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Mbou-Boutambe C, Mombo IM, Rougeron V, Degrugillier F, Gauthier P, Makanga B, Ngoubangoye B, Leroy EM, Prugnolle F, Boundenga L. Investigation of caliciviruses and astroviruses in Gabonese rodents: A possible influence of national and international trade on the spread of enteric viruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105607. [PMID: 38806078 DOI: 10.1016/j.meegid.2024.105607] [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: 04/04/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Caliciviruses (Caliciviridae) and astroviruses (Astroviridae) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of Rattus rattus species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to Mamastrovirus genus in which they were genetically related to R. rattus related AstVs previously detected in Gabon or in Rattus spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.
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Affiliation(s)
- Clark Mbou-Boutambe
- Unité de Recherche en Écologie de la Santé (URES), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon; Ecole Doctorale Régionale d'Afrique Centrale en Infectiologie Tropicale (EDR), Franceville, BP 876, Gabon.
| | - Illich Manfred Mombo
- Unité Émergence des Maladies Virales, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon; Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Virginie Rougeron
- International Research Laboratory-REHABS, CNRS-Université Lyon 1-Nelson Mandela University, Nelson Mandela University George Campus, George 6531, South Africa
| | - Fanny Degrugillier
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Philippe Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Boris Makanga
- Institut de Recherche en Écologie Tropicale (IRET/CENAREST), Libreville, BP 13354, Gabon
| | - Barthélemy Ngoubangoye
- Centre de Primatologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Eric M Leroy
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Franck Prugnolle
- International Research Laboratory-REHABS, CNRS-Université Lyon 1-Nelson Mandela University, Nelson Mandela University George Campus, George 6531, South Africa
| | - Larson Boundenga
- Unité de Recherche en Écologie de la Santé (URES), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon; Département d'Anthropologie, Université de Durham, South Road, Durham DH1 3LE, UK
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Akari Y, Hatazawa R, Kuroki H, Ito H, Negoro M, Tanaka T, Miwa H, Sugiura K, Umemoto M, Tanaka S, Ogawa M, Ito M, Fukuda S, Murata T, Taniguchi K, Suga S, Kamiya H, Nakano T, Taniguchi K, Komoto S. Full genome-based characterization of an Asian G3P[6] human rotavirus strain found in a diarrheic child in Japan: Evidence for porcine-to-human zoonotic transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105507. [PMID: 37757900 DOI: 10.1016/j.meegid.2023.105507] [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: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains.
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Affiliation(s)
- Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Haruo Kuroki
- Sotobo Children's Clinic, Isumi, Chiba 299-4503, Japan
| | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center, Kamogawa, Chiba 296-8602, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Haruna Miwa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Katsumi Sugiura
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | | | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Masahiro Ogawa
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Ise, Mie 516-8512, Japan
| | - Saori Fukuda
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Kiyosu Taniguchi
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Koki Taniguchi
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, Oita 879-5593, Japan.
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Sawant P, Kulkarni A, Mane R, Patil R, Lavania M. Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India. Front Cell Infect Microbiol 2023; 13:1258660. [PMID: 37965252 PMCID: PMC10642067 DOI: 10.3389/fcimb.2023.1258660] [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: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.
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Affiliation(s)
- Pradeep Sawant
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajkumar Mane
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Renu Patil
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Mallika Lavania
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
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Mao H, Li J, Liao G, Gao M, Yang G, Bao J. The prevention strategies of swine viruses related to xenotransplantation. Virol J 2023; 20:121. [PMID: 37312151 DOI: 10.1186/s12985-023-02090-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023] Open
Abstract
Xenotransplantation is considered a solution for the shortage of organs, and pigs play an indispensable role as donors in xenotransplantation. The biosecurity of pigs, especially the zoonotic viruses carried by pigs, has attracted attention. This review introduces several viruses, including porcine endogenous retroviruses that are integrated into the pig genome in a DNA form, herpesviruses that have been proven to clearly affect recipient survival time in previous xenotransplant surgeries, the zoonotic hepatitis E virus, and the widely distributed porcine circoviruses. The detail virus information, such as structure, caused diseases, transmission pathways, and epidemiology was introduced in the current review. Diagnostic and control measures for these viruses, including detection sites and methods, vaccines, RNA interference, antiviral pigs, farm biosecurity, and drugs, are discussed. The challenges faced, including those posed by other viruses and newly emerged viruses, and the challenges brought by the modes of transmission of the viruses are also summarized.
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Grants
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
- 82270662,82070640,81770618 National Natural Scientific Foundations of China
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Affiliation(s)
- Hongzhen Mao
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Center of Infectious Diseases & Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinyang Li
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guangneng Liao
- Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengyu Gao
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guang Yang
- Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ji Bao
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Transcriptomic and antiviral analyses of PoIFN-Delta5 against porcine enteric viruses in porcine intestinal epithelial cells. Vet Microbiol 2023; 280:109718. [PMID: 36871521 DOI: 10.1016/j.vetmic.2023.109718] [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: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
The interferon-delta family was first reported in domestic pigs and belongs to the type I interferon (IFN-I) family. The enteric viruses could cause diarrhea in newborn piglets with high morbidity and mortality. We researched the function of the porcine IFN-delta (PoIFN-δ) family in the porcine intestinal epithelial cells (IPEC-J2) cells infected with porcine epidemic diarrhea virus (PEDV). Our study found that all PoIFN-δs shared a typical IFN-I signature and could be divided into five branches in the phylogenic tree. Different strains of PEDV could induce typical IFN transitorily, and the virulent strain AH2012/12 had the strongest induction of porcine IFN-δ and IFN-alpha (PoIFN-α) in the early stage of infection. In addition, it was found that PoIFN-δ5/6/9/11 and PoIFN-δ1/2 were highly expressed in the intestine. PoIFN-δ5 had a better antiviral effect on PEDV compared to PoIFN-δ1 due to its higher induction of ISGs. PoIFN-δ1 and PoIFN-δ5 also activated JAK-STAT and IRS signaling. For other enteric viruses, transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine rotavirus (PoRV), PoIFN-δ1 and PoIFN-δ5 both showed an excellent antiviral effect. Transcriptome analyses uncovered the differences in host responses to PoIFN-α and PoIFN-δ5 and revealed thousands of differentially expressed genes were mainly enriched in the inflammatory response, antigen processing and presentation, and other immune-related pathways. PoIFN-δ5 would be a potential antiviral drug, especially against porcine enteric viruses. These studies were the first to report the antiviral function against porcine enteric viruses and broaden the new acquaintances of this type of interferon though not novelly discovered.
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Virus Safety of Xenotransplantation. Viruses 2022; 14:v14091926. [PMID: 36146732 PMCID: PMC9503113 DOI: 10.3390/v14091926] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/06/2023] Open
Abstract
The practice of xenotransplantation using pig islet cells or organs is under development to alleviate the shortage of human donor islet cells or organs for the treatment of diabetes or organ failure. Multiple genetically modified pigs were generated to prevent rejection. Xenotransplantation may be associated with the transmission of potentially zoonotic porcine viruses. In order to prevent this, we developed highly sensitive PCR-based, immunologicals and other methods for the detection of numerous xenotransplantation-relevant viruses. These methods were used for the screening of donor pigs and xenotransplant recipients. Of special interest are the porcine endogenous retroviruses (PERVs) that are integrated in the genome of all pigs, which are able to infect human cells, and that cannot be eliminated by methods that other viruses can. We showed, using droplet digital PCR, that the number of PERV proviruses is different in different pigs (usually around 60). Furthermore, the copy number is different in different organs of a single pig, indicating that PERVs are active in the living animals. We showed that in the first clinical trials treating diabetic patients with pig islet cells, no porcine viruses were transmitted. However, in preclinical trials transplanting pig hearts orthotopically into baboons, porcine cytomegalovirus (PCMV), a porcine roseolovirus (PCMV/PRV), and porcine circovirus 3 (PCV3), but no PERVs, were transmitted. PCMV/PRV transmission resulted in a significant reduction of the survival time of the xenotransplant. PCMV/PRV was also transmitted in the first pig heart transplantation to a human patient and possibly contributed to the death of the patient. Transmission means that the virus was detected in the recipient, however it remains unclear whether it can infect primate cells, including human cells. We showed previously that PCMV/PRV can be eliminated from donor pigs by early weaning. PERVs were also not transmitted by inoculation of human cell-adapted PERV into small animals, rhesus monkey, baboons and cynomolgus monkeys, even when pharmaceutical immunosuppression was applied. Since PERVs were not transmitted in clinical, preclinical, or infection experiments, it remains unclear whether they should be inactivated in the pig genome by CRISPR/Cas. In summary, by using our sensitive methods, the safety of xenotransplantation can be ensured.
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