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Devaux CA, Pontarotti P, Levasseur A, Colson P, Raoult D. Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis? Front Public Health 2024; 11:1284337. [PMID: 38259741 PMCID: PMC10801389 DOI: 10.3389/fpubh.2023.1284337] [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: 08/28/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
The polioviruses (PVs) are mainly transmitted by direct contact with an infected person through the fecal-oral route and respiratory secretions (or more rarely via contaminated water or food) and have a primary tropism for the gut. After their replication in the gut, in rare cases (far less than 1% of the infected individuals), PVs can spread to the central nervous system leading to flaccid paralysis, which can result in respiratory paralysis and death. By the middle of the 20th century, every year the wild polioviruses (WPVs) are supposed to have killed or paralyzed over half a million people. The introduction of the oral poliovirus vaccines (OPVs) through mass vaccination campaigns (combined with better application of hygiene measures), was a success story which enabled the World Health Organization (WHO) to set the global eradication of poliomyelitis as an objective. However this strategy of viral eradication has its limits as the majority of poliomyelitis cases today arise in individuals infected with circulating vaccine-derived polioviruses (cVDPVs) which regain pathogenicity following reversion or recombination. In recent years (between January 2018 and May 2023), the WHO recorded 8.8 times more cases of polio which were linked to the attenuated OPV vaccines (3,442 polio cases after reversion or recombination events) than cases linked to a WPV (390 cases). Recent knowledge of the evolution of RNA viruses and the exchange of genetic material among biological entities of the intestinal microbiota, call for a reassessment of the polio eradication vaccine strategies.
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Affiliation(s)
- Christian Albert Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Pierre Pontarotti
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Anthony Levasseur
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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2
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Kamau E, Bessaud M, Majumdar M, Martin J, Simmonds P, Harvala H. Estimating prevalence of Enterovirus D111 in human and non-human primate populations using cross-sectional serology. J Gen Virol 2023; 104:001915. [PMID: 37910158 PMCID: PMC10768692 DOI: 10.1099/jgv.0.001915] [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: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
Enteroviruses primarily affect young children with a varying severity of disease. Recent outbreaks of severe respiratory and neurological disease due to EV-D68 and EV-A71, as well as atypical hand-foot-and-mouth-disease due to CVA6, have brought to light the potency of enteroviruses to emerge as severe human pathogens. Enterovirus D111 (EV-D111) is an enteric pathogen initially detected in Central Africa in human and wildlife samples and was recently detected in environmental samples. The natural history and epidemiology of EV-D111 are poorly studied. Here, the presence of serum neutralizing antibodies to EV-D111 was estimated in human and wildlife samples from five countries. We report high prevalence of neutralizing antibodies measured against EV-D111 in human populations (range, 55-83 %), a proxy for previous infection, which indicates active virus circulation in absence of detection in clinical cases and a high number of undiagnosed infections. Notably, seroprevalence in samples from the UK varied by age and was higher in children and older adults (1-5 and >60 years old), but lower in ages 11-60. EV-D111 seroprevalence in apes and Old World monkeys was 50 % (33-66 %), which also suggests prior exposure and supports existing knowledge of enterovirus circulation in wild and captive apes and Old World monkeys. Generally, reported cases of infection likely underestimate the prevalence of infection particularly when the knowledge of community transmission is limited. Continued serologic surveillance and detection of EV-D111 in clinical and environmental samples will allow for a more robust assessment of EV-D111 epidemiology.
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Affiliation(s)
- Everlyn Kamau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mael Bessaud
- Institut Pasteur-Unité de Biologie des Virus Entériques, Paris, France
- WHO Collaborating Centre for Enteroviruses and Viral Vaccines, Paris, France
| | - Manasi Majumdar
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Javier Martin
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Microbiology Services, NHS Blood Transfusion, London, UK
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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4
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Andino R, Kirkegaard K, Macadam A, Racaniello VR, Rosenfeld AB. The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J Infect Dis 2023; 228:S427-S445. [PMID: 37849401 DOI: 10.1093/infdis/jiac426] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Picornaviruses are nonenveloped particles with a single-stranded RNA genome of positive polarity. This virus family includes poliovirus, hepatitis A virus, rhinoviruses, and Coxsackieviruses. Picornaviruses are common human pathogens, and infection can result in a spectrum of serious illnesses, including acute flaccid myelitis, severe respiratory complications, and hand-foot-mouth disease. Despite research on poliovirus establishing many fundamental principles of RNA virus biology and the first transgenic animal model of disease for infection by a human virus, picornaviruses are understudied. Existing knowledge gaps include, identification of molecules required for virus entry, understanding cellular and humoral immune responses elicited during virus infection, and establishment of immune-competent animal models of virus pathogenesis. Such knowledge is necessary for development of pan-picornavirus countermeasures. Defining enterovirus A71 and D68, human rhinovirus C, and echoviruses 29 as prototype pathogens of this virus family may provide insight into picornavirus biology needed to establish public health strategies necessary for pandemic preparedness.
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Affiliation(s)
- Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Karla Kirkegaard
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California, USA
| | - Andrew Macadam
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom
| | - Vincent R Racaniello
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Amy B Rosenfeld
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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5
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Cheng D, Chiu YW, Huang SW, Lien YY, Chang CL, Tsai HP, Wang YF, Wang JR. Genetic and Cross Neutralization Analyses of Coxsackievirus A16 Circulating in Taiwan from 1998 to 2021 Suggest Dominant Genotype B1 can Serve as Vaccine Candidate. Viruses 2022; 14:2306. [PMID: 36298861 PMCID: PMC9608817 DOI: 10.3390/v14102306] [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: 08/23/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 07/30/2023] Open
Abstract
Coxsackievirus A16 (CVA16) is well known for causing hand-foot-and-mouth disease (HFMD) and outbreaks were frequently reported in Taiwan in the past twenty years. The epidemiology and genetic variations of CVA16 in Taiwan from 1998 to 2021 were analyzed in this study. CVA16 infections usually occurred in early summer and early winter, and showed increased incidence in 1998, 2000-2003, 2005, 2007-2008, and 2010 in Taiwan. Little or no CVA16 was detected from 2017 to 2021. CVA16 infection was prevalent in patients between 1 to 3 years old. A total of 69 isolates were sequenced. Phylogenetic analysis based on the VP1 region showed that CVA16 subgenotype B1 was dominantly isolated in Taiwan from 1998 to 2019, and B2 was identified only from isolates collected in 1999 and 2000. There was a high frequency of synonymous mutations in the amino acid sequences of the VP1 region among CVA16 isolates, with the exception of position 145 which showed positive selection. The recombination analysis of the whole genome of CVA16 isolates indicated that the 5'-untranslated region and the non-structural protein region of CVA16 subgenotype B1 were recombined with Coxsackievirus A4 (CVA4) and enterovirus A71 (EVA71) genotype A, respectively. The recombination pattern of subgenotype B2 was similar to B1, however, the 3D region was similar to EVA71 genotype B. Cross-neutralization among CVA16 showed that mouse antisera from various subgenotypes viruses can cross-neutralize different genotype with high neutralizing antibody titers. These results suggest that the dominant CVA16 genotype B1 can serve as a vaccine candidate for CVA16.
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Affiliation(s)
- Dayna Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yo-Wei Chiu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
| | - Yun-Yin Lien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Chia-Lun Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Fang Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jen-Ren Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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6
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Piralla A, Pariani E. Editorial for the Special Issue "Epidemiology of Enterovirus Disease". Microorganisms 2022; 10:microorganisms10061221. [PMID: 35744739 PMCID: PMC9228421 DOI: 10.3390/microorganisms10061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Enteroviruses (Enterovirus genus, Picornaviridae family) are distributed worldwide and are among the most common causes of human disease globally [...].
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Affiliation(s)
- Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Correspondence: ; Tel.: +39-038-250-2420
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milano, Italy;
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7
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Burel E, Colson P, Lagier JC, Levasseur A, Bedotto M, Lavrard-Meyer P, Fournier PE, La Scola B, Raoult D. Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient. Viruses 2022; 14:1266. [PMID: 35746737 PMCID: PMC9227898 DOI: 10.3390/v14061266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient's sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient's follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.
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Affiliation(s)
- Emilie Burel
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marielle Bedotto
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
| | - Philippe Lavrard-Meyer
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
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8
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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9
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. Antimicrob Agents Chemother 2021; 65:e0255720. [PMID: 34152818 DOI: 10.1128/aac.02557-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (n = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (n = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The blaOXA-48 and the blaKPC-2 genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried blaCTX-M-15, blaTEM-1B, and blaOXA-1 genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.
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10
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Davoust B, Watier-Grillot S, Roqueplo C, Raoult D, Mediannikov O. Detection of zoonotic pathogens in animals performed at the University Hospital Institute Méditerranée Infection (Marseille - France). One Health 2021; 12:100210. [PMID: 33437857 PMCID: PMC7786111 DOI: 10.1016/j.onehlt.2020.100210] [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: 11/12/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022] Open
Abstract
At the University Hospital Institute Méditerranée Infection (IHU, Marseille, France), for almost thirty years, veterinarians have been carrying out epidemiological investigations, together with doctors, on animals living near human cases of zoonoses, on the one hand, and on the other hand, transverse and longitudinal epidemiological surveillance studies on animals which are reservoirs, vectors or sentinels of potentially zoonotic infections,. This article presents the methods adopted and the results obtained from these studies. They have been the subject of 76 peer-reviewed publications relating to wild animals (37 publications) and/or domestic animals (48 publications). These studies were often carried out in the field with veterinarians from the French army's health service (39 publications). They were at the origin of the detection of some thirty zoonotic pathogens in the laboratories of the IHU (64 publications) and/or other French laboratories (18 publications). Our approach is an original embodiment of the "One Health" concept.
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Affiliation(s)
- Bernard Davoust
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- French military health service, Animal epidemiology expert group, Tours, France
| | - Stéphanie Watier-Grillot
- French military health service, Animal epidemiology expert group, Tours, France
- French army center for epidemiology and public health, Marseille, France
| | - Cédric Roqueplo
- French military health service, Animal epidemiology expert group, Tours, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Stool Serology: Development of a Non-Invasive Immunological Method for the Detection of Enterovirus-Specific Antibodies in Congo Gorilla Faeces. Microorganisms 2021; 9:microorganisms9040810. [PMID: 33921300 PMCID: PMC8068960 DOI: 10.3390/microorganisms9040810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The incidence of poliovirus has been significantly reduced by as much as 99.9% globally. Alongside this, however, vaccine-associated paralytic poliomyelitis has emerged. Previously, our team reported in the Lésio-Louna-Léfini Nature Reserve (Republic of Congo) the presence of a new Enterovirus C (Ibou002) in a male gorilla that was put away because of clinical symptoms of facial paralysis. This new virus, isolated was from the stool samples of this gorilla but also from the excrement of an eco-guardian, is very similar to Coxsackievirus (EV-C99) as well as poliovirus 1 and 2. We hypothesised that these symptoms might be due to poliovirus infection. To test our hypothesis, we developed and optimised a non-invasive immunoassay for the detection of Enterovirus-specific antibodies in gorilla faeces that could be useful for routine serosurveillance in such cases. Methods: In order to assess the potential role of poliovirus infection, we have developed and optimised a protocol, based on the lyophilisation and solubilisation of small volumes of stool extracts from 16 gorilla and 3 humans, to detect specific antibodies by western blot and ELISA. Results: First, total immunoglobulins were detected in the concentrated stool extracts. Specific antibodies were then detected in 4/16 gorilla samples and 2/3 human samples by western blot using both the polio vaccine antigen and the Ibou002 antigen and by ELISA using the polio vaccine antigen. Humoral responses were greater with the Ibou002 antigen. Conclusion: We therefore suggest that this recombinant virus could lead to a polio-like disease in the endangered western lowland gorilla. The development of a non-invasive approach to detect microorganism-specific immunoglobulins from faecal samples opens numerous prospects for application in zoonotic infectious diseases and could revolutionise the screening of animals for important emerging infections, such as Ebola fever, rabies and coronavirus infections.
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