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Dong HV, Tran GTH, Rattanasrisomporn A, Rungsuriyawiboon O, Rapichai W, Rattanasrisomporn J. Genetic detection and analysis of porcine norovirus in pigs farmed in north Vietnam. Heliyon 2024; 10:e31946. [PMID: 38882286 PMCID: PMC11176758 DOI: 10.1016/j.heliyon.2024.e31946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Norovirus (NoV) causing gastroenteritis symptoms, which has been reported in several hosts, including humans, pigs, and rats. This study was conducted to identify porcine viral infection and to characterize NoV strains from pigs in some provinces in north Vietnam. Totally, 102 fecal samples from diarrheal pigs on farms in six cities and provinces in northern Vietnam during July 2022 to March 2023 were collected. Polymerase chain reaction was used to identify the viral genome. Positive samples were used for nucleotide sequencing of the partial RNA-dependent RNA polymerase gene sequence. Five (4.9 %) positive stool samples were detected from animals farmed in five different farms, with one positive animal identified in each farm. Genetic analysis indicated that nucleotide identity was in the range 97.77-99.62 % among the 5 NoVs in this study. Phylogenetic analysis pointed out that the five NoVs were Genotype II.19 viruses. Genetically, these strains were closely related to porcine NoV strains that were reported in China in 2009.
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Affiliation(s)
- Hieu Van Dong
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi, 131000, Viet Nam
| | - Giang Thi Huong Tran
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi, 131000, Viet Nam
| | - Amonpun Rattanasrisomporn
- Interdisciplinary of Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok, 10900, Thailand
| | - Oumaporn Rungsuriyawiboon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, 10900, Thailand
| | - Witsanu Rapichai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Jatuporn Rattanasrisomporn
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
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Abid I, Blanco A, Al-Otaibi N, Guix S, Costafreda MI, Pintó RM, Bosch A. Dynamic and Seasonal Distribution of Enteric Viruses in Surface and Well Water in Riyadh (Saudi Arabia). Pathogens 2023; 12:1405. [PMID: 38133289 PMCID: PMC10747075 DOI: 10.3390/pathogens12121405] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Enteric viruses are the major cause of gastroenteritis and enteric hepatitis worldwide, but in some areas like Saudi Arabia, little is known about their presence in water sources. The available information from clinical samples is not enough to figure out their actual prevalence. The aim of this study was to gather information for the first time in Saudi Arabia on the presence of the Norovirus (NoV) genogroup GI and GII, hepatitis A virus (HAV), and hepatitis E virus (HEV) in water. For this purpose, thirteen monthly samples were collected from Lake Wadi Hanifa and surrounding wells from December 2014 to November 2015. Viruses were detected and quantified using real-time RT-qPCR. Despite HEV findings being anecdotic, our results highlight interesting behaviors of the other viruses. There was a higher prevalence of noroviruses in Wadi Hanifa samples than in well water samples (46.43% vs. 12.5% of NoV GI; 66.67% vs. 8.33% of NoV GII). On the contrary, similar levels of HAV positivity were observed (40.48% in surface water vs. 43.06% in well water). Also, a strong influence of flooding events on HAV and NoV GI occurrence was observed in both surface and well water samples, with NoV GII apparently not affected.
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Affiliation(s)
- Islem Abid
- Center of Excellence in Biotechnology Research, College of Applied Medical Science, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Albert Blanco
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Nawal Al-Otaibi
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Maria I. Costafreda
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
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Koutsoumanis K, Allende A, Alvarez Ordoñez A, Bolton D, Bover‐Cid S, Chemaly M, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Skandamis P, Suffredini E, Fernandez Escamez P, Gonzales‐Barron U, Roberts H, Ru G, Simmons M, Cruz RB, Lourenço Martins J, Messens W, Ortiz‐Pelaez A, Simon AC, De Cesare A. Assessment on the efficacy of methods 2 to 5 and method 7 set out in Commission Regulation (EU) No 142/2011 to inactivate relevant pathogens when producing processed animal protein of porcine origin intended to feed poultry and aquaculture animals. EFSA J 2023; 21:e08093. [PMID: 37416785 PMCID: PMC10320699 DOI: 10.2903/j.efsa.2023.8093] [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: 07/08/2023] Open
Abstract
An assessment was conducted on the level of inactivation of relevant pathogens that could be present in processed animal protein of porcine origin intended to feed poultry and aquaculture animals when methods 2 to 5 and method 7, as detailed in Regulation (EU) No 142/2011, are applied. Five approved scenarios were selected for method 7. Salmonella Senftenberg, Enterococcus faecalis, spores of Clostridium perfringens and parvoviruses were shortlisted as target indicators. Inactivation parameters for these indicators were extracted from extensive literature search and a recent EFSA scientific opinion. An adapted Bigelow model was fitted to retrieved data to estimate the probability that methods 2 to 5, in coincidental and consecutive modes, and the five scenarios of method 7 are able to achieve a 5 log10 and a 3 log10 reduction of bacterial indicators and parvoviruses, respectively. Spores of C. perfringens were the indicator with the lowest probability of achieving the target reduction by methods 2 to 5, in coincidental and consecutive mode, and by the five considered scenarios of method 7. An expert knowledge elicitation was conducted to estimate the certainty of achieving a 5 log10 reduction of spores of C. perfringens considering the results of the model and additional evidence. A 5 log10 reduction of C. perfringens spores was judged: 99-100% certain for methods 2 and 3 in coincidental mode; 98-100% certain for method 7 scenario 3; 80-99% certain for method 5 in coincidental mode; 66-100% certain for method 4 in coincidental mode and for method 7 scenarios 4 and 5; 25-75% certain for method 7 scenario 2; and 0-5% certain for method 7 scenario 1. Higher certainty is expected for methods 2 to 5 in consecutive mode compared to coincidental mode.
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Patterns and Temporal Dynamics of Natural Recombination in Noroviruses. Viruses 2023; 15:v15020372. [PMID: 36851586 PMCID: PMC9961210 DOI: 10.3390/v15020372] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although recombination was most prominent between members of GII, the most common genogroup that infects humans. The half-life times of recombinant forms (clades without evidence of recombination) of human GI and GII noroviruses were 10.4 and 8.4-11.3 years, respectively. There was evidence of many recent recombination events, and most noroviruses that differed by more than 18% of nucleotide sequence were recombinant relative to each other. However, there were no distinct recombination events between viruses that differed by over 42% in ORF2/3, consistent with the absence of systematic recombination between different genogroups. The few inter-genogroup recombination events most likely occurred between ancient viruses before they diverged into contemporary genogroups. The recombination events within ORF1 or between ORF2/3 were generally rare. Thus, noroviruses routinely exchange full structural and nonstructural blocks of the genome, providing a modular evolution.
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Lanrewaju AA, Enitan-Folami AM, Sabiu S, Edokpayi JN, Swalaha FM. Global public health implications of human exposure to viral contaminated water. Front Microbiol 2022; 13:981896. [PMID: 36110296 PMCID: PMC9468673 DOI: 10.3389/fmicb.2022.981896] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 01/08/2023] Open
Abstract
Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.
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Affiliation(s)
| | - Abimbola Motunrayo Enitan-Folami
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
- *Correspondence: Abimbola Motunrayo Enitan-Folami,
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
| | - Joshua Nosa Edokpayi
- Water and Environmental Management Research Group, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
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Cavicchio L, Laconi A, Piccirillo A, Beato MS. Swine Norovirus: Past, Present, and Future. Viruses 2022; 14:v14030537. [PMID: 35336944 PMCID: PMC8953536 DOI: 10.3390/v14030537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 01/18/2023] Open
Abstract
Norovirus, an ssRNA + virus of the family Caliciviridae, is a leading disease burden in humans worldwide, causing an estimated 600 million cases of acute gastroenteritis every year. Since the discovery of norovirus in the faeces of swine in Japan in the 1990s, swine norovirus has been reported in several countries on several continents. The identification of the human-associated GII.4 genotype in swine has raised questions about this animal species as a reservoir of norovirus with zoonotic potential, even if species-specific P-types are usually detected in swine. This review summarises the available data regarding the geographic distribution of norovirus in swine, the years of detection, the genotype characterisation, and the prevalence in specific production groups. Furthermore, we discuss the major bottlenecks for the detection and characterisation of swine noroviruses.
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Affiliation(s)
- Lara Cavicchio
- Diagnostic Virology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVE), Viale dell’Università 10, Legnaro, 35020 Padua, Italy;
| | - Andrea Laconi
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (A.L.); (A.P.)
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (A.L.); (A.P.)
| | - Maria Serena Beato
- National Reference Laboratory for African Swine Fever and Ruminant retroviruses, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche (IZSUM), Via G. Salvemini, 1, 06126 Perugia, Italy
- Correspondence:
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Cavicchio L, Tassoni L, Laconi A, Cunial G, Gagliazzo L, Milani A, Campalto M, Di Martino G, Forzan M, Monne I, Beato MS. Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy. Sci Rep 2020; 10:9217. [PMID: 32513947 PMCID: PMC7280493 DOI: 10.1038/s41598-020-66140-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/13/2020] [Indexed: 12/02/2022] Open
Abstract
Noroviruses (NoVs) are one of the major causative agents of non-bacterial gastroenteritis in humans worldwide. NoVs, belonging to Caliciviridae, are classified into ten genogroups (G) and eight P-groups based on major capsid protein (VP1) and of the RNA-dependent-RNA-polymerase (RdRp), respectively. In swine, the main genogroup and P-group identified are GII and GII.P; which can infect humans too. To date, only one case of GIIP.11 have been identified in swine in Italy while the circulation of other P-types is currently unknown. In the present study, 225 swine faecal samples were collected from 74 swine herds in Veneto region through on-farm monitoring. NoV circulation was particularly high in older pigs. The phylogenetic analysis showed the co-circulation of NoVs belonging to two different P-types: GII.P11 and GII.P18, here described for the first time in Italy, presenting an extensive genetic diversity, never described before worldwide. Distinct NoV genetic subgroups and unique amino acid mutations were identified for each P-type for the first time. This study demonstrated the co-circulation of diverse swine NoVs subgroups in Italy, raising questions on the origin of such diversity and suggesting that continuous monitoring of swine NoVs is needed to track the emergence of potentially zoonotic viruses by recombination events.
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Affiliation(s)
- L Cavicchio
- Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - L Tassoni
- Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - A Laconi
- EU, OIE/FAO and National Reference Laboratory for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - G Cunial
- Epidemiology Department, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - L Gagliazzo
- Epidemiology Department, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - A Milani
- EU, OIE/FAO and National Reference Laboratory for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - M Campalto
- Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - G Di Martino
- Epidemiology Department, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - M Forzan
- Department of Veterinary Virology, University of Pisa, Viale delle Piagge 2, 56124, Pisa, Italy
| | - I Monne
- EU, OIE/FAO and National Reference Laboratory for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy
| | - M S Beato
- Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro, Padua, Italy.
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