1
|
Yokoyama M, Doan YH, Motomura K, Sato H, Oka T. Strong evolutionary constraints against amino acid changes in the P2 subdomain of sapovirus GI.1 capsid protein VP1. Biochem Biophys Res Commun 2024; 710:149878. [PMID: 38608492 DOI: 10.1016/j.bbrc.2024.149878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Sapovirus (SaV) is a nonenveloped RNA virus that causes acute gastroenteritis in humans. Although SaV is a clinically important pathogen in children, an effective vaccine is currently unavailable. The capsid protein VP1 of SaVs forms the outer shell of the virion and is highly diverse, as often seen in the virion-surface proteins of RNA viruses, creating an obstacle for vaccine development. We here report a unique phenomenon pertaining to the variation of SaV VP1. Phylogenetic and information entropy analyses using full-length VP1 sequences from a public database consistently showed that the amino acid sequences of the VP1 protein have been highly conserved over more than 40 years in the major epidemic genotype GI.1 but not in GI.2. Structural modeling showed that even the VP1 P2 subdomain, which is arranged on the outermost shell of the virion and presumably exposed to anti-SaV antibodies, remained highly homogeneous in GI.1 but not in GI.2. These results suggest strong evolutionary constraints against amino acid changes in the P2 subdomain of the SaV GI.1 capsid and illustrate a hitherto unappreciated mechanism, i.e., preservation of the VP1 P2 subdomain, involved in SaV survival. Our findings could have important implications for the development of an anti-SaV vaccine.
Collapse
Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazushi Motomura
- Osaka Institute of Public Health, Osaka, Japan; Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Thailand; Research Institute of Microbial Diseases, Osaka University, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
| |
Collapse
|
2
|
Balázs B, Boros Á, Pankovics P, Nagy G, Szekeres S, Urbán P, Reuter G. Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary. Arch Virol 2024; 169:100. [PMID: 38630394 PMCID: PMC11024015 DOI: 10.1007/s00705-024-06034-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.
Collapse
Affiliation(s)
- Benigna Balázs
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Gábor Nagy
- Department of Animal Physiology and Health, Hungarian University of Agriculture and Life Science, Kaposvár, Hungary
| | - Sándor Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
- HUN-REN-UVMB Climate Change: New Blood-Sucking Parasites and Vector-Borne Pathogens Research Group, Budapest, Hungary
| | - Péter Urbán
- Szentágothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary.
| |
Collapse
|
3
|
Ibrahim C, Hammami S, Khelifi N, Pothier P, Hassen A. Activated sludge and UV-C 254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing. Int J Environ Health Res 2024; 34:1995-2014. [PMID: 37086061 DOI: 10.1080/09603123.2023.2203906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
In this study, the detection rates of four enteric viruses, Human Astrovirus (HAstVs), Aichivirus (AiVs), Human Adenovirus (HAdVs), and Sapovirus (SaVs) are carried out to assess the virological quality of the treated wastewater. A total of 140 samples was collected from wastewater treatment plant WWTP of Tunis-City. Real-time RT-PCR and conventional RT-PCR results showed high frequencies of detection of the four enteric viruses investigated at the entry and exit of the biological activated sludge procedure and a significant reduction in viral titers after tertiary treatment with UV-C254 irradiation. These results revealed the ineffectiveness of the biological activated sludge treatment in removing viruses and the poor quality of the treated wastewater intended for recycling, agricultural reuse, and safe discharge into the natural environment. The UV-C254 irradiation, selected while considering the non-release of known disinfection by-products because of eventual reactions with the large organic and mineral load commonly present in the wastewater.
Collapse
Affiliation(s)
- Chourouk Ibrahim
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, the University of Tunis El Manar, Tunis, Tunisia
- Microbiology Laboratory, Beja University Hospital, Beja,Tunisia
| | - Salah Hammami
- National School of Veterinary Medicine at Sidi Thabet, University of Manouba, Tunis, Tunisia
| | - Nesserine Khelifi
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
| | - Pierre Pothier
- National Reference Center for Enteric Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France
| | - Abdennaceur Hassen
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
| |
Collapse
|
4
|
Cintron M, Jani K, Madhavappallil J, Kamboj M, Babady NE. Prevalence of astrovirus and sapovirus among adult oncology patients with acute gastroenteritis using a multiplexed gastrointestinal pathogen PCR panel. Eur J Clin Microbiol Infect Dis 2024; 43:525-531. [PMID: 38216845 DOI: 10.1007/s10096-024-04748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Multiplex syndromic gastrointestinal panels (GIPCR) have streamlined the diagnosis of infectious diarrhea. Additionally, they have expanded the number of pathogens that can be routinely evaluated, allowing further understanding of the prevalence of enteric pathogens in various patient populations. The goal of this study was to investigate the prevalence and clinical presentation of astrovirus and sapovirus gastroenteritis in adult oncology patients as detected by the FilmArray GIPCR. METHODS All GIPCR panel results from December 2017 to June 2021 were retrospectively reviewed to determine the prevalence of astrovirus and sapovirus in adult oncology patients. Medical records were also reviewed to obtain clinical information. Repeat GIPCR positivity and symptom duration were used to estimate prolonged viral shedding. RESULTS A total of 18,014 panels were performed on samples collected from 9303 adults. Overall, astrovirus and sapovirus were detected in 0.35% (33/9303) and 0.45% (42/9303) GIPCRs respectively. At least one viral target was detected in 424 (4.4%) patients. Astrovirus accounted for 7.8% (33/424) and sapovirus 9.9% (42/424) of patients. Diarrhea was the most common symptom documented. A subset of transplant patients had protracted viral detection with a median of ~27 days (range 23-43 days) for astrovirus and 97 days (range 11-495) for sapovirus. No clusters or outbreaks were identified during the study period. CONCLUSION In oncology patients with viral gastroenteritis, astrovirus and sapovirus were the causative agents in 18% of the cases. Both viruses were associated with mild disease. Prolonged diarrhea and viral shedding were observed in a few transplant patients.
Collapse
Affiliation(s)
- Melvili Cintron
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jerin Madhavappallil
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| |
Collapse
|
5
|
Georgana I, Hosmillo M, Jahun AS, Emmott E, Sorgeloos F, Cho KO, Goodfellow IG. Porcine Sapovirus Protease Controls the Innate Immune Response and Targets TBK1. Viruses 2024; 16:247. [PMID: 38400023 PMCID: PMC10892870 DOI: 10.3390/v16020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Human sapoviruses (HuSaVs) and noroviruses are considered the leading cause of acute gastroenteritis worldwide. While extensive research has focused on noroviruses, our understanding of sapoviruses (SaVs) and their interactions with the host's immune response remains limited. HuSaVs have been challenging to propagate in vitro, making the porcine sapovirus (PSaV) Cowden strain a valuable model for studying SaV pathogenesis. In this study we show, for the first time, that PSaV Cowden strain has mechanisms to evade the host's innate immune response. The virus 3C-like protease (NS6) inhibits type I IFN production by targeting TBK1. Catalytically active NS6, both during ectopic expression and during PSaV infection, targets TBK1 which is then led for rapid degradation by the proteasome. Moreover, deletion of TBK1 from porcine cells led to an increase in PSaV titres, emphasizing its role in regulating PSaV infection. Additionally, we successfully established PSaV infection in IPEC-J2 cells, an enterocytic cell line originating from the jejunum of a neonatal piglet. Overall, this study provides novel insights into PSaV evasion strategies, opening the way for future investigations into SaV-host interactions, and enabling the use of a new cell line model for PSaV research.
Collapse
Affiliation(s)
- Iliana Georgana
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
| | - Aminu S. Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Frederic Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
- Université catholique de Louvain, de Duve Institute, MIPA-VIRO 74-49, 74 Avenue Hippocrate, B-1200 Brussels, Belgium
| | - Kyoung-Oh Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Ian G. Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (M.H.); (A.S.J.); (E.E.)
| |
Collapse
|
6
|
Ji X, Guo C, Dai Y, Chen L, Chen Y, Wang S, Sun Y. Genomic Characterization and Molecular Evolution of Sapovirus in Children under 5 Years of Age. Viruses 2024; 16:146. [PMID: 38275956 PMCID: PMC10819405 DOI: 10.3390/v16010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area.
Collapse
Affiliation(s)
- Xiaolei Ji
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Chen Guo
- Department of Laboratory Medicine, Nantong Chongchuan Center for Disease Control and Prevention, 47 Zhongxiu Middle Road, Nantong 226001, China;
| | - Yaoyao Dai
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Lu Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yujia Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Shifang Wang
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yihua Sun
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| |
Collapse
|
7
|
Rubio-Mora E, Carrascoso GR, Rodríguez JG. Sapovirus infection as another cause of persistent viral diarrhea: case series and review of the literature. Eur J Clin Microbiol Infect Dis 2024; 43:55-59. [PMID: 37924444 DOI: 10.1007/s10096-023-04695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
Human sapovirus (HuSaV) is a common cause of gastroenteritis worldwide and is responsible for approximately 4% of acute gastroenteritis episodes in Europe. As reported with norovirus, patients with immunocompromised states are at increased risk of developing HuSaV infection, which can lead to persistent diarrhea and chronic viral shedding in some individuals. Chronic infections are incompletely investigated in these patients, and, due to the lack of specific treatment for HuSaV infection, different clinical approaches were carried out in order to provide further evidence on clinical evolution of these patients with different treatments. In this retrospective study, we report five immunocompromised pediatric patients with recurrent diarrhea caused by HuSaV and long-term viral shedding. Stool samples were analyzed by real-time PCR and tested for enteropathogenic viruses and bacteria and protozoa. Among transplant recipients, reduction of immunosuppressant therapy led to clinical improvement and relief of symptoms, maintaining a balance between managing the infection and preventing graft rejection. Nitazoxanide for 14 days was only used in one of these patients, showing to be an effective therapy to achieve reduction in time to resolution of symptoms. Neither nitazoxanide nor modification of immunosuppressant therapy could avoid recurrences. Further investigations are needed to develop new approaches that can both clear the infection and avoid persistent diarrhea in these patients.
Collapse
Affiliation(s)
- Eduardo Rubio-Mora
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain.
| | - Guillermo Ruiz Carrascoso
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Julio García Rodríguez
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain
| |
Collapse
|
8
|
Ando H, Ahmed W, Okabe S, Kitajima M. Tracking the effects of the COVID-19 pandemic on viral gastroenteritis through wastewater-based retrospective analyses. Sci Total Environ 2023; 905:166557. [PMID: 37633393 DOI: 10.1016/j.scitotenv.2023.166557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
The COVID-19 pandemic possibly disrupted the circulation and seasonality of gastroenteritis viruses (e.g., Norovirus (NoV), Sapovirus (SaV), group A rotavirus (ARoV), and Aichivirus (AiV)). Despite the growing application of wastewater-based epidemiology (WBE), there remains a lack of sufficient investigations into the actual impact of the COVID-19 pandemic on the prevalence of gastroenteritis viruses. In this study, we measured NoV GI and GII, SaV, ARoV, and AiV RNA concentrations in 296 influent wastewater samples collected from three wastewater treatment plants (WWTPs) in Sapporo, Japan between October 28, 2018 and January 12, 2023 using the highly sensitive EPISENS™ method. The detection ratios of SaV and ARoV after May 2020 (SaV: 49.8 % (134/269), ARoV: 57.4 % (151/263)) were significantly lower than those before April 2020 (SaV: 93.9 % (31/33), ARoV: 97.0 % (32/33); SaV: p < 3.5×10-7, ARoV: p < 1.5×10-6). Furthermore, despite comparable detection ratios before (88.5 %, 23/26) and during (66.7 %, 80/120) the COVID-19 pandemic (p = 0.032), the concentrations of NoV GII revealed a significant decrease after the onset of the pandemic (p < 1.5×10-7, Cliff's delta = 0.72). NoV GI RNA were sporadically detected (24.7 %, 8/33) before April 2020 and after May 2020 (6.5 %, 17/263), whereas AiV was consistently (100 %, 33/33) detected from wastewater throughout the study period (95.8 %, 252/263). The WBE results demonstrated the significant influence of COVID-19 countermeasures on the circulation of gastroenteritis viruses, with variations observed in the magnitude of their impact across different types of viruses. These epidemiological findings highlight that the hygiene practices implemented to prevent COVID-19 infections may also be effective for controlling the prevalence of gastroenteritis viruses, providing invaluable insights for public health units and the development of effective disease management guidelines.
Collapse
Affiliation(s)
- Hiroki Ando
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| |
Collapse
|
9
|
Su L, Mao H, Sun Y, Yan H, Ge Q, Gong L, Zhang Y. The analysis of the genotype of Sapovirus outbreaks in Zhejiang Province. Virol J 2023; 20:268. [PMID: 37974193 PMCID: PMC10655437 DOI: 10.1186/s12985-023-02202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Sapovirus (SaV) infection is increasing globally. Concurrently, several SaV-outbreaks were observed in children of Zhejiang province, China, in recent years, In this study, the genotypes of Sapovirus from seven outbreaks in the Zhejiang province were analysed. METHODS A total of 105 faecal samples were collected from children aged between 4 and 17 years from the Zhejiang Provincial Center for Disease Control and Prevention between October 2021 and February 2023. Genotypes were processed using reverse transcription polymerase chain reaction and Sanger sequencing, while next-generation sequencing was used to generate a complete viral genome. Deduced amino acid sequences were analysed to detect VP1 gene mutations. RESULTS In total, 60 SaV-positive patients were detected at a 57.14% (60/105) positivity rate. Positive rates in the seven outbreaks were: 22.22% (2/9), 15.00% (3/20), 93.10% (27/29), 84.21% (16/19), 28.57% (2/7), 53.33% (8/15) and 33.33% (2/6), respectively. Four genotypes were identified in the seven outbreaks, of which, GI.1 accounted for 14.29% (1/7), GI.2 accounted for 14.29% (1/7), GI.6 and GII.5 accounted for 14.29% (1/7), and GI.6 accounted for 57.14% (4/7). All patients were children and outbreaks predominantly occurred in primary schools and during cold seasons. Additionally, the complete sequence from the GI.6 outbreak strain showed high homology (identity: 99.99%) with few common substitutions (Y300S, N302S and L8M) in VP1 protein. CONCLUSIONS SaV genotype diversity was observed in the seven outbreaks, with GI.6 being the main SaV genotype in Zhejiang province. It demonstrated high homology and may provide a platform for SaV prevention and control measures.
Collapse
Affiliation(s)
- Lingxuan Su
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Haiyan Mao
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Yi Sun
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Hao Yan
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Qiong Ge
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Liming Gong
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China.
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China.
| |
Collapse
|
10
|
Matsumoto N, Kurokawa S, Tamiya S, Nakamura Y, Sakon N, Okitsu S, Ushijima H, Yuki Y, Kiyono H, Sato S. Replication of Human Sapovirus in Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Cells. Viruses 2023; 15:1929. [PMID: 37766335 PMCID: PMC10536750 DOI: 10.3390/v15091929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Sapoviruses, like noroviruses, are single-stranded positive-sense RNA viruses classified in the family Caliciviridae and are recognized as a causative pathogen of diarrhea in infants and the elderly. Like human norovirus, human sapovirus (HuSaV) has long been difficult to replicate in vitro. Recently, it has been reported that HuSaV can be replicated in vitro by using intestinal epithelial cells (IECs) derived from human tissues and cell lines derived from testicular and duodenal cancers. In this study, we report that multiple genotypes of HuSaV can sufficiently infect and replicate in human-induced pluripotent stem cell-derived IECs. We also show that this HuSaV replication system can be used to investigate the conditions for inactivation of HuSaV by heat and alcohol, and the effects of virus neutralization of antisera obtained by immunization with vaccine antigens, under conditions closer to the living environment. The results of this study confirm that HuSaV can also infect and replicate in human normal IECs regardless of their origin and are expected to contribute to future virological studies.
Collapse
Affiliation(s)
- Naomi Matsumoto
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Shiho Kurokawa
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Shigeyuki Tamiya
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Yutaka Nakamura
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yoshikazu Yuki
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Hiroshi Kiyono
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba 263-8522, Japan
- CU-UCSD Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Departments of Medicine and Pathology, University of California, San Diego, CA 92093-0956, USA
| | - Shintaro Sato
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| |
Collapse
|
11
|
Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
Collapse
Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| |
Collapse
|
12
|
Hoque SA, Pham NTK, Onda-Shimizu Y, Nishimura S, Sugita K, Kobayashi M, Islam MT, Okitsu S, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Sapovirus infections in Japan before and after the emergence of the COVID-19 pandemic: An alarming update. J Med Virol 2023; 95:e29023. [PMID: 37543991 DOI: 10.1002/jmv.29023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/19/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
An increasing trend of sapovirus (SaV) infections in Japanese children during 2009-2019, particularly after the introduction of the voluntary rotavirus (RV)-vaccination program has been observed. Herein, we investigated the epidemiological situation of SaV infections from 2019 to 2022 when people adopted a precautionary lifestyle due to the emergence of the COVID-19 pandemic, and RV vaccines had been implemented as routine vaccines. Stool samples were collected from children who attended outpatient clinics with acute gastroenteritis and analyzed by reverse transcriptase-polymerase chain reaction to determine viral etiology. Among 961 stool samples, 80 (8.3%) were positive for SaV: 2019-2020 (6.5%), 2020-2021 (0%), and 2021-2022 (12.8%). The trend of SaV infection in Japanese children yet remained upward with statistical significance (p = 0.000). The major genotype was GI.1 (75%) which caused a large outbreak in Kyoto between December 2021 and February 2022. Phylogenetic, gene sequence and deduced amino acid sequence analyses suggested that these GI.1 strains detected in the outbreak and other places during 2021-2022 or 2019-2020 remained genetically identical and widely spread. This study reveals that SaV infection is increasing among Japanese children which is a grave concern and demands immediate attention to be paid before SaV attains a serious public health problem.
Collapse
Affiliation(s)
- Sheikh Ariful Hoque
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Ngan Thi Kim Pham
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuko Onda-Shimizu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shuichi Nishimura
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Kumiko Sugita
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | - Masaaki Kobayashi
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | | | - Shoko Okitsu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Satoshi Hayakawa
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| |
Collapse
|
13
|
Mageau A, Ambert-Balay K, Boutolleau D, Schuffenecker I, Burrel S, Kaplon J, Nguyen Quoc S, Uzunov M, Souchet L, de Rougemont A, Roos-Weil D, Baron M. Norovirus and sapovirus infections after allogeneic hematopoietic stem cell transplantation: is it worth it to look for them? Leuk Lymphoma 2023; 64:1295-1303. [PMID: 37165601 DOI: 10.1080/10428194.2023.2211186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/26/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
Norovirus (NoV) and Sapovirus (SaV) are potential causative agents of diarrhea after allogeneic HSCT but little is known in this population. We performed a retrospective analysis by RT-PCR of calicivirus (NoV and SaV), Human adenovirus (HAdV), rotavirus (RV), Aichi virus (AiV), enterovirus (EV), human parechovirus (HPeV) and Human bocavirus (HBoV) in the diarrheal stools of patients after allogeneic HSCT. 49/162 patients had positive viral assays: HAdV (17%), EV (7%), NoV (4.3%), RV and HBoV (3.1% each), SaV (1.9%), AiV (1.2%), HPeV (0.6%). Seven patients were positive for NoV and 3 for SaV. Among viruses-positive samples, the frequency of caliciviruses cases was 7% in the 6 months post-HSCT compared to 40% after (p < 0.0001). The median duration of symptom was 0.7 months but 2 cases, occurring more than one year after HSCT, were chronic, undiagnosed and strongly contributed to morbidity. Systematic testing of caliciviruses appears especially useful in late chronic diarrhea.
Collapse
Affiliation(s)
- Arthur Mageau
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Katia Ambert-Balay
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
| | - David Boutolleau
- Sorbonne Université, Service de virologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Isabelle Schuffenecker
- Centre National de Référence des Entérovirus et Paréchovirus, Laboratoire de Virologie, Centre de Biologie et de Pathologie Nord, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, France
| | - Sonia Burrel
- Sorbonne Université, Service de virologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Jérome Kaplon
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
| | - Stéphanie Nguyen Quoc
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Madalina Uzunov
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Laetitia Souchet
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Alexis de Rougemont
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
- UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Damien Roos-Weil
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Marine Baron
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| |
Collapse
|
14
|
Wei R, Shang R, Cheng K, Wang S, Wu J, Yu Z. A novel recombinant porcine sapovirus infection in piglets with diarrhea in Shandong Province, China, 2022. Braz J Microbiol 2023; 54:1309-1314. [PMID: 37036658 PMCID: PMC10235293 DOI: 10.1007/s42770-023-00963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 04/11/2023] Open
Abstract
Sapporo virus (SaV) is an emerging enteric virus causing acute gastroenteritis in animals. Here, we found a novel porcine SaV (PoSaV) strain (named SD2202) from the piglets with diarrhea in China in 2022. The highest nucleotide homology of SD2202 with other PoSaV strains is only 90.67%, and there are four amino acids insertion in the viral capsid protein and minor structural protein compared to other PoSaV; furthermore, we found that SD2202 belongs to a new GIII genogroup clade (GIII-6 clade). Interestingly, we found that SD2202 may be an intra-genogroup recombinant strain. Taken together, we found a novel PoSaV implicated in the piglet diarrhea epidemic and emphasized the importance of continuous surveillance of PoSaV.
Collapse
Affiliation(s)
- Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Rui Shang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Kaihui Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Song Wang
- Medical Integration and Practice Center, Shandong University, Jinan, 250012, China
| | - Jiaqiang Wu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| |
Collapse
|
15
|
González F, Diez-Valcarce M, Reyes Y, Vielot NA, Toval-Ruíz C, Gutiérrez L, Zepeda O, Cuadra EC, Blandón P, Browne H, Bowman NM, Vílchez S, Vinjé J, Becker-Dreps S, Bucardo F. Timing and genotype distribution of symptomatic and asymptomatic sapovirus infections and re-infections in a Nicaraguan birth cohort. Clin Microbiol Infect 2023; 29:540.e9-540.e15. [PMID: 36423864 PMCID: PMC10077563 DOI: 10.1016/j.cmi.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVES To characterize the timing and genotype distribution of symptomatic and asymptomatic sapovirus infections and re-infections in a Nicaraguan birth cohort. METHODS Infants (N = 444) were enrolled at 10-14 days of life and observed weekly until 2 years of age. Stool samples were collected for each acute gastroenteritis (AGE) episode, and routine stool samples were collected monthly. Stool samples were tested for sapovirus using RT-qPCR, and positive samples were genotyped. RESULTS A total of 348 children completed 2 years of AGE weekly surveillance; 93 (26.7%) of them experienced sapovirus AGE. Most infections occurred after 5 months of age and mainly during the second year of life (62.4%, 58/93) and early in the rainy season. Sapovirus screening in all stools from a subset of 67 children who consistently provided samples showed sapovirus infections in 91 of 330 (27.6%) AGE episodes and in 39 of 1350 (2.9%) routine stools. In this subset, the median age at the first sapovirus AGE was 11.2 months (95% CI, 9.3-15.9 months); 38 of 67 (57%) children experienced re-infections, 19 symptomatic and 19 asymptomatic. On average, sapovirus re-infections were reported 7.2 months after symptomatic and 5.3 months after asymptomatic infections. Genogroup GI (64%, 69/108) was the most common detected. Sapovirus GI.1 was more frequently detected in AGE stool samples than in routine stool samples (47.2%, 43/91 vs. 25.6%, 10/39; p 0.005), and re-infection with the same genotype was uncommon. DISCUSSION The first sapovirus infections occurred at approximately 11 months of age, whereas the median time to symptomatic re-infection was 7.2 months. Re-infections with the same sapovirus genotype were rare during 2 years of life suggesting genotype-specific protection after natural infection.
Collapse
Affiliation(s)
- Fredman González
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Marta Diez-Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Yaoska Reyes
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christian Toval-Ruíz
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Lester Gutiérrez
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Omar Zepeda
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Edwing Centeno Cuadra
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Patricia Blandón
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Hannah Browne
- National Foundation for the Centers for Disease Control and Prevention Inc., Atlanta, GA, USA
| | - Natalie M Bowman
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel Vílchez
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Jan Vinjé
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Filemón Bucardo
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua.
| |
Collapse
|
16
|
Vielot NA, François R, Huseynova E, González F, Reyes Y, Gutierrez L, Nordgren J, Toval-Ruiz C, Vilchez S, Vinjé J, Becker-Dreps S, Bucardo F. Association between breastfeeding, host genetic factors, and calicivirus gastroenteritis in a Nicaraguan birth cohort. PLoS One 2022; 17:e0267689. [PMID: 36240197 PMCID: PMC9565698 DOI: 10.1371/journal.pone.0267689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Norovirus and sapovirus are important causes of childhood acute gastroenteritis (AGE). Breastfeeding prevents AGE generally; however, it is unknown if breastfeeding prevents AGE caused specifically by norovirus and sapovirus. METHODS We investigated the association between breastfeeding and norovirus or sapovirus AGE episodes in a birth cohort. Weekly data on breastfeeding and AGE episodes were captured during the first year of life. Stools were collected from children with AGE and tested by RT-qPCR for norovirus and sapovirus. Time-dependent Cox models estimated associations between weekly breastfeeding and time to first norovirus or sapovirus AGE. FINDINGS From June 2017 to July 2018, 444 newborns were enrolled in the study. In the first year of life, 69 and 34 children experienced a norovirus and a sapovirus episode, respectively. Exclusive breastfeeding lasted a median of 2 weeks, and any breastfeeding lasted a median of 43 weeks. Breastfeeding in the last week did not prevent norovirus (HR: 1.09, 95% CI: 0.62, 1.92) or sapovirus (HR: 1.00, 95% CI: 0.82, 1.21) AGE in a given week, adjusting for household sanitation, consumption of high-risk foods, and mother's and child's histo-blood group phenotypes. Maternal secretor-positive phenotype was protective against norovirus AGE, whereas child's secretor-positive phenotype was a risk factor for norovirus AGE. INTERPRETATION Exclusive breastfeeding in this population was short-lived, and no conclusions could be drawn about its potential to prevent norovirus or sapovirus AGE. Non-exclusive breastfeeding did not prevent norovirus or sapovirus AGE in the first year of life. However, maternal secretor-positive phenotype was associated with a reduced hazard of norovirus AGE.
Collapse
Affiliation(s)
- Nadja Alexandra Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ruthly François
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Emilya Huseynova
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Fredman González
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Yaoska Reyes
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Lester Gutierrez
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Johan Nordgren
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Christian Toval-Ruiz
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Samuel Vilchez
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| | - Filemon Bucardo
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua–León, León, Nicaragua
| |
Collapse
|
17
|
Phengma P, Khamrin P, Jampanil N, Yodmeeklin A, Ukarapol N, Maneekarn N, Kumthip K. Molecular epidemiology and characterization of norovirus and sapovirus in pediatric patients with acute diarrhea in Thailand, 2019-2020. J Infect Public Health 2022; 15:1013-1019. [PMID: 35994998 DOI: 10.1016/j.jiph.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/04/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Human enteric pathogens in the family Caliciviridae including norovirus (NoV) and sapovirus (SaV) are associated with acute diarrheal disease globally and are considered as one of the viruses with high genetic diversity. METHODS In order to investigate the epidemiology of NoV and SaV in pediatric patients with acute diarrhea in Chiang Mai, Thailand from January 2019 to December 2020, a total of 675 stool specimens were collected and examined for the presence of NoV and SaV by RT-multiplex PCR. RESULTS 126 (18.7 %) and 6 (0.9 %) stool samples were positive for NoV and SaV, respectively. Mixed infection of NoV and SaV was detected in one patient (0.2 %). Among 10 different NoV strains detected in this study, NoV genogroup II genotype 4 (GII.4) Sydney 2012 was the most predominant genotype (51.2 %) followed by GII.3, GII.2, GII.6, GII.12, GII.7, GII.17, GI.4, GII.14, and GI.3. Interestingly, monthly distribution of NoV genotypes revealed that NoV GII.3 increased dramatically in August 2019, suggesting an outbreak of NoV GII.3 might occur in the community. In addition, 3 genotypes of SaV were detected in this study with SaV GI.1 being the most common genotype (71.4 %) followed by GI.2 and GII.5 (each at 14.3 %). CONCLUSIONS This study demonstrates the prevalence and genetic diversity of NoV and SaV circulating in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand during 2019-2020 and shows an emergence of NoV GII.3 infection in 2019.
Collapse
Affiliation(s)
- Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nuthapong Ukarapol
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand.
| |
Collapse
|
18
|
Vielot NA, Reyes Y, Blette B, González F, Toval-Ruiz C, Gutiérrez L, Vílchez S, Diez-Valcarce M, Vinjé J, Becker-Dreps S, Bucardo F. First Episodes of Norovirus and Sapovirus Gastroenteritis Protect Against Subsequent Episodes in a Nicaraguan Birth Cohort. Epidemiology 2022; 33:650-653. [PMID: 35700200 PMCID: PMC9378628 DOI: 10.1097/ede.0000000000001500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Norovirus and sapovirus cause a large burden of acute gastroenteritis (AGE) in young children. We assessed protection conferred by norovirus and sapovirus AGE episodes against future episodes. METHODS Between June 2017 and July 2018, we recruited 444 newborns in León, Nicaragua. Weekly household surveys identified AGE episodes over 36 months, and AGE stools were tested by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) for norovirus genogroup (G)I/GII and sapovirus. We used recurrent-event Cox models and negative control methods to estimate protection conferred by first episodes, controlling for observed and unobserved risk factors, respectively. RESULTS Sapovirus episodes conferred a 69% reduced hazard of subsequent episodes using the negative control method. Norovirus GI (hazard ratio [HR] = 0.67; 95% confidence interval [CI] = 0.31, 1.3) and GII (HR = 0.20; 95% CI = 0.04, 0.44) episodes also appeared highly protective. Protection against norovirus GII was enhanced following two episodes. CONCLUSIONS Evidence of natural immunity in early childhood provides optimism for the future success of pediatric norovirus and sapovirus vaccines.
Collapse
Affiliation(s)
- Nadja A. Vielot
- Department of Family Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yaoska Reyes
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| | - Bryan Blette
- Department of Biostatistics, University of North Carolina. Chapel Hill, North Carolina, USA
| | - Fredman González
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| | - Christian Toval-Ruiz
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| | - Lester Gutiérrez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| | - Samuel Vílchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| | - Marta Diez-Valcarce
- Division of Viral Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
- Emory University, Rollins School of Public Health, Atlanta, GA, USA
| | - Jan Vinjé
- Division of Viral Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Filemón Bucardo
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua – León. León, Nicaragua
| |
Collapse
|
19
|
Shen H, Zhang J, Gauger PC, Burrough ER, Zhang J, Harmon K, Wang L, Zheng Y, Petznick T, Li G. Genetic characterization of porcine sapoviruses identified from pigs during a diarrhoea outbreak in Iowa, 2019. Transbound Emerg Dis 2022; 69:1246-1255. [PMID: 33780163 DOI: 10.1111/tbed.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
Porcine sapovirus (SaV) was first identified by electron microscopy in the United States in 1980 and has since been reported from both asymptomatic and diarrhoeic pigs usually in mixed infection with other enteric pathogens. SaV as the sole aetiological agent of diarrhoea in naturally infected pigs has not previously been reported in the United States. Here, we used four independent lines of evidence including metagenomics analysis, real-time RT-PCR (rRT-PCR), histopathology, and in situ hybridization to confirm porcine SaV genogroup III (GIII) as the sole cause of enteritis and diarrhoea in pigs. A highly sensitive and specific rRT-PCR was established to detect porcine SaV GIII. Examination of 184 faecal samples from an outbreak of diarrhoea on a pig farm showed that pigs with clinical diarrhoea had significantly lower Ct values (15.9 ± 0.59) compared to clinically unaffected pigs (35.8 ± 0.71). Further survey of 336 faecal samples from different states in the United States demonstrated that samples from pigs with clinical diarrhoea had a comparable positive rate (45.3%) with those from asymptomatic pigs (43.1%). However, the SaV-positive pigs with clinical diarrhoea had significantly higher viral loads (Ct = 26.0 ± 0.5) than the SAV-positive but clinically healthy pigs (Ct = 33.2 ± 0.9). Phylogenetic analysis of 20 field SaVs revealed that all belonged to SaV GIII and recombination analysis indicated that intragenogroup recombination had occurred within the field isolates of SaV GIII. These results suggest that porcine SaV GIII plays an important aetiologic role in swine enteritis and diarrhoea and rRT-PCR is a reliable method to detect porcine SaV. Our findings provide significant insights to better understand the epidemiology and pathogenicity of porcine SaV infection.
Collapse
Affiliation(s)
- Huigang Shen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianfeng Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eric R Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| |
Collapse
|
20
|
Pitkänen O, Markkula J, Hemming-Harlo M. Sapovirus, Norovirus and Rotavirus Detections in Stool Samples of Hospitalized Finnish Children With and Without Acute Gastroenteritis. Pediatr Infect Dis J 2022; 41:e203-e207. [PMID: 35185141 PMCID: PMC8997665 DOI: 10.1097/inf.0000000000003493] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Sapovirus, norovirus and rotavirus are major causes of childhood acute gastroenteritis (AGE) globally. Asymptomatic infections of these viruses have not been extensively studied. AIM To examine the prevalence and the genetic variations of sapovirus, norovirus and rotavirus in children with and without symptoms of AGE. METHODS We collected 999 stool samples from children under 16 years old from September 2009 to August 2011 at Tampere University Hospital, Finland. In total 442 children (44%) had symptoms of AGE and 557 patients (56%) had acute respiratory tract infection (ARTI) only. Samples were examined for sapovirus, norovirus and rotavirus using reverse transcription-polymerase chain reaction and the positive amplicons were sequenced. RESULTS Totally 54% and 14% of the patients in AGE and ARTI groups, respectively, tested positive. All viruses were more frequently detected in AGE patients than in ARTI patients (norovirus, 25% vs. 7.2%, respectively; rotavirus, 24% vs. 6.1%; sapovirus, 5.2% vs. 1.4%). In ARTI patients, the cases were seen most frequently during the first two years of life. Norovirus was the most detected pathogen in both groups with genogroup GII covering ≥97% of norovirus strains. Sapovirus was mostly detected in children under 18 months old without predominating genotype. Rotavirus was often detected after recent rotavirus vaccination and 18% and 88% of the strains were rotavirus vaccine-derived in AGE and ARTI groups, respectively. CONCLUSIONS We showed that the most common viruses causing gastroenteritis in children may be found in the stools of an asymptomatic carrier which may function as a potential reservoir for AGE.
Collapse
Affiliation(s)
| | - Jukka Markkula
- From the Vaccine Research Center
- Tampere Center for Child Health Research, Arvo Ylpön katu 34, University of Tampere, Finland
| | - Maria Hemming-Harlo
- Tampere Center for Child Health Research, Arvo Ylpön katu 34, University of Tampere, Finland
- The Pediatric Research Center, Biomedicum Haartmaninkatu 8, University of Helsinki, Finland
| |
Collapse
|
21
|
Bruijnesteijn van Coppenraet LES, Flipse J, Wallinga JA, Vermeer M, van der Reijden WA, Weel JFL, van der Zanden AGM, Schuurs TA, Ruijs GJHM. From a case-control survey to a diagnostic viral gastroenteritis panel for testing of general practitioners' patients. PLoS One 2021; 16:e0258680. [PMID: 34731182 PMCID: PMC8565752 DOI: 10.1371/journal.pone.0258680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE To evaluate the pathogenicity of a broad range of 11 possible gastroenteritis viruses, by means of statistical relationships with cases vs. controls, or Ct-values, in order to establish the most appropriate diagnostic panel for our general practitioner (GP) patients in the Netherlands (2010-2012). METHODS Archived stool samples from 1340 cases and 1100 controls were retested using internally controlled multiplex real-time PCRs for putative pathogenic gastroenteritis viruses: adenovirus, astrovirus, bocavirus, enterovirus, norovirus GI and GII, human parechovirus, rotavirus, salivirus, sapovirus, and torovirus. RESULTS The prevalence of any virus in symptomatic cases and asymptomatic controls was 16.6% (223/1340) and 10.2% (112/1100), respectively. Prevalence of astrovirus (adjusted odds ratio (aOR) 10.37; 95% confidence interval (CI) 1.34-80.06) and norovirus GII (aOR 3.10; CI 1.62-5.92) was significantly higher in cases versus controls. Rotavirus was encountered only in cases. We did not find torovirus and there was no statistically significant relationship with cases for salivirus (aOR 1,67; (CI) 0.43-6.54)), adenovirus non-group F (aOR 1.20; CI 0.75-1.91), bocavirus (aOR 0.85; CI 0.05-13.64), enterovirus (aOR 0.83; CI 0.50-1.37), human parechovirus (aOR 1.61; CI 0.54-4.77) and sapovirus (aOR 1.15; CI 0.67-1.98). Though adenovirus group F (aOR 6.37; CI 0.80-50.92) and norovirus GI (aOR 2.22, CI: 0.79-6.23) are known enteropathogenic viruses and were more prevalent in cases than in controls, this did not reach significance in this study. The Ct value did not discriminate between carriage and disease in PCR-positive subjects. CONCLUSIONS In our population, diagnostic gastroenteritis tests should screen for adenovirus group F, astrovirus, noroviruses GI and GII, and rotavirus. Case-control studies as ours are lacking and should also be carried out in populations from other epidemiological backgrounds.
Collapse
Affiliation(s)
| | - Jacky Flipse
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
| | - Janny A. Wallinga
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
| | - Marloes Vermeer
- ZGT Academy, Ziekenhuisgroep Twente, Almelo, The Netherlands
| | - Wil A. van der Reijden
- Regional Laboratory for Medical Microbiology and Public Health Kennemerland, Haarlem, The Netherlands
| | - Jan F. L. Weel
- Izore, Center for Infectious Diseases Friesland, Leeuwarden, The Netherlands
| | | | - Theo A. Schuurs
- Izore, Center for Infectious Diseases Friesland, Leeuwarden, The Netherlands
| | - Gijs J. H. M. Ruijs
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
- * E-mail:
| |
Collapse
|
22
|
Mattison CP, Dunn M, Wikswo ME, Kambhampati A, Calderwood L, Balachandran N, Burnett E, Hall AJ. Non-Norovirus Viral Gastroenteritis Outbreaks Reported to the National Outbreak Reporting System, USA, 2009-2018. Emerg Infect Dis 2021; 27:560-564. [PMID: 33496216 PMCID: PMC7853577 DOI: 10.3201/eid2702.203943] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2009–2018, four adenovirus, 10 astrovirus, 123 rotavirus, and 107 sapovirus gastroenteritis outbreaks were reported to the US National Outbreak Reporting System (annual median 30 outbreaks). Most were attributable to person-to-person transmission in long-term care facilities, daycares, and schools. Investigations of norovirus-negative gastroenteritis outbreaks should include testing for these viruses.
Collapse
|
23
|
Barsoum Z. Pediatric Sapovirus Gastroenteritis in Ireland-Disease Virulence, Viral Dual-Infection, and Regional Seasonal Trends. Indian J Pediatr 2021; 88:612. [PMID: 33683581 DOI: 10.1007/s12098-021-03711-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Zakaria Barsoum
- Department of Pediatrics, South West Acute Hospital, 124 Irvinestown Rd, Enniskillen, Northern Ireland, BT 74 6DN, UK.
| |
Collapse
|
24
|
Song K, Lin X, Liu Y, Ji F, Zhang L, Chen P, Zhao C, Song Y, Tao Z, Xu A. Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing. Food Environ Virol 2021; 13:270-280. [PMID: 33755873 PMCID: PMC7985922 DOI: 10.1007/s12560-021-09469-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.
Collapse
Affiliation(s)
- Ke Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Yao Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Li Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Peng Chen
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, 44-1 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Chenxu Zhao
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Yanyan Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China.
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China.
| | - Aiqiang Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| |
Collapse
|
25
|
García-Hernández ME, Trujillo-Ortega ME, Alcaraz-Estrada SL, Lozano-Aguirre-Beltrán L, Sandoval-Jaime C, Taboada-Ramírez BI, Sarmiento-Silva RE. Molecular Detection and Characterization of Porcine Epidemic Diarrhea Virus and Porcine Aichivirus C Coinfection in México. Viruses 2021; 13:v13050738. [PMID: 33922604 PMCID: PMC8146670 DOI: 10.3390/v13050738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
Swine enteric viral infections are responsible for substantial economic losses in the pork industry worldwide. Porcine epidemic diarrhea (PEDV) is one of the main causative agents of diarrhea in lactating pigs, and reports of PEDV coinfection with other enteric viruses highlight the importance of viral interactions for disease presentation and outcomes. Using next-generation sequencing (NGS) and sequence analyses from samples taken from piglets with acute diarrhea, we explored the possible interactions between PEDV and other less reported pathogens. PEDV coinfection with porcine kobuvirus (PKV) was detected in 36.4% (27/74) of samples. Full genomes from porcine coronavirus and kobuvirus were obtained, as was a partial porcine sapovirus genome (PSaV). The phylogenetic results show the clustering of these strains corresponding to the geographical relationship. To our knowledge, this is the first full genome and isolation report for porcine kobuvirus in México, as well as the first phylogenetic analysis for porcine sapovirus in the country. The NGS approach provides a better perspective of circulating viruses and other pathogens in affected production units.
Collapse
Affiliation(s)
- Montserrat-Elemi García-Hernández
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
| | - María-Elena Trujillo-Ortega
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
| | - Sofía-Lizbeth Alcaraz-Estrada
- División de Medicina Genómica y Genética Clínica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Av. Félix Cuevas #540, Ciudad de México 03100, Mexico;
| | - Luis Lozano-Aguirre-Beltrán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico;
| | - Carlos Sandoval-Jaime
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico; (C.S.-J.); (B.I.T.-R.)
| | - Blanca Itzel Taboada-Ramírez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico; (C.S.-J.); (B.I.T.-R.)
| | - Rosa-Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
- Correspondence: ; Tel.: +55-56225900 (ext. 33)
| |
Collapse
|
26
|
Magwalivha M, Ngandu JPK, Traore AN, Potgieter N. Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017-2020. Viruses 2021; 13:393. [PMID: 33804579 PMCID: PMC8000493 DOI: 10.3390/v13030393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/29/2022] Open
Abstract
Diarrhoeal disease is considered an important cause of morbidity and mortality in developing areas, and a large contributor to the burden of disease in children younger than five years of age. This study investigated the prevalence and genogroups of human sapovirus (SV) in children ≤5 years of age in rural communities of Vhembe district, South Africa. Between 2017 and 2020, a total of 284 stool samples were collected from children suffering with diarrhoea (n = 228) and from children without diarrhoea (n = 56). RNA extraction using Boom extraction method, and screening for SV using real-time PCR were done in the lab. Positive samples were subjected to conventional RT-PCR targeting the capsid fragment. Positive sample isolates were genotyped using Sanger sequencing. Overall SV were detected in 14.1% (40/284) of the stool samples (16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples). Significant correlation between SV positive cases and water sources was noted. Genogroup-I was identified as the most prevalent strain comprising 81.3% (13/16), followed by SV-GII 12.5% (2/16) and SV-GIV 6.2% (1/16). This study provides valuable data on prevalence of SV amongst outpatients in rural and underdeveloped communities, and highlights the necessity for further monitoring of SV circulating strains as potential emerging strains.
Collapse
Affiliation(s)
- Mpho Magwalivha
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (J.-P.K.N.); (A.N.T.); (N.P.)
| | | | | | | |
Collapse
|
27
|
Halasa N, Piya B, Stewart LS, Rahman H, Payne DC, Woron A, Thomas L, Constantine-Renna L, Garman K, McHenry R, Chappell J, Spieker AJ, Fonnesbeck C, Batarseh E, Hamdan L, Wikswo ME, Parashar U, Bowen MD, Vinjé J, Hall AJ, Dunn JR. The Changing Landscape of Pediatric Viral Enteropathogens in the Post-Rotavirus Vaccine Era. Clin Infect Dis 2021; 72:576-585. [PMID: 32009161 PMCID: PMC7884803 DOI: 10.1093/cid/ciaa100] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute gastroenteritis (AGE) is a common reason for children to receive medical care. However, the viral etiology of AGE illness is not well described in the post-rotavirus vaccine era, particularly in the outpatient (OP) setting. METHODS Between 2012 and 2015, children 15 days through 17 years old presenting to Vanderbilt Children's Hospital, Nashville, Tennessee, with AGE were enrolled prospectively from the inpatient, emergency department, and OP settings, and stool specimens were collected. Healthy controls (HCs) were enrolled and frequency matched for period, age group, race, and ethnicity. Stool specimens were tested by means of reverse-transcription real-time quantitative polymerase chain reaction for norovirus, sapovirus, and astrovirus RNA and by Rotaclone enzyme immunoassay for rotavirus antigen, followed by polymerase chain reaction verification of antigen detection. RESULTS A total of 3705 AGE case patients and 1563 HCs were enrolled, among whom 2885 case patients (78%) and 1110 HCs (71%) provided stool specimens that were tested. All 4 viruses were more frequently detected in AGE case patients than in HCs (norovirus, 22% vs 8%, respectively; rotavirus, 10% vs 1%; sapovirus, 10% vs 5%; and astrovirus, 5% vs 2%; P < .001 for each virus). In the OP setting, rates of AGE due to norovirus were higher than rate for the other 3 viruses. Children <5 years old had higher OP AGE rates than older children for all viruses. CONCLUSIONS Norovirus remains the most common virus detected in all settings, occurring nearly twice as frequently as the next most common pathogens, sapovirus and rotavirus. Combined, norovirus, sapovirus, rotavirus, and astrovirus were associated with almost half of all AGE visits and therefore are an important reason for children to receive medical care.
Collapse
Affiliation(s)
- Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhinnata Piya
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Herdi Rahman
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel C Payne
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy Woron
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Linda Thomas
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Lisha Constantine-Renna
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Katie Garman
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Rendie McHenry
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher Fonnesbeck
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Einas Batarseh
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lubna Hamdan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Wikswo
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh Parashar
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael D Bowen
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J Hall
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R Dunn
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| |
Collapse
|
28
|
de Oliveira-Tozetto S, Santiso-Bellón C, Ferrer-Chirivella JM, Navarro-Lleó N, Vila-Vicent S, Rodríguez-Díaz J, Buesa J. Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain). Viruses 2021; 13:v13020184. [PMID: 33530573 PMCID: PMC7911121 DOI: 10.3390/v13020184] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023] Open
Abstract
Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.
Collapse
Affiliation(s)
- Sibele de Oliveira-Tozetto
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Cristina Santiso-Bellón
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Correspondence: (C.S.-B.); (J.B.)
| | - Josep M. Ferrer-Chirivella
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Noemi Navarro-Lleó
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Susana Vila-Vicent
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Correspondence: (C.S.-B.); (J.B.)
| |
Collapse
|
29
|
Cho SR, Yun SJ, Chae SJ, Jung S, Kim JH, Yong KC, Cho EH, Choi W, Lee DY. An Outbreak Associated with Sapovirus GI.3 in an Elementary School in Gyeonggi-do, Korea. J Korean Med Sci 2020; 35:e281. [PMID: 32864904 PMCID: PMC7458851 DOI: 10.3346/jkms.2020.35.e281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/26/2020] [Indexed: 11/20/2022] Open
Abstract
On October 4, 2018, an outbreak of gastroenteritis associated with sapovirus occurred among elementary school students in Gyeonggi-do, Korea. Epidemiologic studies were conducted in a retrospective cohort approach. Using self-administered questionnaires, we collected information on symptoms and food items consumed. Of the 999 subjects, 17 developed patients that met the case definition. The main symptom was vomiting (100%), and the symptomatic age was 6-12 years. Positive samples were identified by conventional reverse transcription polymerase chain reaction for sequencing. They were classified into genotype GI.3 by phylogenetic analysis. This is the first report of an outbreak associated with sapovirus GI.3 in Korea.
Collapse
Affiliation(s)
- Seung Rye Cho
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Su Jung Yun
- Division of Infectious Disease Research, Gyeonggi-do Institute of Health and Environment, Suwon, Korea
| | - Su Jin Chae
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Sunyoung Jung
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Jong Hwa Kim
- Division of Infectious Disease Research, Gyeonggi-do Institute of Health and Environment, Suwon, Korea
| | - Kum Chan Yong
- Division of Infectious Disease Research, Gyeonggi-do Institute of Health and Environment, Suwon, Korea
| | - Eul Ho Cho
- Bundang-gu Health Center Infectious Disease Response Team, Seongnam, Korea
| | - Wooyoung Choi
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Deog Yong Lee
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea.
| |
Collapse
|
30
|
Makhaola K, Moyo S, Kebaabetswe LP. Distribution and Genetic Variability of Sapoviruses in Africa. Viruses 2020; 12:v12050490. [PMID: 32349380 PMCID: PMC7291139 DOI: 10.3390/v12050490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were searched for studies conducted in African countries and published between Jan 2005 and Mar 2019. Only studies where RT- PCR was used for initial detection were included in the systematic review. We identified 27 studies from 14 African countries with 18 focused on human sapoviruses, two on animal sapoviruses and seven on sapoviruses observed in the environment. Samples. The overall estimated pooled prevalence of human sapovirus infections among symptomatic and asymptomatic individuals was similar at 5.0% (95% Confidence Interval (CI): 3.0–7.0) and 2.0% (95% CI: 1.0–3.0), respectively. In environmental samples sapovirus detection rates ranged from 0% to 90% while in animal studies it was 1.7% to 34.8%. Multiple causes of gastroenteritis, sensitivity of detection method used, diversity of sapovirus strains and rotavirus vaccine coverage rate are some of the factors that could have contributed to the wide range of sapovirus detection rates that were reported. The studies reported human genogroups GI, GII, and GIV, with genogroup GI being the most prevalent. Some potential novel strains were detected from animal samples. Most studies genotyped a small portion of either the capsid and/or polymerase region. However, this is a limitation as it does not allow for detection of recombinants that occur frequently in sapoviruses. More studies with harmonized genotyping protocols that cover longer ranges of the sapovirus genome are needed to provide more information on the genomic characterization of sapoviruses circulating in African countries. Further investigations on animal to human transmission for sapoviruses are needed as inter-species transmissions have been documented for other viruses.
Collapse
Affiliation(s)
- Kgomotso Makhaola
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H Chan School of Public Health, Boston, MA 02115, USA
| | - Lemme P. Kebaabetswe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
- Correspondence:
| |
Collapse
|
31
|
Li W, Dong S, Xu J, Zhou X, Han J, Xie Z, Gong Q, Peng H, Zhou C, Lin M. Viral metagenomics reveals sapoviruses of different genogroups in stool samples from children with acute gastroenteritis in Jiangsu, China. Arch Virol 2020; 165:955-958. [PMID: 32048042 PMCID: PMC7131977 DOI: 10.1007/s00705-020-04549-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/13/2020] [Indexed: 11/26/2022]
Abstract
Sapoviruses (SAVs), including several genogroups (GI to GV), are one of the causes of acute gastroenteritis (AGE). In this study, viral metagenomics revealed the presence of sapoviruses of different genogroups in stool from children with AGE. Eight different complete SAV genomes were determined, of which five belonged to GI and the other three belonged to GII, GIV and GV, respectively. Although they were highly similar to published sequences, the GIV and GV were the first complete genome sequences of these SAVs found in China. In a prevalence investigation, 19% of subjects with AGE were positive for SAVs, while none of the control group was positive.
Collapse
Affiliation(s)
- Wang Li
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Surong Dong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Juan Xu
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Xiaobin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Junling Han
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Zhaqing Xie
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Qin Gong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Hailin Peng
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
| | - Mei Lin
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
| |
Collapse
|
32
|
Wang L, Marthaler D, Fredrickson R, Gauger PC, Zhang J, Burrough ER, Petznick T, Li G. Genetically divergent porcine sapovirus identified in pigs, United States. Transbound Emerg Dis 2020; 67:18-28. [PMID: 31461567 DOI: 10.1111/tbed.13337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 02/05/2023]
Abstract
Porcine sapoviruses (SaVs) are genetically diverse and widely distributed in pig-producing countries. Eight genogroups of porcine SaV have been identified, and genogroup III is the predominant type. Most of the eight genogroups of porcine SaV are circulating in the United States. In the present study, we report detection of porcine SaVs in pigs at different ages with clinical diarrhoea using next-generation sequencing and genetic characterization. All seven cases have porcine SaV GIII strains detected and one pooled case was found to have a porcine SaV GVI strain IA27912-B-2018. Sequence analysis showed that seven GIII isolates were genetically divergent and formed four different lineages on the trees of complete genome, RdRP, VP1 and VP2. In addition, these seven GIII isolates had three different deletion/insertion patterns in an identified variable region close to the 3' end of VP2. The GVI strain IA27912-B-2018 was closely related to strains previously detected in the United States and Japan. A 3-nt deletion in VP1 region of GVI IA27912-B-2018 was identified. Our study showed that genetically divergent SaVs of different genogroups are co-circulating in pigs in the United States. Future studies comparing the virulence of these different genogroups in pigs are needed to better understand this virus and to determine if surveillance and vaccine development are needed to monitor and control porcine SaVs.
Collapse
Affiliation(s)
- Leyi Wang
- Department of Veterinary Clinical Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Douglas Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Richard Fredrickson
- Department of Veterinary Clinical Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eric R Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
33
|
Mann P, Pietsch C, Liebert UG. Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008-2018. Viruses 2019; 11:v11080726. [PMID: 31394867 PMCID: PMC6723979 DOI: 10.3390/v11080726] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/28/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: (1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and (2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.
Collapse
Affiliation(s)
- Pia Mann
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany.
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
| |
Collapse
|
34
|
Ibrahim C, Hammami S, Chérif N, Mejri S, Pothier P, Hassen A. Detection of Sapoviruses in two biological lines of Tunisian hospital wastewater treatment. Int J Environ Health Res 2019; 29:400-413. [PMID: 30474395 DOI: 10.1080/09603123.2018.1546835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The efficiency of rotating biodisks and natural oxidizing lagoon procedures is investigated at a Tunisian semi-industrial pilot plant, El Menzeh I, where the wastewater is mainly provided by three different neighbouring hospital clinics. Throughout 2011, 102 wastewater samples were collected from the two mentioned wastewater treatment procedures. Results showed that the Sapovirus (SaV) frequency was approximately 29.4% using the real-time reverse transcription polymerase chain reaction (RT-PCR) technique, and about 16.6% using the conventional RT-PCR. Also, the SaV genogroups and genotypes were identified and genotyping revealed that all of the four Tunisian SaV strains obtained belonged to the two genogroups GIV.1 and GGI.3. In addition, two new genotypes, D and C, were detected. A moderate decrease in the SaV frequencies was observed at the exit of the two treatment processes and the SaV removal rate was around 90% in the natural oxidizing lagoons and 94% in the rotating biodisks procedure showing the temperate sensitivity of these viruses to the implemented biological wastewater. Therefore, an urgent disinfection process should be implemented downstream of the two biological treatment procedures for safe release of treated effluent in the different natural environments. Abbreviations: NoV: Noroviruses; SaV: Sapoviruses; EC: Electrical Conductivity; COD: Chemical Oxygen Demand; BOD5: Biological Oxygen Demand; SS: Suspended Solids; NH4-N: Ammonium Nitrogen; P-PO4: Ortho-Phosphate; AlCl3: aluminum chloride.
Collapse
Affiliation(s)
- Chourouk Ibrahim
- a Faculty of Mathematical, Physical and Natural Sciences of Tunis , University of Tunis El Manar , Tunis , Tunisia
- b Laboratory of Treatment and Wastewater Valorization, Centre of Research and Water Technologies (CERTE) , Techno Park of Borj-Cedria 8020 , Tunis , Tunisia
| | - Salah Hammami
- c National School of Veterinary Medicine at Sidi-Thabet , University of Manouba, Institution of Agricultural Research and Higher Education (IRESA) , Tunis , Tunisia
| | - Nadia Chérif
- d Unit Virology of Marine organisms, Aquaculture Laboratory , National Institute of Sea Science and Technologies , Tunis , Tunisia
| | - Selma Mejri
- e Veterinary Research Institute of Tunisia, Laboratory of Virology , University of Tunis El Manar, Institution of Agricultural Research and Higher Education (IRESA), La Rabta , Tunis , Tunisia
| | - Pierre Pothier
- f National Reference Centre for Enteric Viruses, Laboratory of Virology , University Hospital of Dijon , Dijon , France
| | - Abdennaceur Hassen
- a Faculty of Mathematical, Physical and Natural Sciences of Tunis , University of Tunis El Manar , Tunis , Tunisia
| |
Collapse
|
35
|
Goldar S, Rajbongshi G, Chamuah K, Alam ST, Sharma A. Occurrence of viral gastroenteritis in children below 5 years: A hospital-based study from Assam, India. Indian J Med Microbiol 2019; 37:415-417. [PMID: 32003342 DOI: 10.4103/ijmm.ijmm_19_79] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Viral gastroenteritis is an important cause of mortality and morbidity in children under 5 years of age. Many a time, these cases go unnoticed causing immense scarcity of data on viral diarrhoea. The study aimed to determine the occurrence of viral gastroenteritis among children below 5 years and the aetiological viral agents. Stool samples were collected from patients suffering from acute gastroenteritis. Real-time polymerase chain reaction was done for detection of rotavirus, adenovirus, norovirus, astrovirus and sapovirus. Viruses were detected in 55% of children. Adenovirus was found to be the most common virus (33.7%), followed by rotavirus infection (28.7%).
Collapse
Affiliation(s)
- Shalini Goldar
- Department of Microbiology, Gauhati Medical College, Guwahati, Assam, India
| | - Gitika Rajbongshi
- Department of Microbiology, Gauhati Medical College, Guwahati, Assam, India
| | - Kailash Chamuah
- Department of Microbiology, Gauhati Medical College, Guwahati, Assam, India
| | - Syed Tanwir Alam
- Department of Microbiology, Gauhati Medical College, Guwahati, Assam, India
| | - Ajanta Sharma
- Department of Microbiology, Gauhati Medical College, Guwahati, Assam, India
| |
Collapse
|
36
|
Xue L, Cai W, Gao J, Jiang Y, Wu H, Zhang L, Zuo Y, Dong R, Pang R, Zeng H, Wu S, Wang J, Zhang J, Wu Q. Genome characteristics and molecular evolution of the human sapovirus variant GII.8. Infect Genet Evol 2019; 73:362-367. [PMID: 31146046 DOI: 10.1016/j.meegid.2019.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/16/2019] [Accepted: 05/25/2019] [Indexed: 12/26/2022]
Abstract
Human sapovirus is regarded as an important viral agent for acute diarrhea worldwide. GII.8, a recently reported genotype, has been detected in a few countries and regions. In this study, we obtained the first genome sequence of a sapovirus GII.8 strain isolated in mainland China, and comprehensively analyzed the genetic diversity and evolutionary process of this genotype. The viral genome of the new GII.8 Guangzhou strain GZ2014-L231 comprised 7433 nucleotides, including two ORFs. Pairwise alignments of the new genome with representative sequences of different genotypes showed inconsistent homology between different protein-encoding regions, of which NS1 and VP2 were found as the variable proteins, and NS3, NS5, and NS6/7 were found as the conserved ones. Compared with other reported GII.8 genomes, the Guangzhou strain introduced 34 new nucleotide changes and one new amino acid change. Phylogenetic analysis based on full-length VP1 sequences demonstrated that 11 GII.8 strains could be divided into 4 clusters A-D, with 88 SNP and 10 SAP spots occurred during their evolutionary process. The Guangzhou strain has higher homology with seven GII.8 strain detected after 2014, especially the US and Peruvian strains of 2015/2016, which have the identical VP1 amino acid sequences. Using a Bayesian coalescent method based on VP1 sequences, GII.8 was predicted to emerge in 2001 with the evolution rate of 1.45 × 10-3 nucleotide substitutions/site/year (strict clock). In summary, the data in this study not only provided reference data from mainland China for sapovirus researches in future, but also firstly described the evolutionary process of the GII.8 genotype.
Collapse
Affiliation(s)
- Liang Xue
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Weicheng Cai
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Junshan Gao
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, PR China
| | - Haoming Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Le Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Yueting Zuo
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Ruimin Dong
- Department of Cardiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, PR China
| | - Rui Pang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Haiyan Zeng
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Shi Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
| | - Qingping Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China.
| |
Collapse
|
37
|
Varela MF, Monteiro S, Rivadulla E, Santos R, Romalde JL. Development of a novel digital RT-PCR method for detection of human sapovirus in different matrices. J Virol Methods 2018; 254:21-24. [PMID: 29407209 DOI: 10.1016/j.jviromet.2018.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/27/2022]
Abstract
A new nanofluidic digital RT-PCR method was developed for sapovirus (SaV) using control material obtained according to standards for enteric viruses. Primers employed amplify a fragment of 112 bp of the polymerase capsid junction, allowing the detection of human genogroups I, II and IV. Analytical validation was performed in clinical, shellfish and environmental water samples. This novel protocol rendered great effectiveness and repetitiveness, as well as higher sensitivity than real time RT-PCR assay, with differences in quantification ranging from 0.1 to 2.6 log-units. The method described here can constitute a promising tool for standardizing SaV quantification.
Collapse
Affiliation(s)
- Miguel F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Silvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001, Lisboa, Portugal
| | - Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001, Lisboa, Portugal
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| |
Collapse
|
38
|
Esseili MA, Meulia T, Saif LJ, Wang Q. Tissue Distribution and Visualization of Internalized Human Norovirus in Leafy Greens. Appl Environ Microbiol 2018; 84:e00292-18. [PMID: 29625983 PMCID: PMC5981073 DOI: 10.1128/aem.00292-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/03/2018] [Indexed: 12/21/2022] Open
Abstract
Lettuce has been implicated in human norovirus (HuNoV) outbreaks. The virus is stable on the leaf surface for at least 2 weeks; however, the dynamics of virus internalization have not been fully investigated. The purpose of this study was to assess the internalization and distribution of HuNoV and two surrogate viruses, porcine sapovirus (SaV) and Tulane virus (TV), in lettuce and spinach. Viral inoculations through the roots of seedlings and the petiole of leaves from mature plants were performed, and the viruses were tracked on days 1 and 6 post-root inoculation and at 16 h and 72 h post-petiole inoculation. Confocal microscopy was used to visualize root-internalized HuNoV. In both lettuce and spinach, (i) HuNoV was internalized into the roots and leaves at similar RNA titers, whereas surrogate viruses were more restricted to the roots, (ii) all three viruses were stable inside the roots and leaves for at least 6 days, and (iii) HuNoV disseminated similarly inside the central veins and leaf lamina, whereas surrogate viruses were more restricted to the central veins. Infectious TV, but not SaV, was detectable in all tissues, suggesting that TV has greater stability than SaV. HuNoV was visualized inside the roots' vascular bundle and the leaf mesophyll of both plants. In conclusion, using surrogate viruses may underestimate the level of HuNoV internalization into edible leaves. The internalization of HuNoV through roots and cut leaves and the dissemination into various spinach and lettuce tissues raise concerns of internal contamination through irrigation and/or wash water.IMPORTANCE Human noroviruses are the leading cause of foodborne outbreaks, with lettuce being implicated in the majority of outbreaks. The virus causes acute gastroenteritis in all age groups, with more severe symptoms in children, the elderly, and immunocompromised patients, contributing to over 200,000 deaths worldwide annually. The majority of deaths due to HuNoV occur in the developing world, where limited sanitation exists along with poor wastewater treatment facilities, resulting in the contamination of water resources that are often used for irrigation. Our study confirms the ability of lettuce and spinach to internalize HuNoV from contaminated water through the roots into the edible leaves. Since these leafy greens are consumed with minimal processing that targets only surface pathogens, the internalized HuNoV presents an added risk to consumers. Thus, preventive measures should be in place to limit the contamination of irrigation water. In addition, better processing technologies are needed to inactivate internalized viral pathogens.
Collapse
Affiliation(s)
- Malak A Esseili
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Tea Meulia
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| |
Collapse
|
39
|
Miura T, Schaeffer J, Le Saux JC, Le Mehaute P, Le Guyader FS. Virus Type-Specific Removal in a Full-Scale Membrane Bioreactor Treatment Process. Food Environ Virol 2018; 10:176-186. [PMID: 29214559 DOI: 10.1007/s12560-017-9330-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/01/2017] [Indexed: 05/09/2023]
Abstract
We investigated removal of noroviruses, sapoviruses, and rotaviruses in a full-scale membrane bioreactor (MBR) plant by monitoring virus concentrations in wastewater samples during two gastroenteritis seasons and evaluating the adsorption of viruses to mixed liquor suspended solids (MLSS). Sapoviruses and rotaviruses were detected in 25% of MBR effluent samples with log reduction values of 3- and 2-logs in geometric mean concentrations, respectively, while noroviruses were detected in only 6% of the samples. We found that norovirus and sapovirus concentrations in the solid phase of mixed liquor samples were significantly higher than in the liquid phase (P < 0.01, t test), while the concentration of rotaviruses was similar in both phases. The efficiency of adsorption of the rotavirus G1P[8] strain to MLSS was significantly less than norovirus GI.1 and GII.4 and sapovirus GI.2 strains (P < 0.01, t test). Differences in the adsorption of viruses to MLSS may cause virus type-specific removal during the MBR treatment process as shown by this study.
Collapse
Affiliation(s)
- Takayuki Miura
- Laboratoire de Microbiologie, LSEM-SG2 M, IFREMER, Nantes, France.
- Department of Environmental Health, National Institute of Public Health, 2-3-6 Minami, Wako, Saitama, 351-0197, Japan.
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM-SG2 M, IFREMER, Nantes, France
| | | | | | | |
Collapse
|
40
|
Diez-Valcarce M, Castro CJ, Marine RL, Halasa N, Mayta H, Saito M, Tsaknaridis L, Pan CY, Bucardo F, Becker-Dreps S, Lopez MR, Magaña LC, Ng TFF, Vinjé J. Genetic diversity of human sapovirus across the Americas. J Clin Virol 2018; 104:65-72. [PMID: 29753103 DOI: 10.1016/j.jcv.2018.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). RESULTS VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. CONCLUSIONS Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.
Collapse
Affiliation(s)
| | | | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Holger Mayta
- Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Department of Virology, Tohoku University, Graduate School of Medicine, Sendai, Japan
| | | | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Filemon Bucardo
- Department of Microbiology, University of Leon, Leon, Nicaragua
| | - Sylvia Becker-Dreps
- Department of Family Medicine and Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | | | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| |
Collapse
|
41
|
Chhabra P, Gregoricus N, Weinberg GA, Halasa N, Chappell J, Hassan F, Selvarangan R, Mijatovic-Rustempasic S, Ward ML, Bowen M, Payne DC, Vinjé J. Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses. J Clin Virol 2017; 95:66-71. [PMID: 28889082 DOI: 10.1016/j.jcv.2017.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available. OBJECTIVE/STUDY DESIGN We evaluated the performance of three multiplex platforms including Biofire's Gastrointestinal Panel (FilmArray), Luminex xTAG® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples. RESULTS The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC. CONCLUSION The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms.
Collapse
Affiliation(s)
- Preeti Chhabra
- Synergy America, Inc., Atlanta, GA, United States; Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nicole Gregoricus
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY, United States
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt Vaccine Research Program, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James Chappell
- Department of Pediatrics, Vanderbilt Vaccine Research Program, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, United States
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, United States
| | - Slavica Mijatovic-Rustempasic
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - M Leanne Ward
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Michael Bowen
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Daniel C Payne
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States.
| |
Collapse
|
42
|
Hergens MP, Nederby Öhd J, Alm E, Askling HH, Helgesson S, Insulander M, Lagerqvist N, Svenungsson B, Tihane M, Tolfvenstam T, Follin P. Investigation of a food-borne outbreak of gastroenteritis in a school canteen revealed a variant of sapovirus genogroup V not detected by standard PCR, Sollentuna, Sweden, 2016. Euro Surveill 2017; 22:30543. [PMID: 28602163 PMCID: PMC5479987 DOI: 10.2807/1560-7917.es.2017.22.22.30543] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/10/2017] [Indexed: 01/19/2023] Open
Abstract
A food-borne outbreak of gastroenteritis with more than 650 suspected cases occurred in April 2016 in Sollentuna, Sweden. It originated in a school kitchen serving a total of 2,700 meals daily. Initial microbiological testing (for Campylobacter, Salmonella, Shigella, Yersinia, Giardia, Cryptosporidium, Entamoeba histolytica, adeno-, astro-, noro-, rota- and sapovirus) of stool samples from 15 symptomatic cases was negative, despite a clinical presentation suggestive of calicivirus. Analyses of the findings from both the Sollentuna municipality environmental team and a web-based questionnaire suggested that the source of the outbreak was the salad buffet served on 20 April, although no specific food item could be identified. Subsequent electron microscopic examination of stool samples followed by whole genome sequencing revealed a variant of sapovirus genogroup V. The virus was not detected using standard PCR screening. This paper describes the epidemiological outbreak investigation and findings leading to the discovery.
Collapse
Affiliation(s)
- Maria-Pia Hergens
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
- Department of Medicine Solna, Infectious Disease Unit, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Nederby Öhd
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
| | - Erik Alm
- Public Health Agency of Sweden, Stockholm, Sweden
| | - Helena H Askling
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
- Department of Medicine Solna, Infectious Disease Unit, Karolinska Institutet, Stockholm, Sweden
| | | | - Mona Insulander
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
| | | | - Bo Svenungsson
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
| | - Malin Tihane
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
| | | | - Per Follin
- Department of Communicable Disease Control and Prevention, Stockholm County Council, Sweden
- Department of Medicine Solna, Infectious Disease Unit, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
43
|
Bennett S, Gunson RN. The development of a multiplex real-time RT-PCR for the detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. J Virol Methods 2017; 242:30-34. [PMID: 28040514 PMCID: PMC7173313 DOI: 10.1016/j.jviromet.2016.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 11/07/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Abstract
Viral gastroenteritis is a major health problem with significant morbidity and economic consequences. Viral gastroenteritis is caused by a number of viruses, including norovirus, rotavirus, adenovirus, astrovirus, and sapovirus. Conventional diagnosis is based on direct antigen detection and electron microscopy, however enzyme immunoassay's are insensitive and not available for all relevant pathogens, and electron microscope (EM) is no longer routinely carried out in most laboratories. Most laboratories now offer norovirus real-time PCR testing however the availability of other assays is variable. Commercial methods for the detection of inflectional intestinal disease (IID) are available but these can be expensive and are not commonly used. This paper describes the development of a single multiplex assay for the simultaneous detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. The multiplex was evaluated by assessing endpoint sensitivity, specificity, panel of clinical samples, quality control (QC) panel and the robustness and reproducibility of the multiplex.
Collapse
Affiliation(s)
- Susan Bennett
- West of Scotland Specialist Virology Centre, United Kingdom.
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, United Kingdom
| |
Collapse
|
44
|
Zhou X, Sun Y, Shang X, Gao J, Zhao X, Shuai H, Zhang R, Zhang Y. Complete genome sequence of a sapovirus from a child in Zhejiang, China. Virus Genes 2016; 52:706-10. [PMID: 27122130 PMCID: PMC5002278 DOI: 10.1007/s11262-016-1343-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 04/16/2016] [Indexed: 11/25/2022]
Abstract
Although Sapovirus (Caliciviridae) has been accepted as one of the causes of acute gastroenteritis worldwide, little is known about the genetic characteristics of the whole genome of sapoviruses in China, especially those that infect humans. Here we report the complete genome sequence of a sapovirus strain, Human/Zhejiang1/2015/China, obtained from a child with acute gastroenteritis in Hangzhou, Zhejiang Province, China. Samples were collected and delivered to the CDC laboratories and were detected by RT-PCR. Sanger sequencing was used to obtain the full genome and molecular characterization of the genome was determined. A phylogenetic analysis of the genome was also performed. The results indicated that Human/Zhejiang1/2015/China belongs to Genogroup I. No recombination events were detected. This is the first complete sequence from a child to be reported in China. The sequence information is important for surveillance of this emerging gastrointestinal infection.
Collapse
Affiliation(s)
- Xiaohong Zhou
- Xiacheng District Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Yi Sun
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Xiaochun Shang
- Xiacheng District Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Jian Gao
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Xueqin Zhao
- Xiacheng District Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Huiqun Shuai
- Xiacheng District Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Rui Zhang
- Xiacheng District Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, Zhejiang, China.
| |
Collapse
|
45
|
Varela MF, Hooper AS, Rivadulla E, Romalde JL. Human Sapovirus in Mussels from Ría do Burgo, A Coruña (Spain). Food Environ Virol 2016; 8:187-193. [PMID: 27156175 DOI: 10.1007/s12560-016-9242-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/02/2016] [Indexed: 06/05/2023]
Abstract
The prevalence and genetical diversity of human Sapovirus were studied during an 18-month study in Ría do Burgo, an estuary nearby the city of A Coruña in Galicia (NW Spain). Sapovirus was detected using RT-qPCR procedure in 30 out of 80 mussel samples (37.5 %). Quantifications ranged from 2.2 × 10(3) to 2.1 × 10(5) RNA copies per gram of digestive tissue. Detection occurred mainly during the cold and rainy seasons of the period studied. Sequences obtained could be distributed into 5 genotypes being the most abundant GI.1 and GI.3. Results obtained indicate that the hydrodynamic characteristics of the harvesting area and the proximity of population density clearly influence the presence of the virus in shellfish.
Collapse
Affiliation(s)
- Miguel F Varela
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Annalise S Hooper
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- School of Marine Sciences, University of Portsmouth, Portsmouth, UK
| | - Enrique Rivadulla
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| |
Collapse
|
46
|
Portal TM, Siqueira JAM, Costa LCPDN, Lima ICGD, Lucena MSSD, Bandeira RDS, Linhares ADC, Luz CRNED, Gabbay YB, Resque HR. Caliciviruses in hospitalized children, São Luís, Maranhão, 1997-1999: detection of norovirus GII.12. Braz J Microbiol 2016; 47:724-30. [PMID: 27161199 PMCID: PMC4927645 DOI: 10.1016/j.bjm.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 01/04/2016] [Indexed: 01/12/2023] Open
Abstract
Gastroenteritis is one of the most common diseases during childhood, with norovirus (NoV) and sapovirus (SaV) being two of its main causes. This study reports for the first time the incidence of these viruses in hospitalized children with and without gastroenteritis in São Luís, Maranhão. A total of 136 fecal samples were tested by enzyme immunoassays (EIA) for the detection of NoV and by reverse transcription-polymerase chain reaction (RT-PCR) for detection of both NoV and SaV. Positive samples for both agents were subjected to sequencing. The overall frequency of NoV as detected by EIA and RT-PCR was 17.6% (24/136) and 32.6% (15/46), respectively in diarrheic patients and 10.0% (9/90) in non-diarrheic patients (p<0.01). Of the diarrheic patients, 17% had fever, vomiting and anorexia, and 13% developed fever, vomiting and abdominal pain. Of the 24 NoV-positive samples, 50% (12/24) were sequenced and classified as genotypes GII.3 (n=1), GII.4 (6), GII.5 (1), GII.7 (2), GII.12 (1) and GII.16 (1). SaV frequency was 9.8% (11/112), with 22.6% (7/31) in diarrheic patients and 4.9% (4/81) in nondiarrheic (p=0.04) ones. In diarrheic cases, 27.3% had fever, vomiting and anorexia, whereas 18.2% had fever, anorexia and abdominal pain. One SaV-positive sample was sequenced and classified as GII.1. These results show a high genetic diversity of NoV and higher prevalence of NoV compared to SaV. Our data highlight the importance of NoV and SaV as enteropathogens in São Luís, Maranhão.
Collapse
Affiliation(s)
- Thayara Morais Portal
- Programa de Pós-Graduação em Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém, Pará, Brazil
| | | | | | | | | | | | | | | | | | - Hugo Reis Resque
- Seção de Virologia, Instituto Evandro Chagas/SVS/MS, Ananindeua, Pará, Brazil.
| |
Collapse
|
47
|
Oka T, Lu Z, Phan T, Delwart EL, Saif LJ, Wang Q. Genetic Characterization and Classification of Human and Animal Sapoviruses. PLoS One 2016; 11:e0156373. [PMID: 27228126 PMCID: PMC4881899 DOI: 10.1371/journal.pone.0156373] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 12/04/2022] Open
Abstract
Sapoviruses (SaVs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans, pigs, mink, dogs, sea lions, chimpanzees, and rats. They show a high level of diversity. A SaV genome commonly encodes seven nonstructural proteins (NSs), including the RNA polymerase protein NS7, and two structural proteins (VP1 and VP2). We classified human and animal SaVs into 15 genogroups (G) based on available VP1 sequences, including three newly characterized genomes from this study. We sequenced the full length genomes of one new genogroup V (GV), one GVII and one GVIII porcine SaV using long range RT-PCR including newly designed forward primers located in the conserved motifs of the putative NS3, and also 5' RACE methods. We also determined the 5’- and 3’-ends of sea lion GV SaV and canine GXIII SaV. Although the complete genomic sequences of GIX-GXII, and GXV SaVs are unavailable, common features of SaV genomes include: 1) “GTG” at the 5′-end of the genome, and a short (9~14 nt) 5′-untranslated region; and 2) the first five amino acids (M [A/V] S [K/R] P) of the putative NS1 and the five amino acids (FEMEG) surrounding the putative cleavage site between NS7 and VP1 were conserved among the chimpanzee, two of five genogroups of pig (GV and GVIII), sea lion, canine, and human SaVs. In contrast, these two amino acid motifs were clearly different in three genogroups of porcine (GIII, GVI and GVII), and bat SaVs. Our results suggest that several animal SaVs have genetic similarities to human SaVs. However, the ability of SaVs to be transmitted between humans and animals is uncertain.
Collapse
Affiliation(s)
- Tomoichiro Oka
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, United States of America
- Department of Virology II, National Institute of Infectious Diseases, Musashi-murayama, Tokyo, Japan
| | - Zhongyan Lu
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, United States of America
| | - Tung Phan
- Blood System Research Institute, 270 Masonic Avenue, San Francisco, CA, United States of America
- University of California San Francisco, Dept of Laboratory Medicine, San Francisco, CA, United States of America
| | - Eric L. Delwart
- Blood System Research Institute, 270 Masonic Avenue, San Francisco, CA, United States of America
- University of California San Francisco, Dept of Laboratory Medicine, San Francisco, CA, United States of America
| | - Linda J. Saif
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, United States of America
- * E-mail: (QW); (LJS)
| | - Qiuhong Wang
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, United States of America
- * E-mail: (QW); (LJS)
| |
Collapse
|
48
|
Torner N, Martinez A, Broner S, Moreno A, Camps N, Domínguez A. Epidemiology of Acute Gastroenteritis Outbreaks Caused by Human Calicivirus (Norovirus and Sapovirus) in Catalonia: A Two Year Prospective Study, 2010-2011. PLoS One 2016; 11:e0152503. [PMID: 27120472 PMCID: PMC4847761 DOI: 10.1371/journal.pone.0152503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 03/15/2016] [Indexed: 12/25/2022] Open
Abstract
Background The epidemiology of cases of acute gastroenteritis (AGE) of viral etiology is a relevant public health issue. Due to underreporting, the study of outbreaks is an accepted approach to investigate their epidemiology. The objective of this study was to investigate the epidemiological characteristics of AGE outbreaks due to norovirus (NoV) and sapovirus (SV) in Catalonia. Material and Methods Prospective study of AGE outbreaks of possible viral etiology notified during two years in Catalonia. NoV and SV were detected by real time reverse transcription polymerase (RT-PCR). Results A total of 101 outbreaks were registered affecting a total of 2756 persons and 12 hospitalizations (hospitalization rate: 0.8x1,000,000 persons-year); 49.5% of outbreaks were foodborne, 45.5% person to person and 5% waterborne. The distribution of outbreaks according to the setting showed a predominance of catering services (39.6%), nursing homes and long term care facilities (26.8%) and schools (11.9%). The median number of cases per outbreak was 17 (range 2–191). The total Incidence rate (IR) was 18.3 per 100,000 persons-years (95%CI: 17.6–19.0). The highest IR was in persons aged ≥65 years (43.6x100,000 (95% CI: 41.0–46.2)) (p<0.001). A total of 1065 samples were analyzed with a positivity rate of 60.8%. 98% of positive samples were NoV (GII 56.3%; GI 4.2%; GII+GI 4.2%; non- typable 33.0%). SV was identified in two person-to-person transmission outbreaks in children. Conclusions These results confirm the relevance of viral AGE outbreaks, both foodborne and person-to-person, especially in institutionalized persons. SV should be taken into account when investigating viral AGE outbreaks.
Collapse
Affiliation(s)
- Nuria Torner
- Public Health Agency of Catalonia, Barcelona, Spain
- CIBER Epidemiología y Salud Pública CIBERESP, Carlos III Health Institute, Madrid, Spain
- Public Health Department, University of Barcelona, Barcelona, Spain
- * E-mail:
| | - Ana Martinez
- Public Health Agency of Catalonia, Barcelona, Spain
- CIBER Epidemiología y Salud Pública CIBERESP, Carlos III Health Institute, Madrid, Spain
| | - Sonia Broner
- CIBER Epidemiología y Salud Pública CIBERESP, Carlos III Health Institute, Madrid, Spain
| | | | - Neus Camps
- Public Health Agency of Catalonia, Barcelona, Spain
| | - Angela Domínguez
- CIBER Epidemiología y Salud Pública CIBERESP, Carlos III Health Institute, Madrid, Spain
- Public Health Department, University of Barcelona, Barcelona, Spain
| | | |
Collapse
|
49
|
Kluge M, Campos FS, Tavares M, de Amorim DB, Valdez FP, Giongo A, Roehe PM, Franco AC. Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals. PLoS One 2016; 11:e0151921. [PMID: 26986573 PMCID: PMC4795697 DOI: 10.1371/journal.pone.0151921] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
The Brazilian South coast seasonally hosts numerous marine species, observed particularly during winter months. Some animals, including fur seals, are found dead or debilitated along the shore and may harbor potential pathogens within their microbiota. In the present study, a metagenomic approach was performed to evaluate the viral diversity in feces of fur seals found deceased along the coast of the state of Rio Grande do Sul. The fecal virome of two fur seal species was characterized: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected and viral particles were purified, extracted and amplified with a random PCR. The products were sequenced through Ion Torrent and Illumina platforms and assembled reads were submitted to BLASTx searches. Both viromes were dominated by bacteriophages and included a number of potentially novel virus genomes. Sequences of picobirnaviruses, picornaviruses and a hepevirus-like were identified in A. australis. A rotavirus related to group C, a novel member of the Sakobuvirus and a sapovirus very similar to California sea lion sapovirus 1 were found in A. tropicalis. Additionally, sequences of members of the Anelloviridae and Parvoviridae families were detected in both fur seal species. This is the first metagenomic study to screen the fecal virome of fur seals, contributing to a better understanding of the complexity of the viral community present in the intestinal microbiota of these animals.
Collapse
Affiliation(s)
- Mariana Kluge
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, UFRGS (Federal University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabrício Souza Campos
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, UFRGS (Federal University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
| | - Maurício Tavares
- CECLIMAR (Center for Coastal, Limnology and Marine Studies), UFRGS (Federal University of Rio Grande do Sul), Imbé, Rio Grande do Sul, Brazil
| | - Derek Blaese de Amorim
- CECLIMAR (Center for Coastal, Limnology and Marine Studies), UFRGS (Federal University of Rio Grande do Sul), Imbé, Rio Grande do Sul, Brazil
| | - Fernanda Pedone Valdez
- Genomic and Molecular Biology Laboratory, PUCRS (Pontifical Catholic University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
| | - Adriana Giongo
- IPR (Institute of Petroleum and Natural Resources), PUCRS (Pontifical Catholic University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
| | - Paulo Michel Roehe
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, UFRGS (Federal University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Claudia Franco
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, UFRGS (Federal University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
| |
Collapse
|
50
|
Coudray-Meunier C, Fraisse A, Martin-Latil S, Delannoy S, Fach P, Perelle S. A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System. PLoS One 2016; 11:e0147832. [PMID: 26824897 PMCID: PMC4732599 DOI: 10.1371/journal.pone.0147832] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/08/2016] [Indexed: 12/23/2022] Open
Abstract
Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health.
Collapse
Affiliation(s)
- Coralie Coudray-Meunier
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
- * E-mail:
| |
Collapse
|