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Wolken M, Wang M, Schedler J, Campos RH, Ensor K, Hopkins L, Treangen T, Stadler LB. PreK-12 school and citywide wastewater monitoring of the enteric viruses astrovirus, rotavirus, and sapovirus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172683. [PMID: 38663617 DOI: 10.1016/j.scitotenv.2024.172683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/07/2024]
Abstract
Wastewater monitoring is an efficient and effective way to surveil for various pathogens in communities. This is especially beneficial in areas of high transmission, such as preK-12 schools, where infections may otherwise go unreported. In this work, we apply wastewater disease surveillance using school and community wastewater from across Houston, Texas to monitor three major enteric viruses: astrovirus, sapovirus genogroup GI, and group A rotavirus. We present the results of a 10-week study that included the analysis of 164 wastewater samples for astrovirus, rotavirus, and sapovirus in 10 preK-12 schools, 6 wastewater treatment plants, and 2 lift stations using newly designed RT-ddPCR assays. We show that the RT-ddPCR assays were able to detect astrovirus, rotavirus, and sapovirus in school, lift station, and wastewater treatment plant (WWTP) wastewater, and that a positive detection of a virus in a school sample was paired with a positive detection of the same virus at a downstream lift station or wastewater treatment plant over 97 % of the time. Additionally, we show how wastewater detections of rotavirus in schools and WWTPs were significantly associated with citywide viral intestinal infections. School wastewater can play a role in the monitoring of enteric viruses and in the detection of outbreaks, potentially allowing public health officials to quickly implement mitigation strategies to prevent viral spread into surrounding communities.
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Affiliation(s)
- Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, United States of America
| | - Michael Wang
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, United States of America
| | - Julia Schedler
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, United States of America
| | - Roberto H Campos
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, United States of America
| | - Katherine Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, United States of America
| | - Loren Hopkins
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, United States of America; Houston Health Department, 8000 N. Stadium Dr., Houston, TX, United States of America
| | - Todd Treangen
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, United States of America; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, United States of America.
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2
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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] [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.
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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.
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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] [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.
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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.
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Rippl M, Burkhard-Meier A, Schönermarck U, Fischereder M. Sapovirus: an emerging pathogen in kidney transplant recipients? Infection 2024:10.1007/s15010-024-02242-9. [PMID: 38592660 DOI: 10.1007/s15010-024-02242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024]
Abstract
PURPOSE Diarrhea is an important cause of morbidity and mortality in immunocompromised patients. After including sapovirus to the viral gastroenteritis screening of our institution's laboratory, we noticed an increase in sapovirus infections among kidney transplant recipients. Therefore, we assumed former gastrointestinal tract infections with unidentified pathogens could have been caused by sapovirus. To better understand the characteristics of a sapovirus infection in a high-risk group we initiated this study. METHODS Over a period of 6 months, all transplant recipients with diarrhea and later identified viral/unknown pathogens were included. Kidney function, levels of immunosuppressants and c-reactive protein, acid-base balance, onset of symptoms and time of hospitalization were analyzed. RESULTS Among 13 hospitalized kidney transplant recipients sapovirus was detected in four patients, while in the remaining nine, three were diagnosed with norovirus, one with cytomegalovirus, one with inflammatory bowel disease and in four patients no pathogen was identified. Even though statistically not significant, creatinine levels at admission tended to be higher in sapovirus patients (median: sapovirus: 3.3 mg/dl (1.3; 5.0), non-sapovirus: 2.5 mg/dl (1.1; 4.9), p = 0.710). Also, Tacrolimus levels showed the same trend (sapovirus: 13.6 ng/ml (12.9; 13.6), non-sapovirus: 7.1 ng/ml (2.6; 22.6), p = 0.279). On discharge creatinine levels improved equally in both groups (sapovirus: 1.7 mg/dl (1.4; 3.2), non-sapovirus: 2 mg/dl (1.0; 3.6), p = 0.825). CONCLUSION In high-risk patients, early symptomatic treatment remains crucial to protect the transplant`s function. In our cohort all patients recovered well. Larger cohorts and longer follow-up times are needed to detect the long-term consequences and a potential need for further research regarding specific treatment. TRIAL REGISTRATION The study has been registered on DRKS (trialsearch.who.int), Reg. Nr. DRKS00033311 (December 28th 2023).
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Affiliation(s)
- Michaela Rippl
- Division of Geriatrics, Department of Medicine IV, LMU University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany.
| | - Anton Burkhard-Meier
- Department of Medicine III, LMU University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Ulf Schönermarck
- Division of Nephrology, Department of Medicine IV, LMU University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Michael Fischereder
- Division of Nephrology, Department of Medicine IV, LMU University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
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Ibrahim C, Hammami S, Khelifi N, Pothier P, Hassen A. Activated sludge and UV-C 254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 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] [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.
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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
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Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms 2024; 12:696. [PMID: 38674640 PMCID: PMC11052288 DOI: 10.3390/microorganisms12040696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.
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Affiliation(s)
- Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Naveen Kumar
- Diagnostics and Vaccines Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462021, Madhya Pradesh, India;
| | - Pragya Yadav
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Shubhankar Sircar
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Anita Shete-Aich
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Thomas Launey
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, Punjab, India
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Flynn TG, Olortegui MP, Kosek MN. Viral gastroenteritis. Lancet 2024; 403:862-876. [PMID: 38340741 DOI: 10.1016/s0140-6736(23)02037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/17/2023] [Accepted: 09/18/2023] [Indexed: 02/12/2024]
Abstract
Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.
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Affiliation(s)
- Thomas G Flynn
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Cintron M, Jani K, Madhavappallil J, Kamboj M, Babady NE. Prevalence of astrovirus and sapovirus among adult oncology patients with acute gastroenteritis using a multiplexed gastrointestinal pathogen PCR panel. Eur J Clin Microbiol Infect Dis 2024; 43:525-531. [PMID: 38216845 DOI: 10.1007/s10096-024-04748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Multiplex syndromic gastrointestinal panels (GIPCR) have streamlined the diagnosis of infectious diarrhea. Additionally, they have expanded the number of pathogens that can be routinely evaluated, allowing further understanding of the prevalence of enteric pathogens in various patient populations. The goal of this study was to investigate the prevalence and clinical presentation of astrovirus and sapovirus gastroenteritis in adult oncology patients as detected by the FilmArray GIPCR. METHODS All GIPCR panel results from December 2017 to June 2021 were retrospectively reviewed to determine the prevalence of astrovirus and sapovirus in adult oncology patients. Medical records were also reviewed to obtain clinical information. Repeat GIPCR positivity and symptom duration were used to estimate prolonged viral shedding. RESULTS A total of 18,014 panels were performed on samples collected from 9303 adults. Overall, astrovirus and sapovirus were detected in 0.35% (33/9303) and 0.45% (42/9303) GIPCRs respectively. At least one viral target was detected in 424 (4.4%) patients. Astrovirus accounted for 7.8% (33/424) and sapovirus 9.9% (42/424) of patients. Diarrhea was the most common symptom documented. A subset of transplant patients had protracted viral detection with a median of ~27 days (range 23-43 days) for astrovirus and 97 days (range 11-495) for sapovirus. No clusters or outbreaks were identified during the study period. CONCLUSION In oncology patients with viral gastroenteritis, astrovirus and sapovirus were the causative agents in 18% of the cases. Both viruses were associated with mild disease. Prolonged diarrhea and viral shedding were observed in a few transplant patients.
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Affiliation(s)
- Melvili Cintron
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jerin Madhavappallil
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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Cantelli CP, Tavares GCL, Sarmento SK, Burlandy FM, Fumian TM, Maranhão AG, da Silva EDSRF, Horta MAP, Miagostovich MP, Yang Z, Leite JPG. Assessment of Gastroenteric Viruses in Marketed Bivalve Mollusks in the Tourist Cities of Rio de Janeiro, Brazil, 2022. Viruses 2024; 16:317. [PMID: 38543684 PMCID: PMC10974528 DOI: 10.3390/v16030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 05/23/2024] Open
Abstract
This study investigated the prevalence and genetic diversity of gastroenteric viruses in mussels and oysters in Rio de Janeiro, Brazil. One hundred and thirty-four marketed bivalve samples were obtained between January and December 2022. The viral analysis was performed according to ISO/TS 15216, and the screening revealed the detection of norovirus GII/GI (40.3%), sapovirus (SaV; 12.7%), human mastadenovirus (7.5%), and rotavirus A (RVA; 5.9%). In total, 44.8% (60) of shellfish samples tested positive for one or more viruses, 46.7% (28/60) of the positive samples tested positive for a single viral agent, 26.7% (16) tested positive for two viral agents, 8.3% (5) for three viral agents, and 13.3% (8) for four viral agents. Additionally, three mussel samples were contaminated with the five investigated viruses (5%, 3/60). Norovirus GII showed the highest mean viral load (3.4 × 105 GC/g), followed by SaV (1.4 × 104 GC/g), RVA (1.1 × 104 GC/g), human mastadenovirus (3.9 × 103 GC/g), and norovirus GI (6.7 × 102 GC/g). Molecular characterization revealed that the recovered norovirus strains belonged to genotypes GII.2, GII.6, GII.9, GII.17, and GII.27; SaV belonged to genotypes GI.1 and GIV.1; RVA to genotypes G6, G8, P[8]-III, and human mastadenovirus to types F40 and F41. The GII.27 norovirus characterized in this study is the only strain of this genotype reported in Brazil. This study highlights the dissemination and diversity of gastroenteric viruses present in commercialized bivalves in a touristic area, indicating the potential risk to human health and the contribution of bivalves in the propagation of emerging pathogens.
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Affiliation(s)
- Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | - Sylvia Kahwage Sarmento
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | - Adriana Gonçalves Maranhão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
| | | | | | | | - Zhihui Yang
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20723, USA
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz 21040-360, RJ, Brazil
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10
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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] [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.
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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.)
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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] [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.
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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.)
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12
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Bouazizi A, Ben Hadj Fredj M, Bennour H, Jerbi A, Ouafa kallala, Fodha I, Trabelsi A. Molecular analysis of adenovirus strains responsible for gastroenteritis in children, under five, in Tunisia. Heliyon 2024; 10:e22969. [PMID: 38163238 PMCID: PMC10754908 DOI: 10.1016/j.heliyon.2023.e22969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Purpose of work Enteric Adenovirus (EAdV) is recognized as one of the most commonly identified agents responsible for severe acute gastroenteritis (AGEs) in the stools of infants.We sought to determine the rate of human adenovirus (HAdV) infections, and the genotypic characterization of circulating strains of HAdV in children under 5 years of age with AGEs in university and regional hospitals, located in the Center-East of Tunisia, from January 2014 to December 2016. Methods A classic PCR was performed on 582 stool samples taken within 5 days of the onset of symptoms. Chosen positive samples were sequenced, and some of the results were confirmed by the Next Generation Sequencing technique (NGS). Partial nucleotide sequences of the Hexon gene obtained in this study were compared with the NCBI GenBank database using BLAST. Multiple sequence alignment and phylogenetic analysis were conducted using MEGA6 software. The phylogenetic tree was generated using the maximum-likelihood method and bootstrap analysis was performed with 1000 replications. Results Out of 582 samples, 52 (8.93 %) cases were positive for HAdV, with a male predominance (57.4 %). Phylogenetic analyses showed that Tunisian HAdV strains clustered into five HAdV lineages corresponding to serotypes F41 (14/28), C2 (9/28), C5 (3/28), E4 (1/28), and A18 (1/28). HAdV was more frequent in children aged up to 12 months, as compared to the other age groups. The HAdV activity was noted in almost all the months of the year with a peak in autumn, in 2014 and 2015, and in winter in 2016. Conclusion This study showed that infections with HAdV species were frequent in children suffering from AGE with the predominance of HAdV F41 and C2. This result underlines the importance of regular monitoring of circulating genotypes, and it could be useful for future epidemiological research.
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Affiliation(s)
- Asma Bouazizi
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Mouna Ben Hadj Fredj
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia
| | - Haifa Bennour
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Amira Jerbi
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Ouafa kallala
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Imene Fodha
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Abdelhalim Trabelsi
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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13
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Powell EA, Hata DJ, Starolis MW. Viral pathogen detection using multiplex gastrointestinal molecular panels: The pros and cons of viral target inclusion. J Clin Virol 2023; 169:105612. [PMID: 37866093 DOI: 10.1016/j.jcv.2023.105612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/31/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Diagnosis of gastrointestinal infections has been revolutionized by the development of in vitro diagnostic (IVD) multiplex molecular panels for the detection of viral nucleic acids. In addition to a high degree of accuracy, these panels are commercially available and relatively simple to perform in the clinical laboratory. However, use of these panels must be carefully considered owing to the laboratory costs of the test, limited reimbursement, and potential for overuse. In this review from the Pan American Society for Clinical Virology, we focus on the viral components of GI multiplex panels (GIPs), presenting a brief overview of pathogens included on most panels and a discussion of advantages and challenges of the inclusion of viral targets on GIPs that should be considered before implementation in the clinical laboratory.
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Affiliation(s)
- Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, 234 Goodman St., Cincinnati, OH 45219, United States.
| | - D Jane Hata
- Department of Laboratory Medicine and Pathology, Mayo Clinic Florida, 4500 San Pablo Rd., Jacksonville, FL 32266, United States
| | - Meghan W Starolis
- Quest Diagnostics, 14225 Newbrook Dr., Chantilly, VA 20155, United States
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14
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Cupido DT, de Beer C. Screening for viral pathogens in the gastrointestinal tract from cases of sudden unexpected death in infancy at the Tygerberg Medico-legal Mortuary. Virol J 2023; 20:281. [PMID: 38031160 PMCID: PMC10688011 DOI: 10.1186/s12985-023-02249-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023] Open
Abstract
Sudden and unexpected death in infancy (SUDI) may be triggered by an external risk or exposure. Intestinal infections with enteric viruses may disrupt the gut and enhance bacterial toxins present in SUDI cases. While diarrhoeal disease deaths have decreased worldwide, approximately half a million deaths still occur in children in Sub- Saharan Africa and South Asia. Furthermore, the role of viral enteropathogens in SUDI cases have not been investigated. The aim of this study was to describe specific viral pathogens in stool samples collected from SUDI cases and age-matched, apparently healthy infants in Cape Town, South Africa. Stool samples were collected from 176 SUDI cases between June 2017 and May 2018. In addition, stool samples were collected from the nappies of 30 age-matched, apparently healthy infants as a control group. Real-time polymerase chain reaction was performed on the stool samples for viral detection. A total of 111 SUDI cases were positive for viruses, with rotavirus (38.6%; 68/176) and norovirus GI and GII (30.0%; 53/176) were prevalent in SUDI cases. Adenovirus Type F was present in only 15.9% (28/176), astrovirus in 9.7% (17/176), and sapovirus in 0.6% (1/176) of cases. In the control samples, norovirus GII was detected most frequently (36.7%; 11/30), followed by rotavirus (33.3%; 10/30), and sapovirus in 6.7% (2/30). While there was no significant association between SUDI cases and enteric viruses, the majority of viruses were significantly associated with the seasons. The study confirms the importance of rotavirus vaccination and describes the significance of norovirus infection in children, post rotavirus vaccine introduction.
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Affiliation(s)
- Danielle T Cupido
- Division of Medical Virology, Department of Pathology, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
| | - Corena de Beer
- Division of Medical Virology, Department of Pathology, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
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15
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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] [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.
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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.
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16
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Hata DJ, Powell EA, Starolis MW. Utility and Recommendations for the Use of Multiplex Molecular Gastrointestinal Pathogen Panels. J Appl Lab Med 2023; 8:1148-1159. [PMID: 37102500 DOI: 10.1093/jalm/jfad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/27/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Many molecular gastrointestinal pathogen panels (GIPs) are Food and Drug Administration (FDA) cleared but it is still unclear how to best utilize these new diagnostic tools. GIPs are highly sensitive and specific, simultaneously detect multiple pathogens in one reaction, and can shorten the overall time of diagnosis for infectious gastroenteritis but are also expensive with relatively poor insurance reimbursement. CONTENT In this review, we take a comprehensive approach to discuss issues with utilization of GIPs from a physician perspective, and implementation from a laboratory perspective. The information presented is to assist physicians in deciding on appropriate use of GIPs in diagnostic algorithms for their patients, and to provide information to laboratories that may be considering the addition of these powerful diagnostic assays to their test menu. Some of the important topics discussed are inpatient vs outpatient use, the appropriate panel size and organisms to include, interpretation of results, laboratory validation, and reimbursement. SUMMARY The information in this review provides clear guidance to both clinicians and laboratories in deciding the best use of GIPs for a specific patient population. While this technology provides many benefits over traditional methods, it can also complicate result interpretation and comes with a high cost, which necessitates the need for use recommendations.
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Affiliation(s)
- D Jane Hata
- Department of Laboratory Medicine and Pathology, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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17
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Opere MW. Analysing the interplay of environmental virology, public health, and sanitation: a comprehensive review from a Kenyan perspective. Front Cell Infect Microbiol 2023; 13:1256822. [PMID: 37942480 PMCID: PMC10629379 DOI: 10.3389/fcimb.2023.1256822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
This comprehensive review examines the interplay between environmental virology, public health, and sanitation in the unique context of Kenya. The review sheds light on the specific viral threats faced by the country, including waterborne viruses, zoonotic infections, and emerging viral diseases, and their implications for public health. It explores the prevailing public health challenges in Kenya associated with environmental viromics, such as infectious viral diseases, and the rising burden of other infectious particles. The role of sanitation in mitigating viral infections is highlighted, emphasising the importance of clean water supply, proper waste management, and hygienic practises. The review also presents strategies for strengthening environmental virology research in Kenya, including enhancing laboratory capacities and leveraging technological advancements. Furthermore, the policy implications and recommendations derived from the review emphasise the need for multi-sectoral collaboration, evidence-based decision-making, and long-term investments in infrastructure and behaviour change interventions. Implementing these strategies can enhance the understanding of environmental virology, improve public health outcomes, and ensure sustainable sanitation practises in Kenya, ultimately contributing to the well-being of the population and sustainable development.
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Affiliation(s)
- Michael Wasonga Opere
- School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
- School of Biosciences, The University of Nottingham, Nottingham, United Kingdom
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18
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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] [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.
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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
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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] [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.
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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
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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] [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.
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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
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21
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Jiao Y, Han T, Qi X, Gao Y, Zhao J, Zhang Y, Li B, Zhang Z, Du J, Sun L. Genotypes Diversity of Acute Gastroenteritis Outbreaks Caused by Human Sapovirus - Beijing Municipality, China, 2015-2021. China CDC Wkly 2023; 5:625-631. [PMID: 37520444 PMCID: PMC10372411 DOI: 10.46234/ccdcw2023.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/05/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Human sapovirus (HuSaV) is an enteric virus responsible for sporadic cases and outbreaks of acute gastroenteritis (AGE) globally. A seven-year active surveillance study was conducted to investigate the molecular epidemiology of HuSaVs associated with AGE outbreaks in Chaoyang District of Beijing Municipality, China from January 2015 to December 2021. Methods Fecal and anal swab samples were obtained from patients experiencing AGE outbreaks. HuSaVs were identified through reverse transcription polymerase chain reaction (RT-PCR), and partial viral protein 1 (VP1) sequences (approximately 434 base pairs) were utilized for genotyping, single nucleotide polymorphism (SNP) analysis, and phylogenetic examination. Results HuSaVs were identified in 71 AGE outbreaks, demonstrating a detection rate of 10.5%, second only to norovirus. The primary demographic affected by HuSaV were children under the age of 5 in kindergarten settings. Infection rates tended to peak during two distinct periods: May to June and September to December. Upon genotyping, seven distinct genotypes emerged. GII.3 was the most prevalent, accounting for 54.9% of cases, followed by GI.1 (12.7%), GI.2 (9.9%), GII.5 (7.0%), GI.5 (2.8%), GI.6 (1.4%), GII.1 (1.4%), and untyped cases (9.9%). A phylogenetic analysis of GII.3 identified three distinct groups, with 15 notable SNPs observed. Conclusions This study offers a comprehensive analysis of the persistent prevalence of HuSaV outbreaks in Chaoyang District, Beijing Municipality, China. Over time, the diversity of HuSaV subtypes has shifted, and it is now recognized as the second leading viral agent responsible for AGE outbreaks. This highlights the importance of ongoing surveillance in the future.
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Affiliation(s)
- Yang Jiao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Taoli Han
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Xiao Qi
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Yan Gao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Jianhong Zhao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Yue Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Beibei Li
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Zheng Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Du
- National Institutes for Food and Drug Control, Beijing, China
| | - Lingli Sun
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
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22
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Dong HV, Truong TH, Tran GTH, Rapichai W, Rattanasrisomporn A, Choowongkomon K, Rattanasrisomporn J. Porcine Sapovirus in Northern Vietnam: Genetic Detection and Characterization Reveals Co-Circulation of Multiple Genotypes. Vet Sci 2023; 10:430. [PMID: 37505835 PMCID: PMC10385290 DOI: 10.3390/vetsci10070430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
Porcine sapovirus (PoSaV) has been reported in many countries over the world, which may cause gastroenteritis symptoms in pigs with all ages. There has been no report on PoSaV infection in Vietnam up to now. In this study, a total of 102 samples were collected from piglets, fattening pigs, and sows with diarrhea in several cities and provinces in northern Vietnam. The PoSaV genome was examined using polymerase chain reaction (PCR). Sequencing of the partial RNA-dependent RNA polymerase (RdRp) gene sequences (324 bp) was performed. Of the 102 tested samples, 10 (9.8%) and 7/20 (35%) were detected as positive for the PoSaV RdRp gene using the PCR method at the individual and farm levels, respectively. Genetic analysis of the partial RdRp gene region of about 324 bp indicated that the nucleotide identity of the current 10 Vietnamese viral strains ranged from 61.39% to 100%. Among the 10 strains obtained, 8 belonged to genotype III and the remaining 2 strains were clustered in genotype VIII. The Vietnamese genotype III viruses formed two sub-clusters. The Vietnamese PoSaV strains were closely related to PoSaVs reported in South Korea, Venezuela, and the Netherlands. This research was the first to describe PoSaV infection in northern Vietnam during 2022-2023.
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Affiliation(s)
- Hieu Van Dong
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi 131000, Vietnam
| | - Thai Ha Truong
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi 131000, Vietnam
| | - Giang Thi Huong Tran
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi 131000, Vietnam
| | - Witsanu Rapichai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Amonpun Rattanasrisomporn
- Interdisciplinary of Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jatuporn Rattanasrisomporn
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
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23
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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] [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.
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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
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24
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Shirakawa D, Shirasaki N, Hu Q, Matsushita T, Matsui Y, Takagi H, Oka T. Investigation of removal and inactivation efficiencies of human sapovirus in drinking water treatment processes by applying an in vitro cell-culture system. WATER RESEARCH 2023; 236:119951. [PMID: 37060876 DOI: 10.1016/j.watres.2023.119951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Here, we examined the efficiencies of drinking water treatment processes for the removal and inactivation of human sapovirus (HuSaV). We applied a recently developed in vitro cell-culture system to produce purified solutions of HuSaV containing virus concentrations high enough to conduct virus-spiking experiments, to develop an integrated cell culture-polymerase chain reaction (ICC-PCR) assay to quantify the infectivity of HuSaV, and to conduct virus-spiking experiments. In virus-spiking coagulation-sedimentation-rapid sand filtration (CS-RSF) and coagulation-microfiltration (C-MF) experiments, HuSaV removals of 1.6-3.7-log10 and 1.2->4.3-log10, respectively, were observed. The removal ratios observed with CS-RSF were comparable and correlated with those of murine norovirus (MNV, a widely used surrogate for human noroviruses) and pepper mild mottle virus (PMMoV, a potential surrogate for human enteric viruses in physical and physicochemical drinking water treatment processes), and those observed with C-MF were higher than but still correlated with those of MNV and PMMoV, indicating that MNV and PMMoV are both potential surrogates for HuSaV in CS-RSF and C-MF. For astrovirus (AstV, a representative human enteric virus), removal ratios of 1.8-3.3-log10 and 1.1->4.0-log10 were observed with CS-RSF and C-MF, respectively. The removal ratios of AstV observed with CS-RSF were comparable and correlated with those of PMMoV, and those observed with C-MF were higher than but still correlated with those of PMMoV, indicating that PMMoV is a potential surrogate for AstV in CS-RSF and C-MF. When the efficacy of chlorine treatment was examined by using the developed ICC-PCR assay, 3.8-4.0-log10 inactivation of HuSaV was observed at a CT value (free-chlorine concentration [C] multiplied by contact time [T]) of 0.02 mg-Cl2·min/L. The infectivity reduction ratios of HuSaV were comparable with those of MNV. For AstV, 1.3-1.7-log10 and >3.4-log10 inactivation, as evaluated by ICC-PCR, was observed at CT values of 0.02 and 0.09 mg-Cl2·min/L, respectively. These results indicate that HuSaV and AstV are both highly sensitive to chlorine treatment and more sensitive than a chlorine-resistant virus, coxsackievirus B5 (1.3-log10 inactivation at a CT value of 0.4 mg-Cl2·min/L, as evaluated by the ICC-PCR assay).
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Affiliation(s)
- D Shirakawa
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - N Shirasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - Q Hu
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - T Matsushita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - Y Matsui
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - H Takagi
- Management Department of Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - T Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
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25
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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] [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.
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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.
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26
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Euller-Nicolas G, Le Mennec C, Schaeffer J, Zeng XL, Ettayebi K, Atmar RL, Le Guyader FS, Estes MK, Desdouits M. Human Sapovirus Replication in Human Intestinal Enteroids. J Virol 2023; 97:e0038323. [PMID: 37039654 PMCID: PMC10134857 DOI: 10.1128/jvi.00383-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/12/2023] Open
Abstract
Human sapoviruses (HuSaVs), like human noroviruses (HuNoV), belong to the Caliciviridae family and cause acute gastroenteritis in humans. Since their discovery in 1976, numerous attempts to grow HuSaVs in vitro were unsuccessful until 2020, when these viruses were reported to replicate in a duodenal cancer cell-derived line. Physiological cellular models allowing viral replication are essential to investigate HuSaV biology and replication mechanisms such as genetic susceptibility, restriction factors, and immune responses to infection. In this study, we demonstrate replication of two HuSaV strains in human intestinal enteroids (HIEs) known to support the replication of HuNoV and other human enteric viruses. HuSaVs replicated in differentiated HIEs originating from jejunum, duodenum and ileum, but not from the colon, and bile acids were required. Between 2h and 3 to 6 days postinfection, viral RNA levels increased up from 0.5 to 1.8 log10-fold. Importantly, HuSaVs were able to replicate in HIEs independent of their secretor status and histo-blood group antigen expression. The HIE model supports HuSaV replication and allows a better understanding of host-pathogen mechanisms such as cellular tropism and mechanisms of viral replication. IMPORTANCE Human sapoviruses (HuSaVs) are a frequent but overlooked cause of acute gastroenteritis, especially in children. Little is known about this pathogen, whose successful in vitro cultivation was reported only recently, in a cancer cell-derived line. Here, we assessed the replication of HuSaV in human intestinal enteroids (HIEs), which are nontransformed cultures originally derived from human intestinal stem cells that can be grown in vitro and are known to allow the replication of other enteric viruses. Successful infection of HIEs with two strains belonging to different genotypes of the virus allowed discovery that the tropism of these HuSaVs is restricted to the small intestine, does not occur in the colon, and replication requires bile acid but is independent of the expression of histo-blood group antigens. Thus, HIEs represent a physiologically relevant model to further investigate HuSaV biology and a suitable platform for the future development of vaccines and antivirals.
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Affiliation(s)
| | - Cécile Le Mennec
- MASAE Microbiologie Aliment Santé Environnement, Ifremer, Nantes, France
| | - Julien Schaeffer
- MASAE Microbiologie Aliment Santé Environnement, Ifremer, Nantes, France
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | | | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Marion Desdouits
- MASAE Microbiologie Aliment Santé Environnement, Ifremer, Nantes, France
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27
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Kumazaki M, Usuku S. Influence of herd immunity on norovirus: a long-term field study of repeated viral gastroenteritis outbreaks at the same facilities. BMC Infect Dis 2023; 23:265. [PMID: 37101126 PMCID: PMC10132420 DOI: 10.1186/s12879-023-08251-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Viral acute gastroenteritis (AG) is detected worldwide annually. Outbreaks caused by viruses associated with gastroenteritis have been reported repeatedly at the same facilities in Yokohama, Japan over several years. We investigated the statuses of these repeated outbreaks to consider herd immunity at the facility level. METHODS Between September 2007 and August 2017, 1459 AG outbreaks were reported at 1099 facilities. Stool samples were collected for virological testing, and the norovirus gene was amplified and sequenced to determine the genotype using the N-terminal region of the capsid. RESULTS The outbreaks were caused by norovirus, sapovirus, rotavirus A, and rotavirus C. Norovirus was consistently predominant over the 10-year period. Of 1099 facilities, 227 reported multiple outbreaks, of which norovirus-only combinations accounted for 76.2%. More outbreaks were due to different genotype combinations than the same genotype combinations. For facilities that experienced two norovirus outbreaks, the average interval between outbreaks was longer for groups with the same combinations than for groups with different genogroup or genotype combinations, although no statistically significant differences were observed. At 44 facilities, outbreaks occurred repeatedly during the same AG season, and most exhibited combinations of different norovirus genotypes or viruses. Among 49 combinations with the same norovirus genotype at the same facilities over 10 years, the most prevalent genotypes were combinations of genogroup II genotype 4 (GII.4), followed by GII.2, GII.6, GII.3, GII.14, and GI.3. The mean interval between outbreaks was 31.2 ± 26.8 months for all combinations, and the mean intervals were longer for non-GII.4 genotype cases than for GII.4 cases, and statistically significant differences were observed (t-test, P < 0.05). Additionally, these average intervals were longer for kindergarten/nursery schools and primary schools than for nursing homes for older adults (t-test, P < 0.05). CONCLUSIONS Repeated AG outbreaks at the same facilities in Yokohama during the 10-year study period included mainly norovirus combinations. Herd immunity at the facility level was maintained for at least the same AG season. Norovirus genotype-specific herd immunity was maintained for an average of 31.2 months during the study period, and these intervals differed depending on genotype.
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Affiliation(s)
- Makoto Kumazaki
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan.
| | - Shuzo Usuku
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan
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28
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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] [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.
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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.
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29
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Doan YH, Yamashita Y, Shinomiya H, Motoya T, Sakon N, Suzuki R, Shimizu H, Shigemoto N, Harada S, Yahiro S, Tomioka K, Sakagami A, Ueki Y, Komagome R, Saka K, Okamoto-Nakagawa R, Shirabe K, Mizukoshi F, Arita Y, Haga K, Katayama K, Kimura H, Muramatsu M, Oka T. Distribution of Human Sapovirus Strain Genotypes over the last four Decades in Japan: a Global Perspective. Jpn J Infect Dis 2023. [PMID: 37005271 DOI: 10.7883/yoken.jjid.2022.704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Sapovirus (SaV) infections are a public health problem because they cause acute gastroenteritis in humans of all ages both as outbreaks and in sporadic cases. However, publicly-available SaV sequence information, especially whole genome sequences for all the SaV genotypes, is still limited. Therefore, in this study, we determined the full/near-full-length genomic sequences of 138 SaVs from the 2001-2015 seasons in 13 prefectures across Japan. The GI genogroup was predominant (67%, n = 92), followed by GII (18%, n = 25), GIV (9%, n = 12), and GV (6%, n = 9). Within the GI genogroup, four different genotypes were identified, as follows: GI.1 (n=44), GI.2 (n=40), GI.3 (n=7), and GI.5 (n=1). We then compared these Japanese SaV sequences with a total of 3119 public human SaV sequences from 49 countries over the last 46 years. The results indicated that GI.1 and GI.2 have been the predominant genotypes in Japan as well as in other countries over at least four decades. Together with public SaV sequences, the 138 newly determined Japanese SaV sequences could facilitate a better understanding of the evolutionary patterns of SaV genotypes.
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Affiliation(s)
- Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
| | - Yasutaka Yamashita
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental Science, Japan
| | - Hiroto Shinomiya
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental Science, Japan
| | - Takumi Motoya
- Division of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Naomi Sakon
- Department of Microbiology, Virology Section, Osaka Prefectural Institute of Public Health, Japan
| | - Rieko Suzuki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Japan
| | - Naoki Shigemoto
- Public Health Research Division, Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Japan
| | - Seiya Harada
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Japan
| | - Shunsuke Yahiro
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Japan
| | - Kyoko Tomioka
- Virus Group, Saitama Prefectural Institute of Public Health, Japan
| | - Akie Sakagami
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Japan
| | - Rika Komagome
- Division of Virology, Department of Infectious Diseases, Hokkaido Institute of Public Health, Japan
| | - Kyohei Saka
- Microbiology Department, Aomori Prefectural Public Health and Environment Center, Japan
| | - Reiko Okamoto-Nakagawa
- Division of Virology, Yamaguchi Prefectural Institute of Public Health and Environment, Japan
| | - Komei Shirabe
- Division of Virology, Yamaguchi Prefectural Institute of Public Health and Environment, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Japan
| | - Yono Arita
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, Japan
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology,Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology,Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Science, Gunma Paz University, Japan
| | | | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Japan
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El-Heneidy A, Ware RS, Lambert SB, Grimwood K. Sapovirus Infections in an Australian Community-Based Healthy Birth Cohort During the First 2 Years of Life. Clin Infect Dis 2023; 76:1043-1049. [PMID: 36310530 PMCID: PMC10029984 DOI: 10.1093/cid/ciac861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Sapovirus is an important cause of acute gastroenteritis (AGE) in young children. However, knowledge gaps remain in community settings. We investigated the epidemiology, disease characteristics, and healthcare use associated with sapovirus infections in Australian children during their first 2 years of life. METHODS Children in the Brisbane-based Observational Research in Childhood Infectious Diseases birth cohort provided daily gastrointestinal symptoms (vomiting/loose stools), weekly stool swabs, and healthcare data until age 2 years. Swabs were batch-tested for sapovirus using real-time polymerase chain reaction assays. Incidence rates and estimates of associations were calculated. RESULTS Overall, 158 children returned 11 124 swabs. There were 192 sapovirus infection episodes. The incidence rate in the first 2 years of life was 0.89 infections per child-year (95% confidence interval [CI], .76-1.05), and the symptomatic incidence rate was 0.26 episodes per child-year (95% CI, .17-.37). Age ≥6 months, the fall season, and childcare attendance increased disease incidence significantly. Fifty-four of the 180 (30%) infections with linked symptom diaries were symptomatic, with 72% recording vomiting and 48% diarrhea. Prior infection reduced risk of further infections (adjusted hazard ratio, 0.70 [95% CI, .54-.81]) in the study period. Viral loads were higher and viral shedding duration was longer in symptomatic than asymptomatic children. Twenty-three (43%) symptomatic episodes required healthcare, including 6 emergency department presentations and 2 hospitalizations. CONCLUSIONS Sapovirus infections are common in Australian children aged 6-23 months. Efforts to reduce childhood AGE after the global rollout of rotavirus vaccines should include sapovirus where estimates of its incidence in communities will be crucial.
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Affiliation(s)
- Asmaa El-Heneidy
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Robert S Ware
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Stephen B Lambert
- UQ Centre for Clinical Research, The University of Queensland, Herston, Australia
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Gold Coast, Queensland, Australia
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Hu Y, Wu W. Application of Membrane Filtration to Cold Sterilization of Drinks and Establishment of Aseptic Workshop. FOOD AND ENVIRONMENTAL VIROLOGY 2023:10.1007/s12560-023-09551-6. [PMID: 36933166 PMCID: PMC10024305 DOI: 10.1007/s12560-023-09551-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/27/2023] [Indexed: 06/01/2023]
Abstract
Aseptic packaging of high quality beverage is necessary and its cold-pasteurization or sterilization is vital. Studies on application of ultrafiltration or microfiltration membrane to cold- pasteurization or sterilization for the aseptic packaging of beverages have been reviewed. Designing and manufacturing ultrafiltration or microfiltration membrane systems for cold-pasteurization or sterilization of beverage are based on the understanding of size of microorganisms and theoretical achievement of filtration. It is concluded that adaptability of membrane filtration, especially its combination with other safe cold method, to cold- pasteurization and sterilization for the aseptic packaging of beverages should be assured without a shadow of doubt in future.
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Affiliation(s)
- Yunhao Hu
- College of Food Science, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China
| | - Wenbiao Wu
- College of Food Science, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China.
- Research Center of Grains, Oils and Foods Engineering Design, Industrial Research Institute, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China.
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Porcine sapovirus-induced RIPK1-dependent necroptosis is proviral in LLC-PK cells. PLoS One 2023; 18:e0279843. [PMID: 36735696 PMCID: PMC9897573 DOI: 10.1371/journal.pone.0279843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/15/2022] [Indexed: 02/04/2023] Open
Abstract
Sapoviruses belonging to the genus Sapovirus within the family Caliciviridae are commonly responsible for severe acute gastroenteritis in both humans and animals. Caliciviruses are known to induce intrinsic apoptosis in vitro and in vivo, however, calicivirus-induced necroptosis remains to be fully elucidated. Here, we demonstrate that infection of porcine kidney LLC-PK cells with porcine sapovirus (PSaV) Cowden strain as a representative of caliciviruses induces receptor-interacting protein kinase 1 (RIPK1)-dependent necroptosis and acts as proviral compared to the antiviral function of PSaV-induced apoptosis. Infection of LLC-PK cells with PSaV Cowden strain showed that the interaction of phosphorylated RIPK1 (pRIPK1) with RIPK3 (pRIPK3), mixed lineage kinase domain-like protein (pMLKL) increased in a time-dependent manner, indicating induction of PSaV-induced RIPK1-dependent necroptosis. Interfering of PSaV-infected cells with each necroptotic molecule (RIPK1, RIPK3, or MLKL) by treatment with each specific chemical inhibitor or knockdown with each specific siRNA significantly reduced replication of PSaV but increased apoptosis and cell viability, implying proviral action of PSaV-induced necroptosis. In contrast, treatment of PSaV-infected cells with pan-caspase inhibitor Z-VAD-FMK increased PSaV replication and necroptosis, indicating an antiviral action of PSaV-induced apoptosis. These results suggest that PSaV-induced RIPK1-dependent necroptosis and apoptosis‒which have proviral and antiviral effects, respectively‒counterbalanced each other in virus-infected cells. Our study contributes to understanding the nature of PSaV-induced necroptosis and apoptosis and will aid in developing efficient and affordable therapies against PSaV and other calicivirus infections.
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Umair M, Rehman Z, Haider SA, Usman M, Rana MS, Ikram A, Salman M. First report of coinfection and whole-genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan. J Med Virol 2023; 95:e28458. [PMID: 36597899 DOI: 10.1002/jmv.28458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
Acute gastroenteritis is one of the most common diseases in infants and children in developing countries including Pakistan. In Pakistan, rotavirus (RVA) is known to contribute significantly to pediatric diarrheal illness, but the contribution of other viruses is still unclear. In the current study we have identified a case of mixed infection of norovirus (NoV) and sapovirus (SaV) in a 2-year-old child with acute gastroenteritis. The sample was initially processed for the detection of group A RVA through ELISA followed by NoV using RT-PCR assay. The sample tested positive for NoV RNA and was later subjected to whole-genome sequencing using meta-genome approach on Miseq (Illumina) platform. Sequencing results revealed GII.15 genotype of NoV that clustered with viruses from China and USA from 2017 to 2021. We also retrieved the complete genome of SaV (GI.1 genotype) from the same sample and phylogenetic analysis showed clustering with strains reported from Japan, South Korea, US, and Taiwan during 2012-2016. This is the first report from Pakistan that confirms coinfection of NoV and SaV and elucidates their whole genomes. We recommend initiation of NoV and SaV surveillance program to ascertain disease burden and explore genetic diversity, especially as RVA vaccines have been included in national immunization program.
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Affiliation(s)
- Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Syed Adnan Haider
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Usman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
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Zhang Q, Zhu S, Zhang X, Su L, Ni J, Zhang Y, Fang L. Recent insights into reverse genetics of norovirus. Virus Res 2023; 325:199046. [PMID: 36657615 DOI: 10.1016/j.virusres.2023.199046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/23/2022] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Norovirus is the leading cause of viral gastroenteritis globally, and poses substantial threats to public health. Despite substantial progress made in preventing norovirus diseases, the lack of a robust virus culture system has hampered biological research and effective strategies to combat this pathogen. Reverse genetic system is the technique to generate infectious viruses from cloned genetic constructs, which is a powerful tool for the investigation of viral pathogenesis and for the development of novel drugs and vaccines. The strategies of reverse genetics include bacterial artificial chromosomes, vaccinia virus vectors, and entirely plasmid-based systems. Since each strategy has its pros and cons, choosing appropriate approaches will greatly improve the efficiency of virus rescue. Reverse genetic systems that have been employed for norovirus greatly extend its life cycle and facilitate the development of medical countermeasures. In this review, we summarize the current knowledge on the structure, transmission, genetic evolution and clinical manifestations of norovirus, and describe recent advances in the studies of norovirus reverse genetics as well as its future prospects for therapeutics and vaccine development.
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Affiliation(s)
- Qinyi Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China; Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Shuirong Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Lingxuan Su
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Ni
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
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Matamoros DJP, Worsfold CS, Campos RC, Acuña HMB, Chacón EC, Sánchez CFJ. Molecular characterization of norovirus and sapovirus detected in animals and humans in Costa Rica: Zoo-anthropozoonotic potential of human norovirus GII.4. Open Vet J 2023; 13:74-89. [PMID: 36777439 PMCID: PMC9897497 DOI: 10.5455/ovj.2023.v13.i1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Background Noroviruses (NoV) and sapoviruses (SaV) are major causes of acute viral gastroenteritis in humans worldwide, as well as gastrointestinal infections in animals. However, it has not been determined whether these viruses are zoonotic pathogens. Aim In this study, we investigated the presence of NoV and SaV in stool samples from dogs, pigs, cows, and humans to determine some aspects of the molecular epidemiology and the genetic relationship of several strains present in these species. Methods Polymerase chain reaction and sequencing of NoV and SaV strains present in stool samples from humans and dogs with diarrhea, pigs, and cattle with and without diarrhea were carried out during fragmented periods from 2002 to 2012. Results Of all samples analyzed, 11.6% (123/1,061) of the samples were positive for NoV and 0.88% (9/1,023) were positive for SaV. The phylogenetic analysis confirmed 16 human strains of NoV (HuNoV) belonging to HuNoV G?/GII.P2 (1), GII.4/GII.P4 (5), G?/GII.P4 (9), and GII.6/GII.P6 (1) and allowed us to verify and assign three strains of human SaV to genotypes GI.2 (1) and GII.5 (2). In dogs, eight strains of NoV [HuNoV G?/GII.P4 (4) and canine G?/GVI.P1 (4)] and two strains of canine SaV were determined. In pigs, six strains were assigned to HuNoV G?/GII.P4 and four strains to porcine SaV were assigned to genogroup GIII (2), GVIII (1), and GXI (1). In bovines, five strains were characterized as HuNoV G?/GII.P4. Conclusions This study showed that NoV and SaV prototype strains have been present in humans and dogs in Costa Rica. Additionally, it revealed that the zoonotic potential of SaV is very limited, while the zoonotic implications for HuNoV GII.4 are stronger due to the simultaneous circulation of strains related to HuNoV GII.4 in four species, which suggests a zoo-anthropozoonosis.
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Affiliation(s)
- Derling José Pichardo Matamoros
- Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica,Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Corresponding Author: Derling José Pichardo Matamoros. Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica.
| | | | - Rocío Cortés Campos
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
| | - Hilda María Bolaños Acuña
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Elena Campos Chacón
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Carlos Francisco Jiménez Sánchez
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
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Phengma P, Khamrin P, Jampanil N, Yodmeeklin A, Ushijima H, Maneekarn N, Kumthip K. The emergence of recombinant norovirus GII.12[P16] and predominance of GII.3[P12] strains in pediatric patients with acute gastroenteritis in Thailand, 2019-2020. J Med Virol 2023; 95:e28321. [PMID: 36397269 DOI: 10.1002/jmv.28321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/17/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Norovirus (NoV) and sapovirus (SaV) are important pathogens that cause acute gastroenteritis (AGE) in all age groups, commonly in children worldwide. Recently, a number of studies have reported a wide variety of NoV recombinant strains. This study aimed to investigate the distribution of NoV and SaV recombinant strains circulating in Chiang Mai, Thailand, during 2019-2020. One hundred and twenty-four NoV and seven SaV strains detected in children admitted to the hospital with AGE were included in this study. The partial RNA-dependent RNA-polymerase (RdRp)/VP1 regions of these NoV and SaV strains were analyzed by phylogenetic analysis, Simplot, and RDP software. Overall, eight recombination patterns of NoV were detected. NoV GII.4[P16] was the most common strain detected (39.1%), followed by GII.3[P12] (25.0%), GII.4[P31] (17.2%), and other recombinant strains were detected at a lower rate. NoV GII.12[P16] strains were detected for the first time in Thailand. For SaV, none of the recombinant strains was detected. All SaV strains, GI.1/GI.1, GI.2/GI.2, and GII.5/GII.5, exhibited VP1 genotype corresponded to RdRp genotype. In conclusion, this study demonstrates the distribution and diversity of NoV and SaV recombinant strains circulating in pediatric patients with AGE in Chiang Mai, during 2019-2020 with the emergence of NoV GII.3[P12] and GII.12[P16].
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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.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (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
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Mochochoko BM, Pohl CH, O’Neill HG. Candida albicans-enteric viral interactions-The prostaglandin E 2 connection and host immune responses. iScience 2022; 26:105870. [PMID: 36647379 PMCID: PMC9839968 DOI: 10.1016/j.isci.2022.105870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human microbiome comprises trillions of microorganisms residing within different mucosal cavities and across the body surface. The gut microbiota modulates host susceptibility to viral infections in several ways, and microbial interkingdom interactions increase viral infectivity within the gut. Candida albicans, a frequently encountered fungal species in the gut, produces highly structured biofilms and eicosanoids such as prostaglandin E2 (PGE2), which aid in viral protection and replication. These biofilms encompass viruses and provide a shield from antiviral drugs or the immune system. PGE2 is a key modulator of active inflammation with the potential to regulate interferon signaling upon microbial invasion or viral infections. In this review, we raise the perspective of gut interkingdom interactions involving C. albicans and enteric viruses, with a special focus on biofilms, PGE2, and viral replication. Ultimately, we discuss the possible implications of C. albicans-enteric virus associations on host immune responses, particularly the interferon signaling pathway.
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Affiliation(s)
- Bonang M. Mochochoko
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa
| | - Carolina H. Pohl
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
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Jung S, Yeo D, Wang Z, Woo S, Seo Y, Hossain MI, Rhee MS, Choi C. Improvement of nested reverse transcription-polymerase chain reaction (RT-PCR) with high specificity and sensitivity detection of sapovirus in food matrix. J Virol Methods 2022; 309:114609. [PMID: 36028003 DOI: 10.1016/j.jviromet.2022.114609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022]
Abstract
Sapovirus (SaV) is a causative agent of human gastroenteritis in both community outbreaks and sporadic cases worldwide. Shellfish accumulate a variety of pathogens during filter feeding. In particular, the contamination of shellfish by SaV has caused several outbreaks. As reported previously, nested RT-PCR (nRT-PCR) has been widely used in clinical samples, but has not proven suitable for food samples, such as oysters. This study aimed to identify a primer set for the detection of SaV with high specificity and sensitivity in food samples. To accomplish this, primers were improved in RNA-dependent RNA polymerase (RdRp) regions of SaV whole genome sequences. The sensitivity of the improved nRT-PCR was 100-1000 times higher than that of previous nRT-PCR and > 10 times higher than that of the previous real-time RT-PCR assay. Notably, cross-reaction with other viruses or food matrices was not observed by the specificity test. This study improved the reliable primer set to detect SaV in various food matrices with high sensitivity.
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Affiliation(s)
- Soontag Jung
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Daseul Yeo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Zhaoqi Wang
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Seoyoung Woo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Yeeun Seo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Md Iqbal Hossain
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Changsun Choi
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea.
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Van Brussel K, Mahar JE, Ortiz-Baez AS, Carrai M, Spielman D, Boardman WSJ, Baker ML, Beatty JA, Geoghegan JL, Barrs VR, Holmes EC. Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology 2022; 576:42-51. [PMID: 36150229 DOI: 10.1016/j.virol.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 01/04/2023]
Abstract
Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.
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Affiliation(s)
- Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Maura Carrai
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Derek Spielman
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide, SA, 5371, Australia
| | - Michelle L Baker
- CSIRO Australian Centre for Disease Preparedness, Health and Biosecurity Business Unit, Geelong, VIC, 3220, Australia
| | - Julia A Beatty
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington, 5022, New Zealand
| | - Vanessa R Barrs
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China; Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, People's Republic of China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia.
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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] [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.
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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.
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Rouhani S, Peñataro Yori P, Paredes Olortegui M, Lima AA, Ahmed T, Mduma ER, George A, Samie A, Svensen E, Lima I, Mondal D, Mason CJ, Kalam A, Guerrant RL, Lang D, Zaidi A, Kang G, Houpt E, Kosek MN. The Epidemiology of Sapovirus in the Etiology, Risk Factors, and Interactions of Enteric Infection and Malnutrition and the Consequences for Child Health and Development (MAL-ED) Study: Evidence of Protection Following Natural Infection. Clin Infect Dis 2022; 75:1334-1341. [PMID: 36094137 PMCID: PMC9555839 DOI: 10.1093/cid/ciac165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Sapovirus is one of the principal agents of acute viral enteritis in children. Because it has not been routinely included in diagnostic evaluations, the epidemiology and natural history remain poorly described. METHODS A birth cohort of 1715 children from 8 countries contributed surveillance samples (n = 35 620) and diarrheal specimens (n = 6868) from 0 to 24 months of age. Sapovirus was detected by quantitative polymerase chain reaction concurrently to other enteropathogens using multiarray cards. Logistic regression was used to identify risk factors, and longitudinal models were employed to estimate incidence rates and evaluate evidence of protective immunity. RESULTS Sapovirus was detected in 24.7% (n = 1665) of diarrheal stools and 12.8% (n = 4429) of monthly surveillance samples. More than 90% of children were infected and 60% experienced sapovirus diarrhea in the first 2 years of life. Breastfeeding and higher socioeconomic status were associated with reduced incidence of infection and illness. Specimens with sapovirus detected had an increased odds of coinfection with rotavirus (odds ratio [OR], 1.6 [95% confidence interval {CI}, 1.3-2.0]), astrovirus (OR, 1.5 [95% CI, 1.3-1.7]), adenovirus (OR, 1.3 [95% CI, 1.1-1.5]), and Shigella (OR, 1.4 [95% CI, 1.3-1.6]). Prior infection with sapovirus conferred a risk reduction of 22% for subsequent infection (hazard ratio [HR], 0.78 [95% CI, .74-.85]) and 24% for subsequent diarrhea (95% CI, 11.0%-35.0%; HR, 0.76). CONCLUSIONS Sapovirus is a common cause of early childhood diarrhea. Further research on coinfections is warranted. Evidence of acquired immunity was observed even in the absence of genotype-specific analysis for this pathogen of known genetic diversity.
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Affiliation(s)
- Saba Rouhani
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Aldo A Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | | | - Ila Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Dinesh Mondal
- Nutrition Infection Interaction Research Group, Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Dennis Lang
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USAand
| | - Anita Zaidi
- Enteric and Diarrheal Diseases Programme, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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Characterization of a Human Sapovirus Genotype GII.3 Strain Generated by a Reverse Genetics System: VP2 Is a Minor Structural Protein of the Virion. Viruses 2022; 14:v14081649. [PMID: 36016271 PMCID: PMC9414370 DOI: 10.3390/v14081649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
We devised a reverse genetics system to generate an infectious human sapovirus (HuSaV) GII.3 virus. Capped/uncapped full-length RNAs derived from HuSaV GII.3 AK11 strain generated by in vitro transcription were used to transfect HuTu80 human duodenum carcinoma cells; infectious viruses were recovered from the capped RNA-transfected cells and passaged in the cells. Genome-wide analyses indicated no nucleotide sequence change in the virus genomes in the cell-culture supernatants recovered from the transfection or those from the subsequent infection. No virus growth was detected in the uncapped RNA-transfected cells, suggesting that the 5′-cap structure is essential for the virus’ generation and replication. Two types of virus particles were purified from the cell-culture supernatant. The complete particles were 39.2-nm-dia., at 1.350 g/cm3 density; the empty particles were 42.2-nm-dia. at 1.286 g/cm3. Two proteins (58-kDa p58 and 17-kDa p17) were detected from the purified particles; their molecular weight were similar to those of VP1 (~60-kDa) and VP2 (~16-kDa) of AK11 strain deduced from their amino acids (aa) sequences. Protein p58 interacted with HuSaV GII.3-VP1-specific antiserum, suggesting that p58 is HuSaV VP1. A total of 94 (57%) aa of p17 were identified by mass spectrometry; the sequences were identical to those of VP2, indicating that the p17 is the VP2 of AK11. Our new method produced infectious HuSaVs and demonstrated that VP2 is the minor protein of the virion, suggested to be involved in the HuSaV assembly.
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Recent Advances in Early Diagnosis of Viruses Associated with Gastroenteritis by Biosensors. BIOSENSORS 2022; 12:bios12070499. [PMID: 35884302 PMCID: PMC9313180 DOI: 10.3390/bios12070499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
Abstract
Gastroenteritis, as one of the main worldwide health challenges, especially in children, leads to 3–6 million deaths annually and causes nearly 20% of the total deaths of children aged ˂5 years, of which ~1.5 million gastroenteritis deaths occur in developing nations. Viruses are the main causative agent (~70%) of gastroenteritis episodes and their specific and early diagnosis via laboratory assays is very helpful for having successful antiviral therapy and reduction in infection burden. Regarding this importance, the present literature is the first review of updated improvements in the employing of different types of biosensors such as electrochemical, optical, and piezoelectric for sensitive, simple, cheap, rapid, and specific diagnosis of human gastroenteritis viruses. The Introduction section is a general discussion about the importance of viral gastroenteritis, types of viruses that cause gastroenteritis, and reasons for the combination of conventional diagnostic tests with biosensors for fast detection of viruses associated with gastroenteritis. Following the current laboratory detection tests for human gastroenteritis viruses and their limitations (with subsections: Electron Microscope (EM), Cell Culture, Immunoassay, and Molecular Techniques), structural features and significant aspects of various biosensing methods are discussed in the Biosensor section. In the next sections, basic information on viruses causing gastroenteritis and recent developments for fabrication and testing of different biosensors for each virus detection are covered, and the prospect of future developments in designing different biosensing platforms for gastroenteritis virus detection is discussed in the Conclusion and Future Directions section as well.
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Liu X, Song C, Liu Y, Qu K, Bi J, Bi J, Wang Y, Yang Y, Sun J, Guo Z, Li G, Liu J, Yin G. High Genetic Diversity of Porcine Sapovirus From Diarrheic Piglets in Yunnan Province, China. Front Vet Sci 2022; 9:854905. [PMID: 35873674 PMCID: PMC9300989 DOI: 10.3389/fvets.2022.854905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
As one of the most important enteric viruses, sapovirus (SaV) can infect humans and a variety of animals. Until now, 19 SaV genogroups have been identified, among which 4 from human (GI, GII, GIV, and GV) and 8 from swine (GIII, GV–GXI). Porcine sapovirus (PoSaV) GIII has been prevalent in China; however, the status of PoSaV infection in Yunnan province remains unknown. In this study, 202 fecal samples were collected from piglets associated with outbreaks of acute diarrhea in Yunnan between January and May 2020. PoSaV detection revealed that the total PoSaV infection rate in Yunnan was 35.2%, with 21 PoSaV strains determined and phylogenetically analyzed. The phylogenetic tree analyses demonstrated that twenty PoSaV strains belonged to GIII and fell into five genotypes, whereas one PoSaV strain (YNQB) belonged to GV. Sequence alignments revealed deletions in VP2 region in 10 of the 20 GIII strains, as well as deletions and insertions in VP1 region of the GV strain (YNQB). Furthermore, genomic recombination analyses showed that two GIII strains (YNAN and YNJD) were recombinants, closely related to reference sequences MK965898 and LC215880, MK965898 and FJ387164, respectively. In summary, PoSaV-GIII strains were identified in Yunnan in 2020, and for the first time, a PoSaV-GV strain was identified from China, whereas the comprehensive analyses illustrated high genetic diversity of Yunnan PoSaV strains. This study may shed new light on the current PoSaV infections in Yunnan and pave the way toward further control of the PoSaV infections in China.
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Affiliation(s)
- Xiao Liu
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Chunlian Song
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Yinghua Liu
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Junyu Bi
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Junlong Bi
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Yunhua Wang
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Ying Yang
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Junhua Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhigang Guo
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jianping Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- *Correspondence: Jianping Liu
| | - Gefen Yin
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- Gefen Yin
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Impact of the SARS-CoV-2 Pandemic on the Prevalence and Incidence of Gastrointestinal Viruses in Children up to Five Years Old: a Retrospective Cohort Study. Microbiol Spectr 2022; 10:e0266921. [PMID: 35638853 PMCID: PMC9241842 DOI: 10.1128/spectrum.02669-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim is determining the impact of non-pharmaceutical measures (NPIs) against SARS-CoV-2 in the incidence and prevalence of gastrointestinal viruses (GV) in children. Demographic, analytical, and clinical data of children from which samples were received at the Hospital Universitario La Paz (Madrid, Spain) and that had a gastrointestinal infection with a positive sample through multiplex-PCR for GV were collected. The time periods included were prepandemic (P1): March 14, 2019 to March 14, 2020 and pandemic (P2): March 15, 2020 to March 15, 2021. The global prevalence, relative incidence (RI, per 1,000 admissions) and absolute incidence (AI, per 100,000 population) of GV were compared for both time periods. The prevalence of GV versus SARS-CoV-2 was determined for P2. Seven-hundred and 50 out of 2,547 children analyzed in P1 and 106 out of 1,368 in P2 were positive by PCR for GV (46.3% decrease in P2). Prevalence and RI of GV declined in P2, except for the RI of rotavirus. Adenovirus showed the largest decreased of prevalence and RI (100%), followed by sapovirus. Astrovirus reduction was less pronounced (3.1% versus 0.4%). Norovirus was the most frequent virus in both time periods and its prevalence and RI also decreased in P2 (15.2% versus 4.7% and 3.40 versus 1.74, respectively). Rotavirus had the smallest decrease in prevalence (2.6% versus 2.5%), and its RI increased during P2 from 0.7 to 0.93. After removing the rotavirus vaccine strains from the analysis, the prevalence and RI decreased during P2 (2.1% to 0.7% and 0.5 to 0.3, respectively). The AI decreased during P2 in all GV, and the prevalence of SARS-CoV-2 and GV was inversely proportional over time. Prevalence and incidence of GV have decreased during the pandemic, probably due to the implementation of NPIs against this virus and the reduction of health care attention to infections other than COVID-19. The differences in the decrease of prevalence and incidence for each virus may be explained by differences in the transmission and the resistance in the environment. Prevalence and RI of rotavirus might be biased since the PCR used detects both the infecting and the vaccine strains. IMPORTANCE Our original article contains an analysis of the impact of the measures applied against SARS-CoV-2 on the prevalence and incidence of GV in children. The small number of studies published to date that analyze the impact of these measures individually on each of the GV makes our study of great interest at this time.
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Partial Analysis of the Capsid Protein (VP1) of Human Sapovirus Isolated from Children with Diarrhoea in Rural Communities of South Africa. Adv Virol 2022; 2022:9928378. [PMID: 35693126 PMCID: PMC9184228 DOI: 10.1155/2022/9928378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
Background Viral diarrhoea is a concern in acute gastroenteritis cases among children younger than 5 years of age. Sapovirus has been noted as an emerging causative agent of acute gastroenteritis worldwide. Objective/Study Design. The aim of this study was to characterize human sapoviruses targeting the VP1 (NVR and N-terminal) region. Twenty-five samples were randomly selected from 40 sapovirus-positive samples previously detected and analyzed for the VP1 region using the One-Step RT-PCR assay. The PCR products were subjected to Sanger sequencing analysis. Results The polyprotein segment (NVR and N-terminal) was successfully amplified from 10/25 samples. Sapovirus GI.1 was the most predominant strain (6/10; 60%), followed by SV-GII.1 (2/10; 20%) and 10% of each GI.3 and GII.3. Conclusion Through the partial analysis of the VP1 region, this study provides more data to add on the human sapovirus genetic characterization of circulating strains in South Africa, with the proposition of further analysis of sapovirus VP1 fragments for the viral structure and function.
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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] [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.
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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
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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] [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.
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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
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Atomic Structure of the Human Sapovirus Capsid Reveals a Unique Capsid Protein Conformation in Caliciviruses. J Virol 2022; 96:e0029822. [PMID: 35435722 PMCID: PMC9093105 DOI: 10.1128/jvi.00298-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sapovirus (SaV) is a member of the Caliciviridae family, which causes acute gastroenteritis in humans and animals. Human sapoviruses (HuSaVs) are genetically and antigenically diverse, but the lack of a viral replication system and structural information has hampered the development of vaccines and therapeutics. Here, we successfully produced a self-assembled virus-like particle (VLP) from the HuSaV GI.6 VP1 protein, and the first atomic structure was determined using single-particle cryo-electron microscopy (cryo-EM) at a 2.9-Å resolution. The atomic model of the VP1 protein revealed a unique capsid protein conformation in caliciviruses. All N-terminal arms in the A, B, and C subunits interacted with adjacent shell domains after extending through their subunits. The roof of the arched VP1 dimer was formed between the P2 subdomains by the interconnected β strands and loops, and its buried surface was minimized compared to those of other caliciviruses. Four hypervariable regions that are potentially involved in the antigenic diversity of SaV formed extensive clusters on top of the P domain. Potential receptor binding regions implied by tissue culture mutants of porcine SaV were also located near these hypervariable clusters. Conserved sequence motifs of the VP1 protein, “PPG” and “GWS,” may stabilize the inner capsid shell and the outer protruding domain, respectively. These findings will provide the structural basis for the medical treatment of HuSaV infections and facilitate the development of vaccines, antivirals, and diagnostic systems. IMPORTANCE SaV and norovirus, belonging to the Caliciviridae family, are common causes of acute gastroenteritis in humans and animals. SaV and norovirus infections are public health problems in all age groups, which occur explosively and sporadically worldwide. HuSaV is genetically and antigenically diverse and is currently classified into 4 genogroups consisting of 18 genotypes based on the sequence similarity of the VP1 proteins. Despite these detailed genetic analyses, the lack of structural information on viral capsids has become a problem for the development of vaccines or antiviral drugs. The 2.9-Å atomic model of the HuSaV GI.6 VLP presented here not only revealed the location of the amino acid residues involved in immune responses and potential receptor binding sites but also provided essential information for the design of stable constructs needed for the development of vaccines and antivirals.
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Potential zoonotic swine enteric viruses: The risk ignored for public health. Virus Res 2022; 315:198767. [PMID: 35421434 DOI: 10.1016/j.virusres.2022.198767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 12/28/2022]
Abstract
Swine could serve as a natural reservoir for a large variety of viruses, including potential zoonotic enteric viruses. The presence of viruses with high genetic similarity between porcine and human strains may result in the emergence of zoonotic or xenozoonotic infections. Furthermore, the globalization and intensification of swine industries exacerbate the transmission and evolution of zoonotic viruses among swine herds and individuals working in swine-related occupations. To effectively prevent the public health risks posed by zoonotic swine enteric viruses, designing, and implementing a comprehensive measure for early diagnosis, prevention, and mitigation, requires interdisciplinary a collaborative ''One Health" approach from veterinarians, environmental and public health professionals, and the swine industry. In this paper, we reviewed the current knowledge of selected potential zoonotic swine enteric viruses and explored swine intensive production and its associated public health risks.
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