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Cantelli CP, Tavares GCL, Sarmento SK, Burlandy FM, Fumian TM, Maranhão AG, da Silva EDSRF, Horta MAP, Miagostovich MP, Yang Z, Leite JPG. Assessment of Gastroenteric Viruses in Marketed Bivalve Mollusks in the Tourist Cities of Rio de Janeiro, Brazil, 2022. Viruses 2024; 16:317. [PMID: 38543684 PMCID: PMC10974528 DOI: 10.3390/v16030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 05/23/2024] Open
Abstract
This study investigated the prevalence and genetic diversity of gastroenteric viruses in mussels and oysters in Rio de Janeiro, Brazil. One hundred and thirty-four marketed bivalve samples were obtained between January and December 2022. The viral analysis was performed according to ISO/TS 15216, and the screening revealed the detection of norovirus GII/GI (40.3%), sapovirus (SaV; 12.7%), human mastadenovirus (7.5%), and rotavirus A (RVA; 5.9%). In total, 44.8% (60) of shellfish samples tested positive for one or more viruses, 46.7% (28/60) of the positive samples tested positive for a single viral agent, 26.7% (16) tested positive for two viral agents, 8.3% (5) for three viral agents, and 13.3% (8) for four viral agents. Additionally, three mussel samples were contaminated with the five investigated viruses (5%, 3/60). Norovirus GII showed the highest mean viral load (3.4 × 105 GC/g), followed by SaV (1.4 × 104 GC/g), RVA (1.1 × 104 GC/g), human mastadenovirus (3.9 × 103 GC/g), and norovirus GI (6.7 × 102 GC/g). Molecular characterization revealed that the recovered norovirus strains belonged to genotypes GII.2, GII.6, GII.9, GII.17, and GII.27; SaV belonged to genotypes GI.1 and GIV.1; RVA to genotypes G6, G8, P[8]-III, and human mastadenovirus to types F40 and F41. The GII.27 norovirus characterized in this study is the only strain of this genotype reported in Brazil. This study highlights the dissemination and diversity of gastroenteric viruses present in commercialized bivalves in a touristic area, indicating the potential risk to human health and the contribution of bivalves in the propagation of emerging pathogens.
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Affiliation(s)
- Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | - Sylvia Kahwage Sarmento
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | - Adriana Gonçalves Maranhão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | | | | | - Zhihui Yang
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20723, USA
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
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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 AND ENVIRONMENTAL VIROLOGY 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] [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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Bai GH, Tsai MC, Lin SC, Hsu YH, Chen SY. Unraveling the interplay between norovirus infection, gut microbiota, and novel antiviral approaches: a comprehensive review. Front Microbiol 2023; 14:1212582. [PMID: 37485533 PMCID: PMC10359435 DOI: 10.3389/fmicb.2023.1212582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Norovirus infection is a leading cause of acute gastroenteritis worldwide and can also cause harmful chronic infections in individuals with weakened immune systems. The role of the gut microbiota in the interactions between the host and noroviruses has been extensively studied. While most past studies were conducted in vitro or focused on murine noroviruses, recent research has expanded to human noroviruses using in vivo or ex vivo human intestinal enteroids culture studies. The gut microbiota has been observed to have both promoting and inhibiting effects on human noroviruses. Understanding the interaction between noroviruses and the gut microbiota or probiotics is crucial for studying the pathogenesis of norovirus infection and its potential implications, including probiotics and vaccines for infection control. Recently, several clinical trials of probiotics and norovirus vaccines have also been published. Therefore, in this review, we discuss the current understanding and recent updates on the interactions between noroviruses and gut microbiota, including the impact of norovirus on the microbiota profile, pro-viral and antiviral effects of microbiota on norovirus infection, the use of probiotics for treating norovirus infections, and human norovirus vaccine development.
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Affiliation(s)
- Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Chen Tsai
- Department of General Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Allergy, Asthma and Immunology, Shuang Ho Hospital, New Taipei, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, New Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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Li J, Zhang L, Zou W, Yang Z, Zhan J, Cheng J. Epidemiology and genetic diversity of norovirus GII genogroups among children in Hubei, China, 2017-2019. Virol Sin 2023; 38:351-362. [PMID: 37030436 PMCID: PMC10311278 DOI: 10.1016/j.virs.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 04/03/2023] [Indexed: 04/10/2023] Open
Abstract
Norovirus (NoV) is an important cause of viral acute gastroenteritis (AGE). To gain insights into the epidemiological characteristics and genetic diversity of NoV among children in Hubei, 1216 stool samples from children (≤ 5 years) obtained under AGE surveillance from January 2017 to December 2019 were analyzed. The results showed that NoV was responsible for 14.64% of AGE cases, with the highest detection rate in children aged 7-12 months (19.76%). Statistically significant differences were found between male and female infection rates (χ2 = 8.108, P = 0.004). Genetic analysis of RdRp and VP1 sequences showed that NoV GII genotypes were GII.4 Sydney [P31] (34.35%), GII.3 [P12] (25.95%), GII.2 [P16] (22.90%), GII.4 Sydney [P16] (12.98%), GII.17 [P17] (2.29%), GII.6 [P7] and GII.3 [P16] (each at 0.76%). GII.17 [P17] variants were divided into the Kawasaki323-like lineage and the Kawasaki308-like lineage. A unique recombination event was detected between strains of GII.4 Sydney 2012 and GII.4 Sydney 2016. Significantly, all GII.P16 sequences associated with GII.4/GII.2 obtained in Hubei were correlated with novel GII.2 [P16] variants that re-emerged in Germany in 2016. Antigenic site analysis of complete VP1 sequences from all GII.4 variants from Hubei identified notable variable residues of antibody epitopes. Genotyping under continuous AGE surveillance and observation of the antigenic sites of VP1 are important monitoring strategies for emerging NoV strains.
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Affiliation(s)
- Jing Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Lingyao Zhang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Wenjing Zou
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Zhaohui Yang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Jianbo Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China.
| | - Jing Cheng
- Wuhan University of Science and Technology, Wuhan, 430065, China.
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Wang L, Ji L, Li H, Xu D, Chen L, Zhang P, Wang W. Early evolution and transmission of GII.P16-GII.2 norovirus in China. G3 (BETHESDA, MD.) 2022; 12:jkac250. [PMID: 36124949 PMCID: PMC9635637 DOI: 10.1093/g3journal/jkac250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Norovirus is the most common cause of acute gastroenteritis worldwide. During 2016-2017, a novel recombinant GII.P16-GII.2 genotype of norovirus suddenly appeared and over the next several years became the predominant strain in both China and worldwide. To better understand the origin and diffusion of the GII.P16-GII.2 genotype in China, we conducted molecular evolutionary analyses, including phylodynamics and phylogeography. Moreover, to trace person-to-person transmission of GII.P16-GII.2 norovirus, we applied the novel method, TransPhylo, to a historical phylogeny using sequences obtained from a publicly available database. A time-scaled phylogenetic tree indicated that the time to the most recent common ancestor of the GII.P16-GII.2 major capsid protein (VP1) gene diverged from the GII.P2-GII.2 VP1 gene at 2,001.03 with an evolutionary rate of 3.32 × 10-3 substitutions/site/year. The time to the most recent common ancestor of the GII.P16-GII.2 RNA-dependent RNA polymerase region diverged from the GII.P16-GII.4 RNA-dependent RNA polymerase region at 2,013.28 with an evolutionary rate of 9.44 × 10-3 substitutions/site/year. Of these 2 genomic regions, VP1 gene sequence variations were the most influenced by selective pressure. A phylogeographic analysis showed that GII.P16-GII.2 strains in China communicated most frequently with those in the United States, Australia, Thailand, and Russia, suggesting import from Australia to Taiwan and from the United States to Guangdong. TransPhylo analyses indicated that the basic reproductive number (R0) and sampling proportion (pi) of GII.P16-GII.2 norovirus were 1.99 (95% confidence interval: 1.58-2.44) and 0.76 (95% confidence interval: 0.63-0.88), respectively. Strains from the United States and Australia were responsible for large spread during the evolution and transmission of the virus. Coastal cities and places with high population densities should be closely monitored for norovirus.
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Affiliation(s)
| | | | - Hao Li
- School of Public Health, Fudan University, Shanghai 200437, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou 313000, China
| | - Peng Zhang
- Corresponding author: Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou 313000, Zhejiang, China. (PZ)
| | - Weibing Wang
- Corresponding author: School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China. (WW)
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The VP2 protein exhibits cross-interaction to the VP1 protein in norovirus GII.17. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105265. [PMID: 35272046 DOI: 10.1016/j.meegid.2022.105265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis worldwide. Like the major capsid protein (VP1), the minor capsid protein (VP2) also contains a hypervariable domain. Generally, a hypervariable domain is functionally driven. However, many functions of VP2 remain unknown and worth exploring. Without sufficient sequences and an available crystallographic model, it is difficult to explore VP2's mysteries. As a helper of stabilizing and coordinating the formation of virus-like particles (VLPs), we asked whether VP2 interacted with the major capsid protein (VP1) in GII.17 and if so, what the key interaction residues were. Here, we reported cross-interaction among four strains represented four clusters of GII.17, and the VP1 interaction domain of VP2 (174-179aa) was found. However, the VP1 interaction domain of VP2 was not universal in different clusters of GII.17. VP2 might evolve in a different pattern from VP1. Additionally, in contrast to previous reports, we found that VP2 localized in the cytoplasm. More possibilities of VP2 should be further explored.
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Dong L, Jia T, Yu Y, Wang Y. Updating a New Semi-nested PCR Primer Pair for the Specific Detection of GII Norovirus in Oysters. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:149-156. [PMID: 35099705 PMCID: PMC8802746 DOI: 10.1007/s12560-022-09511-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Oysters are major transmission vectors of noroviruses (NoVs) in the environment. Outbreaks of NoVs are often associated with the consumption of NoV-contaminated oysters. Laboratory confirmation of suspected oyster samples is a critical step in the surveillance and control of NoVs. Because of non-specific amplification, false-positive results are frequently obtained by semi-nested RT-PCR with the presently widely used primer set (G2SKF/G2SKR). Here, a novel universal PCR primer set N (NG2OF/NG2OR) specific for genogroup II (GII) NoVs was designed based on all GII NoV sequences available in public databases. Specific products were obtained with the primer set N when the NoV-positive oysters, spiked with each of five representative genotypes of GII NoVs (GII.17, GII.13, GII.4, GII.3, and GII.12), were subjected to analyzing. No products were detected with the primer set N for the NoV-negative oysters, while the primer set C gave various non-specific bands. Twenty-three out of 156 fresh oyster samples were NoV-positive with both the primer set N and the classic primer set, while eight were NoV-positive solely with the primer set N. Compared with the classic primer set, the newly designed primer set N had a higher detection rate and improved specificity for GII NoVs in oyster samples. These results show that the novel PCR primer pair is specific and applicable for the detection of GII NoVs in oysters.
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Affiliation(s)
- Lei Dong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Tianhui Jia
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.
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Raymond P, Paul S, Perron A, Bellehumeur C, Larocque É, Charest H. Detection and Sequencing of Multiple Human Norovirus Genotypes from Imported Frozen Raspberries Linked to Outbreaks in the Province of Quebec, Canada, in 2017. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:40-58. [PMID: 35066807 PMCID: PMC8881426 DOI: 10.1007/s12560-021-09507-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Human noroviruses are among the main causes of acute gastroenteritis worldwide. Frozen raspberries have been linked to several norovirus food-related outbreaks. However, the extraction of norovirus RNA from frozen raspberries remains challenging. Recovery yields are low and PCR inhibitors limit the sensitivity of the detection methodologies. In 2017, 724 people from various regions of the Province of Quebec, Canada, were infected by noroviruses and the outbreak investigation pointed to frozen raspberries as a putative source. A new magnetic silica bead approach was used for the extraction of viruses from different outbreak samples. The RNA extracts were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and five samples were confirmed positive for norovirus by RT-qPCR amplicon sequencing. A multiplex long-range two-step RT-PCR approach was developed to amplify norovirus ORF2 and ORF3 capsid genes from the positive frozen raspberry RNA extracts and other sequencing strategies were also explored. These capsid genes were sequenced by Next-Generation Sequencing. Phylogenetic analyses confirmed the presence of multiple genotypes (GI.3, GI.6, and GII.17) and intra-genotype variants in some of the frozen raspberry samples. Variants of genotype GI.3 and GI.6 had 100% homology with sequences from patient samples. Similar strains were also reported in previous outbreaks. Confirmation approaches based on sequencing the norovirus capsid genes using Next-Generation Sequencing can be applied at trace level contaminations and could be useful to assess risk and assist in source tracking.
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Affiliation(s)
- Philippe Raymond
- Canadian Food Inspection Agency (CFIA), Saint-Hyacinthe Laboratory - Food Virology, Saint-Hyacinthe, QC, Canada.
| | - Sylvianne Paul
- Canadian Food Inspection Agency (CFIA), Saint-Hyacinthe Laboratory - Food Virology, Saint-Hyacinthe, QC, Canada
| | - André Perron
- Canadian Food Inspection Agency (CFIA), Saint-Hyacinthe Laboratory - Food Virology, Saint-Hyacinthe, QC, Canada
| | - Christian Bellehumeur
- Canadian Food Inspection Agency (CFIA), Saint-Hyacinthe Laboratory - Food Virology, Saint-Hyacinthe, QC, Canada
| | - Émilie Larocque
- Canadian Food Inspection Agency (CFIA), Saint-Hyacinthe Laboratory - Food Virology, Saint-Hyacinthe, QC, Canada
| | - Hugues Charest
- Laboratoire de santé publique du Québec et Université de Montréal, département de microbiologie, infectiologie et immunologie, Montréal, QC, Canada
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Li W, Yan H, Liu B, Tian Y, Chen Y, Jia L, Gao Z, Wang Q. Epidemiological characteristics and genetic diversity of norovirus infections among outpatient children with diarrhea under 5 years of age in Beijing, China, 2011-2018. Gut Pathog 2021; 13:77. [PMID: 34952625 PMCID: PMC8709959 DOI: 10.1186/s13099-021-00473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Human noroviruses are the leading cause of sporadic cases and outbreaks of viral acute gastroenteritis in all age groups worldwide. Methods Epidemiological data and fecal specimens were collected between January 2011 and December 2018 from 4911 children < 5 years of age with diarrhea in three districts of Beijing. From 2011 to 2013, One-Step Reverse Transcription Polymerase Chain Reaction (RT-PCR) was used to detect noroviruses, and from January 2014 to December 2018, norovirus GI and GII were screened using duplex quantitative real-time RT-PCR (qRT-PCR). One-Step RT-PCR and RT-seminested PCR were performed to amplify the RNA-dependent polymerase and capsid genes of noroviruses in positive sample. Amplified products were sequenced directly; norovirus was typed using the online Norovirus Genotyping Tool v2.0 and phylogenetic analyses were conducted using MEGA-X. Results From 2011 to 2018, noroviruses were detected in 16.5% of specimens from children with diarrhea. The highest prevalence was observed in children aged 12 to 23 months (22.4%, 319/1421), followed by children aged 6 to 11 months (17.6%, 253/1441). The highest prevalence of norovirus infections occurred in autumn followed by winter, spring, and summer. From 2011 to 2018, the most prevalent dual types (genotype and polymerase type) were GII.4 Sydney[P31] (51.6%, 239/463), followed by GII.3[P12] (24.0%, 111/463), GII.4 2006b[P4 2006b] (7.3%, 34/463), GII.2[P16] (5.0%, 23/463), GII.17[P17] (2.6%, 12/463) and GII.6[P7] (2.6%, 12/463). GII.4 2006b[P4 2006b] predominated in 2011 and 2012. GII.4 Sydney[P31] predominated from 2013 to 2018. In total, 15 genotypes, 15 P-types and 19 dual types were detected in this study, reflecting the genetic diversity. Conclusions There were significant epidemiological characteristics and genetic diversity among outpatient children with norovirus infections < 5 years of age in Beijing from 2011 to 2018. These characteristics differ from those of norovirus outbreaks in Beijing. The complete genome sequences of each genotype are needed to better understand norovirus evolutionary mechanisms.
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Affiliation(s)
- Weihong Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Baiwei Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yanwei Chen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
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Fang Y, Zhang Y, Wang H, Shi O, Wang W, Hou M, Wang L, Wu J, Zhao Y. Molecular epidemiology of norovirus infections in children with acute gastroenteritis in 2017-2019 in Tianjin, China. J Med Virol 2021; 94:616-624. [PMID: 34528724 PMCID: PMC9292362 DOI: 10.1002/jmv.27340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/12/2021] [Indexed: 12/27/2022]
Abstract
Norovirus (NoV) is the leading cause of acute gastroenteritis (AGE) worldwide. Globally, the GII.4 Sydney 2012 strain has predominated since 2012, although GII.4 variant strains have caused AGE outbreaks in China. Recent patterns of NoV genotype distributions in 6011 children with AGE in Tianjin, China were investigated. NoV was detected using real-time reverse-transcriptase polymerase chain reaction and sequencing of partial sequences of the viral capsid gene. NoV genotypes were determined, and phylogenetic analysis was conducted. Epidemiological and clinical data were compared between children infected with different NoV genotypes. NoV was detected in 27.6% of the specimens tested. GII.4 strains comprised 49.4% infections, followed by GII.3 at 39.9%. Genotypes GII.2, GII.13, GII.17, GII.1, GII.6, and GII.14 were also detected. NoV was detected during most of the year, with a peak season of cases in the winter. Diarrhea, vomiting, fever, abdominal pain, and dehydration were present in patients with NoV infection. The main genotypes were GII.4 and GII.3, with a slight increase in GII.2, beginning in March 2017. Among the GII.4 strains, GII.4 Sydney 2012 was the only epidemic strain in Tianjin. Patients with GII.4 genotypes were more likely to present with diarrhea and vomiting than those with GII.3. Children with GII. Others were prone to suffered from dehydration and abdominal pain than those with GII.3. NoV GII has become the main cause of viral AGE in Tianjin, China. The predominant genotypes of NoV were GII.4 and GII.3. Identification of emerging genotypes is crucial for the prevention and control of NoV-caused AGE.
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Affiliation(s)
- Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatmen, Tianjin, China
| | - Yanzhi Zhang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Hong Wang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Ouyan Shi
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatmen, Tianjin, China
| | - Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatmen, Tianjin, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatmen, Tianjin, China
| | - Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatmen, Tianjin, China
| | - Yu Zhao
- Department of Digestion, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
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11
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Tohma K, Lepore CJ, Martinez M, Degiuseppe JI, Khamrin P, Saito M, Mayta H, Nwaba AUA, Ford-Siltz LA, Green KY, Galeano ME, Zimic M, Stupka JA, Gilman RH, Maneekarn N, Ushijima H, Parra GI. Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints. PLoS Pathog 2021; 17:e1009744. [PMID: 34255807 PMCID: PMC8318288 DOI: 10.1371/journal.ppat.1009744] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/28/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
Norovirus is a major cause of acute gastroenteritis worldwide. Over 30 different genotypes, mostly from genogroup I (GI) and II (GII), have been shown to infect humans. Despite three decades of genome sequencing, our understanding of the role of genomic diversification across continents and time is incomplete. To close the spatiotemporal gap of genomic information of human noroviruses, we conducted a large-scale genome-wide analyses that included the nearly full-length sequencing of 281 archival viruses circulating since the 1970s in over 10 countries from four continents, with a major emphasis on norovirus genotypes that are currently underrepresented in public genome databases. We provided new genome information for 24 distinct genotypes, including the oldest genome information from 12 norovirus genotypes. Analyses of this new genomic information, together with those publicly available, showed that (i) noroviruses evolve at similar rates across genomic regions and genotypes; (ii) emerging viruses evolved from transiently-circulating intermediate viruses; (iii) diversifying selection on the VP1 protein was recorded in genotypes with multiple variants; (iv) non-structural proteins showed a similar branching on their phylogenetic trees; and (v) contrary to the current understanding, there are restrictions on the ability to recombine different genomic regions, which results in co-circulating populations of viruses evolving independently in human communities. This study provides a comprehensive genetic analysis of diverse norovirus genotypes and the role of non-structural proteins on viral diversification, shedding new light on the mechanisms of norovirus evolution and transmission. Norovirus is a highly diverse enteric pathogen. The large genomic database accumulated in the last three decades advanced our understanding of norovirus diversity; however, this information is limited by geographical bias, sporadic times of collection, and missing or incomplete genome sequences. In this multinational collaborative study, we mined archival samples collected since the 1970s and sequenced nearly full-length new genomes from 281 historical noroviruses, including the first full-length genomic sequences for three genotypes. Using this novel dataset, we found evidence for restrictions in the recombination of genetically disparate viruses and that diversifying selection results in new variants with different epidemiological profiles. These new insights on the diversification of noroviruses could provide baseline information for the study of future epidemics and ultimately the prevention of norovirus infections.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Cara J. Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Magaly Martinez
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- IICS, National University of Asuncion, Asuncion, Paraguay
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Amy U. Amanda Nwaba
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Lauren A. Ford-Siltz
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Kim Y. Green
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | | | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Robert H. Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Gabriel I. Parra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- * E-mail:
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12
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Fu J, Ai J, Bao C, Zhang J, Wu Q, Zhu L, Hu J, Xing Z. Evolution of the GII.3[P12] Norovirus from 2010 to 2019 in Jiangsu, China. Gut Pathog 2021; 13:34. [PMID: 34039425 PMCID: PMC8149921 DOI: 10.1186/s13099-021-00430-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/12/2021] [Indexed: 12/28/2022] Open
Abstract
Objectives Norovirus genotype GII.3[P12] strains have been an important pathogen for sporadic gastroenteritis infection. In previous studies of GII.3[P12], the number of specimens and time span are relatively small, which is difficult to truly reflect the infection and evolution of this type of norovirus. Here we report a molecular epidemiological study of the NoVs prevalent in Jiangsu between 2010 and 2019 to investigate the evolution of the GII.3[P12] strains in China. Methods In this study 60 GII.3[P12] norovirus strains were sequenced and analyzed for evolution, recombination, and selection pressure using bioanalysis software. Results The GII.3[P12] strains were continuously detected during the study period, which showed a high constituent ratio in males, in winter and among children aged 0–11 months, respectively. A time-scaled evolutionary tree showed that both GII.P12 RdRp and GII.3 VP1 sequences were grouped into three major clusters (Cluster I–III). Most GII.3[P12] strains were mainly located in sub-cluster (SC) II of Cluster III. A SimPlot analysis identified GII.3[P12] strain to be as an ORF1-intragenic recombinant of GII.4[P12] and GII.3[P21]. The RdRp genes of the GII.3[P12] showed a higher mean substitution rate than those of all GII.P12, while the VP1 genes of the GII.3[P12] showed a lower mean substitution rate than those of all GII.3. Alignment of the GII.3 capsid sequences revealed that three HBGA binding sites of all known GII.3 strains remained conserved, while several amino acid mutations in the predicted antibody binding sites were detected. The mutation at 385 was within predicted antibody binding regions, close to host attachment factor binding sites. Positive and negative selection sites were estimated. Two common positively selected sites (sites 385 and 406) were located on the surface of the protruding domain. Moreover, an amino acid substitution (aa204) was estimated to be near the active site of the RdRp protein. Conclusions We conducted a comprehensive analysis on the epidemic and evolution of GII.3[P12] noroviruses and the results suggested that evolution was possibly driven by intergenic recombination and mutations in some key amino acid sites. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00430-8.
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Affiliation(s)
- Jianguang Fu
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, 22 Hankou Road, Gulou District, Nanjing, 210093, China.,Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Ai
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.
| | - Jun Zhang
- Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Qingbin Wu
- Soochow University Affiliated Children's Hospital, Suzhou, China
| | - Liguo Zhu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jianli Hu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Zheng Xing
- College of Veterinary Medicine, Department of Veterinary Biomedical Sciences, University of Minnesota At Twin Cities, Saint Paul, MN, 55108, USA.
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13
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Lu J, Peng J, Fang L, Zeng L, Lin H, Xiong Q, Liu Z, Jiang H, Zhang C, Yi L, Song T, Ke C, Li C, Ke B, He G, Zhu G, He J, Sun L, Li H, Zheng H. Capturing noroviruses circulating in the population: sewage surveillance in Guangdong, China (2013-2018). WATER RESEARCH 2021; 196:116990. [PMID: 33725645 DOI: 10.1016/j.watres.2021.116990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Noroviruses (NoVs) are the leading cause of acute gastroenteritis (AGE) outbreaks. Since 2014, novel genetic variants of NoV have been continuously identified and have caused a sharp increase in the number of AGE outbreaks. The specific geographical distribution and expanding genetic diversity of NoV has posed a challenge to conventional surveillance. Here, we describe the long-term dynamic correlation between NoV distribution in sewage and in the local population through the molecular surveillance of NoV in Guangdong, 2013-2018. The relative viral loads of the GI and GII genotypes in sewage were calculated through RT-PCR. A high-throughput sequencing method and operational taxonomic unit (OTU) clustering pipeline were developed to illustrate the abundances of different genotypes and genetic variants in sewage. Our results showed that the NoV viral loads and the emergence of new variants in sewage were closely associated with NoV outbreak risks in the population. Compared with the outbreaks surveillance, the dominance of the newly emerged variants, GII.P17-GII.17 and GII.P16-GII.2, could be detected one or two months ahead in sewage of a hub city. In addition, the dynamics of pre-epidemic variants, which were rarely detected in clinics, could be captured through sewage surveillance, thus improving our understanding of the origin and evolution of these novel epidemic variants. Our data highlight that sewage surveillance could provide nearly real-time and high-throughput data on NoV circulation in the community. With the advances in sequencing techniques, the sewage surveillance system could also be extended to other related infectious diseases.
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Affiliation(s)
- Jing Lu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; School of Public Health, Southern Medical University, Guangzhou, China.
| | - Jinju Peng
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ling Fang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lilian Zeng
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huifang Lin
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Qianling Xiong
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zhe Liu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huimin Jiang
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chaozheng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lina Yi
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Caixia Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanhao He
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanghu Zhu
- School of Mathematics and Computing Science, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Limei Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Hui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
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14
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Yi Y, Wang X, Wang S, Xiong P, Liu Q, Zhang C, Yin F, Huang Z. Identification of a blockade epitope of human norovirus GII.17. Emerg Microbes Infect 2021; 10:954-963. [PMID: 33929932 PMCID: PMC8143627 DOI: 10.1080/22221751.2021.1925162] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human noroviruses are the dominant causative agent of acute viral gastroenteritis worldwide. During the winter of 2014-2015, genotype GII.17 cluster IIIb strains emerged as the leading cause of norovirus infection in Asia and later spread to other parts of the world. It is speculated that mutation at blockade epitopes may have resulted in virus escape from herd immunity, leading to the emergence of GII.17 cluster IIIb variants. Here, we identify a GII.17 cluster IIIb-specific blockade epitope by monoclonal antibody (mAb)-based epitope mapping. Four mAbs (designated as M1 to M4) were generated from mice immunized with virus-like particle (VLP) of a GII.17 cluster IIIb strain. Among them, M1 and M3 reacted specifically with the cluster IIIb VLP but not with the VLPs from clusters II or IIIa. Moreover, M1 and M3 dose-dependently blocked cluster IIIb VLP binding with its ligand, histo-blood group antigens (HBGAs). Epitope mapping revealed that M1 and M3 recognized the same highly exposed epitope consisting of residues 293-296 and 299 in the capsid protein VP1. Sequence alignment showed that the M1/M3 epitope sequence is highly variable among different GII.17 clusters whereas it is identical for cluster IIIIb strains. These data define a dominant blockade epitope of GII.17 norovirus and provide evidence that blockade epitope evolution contributes to the emergence of GII.17 cluster IIIb strains.
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Affiliation(s)
- Yufang Yi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, People's Republic of China.,Hainan Medical University - The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, People's Republic of China
| | - Xiaoli Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Shuxia Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Pei Xiong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Qingwei Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Feifei Yin
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, People's Republic of China.,Hainan Medical University - The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, People's Republic of China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
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15
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Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. J Infect Dis 2020; 221:S319-S330. [PMID: 31538189 DOI: 10.1093/infdis/jiz220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daryl Domman
- Bioscience Division, Los Alamos National Laboratory, New Mexico
| | - Christopher Ruis
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, New Mexico
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16
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Abstract
Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.
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Affiliation(s)
- Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1308, Silver Spring, MD 20993, USA
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17
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Yi L, Zou L, Peng J, Yu J, Song Y, Liang L, Guo Q, Kang M, Ke C, Song T, Lu J, Wu J. Epidemiology, evolution and transmission of human metapneumovirus in Guangzhou China, 2013-2017. Sci Rep 2019; 9:14022. [PMID: 31575919 PMCID: PMC6773679 DOI: 10.1038/s41598-019-50340-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022] Open
Abstract
Human metapneumovirus (hMPV), first identified in 2001, is a major viral respiratory pathogen that worldwide reported. Fundamental questions concerning the dynamics of viral evolution and transmission at both regional and global scales remain unanswered. In this study, we obtained 32 G gene and 51 F gene sequences of hMPV in Guangzhou, China in 2013–2017. Temporal and spatial phylogenetic analyses were undertaken by incorporating publicly available hMPV G gene (978) and F gene (767) sequences. The phylogenetic results show different global distribution patterns of hMPV before 1990, 1990–2005, and 2006–2017. A sharply increasing hMPV positive rate (11%) was detected in Guangzhou 2017, mainly caused by the B1 lineage of hMPV. A close phylogenetic relation was observed between hMPV strains from China and Japan, suggesting frequent hMPV transmissions between these regions. These results provide new insights into hMPV evolution, transmission, and spatial distribution and highlight Asia as a new epicenter for viral transmission and novel variant seeding after the year 2005. Conducting molecular surveillance of hMPV in Asian countries is critical for understanding the global circulation of hMPV and future vaccine design.
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Affiliation(s)
- Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China.,Guangdong Provincial Institute of Public Health, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Jingju Peng
- Southern Medical University, No. 1838, Shatai Road, Baiyun District, Guangzhou, People's Republic of China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Yingchao Song
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Lijun Liang
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China. .,Guangdong Provincial Institute of Public Health, No. 160, Qunxian Road, Panyu District, Guangzhou, China. .,Southern Medical University, No. 1838, Shatai Road, Baiyun District, Guangzhou, People's Republic of China.
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, No. 160, Qunxian Road, Panyu District, Guangzhou, China.
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18
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Matsushima Y, Mizukoshi F, Sakon N, Doan YH, Ueki Y, Ogawa Y, Motoya T, Tsukagoshi H, Nakamura N, Shigemoto N, Yoshitomi H, Okamoto-Nakagawa R, Suzuki R, Tsutsui R, Terasoma F, Takahashi T, Sadamasu K, Shimizu H, Okabe N, Nagasawa K, Aso J, Ishii H, Kuroda M, Ryo A, Katayama K, Kimura H. Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013-2017. Front Microbiol 2019; 10:2189. [PMID: 31611853 PMCID: PMC6777354 DOI: 10.3389/fmicb.2019.02189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 01/05/2023] Open
Abstract
Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013-2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10-3 and ~2.3 × 10-3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.
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Affiliation(s)
- Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai, Japan
| | - Yasutaka Ogawa
- Division of Virology, Saitama Institute of Public Health, Saitama, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute Public Health and Environment Center, Hiroshima, Japan
| | - Hideaki Yoshitomi
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan
| | | | - Rieko Suzuki
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Japan
| | - Rika Tsutsui
- Aomori Prefecture Public Health and Environment Center, Aomori, Japan
| | - Fumio Terasoma
- Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan
| | - Tomoko Takahashi
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Nobuhiko Okabe
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | | | - Jumpei Aso
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
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Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains. mBio 2019; 10:mBio.02202-19. [PMID: 31551337 PMCID: PMC6759766 DOI: 10.1128/mbio.02202-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Noroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design. GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large proportion (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside the antigenic sites. Residues in the third pattern category formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic makeup of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with three of them (A, C, and G) containing residues (352, 357, 368, and 378) linked with the diversifying selective pressure on the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by stochastic diversification with minimal changes that did not progress toward the next variant. This report provides a methodological framework for antigenic characterization of viruses and expands our understanding of the dynamics of GII.4 noroviruses and could facilitate the design of cross-reactive vaccines.
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Popovici ED, Negru DG, Olariu T, Nagy M, Dinu S, Oprisan G, Zota L, Baditoiu LM. Application of the susceptible-infected-recovered deterministic model in a GII.P17 emergent norovirus strain outbreak in Romania in 2015. Infect Drug Resist 2019; 12:2543-2551. [PMID: 31496766 PMCID: PMC6701636 DOI: 10.2147/idr.s204175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/17/2019] [Indexed: 01/08/2023] Open
Abstract
Purpose This study shows the epidemiological profile of the first gastroenteritis outbreak of GII.P17 in the Romanian territory. An outbreak with such large amplitude in a European territory was previously undocumented. Patients and methods Using a cross-sectional design, with the susceptible-infected-recovered (SIR) deterministic compartmental model for a fixed population, and the cluster method for establishing the high-incidence zones, we carried out our investigation by means of questionnaires containing personal data, affected collectivities, disease onset and duration, symptoms displayed, medical assistance provided, previous antibiotic intake where applicable, food consumption and water sources, and sanitation conditions. The confirmation of cases was done based on the typical norovirus gastroenteritis symptomatology and using three laboratory confirmations (by molecular diagnosis) for GII.P17-GII.17 genotype noroviruses from three patients. Results A gastroenteritis outbreak occurred in October-November 2015, affecting 328 people in Arad, a county in Western Romania, covering 44 neighbouring localities with a total population of 35,440 people. The study detected an inter-human transmission of the infection, with an intrafamilial risk of disease of 2.26 (95% CI 1.76 to 2.90) compared with the community transmission (in school collectivity). The basic reproduction number Ro dropped from 1.26 to 0.18 during weeks 43:44, after controlling the transmission by decontamination and isolation. Conclusion SIR made it possible to highlight the expansion of the emerging norovirus strain infection from community to family collectivities. This study provides practical solutions to limit disease cases, even in the absence of etiology, and shows the importance of sometimes underestimated traditional control methods.
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Affiliation(s)
- Emilian Damian Popovici
- Epidemiology Department, "Victor Babeş" University of Medicine and Pharmacy, Timişoara, Romania.,National Institute of Public Health, Regional Public Health Centre, Timişoara, Romania
| | | | | | - Mariana Nagy
- Department of Mathematics and Computer Science, "Aurel Vlaicu" University of Arad, Arad, Romania
| | - Sorin Dinu
- Molecular Epidemiology Laboratory, Cantacuzino National Medical - Military Institute of Research and Development, Bucharest, Romania
| | - Gabriela Oprisan
- Molecular Epidemiology Laboratory, Cantacuzino National Medical - Military Institute of Research and Development, Bucharest, Romania.,Faculty of Pharmacy, "Titu Maiorescu" University, Bucharest, Romania
| | - Lavinia Zota
- National Institute of Public Health, National Centre for Surveillance and Control of Communicable Diseases, Bucharest, Romania
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21
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Iritani N, Yamamoto SP, Abe N, Kanbayashi D, Kubo H, Uema M, Noda M, Kaida A. GII.17 norovirus infections in outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan during two decades. J Med Virol 2019; 91:2101-2107. [PMID: 31368535 DOI: 10.1002/jmv.25560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/25/2019] [Indexed: 12/18/2022]
Abstract
Norovirus (NoV) is a major cause of viral gastroenteritis, and GII.4 has been the predominant genotype worldwide since the mid-1990s. During the 2014 to 2015 winter, a rare genotype, NoV GII.17, emerged and became prevalent mainly in East Asia. Over the past two decades, NoV molecular surveillance in Osaka City, Japan, has revealed that NoV GII.17 was detected for the first time in February 2001 and that NoV GII.17-associated outbreaks remarkably increased during the 2014 to 2015 season, with higher incidence recorded in January to March 2015. Genetic analysis indicated that 28 GII.17 outbreak strains were closely related to the novel GII.P17-GII.17 variants represented by the Kawasaki308/2015/JP strain, similar to that in other regions. Statistical analysis showed that NoV GII.17 infections were more common in adults than GII.3 and GII.4 infections, suggesting that the affected adults most likely did not have antibodies against NoV GII.17 and the novel GII.17 variant had recently appeared. Regarding transmission, food was one of the most important factors involved in the spread of NoV GII.17 among adults; 61% of GII.17 outbreaks were foodborne, with oysters being the most common vehicle. Interplay between pathogens, hosts, and environmental factors was considered to be important in the 2014 to 2015 NoV GII.17 epidemic.
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Affiliation(s)
- Nobuhiro Iritani
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Seiji P Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Niichiro Abe
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Daiki Kanbayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Masashi Uema
- Division of Biomedical Food Research, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Mamoru Noda
- Division of Biomedical Food Research, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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22
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Razafimahefa RM, Ludwig-Begall LF, Thiry E. Cockles and mussels, alive, alive, oh-The role of bivalve molluscs as transmission vehicles for human norovirus infections. Transbound Emerg Dis 2019; 67 Suppl 2:9-25. [PMID: 31232515 DOI: 10.1111/tbed.13165] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/04/2019] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Abstract
Human noroviruses are recognized as the leading worldwide cause of sporadic and epidemic viral gastroenteritis, causing morbidity and mortality in impoverished developing countries and engendering enormous economic losses in developed countries. Transmitted faecal-orally, either via person-to-person contact, or by consumption of contaminated foods or water, norovirus outbreaks are often reported in institutional settings or in the context of communal dining. Bivalve molluscs, which accumulate noroviruses via filter feeding and are often eaten raw or insufficiently cooked, are a common food vehicle implicated in gastroenteritis outbreaks. The involvement of bivalve molluscs in norovirus outbreaks and epidemiology over the past two decades are reviewed. The authors describe how their physiology of filter feeding can render them concentrated vehicles of norovirus contamination in polluted environments and how high viral loads persist in molluscs even after application of depuration practices and typical food preparation steps. The global prevalence of noroviruses in bivalve molluscs as detected by different monitoring efforts is determined and the various methods currently utilized for norovirus extraction and detection from bivalve matrices described. An overview of gastroenteritis outbreaks affirmatively associated with norovirus-contaminated bivalve molluscs as reported in the past 18 years is also provided. Strategies for risk reduction in shellfish contamination and subsequent human infection are discussed.
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Affiliation(s)
- Ravo M Razafimahefa
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Louisa F Ludwig-Begall
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
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23
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The Antigenic Topology of Norovirus as Defined by B and T Cell Epitope Mapping: Implications for Universal Vaccines and Therapeutics. Viruses 2019; 11:v11050432. [PMID: 31083353 PMCID: PMC6563215 DOI: 10.3390/v11050432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Human norovirus (HuNoV) is the leading cause of acute nonbacterial gastroenteritis. Vaccine design has been confounded by the antigenic diversity of these viruses and a limited understanding of protective immunity. We reviewed 77 articles published since 1988 describing the isolation, function, and mapping of 307 unique monoclonal antibodies directed against B cell epitopes of human and murine noroviruses representing diverse Genogroups (G). Of these antibodies, 91, 153, 21, and 42 were reported as GI-specific, GII-specific, MNV GV-specific, and G cross-reactive, respectively. Our goal was to reconstruct the antigenic topology of noroviruses in relationship to mapped epitopes with potential for therapeutic use or inclusion in universal vaccines. Furthermore, we reviewed seven published studies of norovirus T cell epitopes that identified 18 unique peptide sequences with CD4- or CD8-stimulating activity. Both the protruding (P) and shell (S) domains of the major capsid protein VP1 contained B and T cell epitopes, with the majority of neutralizing and HBGA-blocking B cell epitopes mapping in or proximal to the surface-exposed P2 region of the P domain. The majority of broadly reactive B and T cell epitopes mapped to the S and P1 arm of the P domain. Taken together, this atlas of mapped B and T cell epitopes offers insight into the promises and challenges of designing universal vaccines and immunotherapy for the noroviruses.
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24
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Nirwati H, Donato CM, Mawarti Y, Mulyani NS, Ikram A, Aman AT, Peppelenbosch MP, Soenarto Y, Pan Q, Hakim MS. Norovirus and rotavirus infections in children less than five years of age hospitalized with acute gastroenteritis in Indonesia. Arch Virol 2019; 164:1515-1525. [PMID: 30887229 DOI: 10.1007/s00705-019-04215-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 02/18/2019] [Indexed: 01/19/2023]
Abstract
Rotaviruses and noroviruses are the most important viral causes of acute gastroenteritis in children. While previous studies of acute gastroenteritis in Indonesia mainly focused on rotavirus, here, we investigated the burden and epidemiology of norovirus and rotavirus disease. Children less than five years of age hospitalized with acute gastroenteritis were enrolled in this study from January to December 2015 at three participating hospitals. Rotavirus was detected by enzyme immunoassay (EIA), followed by genotyping by reverse transcription PCR (RT-PCR). Norovirus genogroups were determined by TaqMan-based quantitative RT-PCR. Among 406 enrolled children, 75 (18.47%), 223 (54.93%) and 29 (7.14%) cases were positive for norovirus, rotavirus and both viruses (mixed infections), respectively. Most cases clinically presented with fever, diarrhea, vomiting and some degree of dehydration. The majority (n = 69/75 [92%]) of the noroviruses identified belonged to genogroup II, and several genotypes were identified by sequencing a subset of samples. Among 35 samples tested for rotavirus genotype, the most prevalent genotype was G3P[8] (n = 30/35 [85.6%]). Our study suggests that the burden of norovirus diseases in Indonesian children should not be underestimated. It also shows the emergence of rotavirus genotype G3P[8] in Indonesia.
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Affiliation(s)
- Hera Nirwati
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Celeste M Donato
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Enteric Virus Group, Murdoch Children's Research Institute, Melbourne, Australia
| | - Yuli Mawarti
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nenny S Mulyani
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Aqsa Ikram
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.,Atta-Ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Abu T Aman
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Yati Soenarto
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mohamad S Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia. .,Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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25
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Nearly Complete Genome Sequence of a Human Norovirus GII.P17-GII.17 Strain Isolated from Brazil in 2015. Microbiol Resour Announc 2019; 8:MRA01376-18. [PMID: 30714031 PMCID: PMC6357637 DOI: 10.1128/mra.01376-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/03/2019] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses are the most common cause of nonbacterial acute gastroenteritis worldwide. We report here the nearly complete genome sequence (7,551 nucleotides) of a human norovirus GII.P17-GII.17 strain detected in July 2015 in the stool sample from an adult with acute gastroenteritis in Brazil. Human noroviruses are the most common cause of nonbacterial acute gastroenteritis worldwide. We report here the nearly complete genome sequence (7,551 nucleotides) of a human norovirus GII.P17-GII.17 strain detected in July 2015 in the stool sample from an adult with acute gastroenteritis in Brazil.
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26
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Mugyia AE, Ndze VN, Akoachere JFTK, Browne H, Boula A, Ndombo PK, Cannon JL, Vinjé J, Ndip LM. Molecular epidemiology of noroviruses in children under 5 years of age with acute gastroenteritis in Yaoundé, Cameroon. J Med Virol 2019; 91:738-743. [PMID: 30570784 DOI: 10.1002/jmv.25380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023]
Abstract
Norovirus is a common cause of acute gastroenteritis (AGE) among children in developing countries. Limited data on the prevalence and genetic variability of norovirus are available in Cameroon, where early childhood mortality due to AGE is common. We tested 902 fecal specimens from children younger than 5 years of age hospitalized with AGE between January 2010 and December 2013. Overall, 76 (8.4%) samples tested positive for norovirus, of which 83% (63/76) were among children below 12 months old. Most of the noroviruses detected were in children infected between July and December of each year. All norovirus-positive specimens were genotyped, with 80% (61/76) being GII.4 (three variants detected). Genotypes GI.2, GI.6, GII.1, GII.2, GII.3, GII.6, GII.16, GII.17, and GII.21 were also detected. Interestingly, GII.4 Sydney and GII.17 Kawasaki viruses were found as early as 2010, years before their emergence globally. This study suggests norovirus is a significant cause of moderate to severe gastroenteritis among young children in Cameroon. The results are important to highlight appropriate prevention and control strategies for reducing the burden of norovirus disease.
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Affiliation(s)
- Akongnwi E Mugyia
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Valentine N Ndze
- Department of Paediatrics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon.,Metabiota, Cameroon
| | | | - Hannah Browne
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Angeline Boula
- Deparment of Virology, Rotavirus National Reference Laboratory, Mother and Child Centre of the Chantal Biya Foundation, Yaoundé, Cameroon
| | - Paul Koki Ndombo
- Department of Paediatrics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon.,Deparment of Virology, Rotavirus National Reference Laboratory, Mother and Child Centre of the Chantal Biya Foundation, Yaoundé, Cameroon
| | | | - Jan Vinjé
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Lucy M Ndip
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
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27
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Qian Y, Song M, Jiang X, Xia M, Meller J, Tan M, Chen Y, Li X, Rao Z. Structural Adaptations of Norovirus GII.17/13/21 Lineage through Two Distinct Evolutionary Paths. J Virol 2019; 93:e01655-18. [PMID: 30333166 PMCID: PMC6288326 DOI: 10.1128/jvi.01655-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 09/22/2018] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses (huNoVs), which cause epidemic acute gastroenteritis, recognize histo-blood group antigens (HBGAs) as host attachment factors affecting host susceptibility. HuNoVs are genetically diverse, containing at least 31 genotypes in the two major genogroups (genogroup I [GI] and GII). Three GII genotypes, GII genotype 17 (GII.17), GII.13, and GII.21, form a unique genetic lineage, in which the GII.17 genotype retains the conventional GII HBGA binding site (HBS), while the GII.13/21 genotypes acquire a completely new HBS. To understand the molecular bases behind these evolutionary changes, we solved the crystal structures of the HBGA binding protruding domains of (i) an early GII.17 variant (the 1978 variant) that does not bind or binds weakly to HBGAs, (ii) the new GII.17 variant (the 2014/15 variant) that binds A/B/H antigens strongly via an optimized GII HBS, and (iii) a GII.13 variant (the 2010 variant) that binds the Lewis a (Lea) antigen via the new HBS. These serial, high-resolution structural data enable a comprehensive structural comparison to understand the evolutionary changes of the GII.17/13/21 lineage, including the emergence of the new HBS of the GII.13/21 sublineage and the possible HBS optimization of the recent GII.17 variant for an enhanced HBGA binding ability. Our study elucidates the structural adaptations of the GII.17/13/21 lineage through distinct evolutionary paths, which may allow a theory explaining huNoV adaptations and evolutions to be put forward.IMPORTANCE Our understanding of the molecular bases behind the interplays between human noroviruses and their host glycan ligands, as well as their evolutionary changes over time with alterations in their host ligand binding capability and host susceptibility, remains limited. By solving the crystal structures of the glycan ligand binding protruding (P) domains with or without glycan ligands of three representative noroviruses of the GII.17/13/21 genetic lineage, we elucidated the molecular bases of the human norovirus-glycan interactions of this special genetic lineage. We present solid evidence on how noroviruses of this genetic lineage evolved via different evolutionary paths to (i) optimize their glycan binding site for higher glycan binding function and (ii) acquire a completely new glycan binding site for new ligands. Our data shed light on the mechanism of the structural adaptations of human noroviruses through different evolutionary paths, facilitating our understanding of human norovirus adaptations, evolutions, and epidemiology.
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Affiliation(s)
- Ying Qian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mohan Song
- College of Life Science, Nankai University, Tianjin, China
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Ming Xia
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jarek Meller
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Ming Tan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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28
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Noda M. Current Status of Norovirus Food Poisoning Related to Bivalve Mollusk and Its Control Measures. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2018; 58:12-25. [PMID: 28260728 DOI: 10.3358/shokueishi.58.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Tohma K, Lepore CJ, Ford-Siltz LA, Parra GI. Evolutionary dynamics of non-GII genotype 4 (GII.4) noroviruses reveal limited and independent diversification of variants. J Gen Virol 2018; 99:1027-1035. [DOI: 10.1099/jgv.0.001088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Cara J. Lepore
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Lauren A. Ford-Siltz
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Gabriel I. Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
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30
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Chen C, Yan JB, Wang HL, Li P, Li KF, Wu B, Zhang H. Molecular epidemiology and spatiotemporal dynamics of norovirus associated with sporadic acute gastroenteritis during 2013-2017, Zhoushan Islands, China. PLoS One 2018; 13:e0200911. [PMID: 30021022 PMCID: PMC6051660 DOI: 10.1371/journal.pone.0200911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/04/2018] [Indexed: 11/28/2022] Open
Abstract
A total of 1 590 fecal swabs and stool samples from sporadic acute gastroenteritis patients of all ages were collected from January 2013 to March 2018 in the Zhoushan Islands, China, with 99 (6.23%) samples subsequently identified as human norovirus (HuNoV) positive. Phylogenetic analysis of partial RdRp and VP1 gene regions identified 10 genotypes of the GII genogroup and 3 genotypes of the GI genogroup. The predominant genotype was GII.P17-GII.17 (42.86%, 33/77), followed by GII.Pe-GII.4_Sydney 2012 (24.68%, 19/77) and GII.P16-GII.2 (12.96%, 10/77). However, the prevailing genotype in the Zhoushan Islands has shifted on three separate occasions. The GII.Pe-GII.4_Sydney_2012 strain was dominant in 2013-2014, the GII.P17-17 strain was dominant in 2015-2016, and the GII.P16-GII.2 strain was dominant in 2017. Divergence analysis showed that the re-emerging GII.P16-GII.2 strains clustered with the Japanese 2010-2012 GII.P16-GII.2 strains, and the time of the most recent common ancestor was estimated to have occurred in 2012 to 2013. The evolutionary rates of the RdRp gene region of the GII.P16 genotype and the VP1 gene region of the GII.2 genotype were 2.64 × 10(-3) (95% HPD interval, 2.17-3.08 × 10(-3)) and 3.36 × 10(-3) (95% HPD interval, 2.66-4.04 × 10(-3)) substitutions/site/year, respectively. The migration pattern of the HuNoV GII.2 genotype in China demonstrated that the re-emerging GII.P16-GII.2 strains were first introduced into Hong Kong from Japan, and then spread from Hong Kong to other coastal areas. Our results also showed that the GII.P16-GII.2 strains in the Zhoushan Islands were likely introduced from Jiangsu Province, China, in 2016.
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Affiliation(s)
- Can Chen
- Department of Public Health, Nanchang University, Nanchang, Jiangxi Province, China
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Jian-Bo Yan
- Department of Public Health, Nanchang University, Nanchang, Jiangxi Province, China
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Hong-Ling Wang
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Peng Li
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Ke-Feng Li
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Bing Wu
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Hui Zhang
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
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Chan MCW, Kwok K, Zhang LY, Mohammad KN, Lee N, Lui GCY, Nelson EAS, Lai RWM, Leung TF, Chan PKS. Bimodal Seasonality and Alternating Predominance of Norovirus GII.4 and Non-GII.4, Hong Kong, China, 2014-2017 1. Emerg Infect Dis 2018; 24:767-769. [PMID: 29369754 PMCID: PMC5875276 DOI: 10.3201/eid2404.171791] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report emerging subtropical bimodal seasonality and alternating predominance of norovirus GII.4 and non-GII.4 genotypes in Hong Kong. GII.4 predominated in summer and autumn months and affected young children, whereas emergent non-GII.4 genotypes predominated in winter months and affected all age groups. This highly dynamic epidemiology should inform vaccination strategies.
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Gastroenteritis outbreak at a health function caused by an emerging recombinant strain of Norovirus GII.P16/GII.4 Sydney 2012, Australia. Epidemiol Infect 2018; 146:970-971. [DOI: 10.1017/s0950268818000869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractAn emerging recombinant norovirus GII.P16/GII.4 Sydney 2012 strain caused a gastroenteritis outbreak amongst attendees at a large health function in regional New South Wales, Australia. This was the third outbreak caused by the recombinant GII.P16/GII.4 Sydney 2012 strain in this region in 2017, which appears to be emerging as a common strain in the Hunter New England region.
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Lindesmith LC, Brewer-Jensen PD, Mallory ML, Debbink K, Swann EW, Vinjé J, Baric RS. Antigenic Characterization of a Novel Recombinant GII.P16-GII.4 Sydney Norovirus Strain With Minor Sequence Variation Leading to Antibody Escape. J Infect Dis 2018; 217:1145-1152. [PMID: 29281104 PMCID: PMC5939617 DOI: 10.1093/infdis/jix651] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
Background Human noroviruses are the leading cause of acute gastroenteritis. Strains of the GII.4 genotype cause pandemic waves associated with viral evolution and subsequent antigenic drift and ligand-binding modulation. In November 2015, a novel GII.4 Sydney recombinant variant (GII.P16-GII.4 Sydney) emerged and replaced GII.Pe-GII.4 Sydney as the predominant cause of acute gastroenteritis in the 2016-2017 season in the United States. Methods Virus-like particles of GII.4 2012 and GII.4 2015 were compared for ligand binding and antibody reactivity, using a surrogate neutralization assay. Results Residue changes in the capsid between GII.4 2012 and GII.4 2015 decreased the potency of human polyclonal sera and monoclonal antibodies. A change in epitope A resulted in the complete loss of reactivity of a class of blockade antibodies and reduced levels of a second antibody class. Epitope D changes modulated monoclonal antibody potency and ligand-binding patterns. Conclusions Substitutions in blockade antibody epitopes between GII.4 2012 and GII.4 2015 influenced antigenicity and ligand-binding properties. Although the impact of polymerases on fitness remains uncertain, antigenic variation resulting in decreased potency of antibodies to epitope A, coupled with altered ligand binding, likely contributed significantly to the spread of GII.4 2015 and its replacement of GII.4 2012 as the predominant norovirus outbreak strain.
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Affiliation(s)
- Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | | | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Kari Debbink
- Department of Natural Sciences, Bowie State University, Maryland
| | - Excel W Swann
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill,Correspondence: R. S. Baric, PhD, 3304 Hooker Research Center, 135 Dauer Dr, CB7435, School of Public Health, University of North Carolina–Chapel Hill, Chapel Hill, NC 27599 ()
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Emergence of multiple norovirus strains in Thailand, 2015-2017. INFECTION GENETICS AND EVOLUTION 2018; 61:108-112. [PMID: 29597056 DOI: 10.1016/j.meegid.2018.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 03/15/2018] [Accepted: 03/23/2018] [Indexed: 01/30/2023]
Abstract
Norovirus is a major cause of non-bacterial acute gastroenteritis worldwide. Infection can be sporadic or result in widespread outbreaks. The surveillance of norovirus samples (n = 1591) obtained from patients with diarrhea in Thailand from January 2015 to February 2017 suggested that the predominance of norovirus GII.4 often seen in sporadic infection had been superseded by the emergence of GII.17. More recently, a sharp increase in acute gastroenteritis associated with norovirus GII·P16-GII.2 recombinant strain was observed at the end of 2016. Thus, previously rare norovirus strains and their recombinant derivatives may be more frequently responsible for future outbreaks.
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Genetic diversity of norovirus in children under 5 years of age with acute gastroenteritis from Angola. Epidemiol Infect 2018. [PMID: 29534772 DOI: 10.1017/s0950268818000377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Norovirus (NoV) is a major cause of acute gastroenteritis (AGE). In this study, we investigated the genetic diversity of NoV strains identified in children under 5 years of age with AGE in four provinces of Angola. Faecal samples from 343 children were screened for NoV by an in house real-time PCR assay and genotyping was performed by partial capsid gene sequencing. NoV was detected in 17.4% (58/334) of the samples, with high detection rates in children <6 months old (19%) and in children aged 12-24 months (23%). Genotype diversity was large, as demonstrated by the 11 identified genotypes. GII.4 was the predominant genotype (20% of all NoV-positive samples), followed by GII.6 (15%), GI.3 (12%), GII.7 (10%) and by other genotypes to a lesser extent. Two GII.4 variants, New Orleans 2009 and Sydney 2012, were detected and several genetic clusters were observed for genotypes GI.3, GII.6 and GII.7. The present study shows high detection rates and genetic diversity of circulating NoV genotypes in paediatric AGE samples from Angola. This information emphasises the importance of continuous assessment of NoV burden and evolution in the target population.
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Rasmussen LD, Schultz AC, Uhrbrand K, Jensen T, Fischer TK. Molecular Evidence of Oysters as Vehicle of Norovirus GII.P17-GII.17. Emerg Infect Dis 2018; 22:2024-2025. [PMID: 27767928 PMCID: PMC5088042 DOI: 10.3201/eid2211.161171] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Fu JG, Shi C, Xu C, Lin Q, Zhang J, Yi QH, Zhang J, Bao CJ, Huo X, Zhu YF, Ai J, Xing Z. Outbreaks of acute gastroenteritis associated with a re-emerging GII.P16-GII.2 norovirus in the spring of 2017 in Jiangsu, China. PLoS One 2017; 12:e0186090. [PMID: 29284004 PMCID: PMC5746213 DOI: 10.1371/journal.pone.0186090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/25/2017] [Indexed: 12/11/2022] Open
Abstract
A total of 64 acute gastroenteritis outbreaks with 2,953 patients starting in December of 2016 and occurring mostly in the late spring of 2017 were reported in Jiangsu, China. A recombinant GII.P16-GII.2 norovirus variant was associated with 47 outbreaks (73.4%) for the gastroenteritis epidemic, predominantly occurring in February and March of 2017. Sequence analysis of the RNA-dependent RNA polymerase (RdRp) and capsid protein of the viral isolates from these outbreaks confirmed that this GII.P16-GII.2 strain was the GII.P16-GII.2 variant with the intergenotypic recombination, identified in Taiwan, Hong Kong, and other cities in China in 2016. This GII.P16-GII.2 recombinant variant appeared to a re-emerging strain, firstly identified in 2011-2012 from Japan and USA but might be independently originated from other GII.P16-GII.2 variants for sporadic and outbreaks of gastroenteritis in Japan and China before 2016. Further identification of unique amino acid mutations in both VP1 and RdRp of NoV strain as shown in this report may provide insight in explaining its structural and antigenic changes, potentially critical for the variant recombinant to gain its predominance in causing regional and worldwide epidemics.
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Affiliation(s)
- Jian-Guang Fu
- Medical School and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chao Shi
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Cheng Xu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qin Lin
- Changzhou Center for Disease Control and Prevention, Changzhou, China
| | - Jun Zhang
- Yangzhou Center for Disease Control and Prevention, Yangzhou, China
| | - Qian-Hua Yi
- Taizhou Center for Disease Control and Prevention, Taizhou, China
| | - Jun Zhang
- Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Chang-Jun Bao
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiang Huo
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ye-Fei Zhu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Ai
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Zheng Xing
- Medical School and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
- College of Veterinary Medicine, University of Minnesota at Twin Cities, Saint Paul, Minnesota, United States of America
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Motoya T, Nagasawa K, Matsushima Y, Nagata N, Ryo A, Sekizuka T, Yamashita A, Kuroda M, Morita Y, Suzuki Y, Sasaki N, Katayama K, Kimura H. Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974-2015. Front Microbiol 2017; 8:2399. [PMID: 29259596 PMCID: PMC5723339 DOI: 10.3389/fmicb.2017.02399] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022] Open
Abstract
Human norovirus (HuNoV) is a leading cause of viral gastroenteritis worldwide, of which GII.4 is the most predominant genotype. Unlike other genotypes, GII.4 has created various variants that escaped from previously acquired immunity of the host and caused repeated epidemics. However, the molecular evolutionary differences among all GII.4 variants, including recently discovered strains, have not been elucidated. Thus, we conducted a series of bioinformatic analyses using numerous, globally collected, full-length GII.4 major capsid (VP1) gene sequences (466 strains) to compare the evolutionary patterns among GII.4 variants. The time-scaled phylogenetic tree constructed using the Bayesian Markov chain Monte Carlo (MCMC) method showed that the common ancestor of the GII.4 VP1 gene diverged from GII.20 in 1840. The GII.4 genotype emerged in 1932, and then formed seven clusters including 14 known variants after 1980. The evolutionary rate of GII.4 strains was estimated to be 7.68 × 10−3 substitutions/site/year. The evolutionary rates probably differed among variants as well as domains [protruding 1 (P1), shell, and P2 domains]. The Osaka 2007 variant strains probably contained more nucleotide substitutions than any other variant. Few conformational epitopes were located in the shell and P1 domains, although most were contained in the P2 domain, which, as previously established, is associated with attachment to host factors and antigenicity. We found that positive selection sites for the whole GII.4 genotype existed in the shell and P1 domains, while Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants were under positive selection in the P2 domain. Amino acid substitutions overlapped with putative epitopes or were located around the epitopes in the P2 domain. The effective population sizes of the present strains increased stepwise for Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants. These results suggest that HuNoV GII.4 rapidly evolved in a few decades, created various variants, and altered its evolutionary rate and antigenicity.
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Affiliation(s)
- Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan.,Laboratory of Laboratory Animal Science and Medicine, Faculty of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Noriko Nagata
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yukio Morita
- Department of Food and Nutrition, Tokyo Kasei University, Itabashi-ku, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, Faculty of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan.,Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,School of Medical Technology, Faculty of Health Sciences, Gunma Paz University, Takasaki, Japan
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Dai YC, Xia M, Huang Q, Tan M, Qin L, Zhuang YL, Long Y, Li JD, Jiang X, Zhang XF. Characterization of Antigenic Relatedness between GII.4 and GII.17 Noroviruses by Use of Serum Samples from Norovirus-Infected Patients. J Clin Microbiol 2017; 55:3366-3373. [PMID: 28904188 PMCID: PMC5703803 DOI: 10.1128/jcm.00865-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022] Open
Abstract
A novel GII.17 norovirus variant caused major gastroenteritis epidemics in China in 2014 to 2016. To explore the host immune factors in selection of the emergence of this new variant, we characterized its antigenic relatedness with the GII.4 noroviruses that have dominated in China for decades. Through an enzyme-linked immunosorbent assay (ELISA) and a histo-blood group antigen (HBGA) blocking assay using sera from GII.4 and the GII.17 variant-infected patients, respectively, we observed limited cross-immune reactivity by the ELISA but little reactivity by the HBGA blocking assay between GII.4 norovirus and the new GII.17 variant. Our data suggest that, among other possible factors, GII.4-specific herd immunity had little role in the emergence of the new GII.17 variant. Thus, GII.17 may be an important active antigenic type or immunotype that needs to be considered for future vaccine strategies against human noroviruses.
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Affiliation(s)
- Ying-Chun Dai
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou, Guangdong, China
| | - Ming Xia
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Qiong Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ming Tan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Lin Qin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ya-Li Zhuang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yan Long
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian-Dong Li
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou, Guangdong, China
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xu-Fu Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
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40
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Lindesmith LC, Kocher JF, Donaldson EF, Debbink K, Mallory ML, Swann EW, Brewer-Jensen PD, Baric RS. Emergence of Novel Human Norovirus GII.17 Strains Correlates With Changes in Blockade Antibody Epitopes. J Infect Dis 2017; 216:1227-1234. [PMID: 28973354 PMCID: PMC5853573 DOI: 10.1093/infdis/jix385] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Human norovirus is a significant public health burden, with >30 genotypes causing endemic levels of disease and strains from the GII.4 genotype causing serial pandemics as the virus evolves new ligand binding and antigenicity features. During 2014-2015, genotype GII.17 cluster IIIb strains emerged as the leading cause of norovirus infection in select global locations. Comparison of capsid sequences indicates that GII.17 is evolving at previously defined GII.4 antibody epitopes. Methods Antigenicity of virus-like particles (VLPs) representative of clusters I, II, and IIIb GII.17 strains were compared by a surrogate neutralization assay based on antibody blockade of ligand binding. Results Sera from mice immunized with a single GII.17 VLP identified antigenic shifts between each cluster of GII.17 strains. Ligand binding of GII.17 cluster IIIb VLP was blocked only by antisera from mice immunized with cluster IIIb VLPs. Exchange of residues 393-396 from GII.17.2015 into GII.17.1978 ablated ligand binding and altered antigenicity, defining an important varying epitope in GII.17. Conclusions The capsid sequence changes in GII.17 strains result in loss of blockade antibody binding, indicating that viral evolution, specifically at residues 393-396, may have contributed to the emergence of cluster IIIb strains and the persistence of GII.17 in human populations.
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Affiliation(s)
- Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Jacob F Kocher
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Eric F Donaldson
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Kari Debbink
- Department of Natural Sciences, Bowie State University, Maryland
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Excel W Swann
- Department of Epidemiology, University of North Carolina, Chapel Hill
| | | | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill,Correspondence: R. S. Baric, PhD, 3304 Hooker Research Center, 135 Dauer Dr, CB7435, School of Public Health, University of North Carolina–Chapel Hill, Chapel Hill, NC 27599 ()
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41
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La Rosa G, Della Libera S, Iaconelli M, Proroga YTR, De Medici D, Martella V, Suffredini E. Detection of Norovirus GII.17 Kawasaki 2014 in Shellfish, Marine Water and Underwater Sewage Discharges in Italy. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:326-333. [PMID: 28258477 DOI: 10.1007/s12560-017-9290-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
Norovirus (NoV) is a major cause of non-bacterial acute gastroenteritis worldwide, and the variants of genotype GII.4 are currently the predominant human strains. Recently, a novel variant of NoV GII.17 (GII.P17_GII.17 NoV), termed Kawasaki 2014, has been reported as the cause of gastroenteritis outbreaks in Asia, replacing the pandemic strain GII.4 Sydney 2012. The GII.17 Kawasaki 2014 variant has also been reported sporadically in patients with gastroenteritis outside of Asia, including Italy. In this study, 384 shellfish samples were subjected to screening for human NoVs using real-time PCR and 259 (67.4%) tested positive for Genogroup II (GII) NoV. Of these, 52 samples, selected as representative of different areas and sampling dates, were further amplified by conventional PCR targeting the capsid gene, using broad-range primers. Forty shellfish samples were characterized by amplicon sequencing as GII.4 (n = 29), GII.2 (n = 4), GII.6 (n = 2), GII.12 (n = 2), and GII.17 (n = 3). Sixty-eight water samples (39 seawater samples from the corresponding shellfish production areas and 29 water samples from nearby underwater sewage discharge points) were also tested using the above broad-range assay: eight NoV-positive samples were characterized as GII.1 (n = 3), GII.2 (n = 1), GII.4 (n = 2), and GII.6 (n = 2). Based on full genome sequences available in public databases, a novel RT-PCR nested assay specific for GII.17 NoVs was designed and used to re-test the characterized shellfish (40) and water (8) samples. In this second screening, the RNA of GII.17 NoV was identified in 17 additional shellfish samples and in one water sample. Upon phylogenetic analysis, these GII.17 NoV isolates were closely related to the novel GII.17 Kawasaki 2014. Interestingly, our findings chronologically matched the emergence of the Kawasaki 2014 variant in the Italian population (early 2015), as reported by hospital-based NoV surveillance. These results, showing GII.17 NoV strains to be widespread in shellfish samples collected in 2015 in Italy, provide indirect evidence that this strain has started circulating in the Italian population. Notably, using a specific assay, we were able to detect many more samples positive for GII.17 NoV, indicating that, in food and water matrices, broad-range assays for NoV may grossly underestimate the prevalence of some, less common, NoVs. The detection of the GII.17 strain Kawasaki 2014 in clinical, water and food samples in Italy highlights the need for more systematic surveillance for future disease control and prevention.
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Affiliation(s)
- G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy.
| | - S Della Libera
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - Y T R Proroga
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, via della Salute 2, 80055, Portici, Italy
| | - D De Medici
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - V Martella
- Faculty of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, BA, Italy
| | - E Suffredini
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
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Lu J, Fang L, Sun L, Zeng H, Li Y, Zheng H, Wu S, Yang F, Song T, Lin J, Ke C, Zhang Y, Vinjé J, Li H. Association of GII.P16-GII.2 Recombinant Norovirus Strain with Increased Norovirus Outbreaks, Guangdong, China, 2016. Emerg Infect Dis 2017; 23:1188-1190. [PMID: 28430561 PMCID: PMC5512473 DOI: 10.3201/eid2307.170333] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
An unusual prevalence of recombinant GII.2 noroviruses (GII.P16-GII.2) in Guangdong, China, at the end of 2016 caused a sharp increase in outbreaks of acute gastroenteritis. This event was another non-GII.4 epidemic that emerged after the GII.17 viruses in 2014 and 2015 and warrants global surveillance.
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43
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Phylogenetic Analyses Suggest that Factors Other Than the Capsid Protein Play a Role in the Epidemic Potential of GII.2 Norovirus. mSphere 2017; 2:mSphere00187-17. [PMID: 28529975 PMCID: PMC5437133 DOI: 10.1128/mspheredirect.00187-17] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII.P16 polymerase genotype. In this study, we investigated the evolutionary dynamics of GII.2 to determine the mechanism of this sudden emergence in the human population. The phylogenetic analyses indicated strong linear evolution of the VP1-encoding sequence, albeit with minor changes in the amino acid sequence over time. Without major genetic differences among the strains, a clustering based on the polymerase genotype was observed in the tree. This association did not affect the substitution rate of the VP1. Phylogenetic analyses of the polymerase region showed that reemerging GII.P16-GII.2 strains diverged into a new cluster, with a small number of amino acid substitutions detected on the surface of the associated polymerase. Thus, besides recombination or antigenic shift, point mutations in nonstructural proteins could also lead to novel properties with epidemic potential in different norovirus genotypes. IMPORTANCE Noroviruses are a major cause of gastroenteritis worldwide. Currently, there is no vaccine or specific antiviral available to treat norovirus disease. Multiple norovirus strains infect humans, but a single genotype (GII.4) has been regarded as the most important cause of viral gastroenteritis outbreaks worldwide. Its persistence and predominance have been explained by the continuous replacement of variants that present new antigenic properties on their capsid protein, thus evading the herd immunity acquired to the previous variants. Over the last three seasons, minor genotypes have displaced the GII.4 viruses as the predominant strains. One of these genotypes, GII.2, reemerged as predominant during 2016 to 2017. Here we show that factors such as minor changes in the polymerase may have driven the reemergence of GII.2 during the last season. A better understanding of norovirus diversity is important for the development of effective treatments against noroviruses.
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Genetic and Epidemiologic Trends of Norovirus Outbreaks in the United States from 2013 to 2016 Demonstrated Emergence of Novel GII.4 Recombinant Viruses. J Clin Microbiol 2017; 55:2208-2221. [PMID: 28490488 DOI: 10.1128/jcm.00455-17] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/25/2017] [Indexed: 12/29/2022] Open
Abstract
Noroviruses are the most frequent cause of epidemic acute gastroenteritis in the United States. Between September 2013 and August 2016, 2,715 genotyped norovirus outbreaks were submitted to CaliciNet. GII.4 Sydney viruses caused 58% of the outbreaks during these years. A GII.4 Sydney virus with a novel GII.P16 polymerase emerged in November 2015, causing 60% of all GII.4 outbreaks in the 2015-2016 season. Several genotypes detected were associated with more than one polymerase type, including GI.3, GII.2, GII.3, GII.4 Sydney, GII.13, and GII.17, four of which harbored GII.P16 polymerases. GII.P16 polymerase sequences associated with GII.2 and GII.4 Sydney viruses were nearly identical, suggesting common ancestry. Other common genotypes, each causing 5 to 17% of outbreaks in a season, included GI.3, GI.5, GII.2, GII.3, GII.6, GII.13, and GII.17 Kawasaki 308. Acquisition of alternative RNA polymerases by recombination is an important mechanism for norovirus evolution and a phenomenon that was shown to occur more frequently than previously recognized in the United States. Continued molecular surveillance of noroviruses, including typing of both polymerase and capsid genes, is important for monitoring emerging strains in our continued efforts to reduce the overall burden of norovirus disease.
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Mori K, Motomura K, Somura Y, Kimoto K, Akiba T, Sadamasu K. Comparison of genetic characteristics in the evolution of Norovirus GII.4 and GII.17. J Med Virol 2017; 89:1480-1484. [PMID: 28198556 DOI: 10.1002/jmv.24791] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 01/20/2017] [Indexed: 11/10/2022]
Abstract
The genetic characteristics of Norovirus GII.17 were evaluated. Phylogenetic analysis and comparisons of amino acid (Aa) substitutions and nonsynonymous (NS) substitutions/site/year were performed. The complete VP1 sequence of Tokyo/27-3/1976 clustered independently with GII.P17_GII.17 strains. Aa substitutions were mainly accumulated in the P2 domain. NS substitutions/site/year for Tokyo/27-3/1976 compared to Kawasaki323/2014 and Kawasaki308/2015 were 0.57 × 10-3 and 0.78 × 10-3 , respectively; for GII.4 Sydney/NSW0514/2012 compared to CHDC2094/1974 and CHDC5191/1974 were 0.93 × 10-3 and 1.06 × 10-3 , respectively. These findings imply that evolutionary diversity in the VP1 of GII.17 might be strictly constrained in contrast to that of GII.4.
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Affiliation(s)
- Kohji Mori
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Yoshiko Somura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kana Kimoto
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Tetsuya Akiba
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
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Rupprom K, Chavalitshewinkoon-Petmitr P, Diraphat P, Kittigul L. Evaluation of real-time RT-PCR assays for detection and quantification of norovirus genogroups I and II. Virol Sin 2017; 32:139-146. [PMID: 28224385 DOI: 10.1007/s12250-016-3863-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022] Open
Abstract
Noroviruses are the leading cause of acute gastroenteritis in humans. Real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) is a promising molecular method for the detection of noroviruses. In this study, the performance of three TaqMan real-time RT-PCR assays was assessed, which were one commercially available real-time RT-PCR kit (assay A: Norovirus Real Time RT-PCR kit) and two in-house real-time RT-PCR assays (assay B: LightCycler RNA Master Hybprobe and assay C: RealTime ready RNA Virus Master). Assays A and B showed higher sensitivity than assay C for norovirus GI, while they all had the same sensitivity (103 DNA copies/mL) for GII DNA standard controls. Assay B had the highest efficiency for both genogroups. No cross-reactivity was observed among GI and GII noroviruses, rotavirus, hepatitis A virus, and poliovirus. The detection rates of these assays in GI and GII norovirus-positive fecal samples were not significantly different. However, the mean quantification cycle (Cq) value of assay B for GII was lower than assays A and C with statistical significance (P-value, 0.000). All three real-time RT-PCR assays could detect a variety of noroviruses including GI.2, GII.2, GII.3, GII.4, GII.6, GII.12, GII.17, and GII.21. This study suggests assay B as a suitable assay for the detection and quantification of noroviruses GI and GII due to good analytical sensitivity and higher performance to amplify norovirus on DNA standard controls and clinical samples.
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Affiliation(s)
- Kitwadee Rupprom
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pornphan Diraphat
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | - Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand.
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Parra GI, Squires RB, Karangwa CK, Johnson JA, Lepore CJ, Sosnovtsev SV, Green KY. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity. PLoS Pathog 2017; 13:e1006136. [PMID: 28103318 PMCID: PMC5283768 DOI: 10.1371/journal.ppat.1006136] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/31/2017] [Accepted: 12/17/2016] [Indexed: 12/12/2022] Open
Abstract
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining "static") and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification ("static" versus "evolving"), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as "immunotypes". We propose that "immunotypes" and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population.
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Affiliation(s)
- Gabriel I Parra
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - R Burke Squires
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Consolee K Karangwa
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Jordan A Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Cara J Lepore
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, United States of America
| | - Stanislav V Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Kim Y Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
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Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses. Virus Res 2016; 234:21-33. [PMID: 28041960 PMCID: PMC7114559 DOI: 10.1016/j.virusres.2016.12.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/17/2022]
Abstract
This review summarizes current knowledge on the norovirus RdRp. Multiple X-ray structures of norovirus RdRp show important conformational changes. Norovirus RdRp recognizes specific promotor sequences to initiate RNA synthesis. Anti-HCV nucleoside analogs such as 2CM-C also inhibit Norovirus RdRp. Suramin and its analogs act as allosteric non-nucleoside polymerase inhibitors.
Noroviruses belong to the Caliciviridae family of single-stranded positive-sense RNA viruses. The genus Norovirus includes seven genogroups (designated GI-GVII), of which GI, GII and GIV infect humans. Human noroviruses are responsible for widespread outbreaks of acute gastroenteritis and represent one of the most common causes of foodborne illness. No vaccine or antiviral treatment options are available for norovirus infection. The RNA-dependent RNA polymerase (RdRp) of noroviruses is a key enzyme responsible for transcription and replication of the viral genome. Here, we review the progress made in understanding the structures and functions of norovirus RdRp and its use as a target for small molecule inhibitors. Crystal structures of the RdRp at different stages of substrate interaction have been determined, which shed light on its multi-step catalytic cycle. The in vitro assays and in vivo animal models that have been developed to identify and characterize inhibitors of norovirus RdRp are also summarized, followed by an update on the current antiviral research targeting different regions of norovirus RdRp. In the future, structure-based drug design and rational optimization of known nucleoside and non-nucleoside inhibitors of norovirus RdRp may pave the way towards the next generation of direct-acting antivirals.
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Norovirus Polymerase Fidelity Contributes to Viral Transmission In Vivo. mSphere 2016; 1:mSphere00279-16. [PMID: 27777985 PMCID: PMC5071534 DOI: 10.1128/msphere.00279-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022] Open
Abstract
Virus replication fidelity and hence the intrahost genetic diversity of viral populations are known to be intricately linked to viral pathogenesis and tropism as well as to immune and antiviral escape during infection. In this study, we investigated whether changes in replication fidelity can impact the ability of a virus to transmit between susceptible hosts by the use of a mouse model for norovirus. We show that a variant encoding a high-fidelity polymerase is transmitted less efficiently between mice than the wild-type strain. This constitutes the first experimental demonstration that the polymerase fidelity of viruses can impact transmission of infection in their natural hosts. These results provide further insight into potential reasons for the global emergence of pandemic human noroviruses that display alterations in the replication fidelity of their polymerases compared to nonpandemic strains. Intrahost genetic diversity and replication error rates are intricately linked to RNA virus pathogenesis, with alterations in viral polymerase fidelity typically leading to attenuation during infections in vivo. We have previously shown that norovirus intrahost genetic diversity also influences viral pathogenesis using the murine norovirus model, as increasing viral mutation frequency using a mutagenic nucleoside resulted in clearance of a persistent infection in mice. Given the role of replication fidelity and genetic diversity in pathogenesis, we have now investigated whether polymerase fidelity can also impact virus transmission between susceptible hosts. We have identified a high-fidelity norovirus RNA-dependent RNA polymerase mutant (I391L) which displays delayed replication kinetics in vivo but not in cell culture. The I391L polymerase mutant also exhibited lower transmission rates between susceptible hosts than the wild-type virus and, most notably, another replication defective mutant that has wild-type levels of polymerase fidelity. These results provide the first experimental evidence that norovirus polymerase fidelity contributes to virus transmission between hosts and that maintaining diversity is important for the establishment of infection. This work supports the hypothesis that the reduced polymerase fidelity of the pandemic GII.4 human norovirus isolates may contribute to their global dominance. IMPORTANCE Virus replication fidelity and hence the intrahost genetic diversity of viral populations are known to be intricately linked to viral pathogenesis and tropism as well as to immune and antiviral escape during infection. In this study, we investigated whether changes in replication fidelity can impact the ability of a virus to transmit between susceptible hosts by the use of a mouse model for norovirus. We show that a variant encoding a high-fidelity polymerase is transmitted less efficiently between mice than the wild-type strain. This constitutes the first experimental demonstration that the polymerase fidelity of viruses can impact transmission of infection in their natural hosts. These results provide further insight into potential reasons for the global emergence of pandemic human noroviruses that display alterations in the replication fidelity of their polymerases compared to nonpandemic strains.
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Zou L, Yi L, Wu J, Song Y, Huang G, Zhang X, Liang L, Ni H, Pybus OG, Ke C, Lu J. Evolution and Transmission of Respiratory Syncytial Group A (RSV-A) Viruses in Guangdong, China 2008-2015. Front Microbiol 2016; 7:1263. [PMID: 27574518 PMCID: PMC4983572 DOI: 10.3389/fmicb.2016.01263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/02/2016] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial viruses (RSVs) including subgroups A (RSV-A) and B (RSV-B) are an important cause of acute respiratory tract infections worldwide. RSV-A include major epidemic strains. Fundamental questions concerning the evolution, persistence and transmission of RSV-A are critical for disease control and prevention, yet remain unanswered. In this study, we generated 64 complete G gene sequences of RSV-A strains collected between 2008 and 2015 in Guangdong, China. Phylogenetic analysis was undertaken by incorporating 572 publicly available RSV-A sequences. Current data indicate that genotypes GA1, GA4, and GA5 are endemic with limited epidemic activity. In contrast, the GA2 genotype which likely originated in 1980 has spread rapidly and caused epidemics worldwide. By analyzing GA2 genotype sequences across epidemic seasons within Guangdong, we find that RSV-A epidemics in Guangdong are caused by a combination of virus importation and local persistence, although the magnitude of the latter is likely overestimated due to infrequent sampling in other regions. Our results provide new insights into RSV-A evolution and transmission at global and local scales and highlights the rapid and wide spread of genotype GA2 compared to other genotypes. In order to control RSV transmission and outbreak, both local persistence and external introduction should be taken into account when designing optimal strategies.
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Affiliation(s)
- Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Yingchao Song
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Guofeng Huang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Xin Zhang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lijun Liang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Hanzhong Ni
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | | | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Department of Zoology, University of OxfordOxford, UK
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