandemic and during pandemic at 37.5%. The diversity of most common genotypes in nursing homes and child care facilities showed a different proportion of genotypes causing outbreaks. In nursing homes as well as in child care facilities GII.4 Sydney[P16] was predominant during the whole study period. Compared to the nursing homes, a greater variety of genotypes at the expense of GII.4 Sydney[P16] was detected in child care facilities. Furthermore, the overall proportion of recombinant strain GII.3[P12] increased during the pandemic, due to outbreaks in child care facilities. The COVID-19 pandemic had a high impact on the occurrence of sporadic cases and norovirus outbreaks in Germany, leading to a near suppression of the typical norovirus winter season following the start of the pandemic. The number of norovirus-associated outbreak samples sent to the Consultant Laboratory dropped by 63% during the pandemic. We could not identify a clear influence on circulating norovirus genotypes. The dominance of GII.4 Sydney recombinant strains was independent from the pandemic. Further studies are needed to follow up on the diversity of less predominant genotypes to see if the pandemic could have acted as a bottleneck to the spread of previously minoritized genotypes like GII.3[P12].
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Affiliation(s)
- Sonja Jacobsen
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Mirko Faber
- Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Britta Altmann
- Department of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany
| | - Andreas Mas Marques
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - C-Thomas Bock
- Department of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany
| | - Sandra Niendorf
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany.
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15
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Rexin D, Rachmadi AT, Hewitt J. Persistence of Infectious Human Norovirus in Estuarine Water. Food Environ Virol 2024; 16:58-64. [PMID: 38165609 DOI: 10.1007/s12560-023-09577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/04/2024]
Abstract
Norovirus is the predominant cause of viral acute gastroenteritis globally. While person-to-person is the most reported transmission route, norovirus is also associated with waterborne and foodborne illness, including from the consumption of contaminated bivalve molluscan shellfish. The main cause of shellfish contamination is via the bioaccumulation of norovirus from growing waters impacted by human wastewater. However, data on the persistence of infectious norovirus in the environment are limited due to a lack of a human norovirus culture method in the past. In this study, we applied the recently established method of norovirus replication in human intestinal enteroids to determine the persistence of norovirus in artificial estuarine water at 25 ppt for up to 21 days at 4 °C and 16 °C in the dark. Infectious norovirus was detected for up to 21 days. The relative infectivity declined from 100 to 3% at day 21, with decay rate constants of 0.07 day-1 at 4 °C and 0.17 day-1 at 16 °C. There was no decrease in norovirus titres as measured by reverse transcription-droplet digital PCR (RT-ddPCR), confirming the lack of the relationship between norovirus infectivity and direct detection by PCR. The results confirm that norovirus can remain infectious for at least 3 weeks in an estuarine water environment, presenting associated health risks.
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Affiliation(s)
- Daniel Rexin
- Institute of Environmental Science and Research Ltd. (ESR), Porirua, 5240, New Zealand.
| | - Andri T Rachmadi
- Institute of Environmental Science and Research Ltd. (ESR), Porirua, 5240, New Zealand
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd. (ESR), Porirua, 5240, New Zealand
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16
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Ossio A, Flores-Rodríguez F, Heredia N, García S, Merino-Mascorro JA. Foodborne Viruses and Somatic Coliphages Occurrence in Fresh Produce at Retail from Northern Mexico. Food Environ Virol 2024; 16:109-119. [PMID: 38198031 DOI: 10.1007/s12560-023-09578-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Foodborne disease outbreaks linked to consumption of vegetables have been often attributed to human enteric viruses, such as Norovirus (NoV), Hepatitis A virus (HAV), and Rotavirus (RoV). Information about the occurrence of these viruses is scarce in many fresh-producing countries. Viral contamination detection of indicators, such as somatic coliphages, could indirectly reflect the presence of viral pathogens, being a valuable tool for better viral risk assessment in food industry. This study aimed to establish the occurrence and correlation of foodborne viruses and somatic coliphages in leafy greens in northern Mexico. A total of 320 vegetable samples were collected, resulting in 80 composite rinses, 40 of lettuce and 40 of parsley. Somatic coliphages were determined using the EPA 1602 method, while foodborne viruses (HAV, RoV, NoV GI, and GII) were determined by qPCR. The occurrence of RoV was 22.5% (9/40, mean 2.11 log gc/g) in lettuce and 20% (8/40, mean 1.91 log gc/g) in parsley. NoV and HAV were not detected in any samples. Somatic coliphages were present in all lettuce and parsley samples, with mean levels of 1.85 log PFU/100 ml and 2.28 log PFU/100 ml, respectively. Spearman analysis established the correlation of somatic coliphages and genomic copies of RoV, resulting in an r2 value of - 0.026 in lettuce and 0.349 in parsley. Although NoV or HAV were undetected in the samples, the presence of RoV is a matter of concern as leafy greens are usually eaten raw, which poses a potential risk of infection.
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Affiliation(s)
- Axel Ossio
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Fernanda Flores-Rodríguez
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Norma Heredia
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Santos García
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Jose Angel Merino-Mascorro
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico.
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17
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Campos CJA, Gyawali P, Hewitt J. Study of Shellfish Growing Area During Normal Harvesting Periods and Following Wastewater Overflows in an Urban Estuary With Complex Hydrography. Food Environ Virol 2024; 16:79-96. [PMID: 38329699 DOI: 10.1007/s12560-023-09579-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024]
Abstract
Viral testing combined with hydrographic studies is considered standard good practice in determining microbiological impacts on shellfish growing areas following wastewater overflows. In this study, norovirus genogroup I and II, indicators of viral contamination (F-RNA bacteriophage genogroup II (F-RNA GII), crAssphage, pepper mild mottle virus) and Escherichia coli were monitored during periods of normal harvesting and following overflows in two commercial shellfish growing areas in Otago Harbour (Aotearoa New Zealand). Dye tracing, drogue tracking and analysis of particle tracking modelling were also undertaken to assess the dispersion, dilution and time of travel of wastewater discharged from a pump station discharge that impacts the growing areas. Norovirus was not detected in any of the 218 shellfish samples tested. PMMoV and crAssphage were more prevalent than F-RNA GII as determined by RT-qPCR. The dye study indicated long residence time of the waters (≥5 days) in the embayment impacted by the discharge. No relationships were found between the concentrations of viral indicators or E. coli and wastewater dilution, distance between the discharge and the growing areas or time since the last overflow. For the three spills studied (≤327 m3), there was little evidence of microbiological impact on the growing areas. This was likely associated with a deep shipping channel that enhances water flushing in the harbour and reduces contaminant transport to the growing areas. We recommend flexibility in the approach for closure/reopening growing areas impacted by spills, particularly for small duration/volume spills and when norovirus is not present in the community.
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Affiliation(s)
- Carlos J A Campos
- Cawthron Institute, 98 Halifax Street East, Nelson, 7042, New Zealand.
- Jacobs, 47 Hereford Street Level 2, Wynn Williams Building, Christchurch, 8013, New Zealand.
| | - Pradip Gyawali
- Institute of Environmental Science and Research Limited (ESR), Kenepuru Science Centre, 34 Kenepuru Drive, Kenepuru, Porirua, 5240, New Zealand
| | - Joanne Hewitt
- Institute of Environmental Science and Research Limited (ESR), Kenepuru Science Centre, 34 Kenepuru Drive, Kenepuru, Porirua, 5240, New Zealand
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18
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Hu X, He P, Jiang T, Shen J. Development and Evaluation of a Rapid GII Norovirus Detection Method Based on CRISPR-Cas12a. Pol J Microbiol 2024; 73:89-97. [PMID: 38437462 PMCID: PMC10911698 DOI: 10.33073/pjm-2024-009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024] Open
Abstract
Norovirus is highly infectious and rapidly transmissible and represents a major pathogen of sporadic cases and outbreaks of acute gastroenteritis worldwide, causing a substantial disease burden. Recent years have witnessed a dramatic increase in norovirus outbreaks in China, significantly higher than in previous years, among which GII norovirus is the predominant prevalent strain. Therefore, rapid norovirus diagnosis is critical for clinical treatment and transmission control. Hence, we developed a molecular assay based on RPA combined with the CRISPER-CAS12a technique targeting the conserved region of the GII norovirus genome, the results of which could be displayed by fluorescence curves and immunochromatographic lateral-flow test strips. The reaction only required approximately 50 min, and the results were visible by the naked eye with a sensitivity reaching 102 copies/μl. Also, our method does not cross-react with other common pathogens that cause intestinal diarrhea. Furthermore, this assay was easy to perform and inexpensive, which could be widely applied for detecting norovirus in settings including medical institutions at all levels, particularly township health centers in low-resource areas.
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Affiliation(s)
- Xinyi Hu
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Pei He
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Tong Jiang
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Jilu Shen
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
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19
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Abney SE, Higham CA, Wilson AM, Ijaz MK, McKinney J, Reynolds KA, Gerba CP. Transmission of Viruses from Restroom Use: A Quantitative Microbial Risk Assessment. Food Environ Virol 2024; 16:65-78. [PMID: 38372960 DOI: 10.1007/s12560-023-09580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/30/2023] [Indexed: 02/20/2024]
Abstract
Restroom use has been implicated in a number of viral outbreaks. In this study, we apply quantitative microbial risk assessment to quantify the risk of viral transmission by contaminated restroom fomites. We estimate risk from high-touch fomite surfaces (entrance/exit door, toilet seat) for three viruses of interest (SARS-CoV-2, adenovirus, norovirus) through eight exposure scenarios involving differing user behaviors, and the use of hand sanitizer following each scenario. We assessed the impacts of several sequences of fomite contacts in the restroom, reflecting the variability of human behavior, on infection risks for these viruses. Touching of the toilet seat was assumed to model adjustment of the seat (open vs. closed), a common touch point in single-user restrooms (home, small business, hospital). A Monte Carlo simulation was conducted for each exposure scenario (10,000 simulations each). Norovirus resulted in the highest probability of infection for all exposure scenarios with fomite surfaces. Post-restroom automatic-dispensing hand sanitizer use reduced the probability of infection for each virus by up to 99.75%. Handwashing within the restroom, an important risk-reduction intervention, was not found to be as effective as use of a non-touch hand sanitizer dispenser for reducing risk to near or below 1/1,000,000, a commonly used risk threshold for comparison.
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Affiliation(s)
- Sarah E Abney
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ciara A Higham
- EPSRC Centre for Doctoral Training in Fluid Dynamics, University of Leeds, Leeds, UK
| | - Amanda M Wilson
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - M Khalid Ijaz
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Julie McKinney
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Kelly A Reynolds
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Charles P Gerba
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA.
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20
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Khamrin P, Kumthip K, Yodmeeklin A, Okitsu S, Motomura K, Sato S, Ushijima H, Maneekarn N. Genetic recombination and genotype diversity of norovirus GI in children with acute gastroenteritis in Thailand, 2015-2021. J Infect Public Health 2024; 17:379-385. [PMID: 38237357 DOI: 10.1016/j.jiph.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Human norovirus is a predominant etiological agent responsible for acute gastroenteritis across all age groups. Recently, norovirus recombinant strains have been reported as the cause of norovirus outbreaks in several settings and the strains that cause outbreaks mostly belong to the norovirus GII. However, yet, the norovirus GI recombinant strains have never been reported previously in Thailand. The aims of this study were to investigate the genetic recombination and genotype diversity of norovirus GI strains in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand during a period of seven years from 2015 to 2021. METHODS A total of 2829 stool specimens were screened for norovirus GI by real-time PCR, and the polymerase and capsid genes were sequenced and analyzed. RESULTS Of 2829 specimens tested, 12 (0.4%) were positive for norovirus GI. Of these, 7 out of 12 (58.3%) strains were identified as norovirus GI recombinant strains. Among 7 norovirus GI recombinant strains, 3, 3, and 1 were identified as GI.3[P13], GI.5[P4], and GI.6[P11], respectively. The remaining five strains were identified as non-recombinant strains of the GI.4[P4], GI.5[P5], and GI.6[P6] genotypes. CONCLUSIONS The findings highlight the genetic diversity and multiple intergenotype recombinant strains of norovirus GI circulating in children with acute gastroenteritis in Chiang Mai, Thailand from 2015 to 2021. The detection of multiple intergenotype norovirus GI recombinant strains further underscore the complexity of norovirus GI strains circulating in this region.
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Affiliation(s)
- Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kazushi Motomura
- Epidemiology Section, Division of Public Health, Osaka Institute of Public Health, Osaka, Japan
| | - Shintaro Sato
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Hiroshi Ushijima
- 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; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
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21
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Cintron M, Jani K, Madhavappallil J, Kamboj M, Babady NE. Prevalence of astrovirus and sapovirus among adult oncology patients with acute gastroenteritis using a multiplexed gastrointestinal pathogen PCR panel. Eur J Clin Microbiol Infect Dis 2024; 43:525-531. [PMID: 38216845 DOI: 10.1007/s10096-024-04748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Multiplex syndromic gastrointestinal panels (GIPCR) have streamlined the diagnosis of infectious diarrhea. Additionally, they have expanded the number of pathogens that can be routinely evaluated, allowing further understanding of the prevalence of enteric pathogens in various patient populations. The goal of this study was to investigate the prevalence and clinical presentation of astrovirus and sapovirus gastroenteritis in adult oncology patients as detected by the FilmArray GIPCR. METHODS All GIPCR panel results from December 2017 to June 2021 were retrospectively reviewed to determine the prevalence of astrovirus and sapovirus in adult oncology patients. Medical records were also reviewed to obtain clinical information. Repeat GIPCR positivity and symptom duration were used to estimate prolonged viral shedding. RESULTS A total of 18,014 panels were performed on samples collected from 9303 adults. Overall, astrovirus and sapovirus were detected in 0.35% (33/9303) and 0.45% (42/9303) GIPCRs respectively. At least one viral target was detected in 424 (4.4%) patients. Astrovirus accounted for 7.8% (33/424) and sapovirus 9.9% (42/424) of patients. Diarrhea was the most common symptom documented. A subset of transplant patients had protracted viral detection with a median of ~27 days (range 23-43 days) for astrovirus and 97 days (range 11-495) for sapovirus. No clusters or outbreaks were identified during the study period. CONCLUSION In oncology patients with viral gastroenteritis, astrovirus and sapovirus were the causative agents in 18% of the cases. Both viruses were associated with mild disease. Prolonged diarrhea and viral shedding were observed in a few transplant patients.
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Affiliation(s)
- Melvili Cintron
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jerin Madhavappallil
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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22
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Monnot M, Ollivier J, Taligrot H, Garry P, Cordier C, Stravakakis C, Le Guyader FS, Moulin P. Retention of Virus Versus Surrogate, by Ultrafiltration in Seawater: Case Study of Norovirus Versus Tulane. Food Environ Virol 2024; 16:14-24. [PMID: 38184502 DOI: 10.1007/s12560-023-09574-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024]
Abstract
In the field of chemical engineering and water treatment, the study of viruses, included surrogates, is well documented. Often, surrogates are used to study viruses and their behavior because they can be produced in larger quantities in safer conditions and are easier to handle. In fact, surrogates allow studying microorganisms which are non-infectious to humans but share some properties similar to pathogenic viruses: structure, composition, morphology, and size. Human noroviruses, recognized as the leading cause of epidemics and sporadic cases of gastroenteritis across all age groups, may be mimicked by the Tulane virus. The objectives of this work were to study (i) the ultrafiltration of Tulane virus and norovirus to validate that Tulane virus can be used as a surrogate for norovirus in water treatment process and (ii) the retention of norovirus and the surrogate as a function of water quality to better understand the use of the latter pathogenic viruses. Ultrafiltration tests showed significant logarithmic reduction values (LRV) in viral RNA: around 2.5 for global LRV (i.e., based on the initial and permeate average concentrations) and between 2 and 6 for average LRV (i.e., retention rate considering the increase of viral concentration in the retentate), both for norovirus and the surrogate Tulane virus. Higher reduction rates (from 2 to 6 log genome copies) are obtained for higher initial concentrations (from 101 to 107 genome copies per mL) due to virus aggregation in membrane lumen. Tulane virus appears to be a good surrogate for norovirus retention by membrane processes.
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Affiliation(s)
- M Monnot
- Aix Marseille Univ., CNRS, Centrale Marseille, M2P2 UMR 7340, Equipe Procédés Membranaires (EPM), Europôle de l'Arbois, Pavillon Laennec, Hall C, BP80, 13545, Aix-en-Provence, France
| | - J Ollivier
- Ifremer - U. Microbiologie, Aliment, Santé et Environnement (LSEM/RBE), Rue de l'Ile d'Yeu, BP 21105, 44311, Nantes, Cedex 3, France
| | - H Taligrot
- Aix Marseille Univ., CNRS, Centrale Marseille, M2P2 UMR 7340, Equipe Procédés Membranaires (EPM), Europôle de l'Arbois, Pavillon Laennec, Hall C, BP80, 13545, Aix-en-Provence, France
| | - P Garry
- Ifremer - U. Microbiologie, Aliment, Santé et Environnement (LSEM/RBE), Rue de l'Ile d'Yeu, BP 21105, 44311, Nantes, Cedex 3, France
| | - C Cordier
- Aix Marseille Univ., CNRS, Centrale Marseille, M2P2 UMR 7340, Equipe Procédés Membranaires (EPM), Europôle de l'Arbois, Pavillon Laennec, Hall C, BP80, 13545, Aix-en-Provence, France
| | - C Stravakakis
- Ifremer - EMMA Plateforme Expérimentale Mollusques Marins Atlantique, 85230, Bouin, France
| | - F S Le Guyader
- Ifremer - U. Microbiologie, Aliment, Santé et Environnement (LSEM/RBE), Rue de l'Ile d'Yeu, BP 21105, 44311, Nantes, Cedex 3, France
| | - P Moulin
- Aix Marseille Univ., CNRS, Centrale Marseille, M2P2 UMR 7340, Equipe Procédés Membranaires (EPM), Europôle de l'Arbois, Pavillon Laennec, Hall C, BP80, 13545, Aix-en-Provence, France.
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23
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Wang W, Wang B, Li Q, Tian R, Lu X, Peng Y, Sun J, Bai J, Gao Z, Sun X. Ultrasensitive Detection Strategy of Norovirus Based on a Dual Enhancement Strategy: CRISPR-Responsive Self-Assembled SNA and Isothermal Amplification. J Agric Food Chem 2024; 72:4415-4425. [PMID: 38355417 DOI: 10.1021/acs.jafc.4c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Spherical nucleic acids (SNAs) have been used to construct various nanobiosensors with gold nanoparticles (AuNPs) as nuclei. The SNAs play a critical role in biosensing due to their various physical and chemical properties, programmability, and specificity recognition ability. In this study, CRISPR-responsive self-assembled spherical nucleic acid (CRISPR-rsSNA) detection probes were constructed by conjugating fluorescein-labeled probes to the surface of AuNPs to improve the sensing performance. Also, the mechanism of ssDNA and the role of different fluorescent groups in the self-assembly process of CRISPR-rsSNA were explored. Then, CRISPR-rsSNA and reverse transcription-recombinase polymerase amplification (RT-RPA) were combined to develop an ultrasensitive fluorescence-detection strategy for norovirus. In the presence of the virus, the target RNA sequence of the virus was transformed and amplified by RT-RPA. The resulting dsDNA activated the trans-cleavage activity of CRISPR cas12a, resulting in disintegrating the outer nucleic acid structure of the CRISPR-rsSNA at a diffusible rate, which released reporter molecules. Norovirus was quantitated by fluorescence detection. This strategy facilitated the detection of the norovirus at the attomolar level. An RT-RPA kit for norovirus detected would be developed based on this method. The proposed method would be used for the detection of different viruses just by changing the target RNA and crRNA of the CRISPR cas12a system which provided a foundation for high-throughput detection of various substances.
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Affiliation(s)
- Weiya Wang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Botao Wang
- School of Instrument Science and Optoelectronics Engineering, Beihang University, Beijing 100191, China
| | - Qiaofeng Li
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Run Tian
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Xin Lu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Jiadi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Xiulan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
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24
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Kim NE, Kim MJ, Park BJ, Kwon JW, Lee JM, Park JH, Song YJ. A DNA vaccine against GII.4 human norovirus VP1 induces blocking antibody production and T cell responses. Vaccine 2024; 42:1392-1400. [PMID: 38320930 DOI: 10.1016/j.vaccine.2024.01.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
Human noroviruses (HuNoVs) are highly contagious and a leading cause of epidemics of acute gastroenteritis worldwide. Among the various HuNoV genotypes, GII.4 is the most prevalent cause of outbreaks. However, no vaccines have been approved for HuNoVs to date. DNA vaccines are proposed to serve as an ideal platform against HuNoV since they can be easily produced and customized to express target proteins. In this study, we constructed a CMV/R vector expressing a major structural protein, VP1, of GII.4 HuNoV (CMV/R-GII.4 HuNoV VP1). Transfection of CMV/R-GII.4 HuNoV VP1 into human embryonic kidney 293T (HEK293T) cells resulted in successful expression of VP1 proteins in vitro. Intramuscular or intradermal immunization of mice with the CMV/R-GII.4 HuNoV VP1 construct elicited the production of blocking antibodies and activation of T cell responses against GII.4 HuNoV VP1. Our collective data support the utility of CMV/R-GII.4 HuNoV VP1 as a promising DNA vaccine candidate against GII.4 HuNoV.
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Affiliation(s)
- Na-Eun Kim
- Department of Life Science, Gachon University, Seongnam-Si, South Korea
| | - Mun-Jin Kim
- Department of BioNano Technology, Gachon University, Seongnam-Si, South Korea
| | - Bum Ju Park
- Department of Life Science, Gachon University, Seongnam-Si, South Korea
| | - Jung Won Kwon
- Department of Life Science, Gachon University, Seongnam-Si, South Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Jung-Hwan Park
- Department of BioNano Technology, Gachon University, Seongnam-Si, South Korea
| | - Yoon-Jae Song
- Department of Life Science, Gachon University, Seongnam-Si, South Korea.
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25
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Ma J, Liu J, Huo Y. Characterization of cleavage patterns and assembly of N-terminally modified GII.6 norovirus VP1 proteins. Arch Virol 2024; 169:55. [PMID: 38386207 DOI: 10.1007/s00705-024-05973-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/12/2023] [Indexed: 02/23/2024]
Abstract
When expressed in vitro, the major capsid protein VP1 of a norovirus (NoV) can self-assemble into virus-like particles (VLPs), and its N-terminus can tolerate foreign sequences without the assembly being affected. We explored the effects of adding an N-terminal sequence to the VP1 of a GII.6 NoV strain on its cleavage and assembly. Sequences of varying lengths derived from the minor capsid protein VP2 were added to the VP1 N-terminus. Using a recombinant baculovirus expression system, the fusion proteins were expressed, and their cleavage patterns and assembly were analyzed using mass spectrometry and transmission electron microscopy, respectively. All of the fusion proteins were successfully expressed and exhibited varying degrees of enzyme cleavage, most probably at the N-terminus. LC-MS results revealed that similar fragments were obtained for wild-type VP1 and fusion proteins, indicating that the cleavage sites were conserved. EM analysis indicated that VLPs of different sizes were successfully assembled for certain fusion proteins. The study data demonstrate that NoV VP1 can tolerate foreign sequences of a certain length at its N-terminus and that a conserved cleavage pattern exists, which might facilitate further investigation of the assembly and cleavage mechanisms of NoV.
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Affiliation(s)
- Jie Ma
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, 450000, China
| | - Jinjin Liu
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, 450000, China
| | - Yuqi Huo
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, 450000, China.
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26
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Ishiyama R, Yoshida K, Oikawa K, Takai-Todaka R, Kato A, Kanamori K, Nakanishi A, Haga K, Katayama K. Production of infectious reporter murine norovirus by VP2 trans-complementation. J Virol 2024; 98:e0126123. [PMID: 38226813 PMCID: PMC10878090 DOI: 10.1128/jvi.01261-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Human norovirus (HuNoV) causes gastroenteritis, a disease with no effective therapy or vaccine, and does not grow well in culture. Murine norovirus (MNV) easily replicates in cell cultures and small animals and has often been used as a model to elucidate the structural and functional characteristics of HuNoV. An MNV plasmid-based reverse genetics system was developed to produce the modified recombinant virus. In this study, we attempted to construct the recombinant virus by integrating a foreign gene into MNV ORF3, which encodes the minor structural protein VP2. Deletion of VP2 expression abolished infectious particles from MNV cDNA clones, and supplying exogenous VP2 to the cells rescued the infectivity of cDNA clones without VP2 expression. In addition, the coding sequence of C-terminal ORF3 was essential for cDNA clones compensated with VP2 to produce infectious particles. Furthermore, the recombinant virus with exogenous reporter genes in place of the dispensable region of ORF3 was propagated when VP2 was constitutively supplied. Our findings indicate that foreign genes can be transduced into the norovirus ORF3 region when VP2 is supplied and that successive propagation of modified recombinant norovirus could lead to the development of norovirus-based vaccines or therapeutics.IMPORTANCEIn this study, we revealed that some of the coding regions of ORF3 could be replaced by a foreign gene and infectious virus could be produced when VP2 was supplied. Propagation of this virus depended on VP2 being supplied in trans, indicating that this virus could infect only once. Our findings help to elucidate the functions of VP2 in the virus lifecycle and to develop other caliciviral vectors for recombinant attenuated live enteric virus vaccines or therapeutics tools.
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Affiliation(s)
- Ryoka Ishiyama
- Department of Infection Control and Immunology, Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuhiro Yoshida
- Department of Aging Intervention, National Center for Geriatrics and Gerontology, Laboratory of Gene Therapy, and Laboratory for Radiation Safety, Aichi, Japan
| | - Kazuki Oikawa
- Department of Infection Control and Immunology, Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Infection Control and Immunology, Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akiko Kato
- Department of Aging Intervention, National Center for Geriatrics and Gerontology, Laboratory of Gene Therapy, and Laboratory for Radiation Safety, Aichi, Japan
| | - Kumiko Kanamori
- Department of Aging Intervention, National Center for Geriatrics and Gerontology, Laboratory of Gene Therapy, and Laboratory for Radiation Safety, Aichi, Japan
| | - Akira Nakanishi
- Department of Aging Intervention, National Center for Geriatrics and Gerontology, Laboratory of Gene Therapy, and Laboratory for Radiation Safety, Aichi, Japan
- Department of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kei Haga
- Department of Infection Control and Immunology, Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuhiko Katayama
- Department of Infection Control and Immunology, Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
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27
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Narwankar R, Esseili MA. Replication of Human Norovirus in Human Intestinal Enteroids Is Affected by Fecal Sample Processing. Viruses 2024; 16:241. [PMID: 38400017 PMCID: PMC10893307 DOI: 10.3390/v16020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Human intestinal enteroids (HIEs) culture is an emerging model for assessing the infectivity of human noroviruses (HuNoVs). The model is based on detecting an increase in HuNoV RNA post-infection of HIEs. HuNoV fecal samples used for HIE infection are traditionally processed by serial filtration. Recently, processing HuNoV fecal samples by serial centrifugation was shown to retain vesicles containing HuNoV. The objective of this study was to investigate whether serially centrifuged fecal samples, RNA extraction kit (QIAamp versus MagMaX) and HIE age (newer versus older) affect HuNoV RNA fold increase in HIE. HuNoV GII.1, GII.4 and GII.6 fecal samples were prepared by serial centrifugation and filtration and the viral RNA in HIE was quantified at 1 and 72 h post-infection (hpi) following RNA extraction and RT-qPCR. The serially filtered GII.1, GII.4 and GII.6 showed successful replication in HIE, resulting in mean log increases of 2.2, 2 and 1.2, respectively, at 72 vs. 1 hpi. In contrast, only serially centrifuged GII.1 showed consistently successful replication. However, using newer HIE passages and the MagMAX kit resulted in mean log fold increases for serially centrifuged GII.1, GII.4 and GII.6 (1.6, 2.3 and 1.8 log, respectively) that were similar to serially filtered samples. Therefore, HuNoV fecal sample processing and HIE age can affect virus replication in the HIE model.
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Affiliation(s)
| | - Malak A. Esseili
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223, USA
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28
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Wales SQ, Pandiscia A, Kulka M, Sanchez G, Randazzo W. Challenges for estimating human norovirus infectivity by viability RT-qPCR as compared to replication in human intestinal enteroids. Int J Food Microbiol 2024; 411:110507. [PMID: 38043474 DOI: 10.1016/j.ijfoodmicro.2023.110507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Viability RT-qPCR, a molecular detection method combining viability marker pre-treatment with RT-qPCR, has been proposed to infer infectivity of viruses which is particularly relevant for non-culturable viruses or sophisticated cell culture systems. Being human noroviruses (HuNoV) most frequently associated with foodborne outbreaks, this study compared different viability techniques and infectivity in human intestinal enteroids (HIE) to ultimately determine whether the molecular approaches could serve as rapid assays to predict HuNoV inactivation in high-risk food. To this end, the performance of three viability RT-qPCR assays with different intercalating markers ((Viability PCR Crosslinker Kit (CL), propidium monoazide (PMAxx™), and platinum chloride (PtCl4)) in estimating survival of HuNoV exposed to thermal and high pressure (HPP) treatments was compared to replication tested in the HIE cell culture model. A nearly full-length genomic molecular assay coupled with PMAxx™ to infer HuNoV thermal inactivation was also assessed. The experimental design included HuNoV genogroup I.3 [P13], GII.4 Sydney [P16], GII.6 [P7], along with Tulane virus (TV) serving as surrogate. Finally, viability RT-qPCR was tested in HPP-treated strawberry puree, selected as a food matrix with high viral contamination risk. PMAxx™ and CL performed evenly, while PtCl4 affected HuNoV infectivity. Taking all experimental data together, viability RT-qPCR was demonstrated to be an improved method over direct RT-qPCR to estimate viral inactivation at extreme thermal (95 °C) and HPP (450 MPa) exposures, but not under milder conditions as amplification signals were detected. Despite its complexity and limitations, the HIE demonstrated a more robust model than viability RT-qPCR to assess HuNoV infectivity.
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Affiliation(s)
- Samantha Q Wales
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, United States
| | - Annamaria Pandiscia
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain; Department of Veterinary Medicine, University of Bari, Provincial Road to Casamassima Km 3, Bari, Valenzano 70010, Italy
| | - Michael Kulka
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, United States
| | - Gloria Sanchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
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Kreins AY, Roux E, Pang J, Cheng I, Charles O, Roy S, Mohammed R, Owens S, Lowe DM, Brugha R, Williams R, Howley E, Best T, Davies EG, Worth A, Solas C, Standing JF, Goldstein RA, Rocha-Pereira J, Breuer J. Favipiravir induces HuNoV viral mutagenesis and infectivity loss with clinical improvement in immunocompromised patients. Clin Immunol 2024; 259:109901. [PMID: 38218209 DOI: 10.1016/j.clim.2024.109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Chronic human norovirus (HuNoV) infections in immunocompromised patients result in severe disease, yet approved antivirals are lacking. RNA-dependent RNA polymerase (RdRp) inhibitors inducing viral mutagenesis display broad-spectrum in vitro antiviral activity, but clinical efficacy in HuNoV infections is anecdotal and the potential emergence of drug-resistant variants is concerning. Upon favipiravir (and nitazoxanide) treatment of four immunocompromised patients with life-threatening HuNoV infections, viral whole-genome sequencing showed accumulation of favipiravir-induced mutations which coincided with clinical improvement although treatment failed to clear HuNoV. Infection of zebrafish larvae demonstrated drug-associated loss of viral infectivity and favipiravir treatment showed efficacy despite occurrence of RdRp variants potentially causing favipiravir resistance. This indicates that within-host resistance evolution did not reverse loss of viral fitness caused by genome-wide accumulation of sequence changes. This off-label approach supports the use of mutagenic antivirals for treating prolonged RNA viral infections and further informs the debate surrounding their impact on virus evolution.
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Affiliation(s)
- Alexandra Y Kreins
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Emma Roux
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Juanita Pang
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Iek Cheng
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Pharmacy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Oscar Charles
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sunando Roy
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Reem Mohammed
- Department of Pediatrics, Division of Allergy and Immunology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Stephen Owens
- Department of Paediatric Allergy, Immunology and Infectious Diseases, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - David M Lowe
- Immunology Department, Royal Free Hospital NHS Foundation Trust, London, United Kingdom; Institute of Immunity and Transplantation, University College London, London, UK
| | - Rossa Brugha
- Department of Cardiothoracic Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Rachel Williams
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Evey Howley
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Timothy Best
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - E Graham Davies
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Austen Worth
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Caroline Solas
- Unité des Virus Émergents IRD 190, INSERM 1207, Aix-Marseille Université, Marseille, France; APHM, Laboratoire de Pharmacocinétique et Toxicologie, Hôpital La Timone, Marseille, France
| | - Joseph F Standing
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Pharmacy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Joana Rocha-Pereira
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
| | - Judith Breuer
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Institute of Immunity and Transplantation, University College London, London, UK.
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Shaffer M, Huynh K, Costantini V, Vinjé J, Bibby K. Heat inactivation of aqueous viable norovirus and MS2 bacteriophage. J Appl Microbiol 2024; 135:lxae033. [PMID: 38341278 DOI: 10.1093/jambio/lxae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024]
Abstract
AIMS This study aimed to compare the heat inactivation kinetics of viable human norovirus with the surrogate, MS2 bacteriophage as well as assess the decay of the RNA signal. METHODS AND RESULTS Human intestinal enteroids were used to analyze the heat inactivation kinetics of viable human norovirus compared to the surrogate MS2 bacteriophage, which was cultured using a plaque assay. Norovirus decay rates were 0.22 min-1, 0.68 min-1, and 1.11 min-1 for 50°C, 60°C, and 70°C, respectively, and MS2 bacteriophage decay rates were 0.0065 min-1, 0.045 min-1, and 0.16 min-1 for 50°C, 60°C, and 70°C, respectively. Norovirus had significantly higher decay rates than MS2 bacteriophage at all tested temperatures (P = .002-.007). No decrease of RNA titers as measured by reverse transcription-PCR for both human norovirus and MS2 bacteriophage over time was observed, indicating molecular methods do not accurately depict viable human norovirus after heat inactivation and treatment efficiency is underestimated. CONCLUSIONS Overall, our data demonstrate that MS2 bacteriophage is a conservative surrogate to measure heat inactivation and potentially overestimates the infectious risk of norovirus. Furthermore, this study corroborates that measuring viral RNA titers, as evaluated by PCR methods, does not correlate with the persistence of viable norovirus under heat inactivation.
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Affiliation(s)
- Marlee Shaffer
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN 46556, United States
| | - Kimberly Huynh
- National Calicivirus Laboratory, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Verónica Costantini
- National Calicivirus Laboratory, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jan Vinjé
- National Calicivirus Laboratory, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN 46556, United States
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Kennedy LC, Lowry SA, Boehm AB. Temperature and particles interact to affect human norovirus and MS2 persistence in surface water. Environ Sci Process Impacts 2024; 26:71-81. [PMID: 38078556 DOI: 10.1039/d3em00357d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Modeling the fate and transport of viruses and their genetic material in surface water is necessary to assess risks associated with contaminated surface waters and to inform environmental surveillance efforts. Temperature has been identified as a key variable affecting virus persistence in surface waters, but the effects of the presence of biological and inert particles and of their interaction with temperature have not been well characterized. We assessed these effects on the persistence of human norovirus (HuNoV) genotype II.4 purified from stool and MS2 in surface water. Raw or filter-sterilized creek water microcosms were inoculated and incubated in the dark at 10 °C, 15 °C, and 20 °C. HuNoV (i.e., genome segments and intact capsids) and MS2 (i.e., infectious MS2, genome segments, and intact capsids) concentrations were followed over 36 days. The range in positive, significant first-order decay rate constants for HuNoV in this study was 0.14 to 0.69 day-1 compared with 0.026 to 0.71 day-1 for that of MS2. Decay rate constants for HuNoV genome segments and infectious MS2 were largest in creek water that included biological and inert particles and incubated at higher temperatures. In addition, for HuNoV and MS2 incubated in raw or filter-sterilized creek water at 15 °C, capsid damage was not identified as a dominant inactivation mechanism. Environmental processes and events that affect surface water biological and inert particles, temperature, or both could lead to variable virus decay rate constants. Incorporating the effects of particles, temperature, and their interaction could enhance models of virus fate and transport in surface water.
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Affiliation(s)
- Lauren C Kennedy
- Department of Civil and Environmental Engineering, Stanford University, Y2E2 Room 189, Stanford, CA 94305, USA.
| | - Sarah A Lowry
- Department of Civil and Environmental Engineering, Stanford University, Y2E2 Room 189, Stanford, CA 94305, USA.
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Y2E2 Room 189, Stanford, CA 94305, USA.
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32
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Udompat P, Srimuang K, Doungngern P, Thippamom N, Petcharat S, Rattanatumhi K, Khiewbanyang S, Taweewigyakarn P, Kripattanapong S, Ninwattana S, Supataragul A, Sterling SL, Klungthong C, Joonlasak K, Manasatienkij W, Cotrone TS, Fernandez S, Wacharapluesadee S, Putcharoen O. An unusual diarrheal outbreak in the community in Eastern Thailand caused by Norovirus GII.3[P25]. Virol J 2024; 21:21. [PMID: 38243289 PMCID: PMC10797983 DOI: 10.1186/s12985-024-02296-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Sentinel laboratory surveillance for diarrheal disease determined norovirus to be the most common cause of non-bacterial gastroenteritis in people during the COVID-19 pandemic in Thailand. An increase in patients presenting with diarrhea and vomiting in hospitals across Chanthaburi province between December 2021 and January 2022 led to the need for the identification of viral pathogens that may be responsible for the outbreak. METHODS Fecal samples (rectal swabs or stool) from 93 patients, of which 65 patients were collected during the December 2021 to January 2022 outbreak, were collected and screened for viral infection by real-time RT-PCR. Positive samples for norovirus GII were then genotyped by targeted amplification and sequencing of partial polymerase and capsid genes. Full genome sequencing was performed from the predominant strain, GII.3[P25]. RESULTS Norovirus was the most common virus detected in human fecal samples in this study. 39 of 65 outbreak samples (60%) and 3 of 28 (10%) non-outbreak samples were positive for norovirus genogroup II. One was positive for rotavirus, and one indicated co-infection with rotavirus and norovirus genogroups I and II. Nucleotide sequences of VP1 and RdRp gene were successfully obtained from 28 of 39 positive norovirus GII and used for dual-typing; 25/28 (89.3%) were GII.3, and 24/28 (85.7) were GII.P25, respectively. Norovirus GII.3[P25] was the predominant strain responsible for this outbreak. The full genome sequence of norovirus GII.3[P25] from our study is the first reported in Thailand and has 98.62% and 98.57% similarity to norovirus found in China in 2021 and the USA in 2022, respectively. We further demonstrate the presence of multiple co-circulating norovirus genotypes, including GII.21[P21], GII.17[P17], GII.3[P12] and GII.4[P31] in our study. CONCLUSIONS An unusual diarrhea outbreak was found in December 2021 in eastern Thailand. Norovirus strain GII.3[P25] was the cause of the outbreak and was first detected in Thailand. The positive rate during GII.3[P25] outbreak was six times higher than sporadic cases (GII.4), and, atypically, adults were the primary infected population rather than children.
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Affiliation(s)
| | - Krongkan Srimuang
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
| | - Pawinee Doungngern
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi, 11000, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sininat Petcharat
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
| | - Khwankamon Rattanatumhi
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sirorat Khiewbanyang
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi, 11000, Thailand
| | - Pantila Taweewigyakarn
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi, 11000, Thailand
| | - Somkid Kripattanapong
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi, 11000, Thailand
| | - Sasiprapa Ninwattana
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ananporn Supataragul
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand
| | - Spencer L Sterling
- Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Henry M. Jackson Foundation, Bethesda, MD, USA
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Khajohn Joonlasak
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Thomas S Cotrone
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand.
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok, 10330, Thailand.
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Tao L, Zhang X, Wang X, Ding J. Using molecular methods to delineate norovirus outbreaks: a systematic review. Arch Virol 2024; 169:16. [PMID: 38172375 DOI: 10.1007/s00705-023-05953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Noroviruses are among the major causative agents of human acute gastroenteritis, and the nature of norovirus outbreaks can differ considerably. The number of single-nucleotide polymorphisms (SNPs) between strains is used to assess their relationships. There is currently no universally accepted cutoff value for clustering strains that define an outbreak or linking the individuals involved. This study was conducted to estimate the threshold value of genomic variations among related strains within norovirus outbreaks. We carried out a literature search in the PubMed and Web of Science databases. SNP rates were defined as the number of SNPs/sequence length (bp) × 100%. The Mann-Whitney U-test was used in comparisons of the distribution of SNP rates for different sequence regions, genogroups (GI and GII), transmission routes, and sequencing methods. A total of 25 articles reporting on 108 norovirus outbreaks were included. In 99.1% of the outbreaks, the SNP rates were below 0.50%, and in 89.8%, the SNP rates were under 0.20%. Outbreak strains showed higher SNP rates when the P2 domain was used for sequence analysis (Z = -2.652, p = 0.008) and when an NGS method was used (Z = -3.686, p < 0.001). Outbreaks caused by different norovirus genotypes showed no significant difference in SNP rates. Compared with person-to-person outbreaks, SNP rates were lower in common-source outbreaks, but no significant difference was found when differences in sequencing methods were taken into consideraton. SNP rates under 0.20% and 0.50% could be considered as the rigorous and relaxed threshold, respectively, of strain similarity within a norovirus outbreak. More data are needed to evaluate differences within and between various norovirus outbreaks.
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Affiliation(s)
- Luqiu Tao
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xinyang Zhang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xuan Wang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China.
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China.
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Shen L, Zhang Z, Wang R, Wu S, Wang Y, Fu S. Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source. J Appl Microbiol 2024; 135:lxad310. [PMID: 38130237 DOI: 10.1093/jambio/lxad310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
AIMS Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources. METHODS AND RESULTS We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified. CONCLUSIONS Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
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Affiliation(s)
- Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Shuang Wu
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yongjie Wang
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai 200093, China
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
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Mangeri L, Righi F, Benevenia R, Galuppini E, Tilola M, Bertasi B, Tranquillo V, Rubini S, Losio MN, Filipello V. Monitoring and Genotyping of Norovirus in Bivalve Molluscan Shellfish from Northern Italian Seas (2018-2020). Foodborne Pathog Dis 2024; 21:27-35. [PMID: 37878812 DOI: 10.1089/fpd.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
Norovirus (NoV) is an enteric virus with foodborne transmission. Bivalve shellfish are a main source of infections and outbreaks. In Italy a voluntary based monitoring plan to check the safety of bivalve shellfish was set up at provincial level. This study describes the occurrence and distribution of NoV in the Northern Adriatic Sea and in the Ligurian Sea. From October 2018 to September 2020, 807 bivalve shellfish samples (n = 205 oysters, n = 182 mussels, n = 348 clams, n = 72 other bivalve shellfish) were tested by One-Step Retrotranscription Real-time polymerase chain reaction for NoV GI and GII and quantified according to the ISO 15216-2:2013 and ISO 15216-1:2017. Positive samples were further analyzed to determine genotype by sequencing of the ORF1/ORF2 junction of the viral genome. A total of 126 samples were positive for NoV, mussels, and oysters had the highest probability of being positive and positive samples were found mainly in the colder season. Of these samples, 46% were NoV GII, 13% NoV GI, and 40% carried both genogroups. Thirty-seven samples were typeable (GI n = 12 and GII n = 25) with GI samples belonging to four genotypes and GII samples belonging to five genotypes. GII.3 genotype was the most prevalent, followed by GII.4, particularly Sydney 2012 subtype, a leading cause of infections worldwide, was found in three oysters' and three clams' samples. The phylogenetic analysis revealed a high heterogeneity among the species that are scattered in several clusters. Considering the low infectious dose the overall presence of NoV in edible shellfish, particular those to be eaten raw or undercooked, is moderately high. The presence of genotypes frequently involved in human infections strengthens the need for ongoing monitoring, which should be extended at national level.
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Affiliation(s)
- Lucia Mangeri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Francesco Righi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Roberto Benevenia
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
| | - Elisa Galuppini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Michela Tilola
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Barbara Bertasi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Vito Tranquillo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
| | - Silva Rubini
- Istituto Zooprofilattico della Lombardia e dell'Emilia Romagna (IZSLER), Cassana, Italy
| | - Marina Nadia Losio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Milano, Italy
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36
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Hazan G, Goldstein Y, Greenberg D, Khalde F, Mahajna R, Keren-Naos A, Hershkovitz E, Faingelernt Y, Givon-Lavi N, Danino D. Comparing single versus multiple virus detection in pediatric acute gastroenteritis postimplementation of routine multiplex RT-PCR diagnostic testing. J Med Virol 2024; 96:e29344. [PMID: 38149453 DOI: 10.1002/jmv.29344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Utilizing multiplex real time polymerase chain reaction (RT-PCR) for rapid diagnosis of gastroenteritis, enables simultaneous detection of multiple pathogens. A comparative analysis of disease characteristics was conducted between cases with single and multiple viruses. Rotavirus vaccine was introduced in 2010, reaching a 70% coverage in 2 years. All rectal swabs collected from diarrheic children (<5 years) between December 2017 and March 2022 were included. Detection of the same viruses within 2 months was considered a single episode. Episodes with positive stool bacterial PCR were excluded. A total of 5879 samples were collected, revealing 86.9% (1509) with single virus detection and 13.1% (227) with multiple viruses. The most frequent combination was rotavirus and norovirus (27.8%), these infections followed a winter-spring seasonality akin to rotavirus. Children with multivirus infections exhibited higher immunodeficiency (OR 2.06) rates, but lower food allergy (OR 0.45) and prematurity rates (OR 0.55) compared to single infections. Greater disease severity, evaluated by the Vesikari score, was observed in multivirus episodes (p < 0.001, OR 1.12). Multivirus infections accounted for 13.1% of symptomatic cases in hospitalized young children. Despite vaccination efforts, rotavirus remained prominent, frequently in co-infections with norovirus. Overall, multivirus infections were linked to more severe diseases than single virus cases.
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Affiliation(s)
- Guy Hazan
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Pulmonary Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yoav Goldstein
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - David Greenberg
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Firas Khalde
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Rofaida Mahajna
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Ayelet Keren-Naos
- Clinical Virology Laboratory, Soroka University Medical Center, Beer Sheva, Israel
| | - Eli Hershkovitz
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yaniv Faingelernt
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Gastroenterology Hepatology and Nutrition Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Noga Givon-Lavi
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Dana Danino
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
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37
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Giri S, Chhabra P, Kulkarni R, Reju S, Sabapathy SK, Selvarajan S, Varghese T, Kalaivanan M, Dorairaj P, Kalrao V, Mankar S, Sangamnerkar M, Purushothaman GKC, Srikanth P, Kang G, Vinjé J. Hospital-based norovirus surveillance in children <5 years of age from 2017 to 2019 in India. J Med Virol 2024; 96:e29384. [PMID: 38235830 PMCID: PMC10875411 DOI: 10.1002/jmv.29384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
After the introduction of the rotavirus vaccine into the Universal Immunization Program in India in 2016, relatively few studies have assessed the prevalence and epidemiological patterns of acute gastroenteritis (AGE) among hospitalized children ≤5 years of age. We used a uniform protocol to recruit children with AGE as well as standardized testing and typing protocols. Stool specimens from children with AGE younger than 5 years of age admitted to six hospitals in three cities in India were collected from January 2017 through December 2019. Norovirus was detected by real-time reverse transcription-polymerase chain reaction (RT-qPCR) followed by typing positive specimens by conventional RT-PCR and Sanger sequencing. Norovirus was detected in 322 (14.8%) of 2182 specimens with the highest rate in 2018 (17.6%, 146/829), followed by 2019 (14.4%, 122/849) and 2017 (10.7%, 54/504). Rotavirus vaccine status was known for 91.6% of the children of which 70.4% were vaccinated and 29.6% not. Norovirus positivity in rotavirus-vaccinated children was 16.3% and 12% in unvaccinated children. GII.4 Sydney[P16] (39.3%), GII.4 Sydney[P31] (18.7%), GII.2[P16] (10%), GI.3[P13] (6.8%), GII.3[P16] (5.9%), and GII.13[P16] (5%) accounted for 85.8% (188/219) of the typed strains. Our data highlight the importance of norovirus in Indian children hospitalized with AGE.
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Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Preeti Chhabra
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ruta Kulkarni
- Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth, Pune, India
| | - Sudhabharathi Reju
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Chennai, India
| | - Satheesh Kumar Sabapathy
- Indian Council of Medical Research (ICMR)-National Institute of Epidemiology (NIE), Chennai, India
| | - Sribal Selvarajan
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Chennai, India
| | - Tintu Varghese
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Vijay Kalrao
- Bharati Hospital, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | | | | | | | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Chennai, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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38
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Chhabra P, Tully DC, Mans J, Niendorf S, Barclay L, Cannon JL, Montmayeur AM, Pan CY, Page N, Williams R, Tutill H, Roy S, Celma C, Beard S, Mallory ML, Manouana GP, Velavan TP, Adegnika AA, Kremsner PG, Lindesmith LC, Hué S, Baric RS, Breuer J, Vinjé J. Emergence of Novel Norovirus GII.4 Variant. Emerg Infect Dis 2024; 30:163-167. [PMID: 38063078 PMCID: PMC10756382 DOI: 10.3201/eid3001.231003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
We detected a novel GII.4 variant with an amino acid insertion at the start of epitope A in viral protein 1 of noroviruses from the United States, Gabon, South Africa, and the United Kingdom collected during 2017-2022. Early identification of GII.4 variants is crucial for assessing pandemic potential and informing vaccine development.
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Affiliation(s)
| | | | - Janet Mans
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Sandra Niendorf
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Leslie Barclay
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Jennifer L. Cannon
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Anna M. Montmayeur
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Chao-Yang Pan
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Nicola Page
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Rachel Williams
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Helena Tutill
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Sunando Roy
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Cristina Celma
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Stuart Beard
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Michael L. Mallory
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Gédéon Prince Manouana
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Thirumalaisamy P. Velavan
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Ayola Akim Adegnika
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Peter G. Kremsner
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Lisa C. Lindesmith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Stéphane Hué
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Ralph S. Baric
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Judith Breuer
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P. Chhabra, L. Barclay, J.L. Cannon, A.M. Montmayeur, J. Vinjé)
- London School of Hygiene & Tropical Medicine, London, UK (D.C. Tully, S. Hué)
- University of Pretoria, Pretoria, South Africa (J. Mans, N. Page)
- Robert Koch Institut, Berlin, Germany (S. Niendorf)
- California Department of Public Health, Richmond, California, USA (C.-Y. Pan)
- National Institute for Communicable Diseases, Sandringham, South Africa (N. Page)
- UCL Great Ormond Street Institute of Child Health, London (R. Williams, H. Tutill, S. Roy, J. Breuer)
- UK Health Security Agency, London (C. Celma, S. Beard)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.L. Mallory, L.C. Lindesmith, R.S. Baric)
- Universitätsklinikum Tübingen, Tübingen, Germany (G.P. Manouana, T.P. Velavan, A.A. Adegnika)
- Centre de Recherches Médicales de Lambaréné, Lambarene, Gabon (G.P. Manouana, A.A. Adegnika, P.G. Kremsner)
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam (T.P. Velavan)
- Duy Tan University, Da Nang, Vietnam (T.P. Velavan)
- German Center for Infection Research, Tübingen (A.A. Adegnika)
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Toh JYL, Zwe YH, Tan MTH, Gong Z, Li D. Sequential infection of human norovirus and Salmonella enterica resulted in higher mortality and ACOD1/IRG1 upregulation in zebrafish larvae. Microbes Infect 2024; 26:105229. [PMID: 37739029 DOI: 10.1016/j.micinf.2023.105229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Human norovirus (HNoVs) and Salmonella are both very important foodborne pathogens with mixed infection of HNoV and Salmonella reported clinically. With the use of model organism zebrafish (Danio rerio), it was observed that the sequential infection of HNoVs and Salmonella caused lower survival rates (12.5 ± 4.2%) than the single-pathogen infection by Salmonella (31.6 ± 7.3%, P < 0.05) or HNoVs (no mortality observed). Gene expression study with the use of RT-PCR and global transcriptomic analysis revealed that the mortality of zebrafish larvae was very likely due to the harmful inflammatory responses. Specifically, it was noted that the genes encoding aconitate decarboxylase 1 (ACOD1), also known as immunoresponsive gene 1 (IRG1), were significantly upregulated in the sequentially infected zebrafish larvae. The expression of acod1 could lead to mitochondrial reactive oxygen species (ROS) production. The ROS levels were indeed higher in sequentially infected zebrafish larvae than the single-pathogen infected ones (P < 0.05). An immersion treatment of glutathione or citraconate did not affect the microbial loads of HNoVs and Salmonella but significantly reduced the ROS levels and protected the zebrafish larvae by inducing higher survival rates in the sequentially infected zebrafish larvae (P < 0.05). Taken together, this study accumulated new knowledge over the function of ACOD1/IRG1 pathway in infectious diseases, and proposed possible treatment strategies accordingly.
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Affiliation(s)
- Jillinda Yi Ling Toh
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore
| | - Ye Htut Zwe
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore
| | - Malcolm Turk Hsern Tan
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Dan Li
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore.
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Chuchaona W, Vongpunsawad S, Lawtongkum W, Thepnarong N, Poovorawan Y. Acute Gastroenteritis Associated with Norovirus GII.8[P8], Thailand, 2023. Emerg Infect Dis 2024; 30:194-197. [PMID: 38147526 PMCID: PMC10756372 DOI: 10.3201/eid3001.231264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Acute gastroenteritis associated with human norovirus infection was reported in Phuket, Thailand, in June 2023. We amplified GII.8[P8] from the outbreak stool specimens. Retrospective sample analysis identified infrequent GII.8[P8] in the country beginning in 2018. In all, the 10 whole-genome GII.8[P8] sequences from Thailand we examined had no evidence of genotypic recombination.
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Yu JR, Xie DJ, Li JH, Koroma MM, Wang L, Wang Y, Jing DN, Xu JY, Yu JX, Du HS, Zhou FY, Liang ZY, Zhang XF, Dai YC. Serological surveillance of GI norovirus reveals persistence of blockade antibody in a Jidong community-based prospective cohort, 2014-2018. Front Cell Infect Microbiol 2023; 13:1258550. [PMID: 38188632 PMCID: PMC10766831 DOI: 10.3389/fcimb.2023.1258550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Herd immunity against norovirus (NoV) is poorly understood in terms of its serological properties and vaccine designs. The precise neutralizing serological features of genotype I (GI) NoV have not been studied. Methods To expand insights on vaccine design and herd immunity of NoVs, seroprevalence and seroincidence of NoV genotypes GI.2, GI.3, and GI.9 were determined using blockade antibodies based on a 5-year longitudinal serosurveillance among 449 residents in Jidong community. Results Correlation between human histo-blood group antigens (HBGAs) and GI NoV, and dynamic and persistency of antibodies were also analyzed. Seroprevalence of GI.2, GI.3, and GI.9 NoV were 15.1%-18.0%, 35.0%-38.8%, and 17.6%-22.0%; seroincidences were 10.0, 21.0, and 11.0 per 100.0 person-year from 2014 to 2018, respectively. Blockade antibodies positive to GI.2 and GI.3 NoV were significantly associated with HBGA phenotypes, including blood types A, B (excluding GI.3), and O+; Lewis phenotypes Leb+/Ley+ and Lea+b+/Lex+y+; and secretors. The overall decay rate of anti-GI.2 antibody was -5.9%/year (95% CI: -7.1% to -4.8%/year), which was significantly faster than that of GI.3 [-3.6%/year (95% CI: -4.6% to -2.6%/year)] and GI.9 strains [-4.0%/year (95% CI: -4.7% to -3.3%/year)]. The duration of anti-GI.2, GI.3, and GI.9 NoV antibodies estimated by generalized linear model (GLM) was approximately 2.3, 4.2, and 4.8 years, respectively. Discussion In conclusion, enhanced community surveillance of GI NoV is needed, and even one-shot vaccine may provide coast-efficient health benefits against GI NoV infection.
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Affiliation(s)
- Jing-Rong Yu
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Department of Public Health, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Dong-Jie Xie
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jia-Heng Li
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Mark Momoh Koroma
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lu Wang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yu Wang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Duo-Na Jing
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jia-Yi Xu
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jun-Xuan Yu
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hui-Sha Du
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fei-Yuan Zhou
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zhi-Yan Liang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xu-Fu Zhang
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Ying-Chun Dai
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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Li T, Peng J, Li Q, Li B, Yuan Y, Yang C, Yang D, Tang W, Qi L. Investigation of two norovirus outbreaks linked to drinking water contaminated with multiple GII strains in a rural county-Chongqing, China, 2021. Front Public Health 2023; 11:1259584. [PMID: 38162601 PMCID: PMC10756231 DOI: 10.3389/fpubh.2023.1259584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Backgrounds Norovirus is leading cause of non-bacterial gastroenteritis outbreaks globally, characterized by different strains prevalent in different countries and regions. Methods Cases were defined as individuals experiencing diarrhea ≥3 times/24 h, and/or vomiting ≥2 times/24 h in two villages between January 28 and February 9, 2021. Investigations were conducted to identify causes. Cases were interviewed using a standardized in-person form to collect data on potential risk factors. A retrospective cohort study was conducted to investigate the role of the spring water supply as the outbreak source. Residents from neighboring villages with different water sources served as the unexposed population. Stool specimens, rectal swabs, and water samples were tested using quantitative real-time Polymerase Chain Reaction, with subsequent sequencing performed on pathogen-positive specimens. Results Village-specific attack rates were 21.93% (123/561) and 26.99% (88/326), respectively. Evidence from both epidemiological and laboratory tests was consistent. Drinking spring water was statistically associated with the two outbreaks (RR = 41.8 and 79.2, respectively). In both outbreaks, stool specimens, rectal swabs, and water samples tested positive for norovirus. Specifically, GII.2 (P16) and GII.17 (P17) were identified in outbreak A, and GII.4 Sydney (P16) and GII.1 (P16) in outbreak B. Conclusion These two independent gastroenteritis outbreaks share similarities, both being linked to norovirus GII strains. The contaminated spring drinking water was identified as the probable source and was promptly closed and subjected to disinfection procedures. These findings reinforce the importance of implementing sanitation and environmental disinfection measures in rural areas, especially during the periods of increased rainfall.
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Affiliation(s)
- Tingting Li
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Jingyao Peng
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Qin Li
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Baisong Li
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Yi Yuan
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Chuan Yang
- Xiushan County Center for Disease Control and Prevention, Chongqing, China
| | - Di Yang
- Xiushan County Center for Disease Control and Prevention, Chongqing, China
| | - Wenge Tang
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
| | - Li Qi
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, China
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing, China
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43
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Treagus S, Lowther J, Longdon B, Gaze W, Baker-Austin C, Ryder D, Batista FM. Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing. Food Environ Virol 2023; 15:292-306. [PMID: 37910379 PMCID: PMC7615314 DOI: 10.1007/s12560-023-09569-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV has been reported within wastewater in many countries previously. Here we used amplicon deep sequencing (metabarcoding) to identify norovirus and HEV strains in wastewater samples from England collected in 2019 and 2020. For HEV, we sequenced a fragment of the RNA-dependent RNA polymerase (RdRp) gene targeting genotype three strains. For norovirus, we sequenced the 5' portion of the major capsid protein gene (VP1) of genogroup II strains. Sequencing of the wastewater samples revealed eight different genotypes of norovirus GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.9, GII.13 and GII.17). Genotypes GII.3 and GII.4 were the most commonly found. The HEV metabarcoding assay was able to identify HEV genotype 3 strains in some samples with a very low viral concentration determined by RT-qPCR. Analysis showed that most HEV strains found in influent wastewater were typed as G3c and G3e and were likely to have originated from humans or swine. However, the small size of the HEV nested PCR amplicon could cause issues with typing, and so this method is more appropriate for samples with high CTs where methods targeting longer genomic regions are unlikely to be successful. This is the first report of HEV RNA in wastewater in England. This study demonstrates the utility of wastewater sequencing and the need for wider surveillance of norovirus and HEV within host species and environments.
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Affiliation(s)
- Samantha Treagus
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall, UK.
- UK Health Security Agency, Manor Farm Road, Porton Down, SP4 0JG, Wiltshire, UK.
| | - James Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall, UK
| | - William Gaze
- Faculty of Health and Life Sciences, University of Exeter Medical School, Penryn Campus, Cornwall, UK
| | | | - David Ryder
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
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Li C, Song S, Huang X, Liu X, Lv H, Shen Y, Wei X, Zhang W, Xu Y. Molecular epidemiology and genetic diversity of norovirus among hospitalized patients with acute gastroenteritis in Shandong, China, 2016-2018. J Med Virol 2023; 95:e29339. [PMID: 38130177 DOI: 10.1002/jmv.29339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Norovirus (NoV) infection is a leading cause of acute gastroenteritis (AGE) for people of all ages. Here, we reported the molecular epidemiology and genetic diversity of NoVs among hospitalized patients with AGE between 2016 and 2018 in Shandong Province, China. Two thousand sixty-nine AGE patients from sentinel hospitals were enrolled. The stool samples were collected and tested for NoVs by real-time RT-PCR. The RNA-dependent RNA polymerase (RdRp) and capsid gene of 163 strains were amplified and sequenced for genotyping. Phylogenetic analyses and genomic characterization were conducted with the VP1 and RdRp region of the full genome sequences. Four hundred seventy two (21.76%) samples were NoV-positive. The positive rate in 2016 was higher than those of 2017 and 2018. We observed diverse NoV genotypes. GII.2[P16] emerged in January 2017 and became the dominant genotype between May and June 2017. Phylogenetic analyses showed that our GII.2[P16] genomes clustered in the SC1 in VP1 region, while they belonged to the Emerging GⅡ.P16 (2015-2017) clade in RdRp region. Our GⅡ.4 strains displayed two amino acid mutations, positions R297H and D372N, in epitope A of the VP1 region. Our study highlighted that NoV is an important pathogen of viral AGE in Shandong and, therefore, it is necessary to strengthen its surveillance.
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Affiliation(s)
- Chao Li
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shaoxia Song
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Infectious Disease Prevention and Control, Preventive healthcare Research Institute of Shandong University, Jinan, China
| | - Xianglin Huang
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaolin Liu
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Infectious Disease Prevention and Control, Preventive healthcare Research Institute of Shandong University, Jinan, China
| | - Hui Lv
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Infectious Disease Prevention and Control, Preventive healthcare Research Institute of Shandong University, Jinan, China
| | - Yuanyuan Shen
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xuemin Wei
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenqiang Zhang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Infectious Disease Prevention and Control, Preventive healthcare Research Institute of Shandong University, Jinan, China
| | - Yifei Xu
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, China
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Hoque SA, Saito H, Akino W, Kotaki T, Okitsu S, Onda Y, Kobayashi T, Hossian T, Khamrin P, Motomura K, Maneekarn N, Hayakawa S, Ushijima H. The Emergence and Widespread Circulation of Enteric Viruses Throughout the COVID-19 Pandemic: A Wastewater-Based Evidence. Food Environ Virol 2023; 15:342-354. [PMID: 37898959 DOI: 10.1007/s12560-023-09566-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/31/2023]
Abstract
Growing evidence shed light on the importance of wastewater-based epidemiology (WBE) during the pandemic, when the patients rarely visited the clinics despite the fact that the infections were still prevalent in the community as before. The abundance of infections in the community poses a constant threat of the emergence of new epidemic strains. Herein, we investigated enteric viruses in raw sewage water (SW) from Japan's Tohoku region and compared them to those from the Kansai region to better understand the circulating strains and their distribution across communities during the COVID-19 pandemic. Raw SW was collected between 2019 and 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major AGE viruses by RT-PCR. Sequence-based analyses were used to assess genotypes and evolutionary relationships. The most commonly detected enteric virus was rotavirus A (RVA) at 63.8%, followed by astrovirus (AstV) at 61.1%, norovirus (NoV) GII and adenovirus (AdV) at 33.3%, sapovirus (SV) at 25.0%, enterovirus (EV) at 19.4%, and NoV GI at 13.9%. The highest prevalence (46.0%) was found in the spring. Importantly, enteric viruses did not decline during the pandemic. Rather, several strains like NoV GII.2, DS-1-like human G3 (equine) RVA, MLB1 AstV, and different F41 HAdV emerged throughout the pandemic and spread widely over the Tohoku and Kansai regions. Tohoku's detection rate remained lower than that of the Kansai area (36 vs 58%). This study provides evidence for the emergence and spread of enteric viruses during the pandemic.
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Affiliation(s)
- Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Hiroyuki Saito
- Department of Microbiology, Akita Prefectual Research Center for Public Health and Environment, Akita, Japan
| | - Wakako Akino
- Department of Microbiology, Akita Prefectual Research Center for Public Health and Environment, Akita, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Yuko Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tania Hossian
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
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Srivastava P, Prasad D. Human Norovirus Detection: How Much Are We Prepared? Foodborne Pathog Dis 2023; 20:531-544. [PMID: 37792418 DOI: 10.1089/fpd.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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Sá R, Roque J, Marques Mendes P, Gonçalves I, Sousa J, Matos C, Júnior Á, Coelho A, Belo Correia C, Manageiro V, Minetti C, de Sousa R, Horta Correia F. Prevention, protocols, and lab capacity: lessons from a norovirus outbreak in the Algarve. Arch Virol 2023; 168:299. [PMID: 38015274 DOI: 10.1007/s00705-023-05926-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
This brief report presents the findings of an epidemiological investigation into a large-scale outbreak of norovirus gastroenteritis that occurred in a hotel in Algarve, Portugal, in August 2022. A total of 244 cases were reported, primarily affecting Portuguese families, with the parents aged 40-50 years and the children aged 0-19 years. Reported symptoms included vomiting, nausea, abdominal pain, and diarrhoea. Norovirus genotype GI.3 [P3] was detected in stool samples from eight probable cases, while food samples tested negative for norovirus and common pathogenic bacteria. The investigation data collected suggest that the source of the outbreak was likely in the hotel's common areas, with subsequent person-to-person transmission in other areas. The final report emphasizes the importance of improving outbreak prevention and control measures, including the development of a foodborne outbreak investigation protocol, the establishment of an outbreak response team, and the enhancement of regional laboratory capacity.
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Affiliation(s)
- Regina Sá
- Public Health Unit, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Faro, Portugal.
| | - Joana Roque
- Public Health Unit, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Faro, Portugal
| | - Pedro Marques Mendes
- Public Health Unit, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Faro, Portugal
| | - Inês Gonçalves
- Public Health Unit, Algarve Barlavento Health Centre Grouping, Regional Health Administration of Algarve, Portimão, Portugal
| | - Judite Sousa
- Personalized Health Care Unit (UCSP) Albufeira, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Albufeira, Portugal
| | - Cátia Matos
- Personalized Health Care Unit (UCSP) Albufeira, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Albufeira, Portugal
| | | | - Anabela Coelho
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Cristina Belo Correia
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Vera Manageiro
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Corrado Minetti
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Rita de Sousa
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Filomena Horta Correia
- Public Health Unit, Algarve Central Health Centre Grouping, Regional Health Administration of Algarve, Faro, Portugal
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Bonura F, Filizzolo C, Pizzo M, Sanfilippo GL, Cacioppo F, Palazzotto E, Di Bernardo F, Collura A, Martella V, De Grazia S, Giammanco GM. Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology. Viruses 2023; 15:2303. [PMID: 38140544 PMCID: PMC10747129 DOI: 10.3390/v15122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Chiara Filizzolo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Mariangela Pizzo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giuseppa L. Sanfilippo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Federica Cacioppo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Emilia Palazzotto
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Antonina Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Vito Martella
- Dipartimento di Sanità Pubblica e Zootecnia, Università Aldo Moro di Bari, 70010 Valenzano, Italy;
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giovanni M. Giammanco
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
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49
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Widström J, Andersson ME, Westin J, Wahllöf M, Lindh M, Rydell GE. Complex norovirus transmission dynamics at hospital wards revealed by deep sequencing. J Clin Microbiol 2023; 61:e0060823. [PMID: 37889018 PMCID: PMC10662361 DOI: 10.1128/jcm.00608-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/28/2023] Open
Abstract
Detailed knowledge regarding norovirus transmission within hospitals is limited. We investigated a norovirus hospital outbreak affecting 65 patients at five different wards. PCR showed that 61 (94%) of the patients were infected with genotype II.4 strains. Successful Ion Torrent deep sequencing of GII.4 positive samples from 59 patients followed by phylogenetic analysis revealed that all sequences but two clustered into four distinct clades. Two of the clades belonged to GII.4 Sydney 2012, while the other two belonged to GII.4 New Orleans 2009. One of the clades was predominant at two wards, while two clades were predominant at one ward each. The fourth clade was found in sporadic cases at several wards. Thus, at four out of five wards, variants from one clade were predominant. At one ward, a single clade accounted for all cases, while at three wards the predominant clade accounted for 60%-71% of cases. Analysis of quasispecies variation identified positions that could further discriminate between variants from separate wards. The results illustrate a complex transmission of healthcare-associated norovirus infections and show that sequencing can be used to discriminate between related and unrelated cases.
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Affiliation(s)
- Julia Widström
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria E. Andersson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johan Westin
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martina Wahllöf
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gustaf E. Rydell
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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50
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Chen Q, Ma J, Gao L, Xian R, Wei K, Shi A, Yuan F, Cao M, Zhao Y, Jin M, Kuai W. Determination and analysis of whole genome sequence of recombinant GII.6[P7] norovirus in Ningxia, China. Infect Genet Evol 2023; 115:105499. [PMID: 37734510 DOI: 10.1016/j.meegid.2023.105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
While the GII.4 norovirus was the predominant genotype, non-GII.4 genotype was increasingly focused since the non-GII.4 genotype caused regional epidemics. In this study, the detection rate was16.51% (183/1108) in Ningxia from January to December 2020. Among identified genotypes, GII.4[P31] and GII.4[P16] were the dominant genotypes (n = 20 and 18, respectively) while GII.6[P7] was the main type (n = 6) in non-GII.4 strains which was mainly detected in from May to July. The whole genome sequences of the norovirus diarrhea samples identified as GII.6 [P7] with Ct ≤ 30 collected in 2020 were determined. In this study, the complete genome sequences of norovirus strains PL20-044 and QTX20-071 were identified and analyzed phylogenetically. Phylogenetic analysis of the ORF1and ORF2 regions showed that these strains evolved from the GII·P7-GII.6 strains detected in recent years from different country. The results showed that PL20-044 had intra-type recombination with GII·P7-GII.6c and GII·P7-GII.6a, while QTX20-071 had intre-type recombination within GII·P7-GII.6a. The evolutionary rates of the RdRp gene region of the GII·P7 genotype and the VP1 gene region of the GII.6 genotype were 2.91 × 10-3 (95%HPDs2.32-3.51 × 10-3) and 2.61 × 10-3 (95%HPDs2.14-3.11 × 10-3) substitutions/site/year, respectively. Comparative analysis of the amino acid mutation sites in VP1 with the GII·P7-GII.6a strains before 1997, the later detected strains have changed in aa131 and aa354. Moreover, PL20-044 strains showed special mutations at aa316 and aa395. These results help to understand the norovirus genotype circulating in the human population in Ningxia, and discover the evolutionary characteristics of the GII·P7-GII.6 strain.
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Affiliation(s)
- Qian Chen
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Jiangtao Ma
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China.
| | - Lei Gao
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Ran Xian
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Kaixin Wei
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Anqi Shi
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Fang Yuan
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
| | - Min Cao
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
| | - Yu Zhao
- School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Miao Jin
- National Institute for Viral Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102211, China
| | - Wenhe Kuai
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
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