25 results on '"M. Ar Gouilh"'
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2. Opinion paper: Severe Acute Respiratory Syndrome Coronavirus 2 and domestic animals: what relation?
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G. Meyer, Nicole Pavio, S. Le Poder, E. Khamisse, P. Brown, François Meurens, M. Ar Gouilh, Gaëlle Simon, Elodie Monchatre-Leroy, Charlotte Dunoyer, Unité Evaluation des risques liés à la santé, l’alimentation et au bien-être des animaux (UERSABA), Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Service de Virologie [CHU Caen], CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Virologie UMR1161 (VIRO), and École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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medicine.medical_specialty ,040301 veterinary sciences ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine.disease_cause ,SF1-1100 ,Occupational safety and health ,0403 veterinary science ,Environmental health ,Opinion Paper ,Pandemic ,medicine ,China ,Coronavirus ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,SARS-CoV-2 ,business.industry ,Public health ,0402 animal and dairy science ,COVID-19 ,Outbreak ,04 agricultural and veterinary sciences ,medicine.disease ,040201 dairy & animal science ,Animal culture ,3. Good health ,Domestic animals ,Pneumonia ,Animal Science and Zoology ,MESH: severe acute respiratory syndrome coronavirus 2 [Supplementary Concept] ,business - Abstract
This document was prepared thanks to the collective expertappraisal, carried out by the Anses’expert group‘GECUCovid-19’(ANSES opinion 2020-SA-0037), chaired by Sophie Le Poder and whose members for the animal health component are cited in the authors.; International audience; In late December 2019, an outbreak of clustered cases of pneumonia associated with a novel coronavirus was reported by the Chinese authorities to the World Health Organization (WHO). Several initial confirmed cases were linked to a wetmarket selling live animals and seafood products in Wuhan(Hubei province), China (Huang et al.,2020). On 30 January 2020, the WHO declared the outbreak a Public Health Emergency of International Concern. On 11 February 2020, the causative pathogen was officially named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for Coronavirus Disease 2019 (COVID-19) (DuToit, 2020). Severe Acute Respiratory Syndrome Coronavirus 2 is mainly transmitted from person to person, by direct or indirect contact, through infectious microdroplets emitted wheninfected individuals spit, sneeze or cough (Bernard Stoecklin et al.,2020). The massive circulation of this new pandemiccoronavirus with a probable zoonotic origin raised questions on its ability to spillover to animal species and on the potential consequences of such events on both animals and humans. This public health concern came to the attention of animal health authorities given the close contacts between humans and domestic animals. Therefore, in France, the French Agency for Food, Environmental and Occupational Health and Safety (ANSES) established an Emergency Collective Expert Appraisal Group (Groupe d’Expertise Collective d’Urgence, GECU‘Covid-19’). The GECU ‘Covid-19’ urgently convened on 4 March 2020 and 8 April 2020 to conduct an evaluation of the potential role of domestic animals in the ongoing COVID-19 pandemic.
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- 2020
3. SARS-CoV2 infection in whole lung primarily targets macrophages that display subset-specific responses.
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Vu Manh TP, Gouin C, De Wolf J, Jouneau L, Pascale F, Bevilacqua C, Ar Gouilh M, Da Costa B, Chevalier C, Glorion M, Hannouche L, Urien C, Estephan J, Magnan A, Le Guen M, Marquant Q, Descamps D, Dalod M, Schwartz-Cornil I, and Sage E
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- Humans, Monocytes virology, Monocytes metabolism, Monocytes immunology, Male, Female, Single-Cell Analysis, Middle Aged, COVID-19 virology, COVID-19 immunology, SARS-CoV-2 physiology, Lung virology, Lung immunology, Lung pathology, Macrophages virology, Macrophages metabolism, Macrophages immunology, Macrophages, Alveolar virology, Macrophages, Alveolar immunology, Macrophages, Alveolar metabolism, Cytokines metabolism
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Deciphering the initial steps of SARS-CoV-2 infection, that influence COVID-19 outcomes, is challenging because animal models do not always reproduce human biological processes and in vitro systems do not recapitulate the histoarchitecture and cellular composition of respiratory tissues. To address this, we developed an innovative ex vivo model of whole human lung infection with SARS-CoV-2, leveraging a lung transplantation technique. Through single-cell RNA-seq, we identified that alveolar and monocyte-derived macrophages (AMs and MoMacs) were initial targets of the virus. Exposure of isolated lung AMs, MoMacs, classical monocytes and non-classical monocytes (ncMos) to SARS-CoV-2 variants revealed that while all subsets responded, MoMacs produced higher levels of inflammatory cytokines than AMs, and ncMos contributed the least. A Wuhan lineage appeared to be more potent than a D614G virus, in a dose-dependent manner. Amidst the ambiguity in the literature regarding the initial SARS-CoV-2 cell target, our study reveals that AMs and MoMacs are dominant primary entry points for the virus, and suggests that their responses may conduct subsequent injury, depending on their abundance, the viral strain and dose. Interfering on virus interaction with lung macrophages should be considered in prophylactic strategies., (© 2024. The Author(s).)
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- 2024
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4. Unravelling the acute respiratory infection landscape: virus type, viral load, health status and coinfection do matter.
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Petat H, Corbet S, Leterrier B, Vabret A, and Ar Gouilh M
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- Humans, Infant, Female, Child, Preschool, Male, Child, Health Status, Adult, Respiratory Syncytial Virus Infections virology, Adolescent, Middle Aged, Respiratory Syncytial Virus, Human genetics, Respiratory Syncytial Virus, Human isolation & purification, Nasopharynx virology, Infant, Newborn, Young Adult, Aged, Real-Time Polymerase Chain Reaction, Acute Disease, Genotype, Multiplex Polymerase Chain Reaction, Aged, 80 and over, Viral Load, Coinfection virology, Respiratory Tract Infections virology, Rhinovirus isolation & purification, Rhinovirus genetics
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Introduction: Acute respiratory infections (ARI) are the most common infections in the general population and are mainly caused by respiratory viruses. Detecting several viruses in a respiratory sample is common. To better understand these viral codetections and potential interferences, we tested for the presence of viruses and developed quantitative PCR (Polymerase Chain Reaction) for the viruses most prevalent in coinfections: human rhinovirus (HRV) and respiratory syncytial virus (RSV), and quantified their viral loads according to coinfections and health status, age, cellular abundance and other variables., Materials and Methods: Samples from two different cohorts were analyzed: one included hospitalized infants under 12 months of age with acute bronchiolitis (n=719) and the other primary care patients of all ages with symptoms of ARI (n=685). We performed Multiplex PCR on nasopharyngeal swabs, and quantitative PCR on samples positive for HRV or/and RSV to determine viral loads (VL). Cellular abundance (CA) was also estimated by qPCR targeting the GAPDH gene. Genotyping was performed either directly from first-line molecular panel or by PCR and sequencing for HRV., Results: The risks of viral codetection were 4.1 (IC
95 [1.8; 10.0]) and 93.9 1 (IC95 [48.7; 190.7]) higher in infants hospitalized for bronchiolitis than in infants in primary care for RSV and HRV respectively (p<0.001). CA was higher in samples positive for multiple viruses than in mono-infected or negative samples (p<0.001), and higher in samples positive for RSV (p<0.001) and HRV (p<0.001) than in negative samples. We found a positive correlation between CA and VL for both RSV and HRV. HRV VL was higher in children than in the elderly (p<0.05), but not RSV VL. HRV VL was higher when detected alone than in samples coinfected with RSV-A and with RSV-B. There was a significant increase of RSV-A VL when codetecting with HRV (p=0.001) and when co-detecting with RSV-B+HRV versus RSV-A+ RSV-B (p=0.02)., Conclusions: Many parameters influence the natural history of respiratory viral infections, and quantifying respiratory viral loads can help disentangle their contributions to viral outcome., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Petat, Corbet, Leterrier, Vabret and Ar Gouilh.)- Published
- 2024
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5. Evidence for circulation of Rift Valley fever virus in wildlife and domestic animals in a forest environment in Gabon, Central Africa.
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Becquart P, Bohou Kombila L, Mebaley TN, Paupy C, Garcia D, Nesi N, Olive MM, Vanhomwegen J, Boundenga L, Mombo IM, Piro-Mégy C, Fritz M, Lenguiya LH, Ar Gouilh M, Leroy EM, N'Dilimabaka N, Cêtre-Sossah C, and Maganga GD
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- Animals, Sheep, Dogs, Animals, Domestic, Animals, Wild, Gabon epidemiology, Cross-Sectional Studies, Ecosystem, Phylogeny, Ruminants, Goats, Antibodies, Viral, Forests, Seroepidemiologic Studies, Rift Valley fever virus, Rift Valley Fever
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Rift Valley fever (RVF) is a mosquito-borne viral zoonosis caused by the Rift Valley fever virus (RVFV) that can infect domestic and wild animals. Although the RVFV transmission cycle has been well documented across Africa in savanna ecosystems, little is known about its transmission in tropical rainforest settings, particularly in Central Africa. We therefore conducted a survey in northeastern Gabon to assess RVFV circulation among wild and domestic animals. Among 163 wildlife samples tested using RVFV-specific RT-qPCR, four ruminants belonging to subfamily Cephalophinae were detected positive. The phylogenetic analysis revealed that the four RVFV sequences clustered together with a virus isolated in Namibia within the well-structured Egyptian clade. A cross-sectional survey conducted on sheep, goats and dogs living in villages within the same area determined the IgG RVFV-specific antibody prevalence using cELISA. Out of the 306 small ruminants tested (214 goats, 92 sheep), an overall antibody prevalence of 15.4% (95% CI [11.5-19.9]) was observed with a higher rate in goats than in sheep (20.1% versus 3.3%). RVFV-specific antibodies were detected in a single dog out of the 26 tested. Neither age, sex of domestic animals nor season was found to be significant risk factors of RVFV occurrence. Our findings highlight sylvatic circulation of RVFV for the first time in Gabon. These results stress the need to develop adequate surveillance plan measures to better control the public health threat of RVFV., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Becquart et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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6. Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study.
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Petat H, Schuers M, Marguet C, Humbert X, Le Bas F, Rabiaza A, Corbet S, Leterrier B, Vabret A, and Ar Gouilh M
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- Humans, Prospective Studies, Primary Health Care, Respiratory Tract Infections, Viruses genetics, Virus Diseases epidemiology
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Introduction: Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited., Materials and Methods: ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)]., Results: Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses ( p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV., Conclusion: Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Petat, Schuers, Marguet, Humbert, Le Bas, Rabiaza, Corbet, Leterrier, Vabret and Ar Gouilh.)
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- 2023
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7. Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo.
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Lenguiya LH, Fritz M, De Fonclare DR, Corbet S, Becquart P, Mbou C, Nguie RJ, Mouellet WS, Demboux JEL, N'kaya-Tobi, Issamou Mayengue P, Koukouikila-Koussounda F, Ar Gouilh M, Leroy EM, and Niama FR
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- Animals, Cats, Dogs, Humans, SARS-CoV-2 genetics, Congo epidemiology, COVID-19 Testing, RNA, Viral genetics, Seroepidemiologic Studies, Recombination, Genetic, COVID-19 epidemiology, COVID-19 veterinary, Cat Diseases, Dog Diseases diagnosis, Dog Diseases epidemiology
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Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a "One Health" approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.
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- 2023
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8. The Design and Implementation of the ECOVIR Project: A Primary Health Care Surveillance System to Strengthen Co-Detection of Respiratory Viruses in Normandy.
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Petat H, Schuers M, Corbet S, Humbert X, Le Bas F, Marguet C, Pellerin L, Rabiaza A, Vabret A, and Ar Gouilh M
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Acute respiratory infections (ARIs) need to be better understood and treated, as they are critical to public health, especially during crises such as the SARS-CoV2 pandemic. These are the most abundant infections in the general population and are seen primarily in primary care by general practitioners (GPs). Many different viruses are involved, according to epidemic variations. Viral co-detections account for a significant proportion of ARIs in hospital cohorts. The objective of the ECOVIR cohort was to study viral co-detections by setting up a biobank of respiratory tract samples from patients consulting their general practitioner for ARI symptoms. We report here on the course of the study: the design, the conduct, and the difficulties encountered. ECOVIR (Etude des CO-detections VIrales dans les prélèvements Respiratoires) was a prospective, multicenter cohort conducted in France during two epidemic seasons (2018-2019 and 2019-2020). We recruited GPs. Each GP investigator (GPI) saw patients weekly for examination, clinical data collection, and nasopharyngeal swabbing. Each sample was sent to the virology unit for biobanking and molecular analysis. Clinical and sociodemographic data were collected 7 days after inclusion. ECOVIR involved 36 GPIs. Patients with symptoms of an ARI were included ( n = 685). The median number of inclusions was 16 patients per GPI over both seasons (IC
25-75% [4.75; 27]). Patients aged 18 to 64 years were the most numerous (57%), followed by children (30%), and the elderly (13% over 65 years). This age distribution emphasizes the young adult and middle-aged population. Residents participated in the project and called patients on day 7 to obtain clinical and sociodemographic data. Our study triggered the creation of an original network, which plans to establish a functional link between research and primary health care. Primary care is unfortunately poorly represented in research protocols, particularly in respiratory infections, even though it is a cornerstone of our French health care system, as demonstrated every day in this period of crisis., Competing Interests: The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.- Published
- 2022
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9. Use of LoopDeelab during the COVID-19 Pandemic: An Innovative Device for Field Diagnosis.
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Dossou NC, Gaubert I, Maille E, Morello R, Cassier R, Schanen C, Dutheil JJ, Rocque LM, Vabret A, and Ar Gouilh M
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- COVID-19 Testing, Humans, Nucleic Acid Amplification Techniques methods, Pandemics, Prospective Studies, SARS-CoV-2 genetics, Sensitivity and Specificity, COVID-19 diagnosis, COVID-19 epidemiology
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Rapid and accurate diagnosis of SARS-CoV-2 infection is essential for the management of the COVID-19 outbreak. RT-LAMP LoopDeetect COVID-19 (LoopDeescience, France) is a rapid molecular diagnostic tool which operates with the LoopDeelab (LoopDeescience, France) device. RAPID COVID is a prospective double-blind research protocol which was conducted to evaluate the concordance between Loopdeetect COVID-19 and RT-PCR Allplex 2019 n-Cov (Seegene, Korea). Between 11 May 2020 and 14 June 2021, a total of 1122 nasopharyngeal swab specimens were collected, of which 741 were finally analysed. There were 32 "positive" and "indeterminate" RT-PCR results. The intrinsic performances of Loopdeetect COVID-19 are equivalent to other commercial RT-LAMP PCR COVID-19 kits, with a sensitivity and specificity of 69.23% [CI 95%: 48.21-85.67] and 100% [CI 95%: 99.58-100.00], respectively. To the best of our knowledge, LoopDeelab is the only LAMP PCR diagnostic device allowing such a fast and reliable analysis with low-cost equipment; this makes it a new and innovative technology, designed for field use. This device being portable, the development of other detection kits will be useful for the management of epidemics with a high attack rate and would facilitate the rapid application of health measures.
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- 2022
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10. Detection of SARS-CoV-2 in two cats during the second wave of the COVID-19 pandemic in France.
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Fritz M, Nesi N, Denolly S, Boson B, Legros V, Rosolen SG, Briend-Marchal A, Ar Gouilh M, and Leroy EM
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- Animals, Cats, France epidemiology, Pandemics, SARS-CoV-2, COVID-19 veterinary, Cat Diseases epidemiology
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Although there are several reports in the literature of SARS-CoV-2 infection in cats, few SARS-CoV-2 sequences from infected cats have been published. In this study, SARS-CoV-2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS-CoV-2 infection in two cats, infection status was confirmed by RT-qPCR and, in one cat, serological analysis for antibodies against N-protein and S-protein, as well as neutralizing antibodies. Comparative analysis of five SARS-CoV-2 sequence fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS-CoV-2. This study provides additional information on the clinical, molecular, and serological aspects of SARS-CoV-2 infection in cats., (© 2021 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd.)
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- 2022
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11. First Coronavirus Active Survey in Rodents From the Canary Islands.
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Monastiri A, Martín-Carrillo N, Foronda P, Izquierdo-Rodríguez E, Feliu C, López-Roig M, Miquel J, Ar Gouilh M, and Serra-Cobo J
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Since the beginning of the 21st century five new coronaviruses inducing respiratory diseases in humans have been reported. These emergences has promoted research on coronaviruses in wildlife. We started the first eco-epidemiological study to screen the presence of coronaviruses circulating in mice and rats of four Canary Islands. Between 2015 and 2019, we obtained fecal samples of three rodent species (150 Mus musculus , 109 Rattus rattus and 1 Rattus norvegicus ) captured in urban and rural areas. Fecal samples were analyzed by nRT-PCR and the resulting sequences were compared to known diversity using Bayesian phylogenetic methods. We only found coronavirus RNA in house mice from El Hierro (10.53%), Tenerife (7.02%) and Lanzarote (5.26%) islands. All coronaviruses detected belong to the species Murine coronavirus belonging to the genus Betacoronavirus and subgenus Embecovirus , being all positive house mice captured in anthropogenic environment. The phylogenetic analysis shows that murine coronaviruses from the Canary Islands are related to European murine coronaviruses. Albeit data are still scarce in the region, the most probable origin of M. coronavirus present in the Canary Islands is continental Europe. According to temporal Bayesian phylogenetics, the differentiation between Canary and continental viruses seems to be quite recent. Moreover, murine coronaviruses from El Hierro, Tenerife and Lanzarote islands tend to segregate in different clades. This enlightens the potential role of rodents or other possibly invasive species in disseminating infectious diseases to remote places through exchanges with the continent. It is important to consider these aspects in the sanitary control of islands, for health and biodiversity preservation concerns., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Monastiri, Martín-Carrillo, Foronda, Izquierdo-Rodríguez, Feliu, López-Roig, Miquel, Ar Gouilh and Serra-Cobo.)
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- 2021
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12. Effect of Tenofovir Disoproxil Fumarate and Emtricitabine on nasopharyngeal SARS-CoV-2 viral load burden amongst outpatients with COVID-19: A pilot, randomized, open-label phase 2 trial.
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Parienti JJ, Prazuck T, Peyro-Saint-Paul L, Fournier A, Valentin C, Brucato S, Verdon R, Sève A, Colin M, Lesne F, Guinard J, Ar Gouilh M, Dina J, Vabret A, and Hocqueloux L
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Background: Tenofovir and emtricitabine interfere with the SARS CoV-2 ribonucleic acid (RNA)-dependent RNA polymerase (RdRp). Several cohorts reported that people treated by tenofovir disoproxil fumarate and emtricitabine are less likely to develop SARS CoV-2 infection and related severe COVID-19., Methods: We conducted a pilot randomized, open-label, controlled, phase 2 trial at two hospitals in France. Eligible patients were consecutive outpatients (aged ≥18 years) with RT-PCR-confirmed SARS-CoV-2 infection and an interval from symptom onset to enrolment of 7 days or less. Patients were randomly assigned in a 1:1 ratio to receive oral tenofovir disoproxil fumarate and emtricitabine (2 pills on day 1 followed by 1 pill per day on days 2-7) or the standard of care. The primary and secondary endpoints were SARS-CoV-2 viral clearance from baseline assessed by cycle threshold (Ct) RT-PCR on nasopharyngeal swab collected at day 4 and day 7, respectively. A higher Ct corresponds to a lower SARS CoV-2 viral burden. Other endpoints were the time to recovery and the number of adverse events. This trial is registered with ClinicalTrials.gov, NCT04685512., Findings: From November, 20
th 2020 to March, 19th 2021, 60 patients were enrolled and randomly assigned to a treatment group (30 to tenofovir disoproxil fumarate and emtricitabine and 30 to standard of care). The median number of days from symptom onset to inclusion was 4 days (IQR 3-5) in both groups. Amongst patients who received tenofovir disoproxil fumarate, the difference from standard of care in the increase in Ct RT-PCR from baseline was 2.3 (95% confidence interval [-0.6 to 5.2], p = 0.13) at day 4 and 2.9 (95% CI [0.1 to 5.2], p = 0.044) at day 7. At day 7, 6/30 in the tenofovir disoproxil fumarate and emtricitabine group and 3/30 in the standard of care group reported no COVID-related symptoms. Adverse events included 11 cases of gastrointestinal side effects (grade ≤ 2), three of which leaded to drug discontinuation. Three patients had COVID-19 related hospitalisation, no participant died., Interpretation: In this pilot study of outpatients adult with recent non-severe COVID-19, tenofovir disoproxil fumarate plus emtricitabine appeared to accelerate the natural clearance of nasopharyngeal SARS-CoV-2 viral burden. These findings support the conduct of larger trials of tenofovir-based therapies for the prevention and early treatment of COVID-19., Funding: No external funding., Competing Interests: J.-JP reports personal fees and grant support from Gilead Sciences, Merck Sharp & Dohme and ViiV Healthcare outside the submitted work. L.H. reports personal fees and non-financial support from Gilead Sciences, Janssen-Cilag, Merck Sharp & Dohme and ViiV Healthcare outside the submitted work. Other authors declare no competing interests., (© 2021 The Author(s).)- Published
- 2021
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13. Misconceptions and misinformation about bats and viruses.
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Puechmaille SJ, Ar Gouilh M, Dechmann D, Fenton B, Geiselman C, Medellin R, Mittermeier R, Racey P, Reeder DM, Schaer J, Vicente-Santos A, Sechrest W, Víquez-R L, and Weber N
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- Animals, Communication, Ecosystem, Humans, SARS-CoV-2, COVID-19, Chiroptera, Viruses
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- 2021
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14. Healthcare associated coronavirus disease 2019 among health care workers in Normandy, France: a multi-center study.
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Thibon P, Breton P, Mouet A, Bidon A, Haupais F, Darrigan C, Gautier P, Letourneur T, Perillieux E, Seguineau C, Thibon P, Henry L, Ar Gouilh M, Borgey F, and Le Hello S
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Introduction: In the early phase of the coronavirus disease (COVID-19) epidemic in France, knowledge of SARS-COV-2 characteristics was limited, and personal protective equipment (PPE) was lacking. Thus, health care workers (HCWs) were exposed to nosocomial transmission., Methods: A multicenter regional descriptive study of fifty-two heath care facilities covering 30,533 HCWs in western Normandy, France, from March 3 to March 27, 2020, before the incidence threshold of 10/100,000 inhabitants was crossed in the study area. The incidence rate of COVID-19 in HCWs, the attack rates and the serial interval distribution of nosocomial transmission were computed. Demographic characteristics of HCWs, contacts with index cases, and the use of personal protective equipment were collected by a structured questionnaire., Results: The incidence rate of COVID-19 in HCWs was 2.7‰. Among 19 situations (13 clusters >2 cases), 10 were HCW-HCW and 9 patient-HCW transmission, the global attack rate was 13.7% (95% confidence interval, 10.6%-17.3%), and 68 HCWs were involved (10 index cases, with 58 secondary cases). Exposure of secondary cases was only in the presymptomatic phase of the index case in 29% of cases, 48% for HCW-HCW and 10% for patient-HCW transmission ( P <0.001). The mean serial interval was 5.1 days (95% CI, 4.2-5.9 days). Preventative measures were not optimal., Conclusions: Our investigation demonstrated that HCWs who were not assigned to the care of COVID-19 patients were not prepared for the arrival of this particularly insidious new virus, which spread rapidly from an often asymptomatic colleague or patient., (© 2020 The Authors.)
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- 2021
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15. The risk of SARS-CoV-2 transmission to pets and other wild and domestic animals strongly mandates a one-health strategy to control the COVID-19 pandemic.
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Leroy EM, Ar Gouilh M, and Brugère-Picoux J
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- 2020
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16. Opinion paper: Severe Acute Respiratory Syndrome Coronavirus 2 and domestic animals: what relation?
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Khamisse E, Dunoyer C, Ar Gouilh M, Brown P, Meurens F, Meyer G, Monchatre-Leroy E, Pavio N, Simon G, and Le Poder S
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- 2020
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17. Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon.
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Maganga GD, Pinto A, Mombo IM, Madjitobaye M, Mbeang Beyeme AM, Boundenga L, Ar Gouilh M, N'Dilimabaka N, Drexler JF, Drosten C, and Leroy EM
- Subjects
- Animals, Base Sequence genetics, Coronavirus 229E, Human genetics, Coronavirus Infections virology, Eulipotyphla virology, Gabon epidemiology, Humans, Phylogeny, Prevalence, Primates genetics, RNA, Viral genetics, RNA, Viral isolation & purification, Reverse Transcriptase Polymerase Chain Reaction, Rodentia genetics, Seasons, Alphacoronavirus genetics, Betacoronavirus genetics, Caves, Chiroptera virology, Coronavirus Infections epidemiology, Genetic Variation
- Abstract
Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). We explored the diversity of CoVs and determined the factors driving the infection of CoVs in wild animals. Based on a nested reverse transcription-polymerase chain reaction, only bats, belonging to the Hipposideros gigas (4/156), Hipposideros cf. ruber (13/262) and Miniopterus inflatus (1/249) species, were found infected with CoVs. We identified alphacoronaviruses in H. gigas and H. cf. ruber and betacoronaviruses in H. gigas. All Alphacoronavirus sequences grouped with Human coronavirus 229E (HCoV-229E). Ecological analyses revealed that CoV infection was significantly found in July and October in H. gigas and in October and November in H. cf ruber. The prevalence in the Faucon cave was significantly higher. Our findings suggest that insectivorous bats harbor potentially zoonotic CoVs; highlight a probable seasonality of the infection in cave-dwelling bats from the North-East of Gabon and pointed to an association between the disturbance of the bats' habitat by human activities and CoV infection.
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- 2020
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18. Rabies in Uganda: rabies knowledge, attitude and practice and molecular characterization of circulating virus strains.
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Omodo M, Ar Gouilh M, Mwiine FN, Okurut ARA, Nantima N, Namatovu A, Nakanjako MF, Isingoma E, Arinaitwe E, Esau M, Kyazze S, Bahati M, Mayanja F, Bagonza P, Urri RA, Lovincer MN, Nabatta E, Kidega E, Ayebazibwe C, Nakanjako G, Sserugga J, Ndumu DB, Mwebe R, Mugabi K, Gonzalez JP, and Sekamatte M
- Subjects
- Adolescent, Adult, Animals, Bites and Stings, Brain virology, Child, Dog Diseases diagnosis, Dog Diseases epidemiology, Dog Diseases virology, Dogs, Female, Humans, Male, Phylogeny, Phylogeography, Post-Exposure Prophylaxis, RNA, Viral blood, Rabies epidemiology, Rabies virology, Rabies virus classification, Rabies virus genetics, Uganda, Young Adult, Health Knowledge, Attitudes, Practice, Rabies diagnosis, Rabies virus isolation & purification
- Abstract
Background: Rabies is a deadly preventable viral disease that affects all warm-blooded animals and widespread in many regions including Africa. The disease remains of major public health importance in Uganda. The purpose of this study was to establish Knowledge, Attitude, Practice (KAP) of Rabies in Moyo and Ntoroko districts and to characterize Rabies virus (RABV) strains from seven districts of Uganda with consistent prevalence of rabies., Methods: KAP survey data were collected based on animal biting history by interviewing the head of the veterinary departments, the medical centers and selected households from the study sites. Data were obtained from 84 households in Ntoroko and Moyo districts. Thirty-five (35) brain samples were collected from bovine, dogs, goats, foxes, jackals ad sheep between 2011 and 2013. Samples were tested using fluorescent antibody test (FAT), One step RT-PCR (following RNA extraction) and partial RABV N gene was sequenced by Sanger method before phylogenetic and phylogeographic analyses of sequences., Results: Scarcity of post-exposure prophylaxis services in the health centers was noted. Poor attitude of wound washing and deficiency of knowledge on how to handle wounds related to dog bites and the significance among household participants lacked. There is a high risk of rabies infection due to a limited dog's vaccination. Dog biting episodes in humans were of 75.00 and 62.50% in Moyo and Ntoroko districts respectively. Twenty-seven (27) samples tested positive for rabies by FAT and PCR. Ugandan sequences were closely related (97% nucleotide id) to the rabies virus sequences from Tanzania, Rwanda, Burundi, Nigeria, Central African Republic and Sudan with both the "Africa 1A" and "Africa 1B" RABV clades represented. A putative new clade 1D was also detected., Conclusions: Rabies remains a public health hazard in Uganda. There is urgent need to establish advocacy programs in both schools and communities to curtail the spread of rabies. Increasing the knowledge regarding wound washing, post-exposure prophylaxis and dogs vaccination would enhance prevention of rabies. A strong collaboration between medical and veterinary sectors under a one health platform is required to ensure sufficient preventative services to the communities.
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- 2020
- Full Text
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19. SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world.
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Ar Gouilh M, Puechmaille SJ, Diancourt L, Vandenbogaert M, Serra-Cobo J, Lopez Roïg M, Brown P, Moutou F, Caro V, Vabret A, and Manuguerra JC
- Subjects
- Alphacoronavirus isolation & purification, Animals, Betacoronavirus isolation & purification, Coronavirus Infections virology, Genetic Variation, Phylogeny, Alphacoronavirus genetics, Betacoronavirus genetics, Chiroptera virology, Coronavirus Infections veterinary, Severe acute respiratory syndrome-related coronavirus genetics
- Abstract
The emergence of SARS-CoV and MERS-CoV, triggered the discovery of a high diversity of coronaviruses in bats. Studies from Europe have shown that coronaviruses circulate in bats in France but this reflects only a fraction of the whole diversity. In the current study the diversity of coronaviruses circulating in western Europe was extensively explored. Ten alphacoronaviruses in eleven bat species belonging to the Miniopteridae, Vespertilionidae and Rhinolophidae families and, a SARS-CoV-related Betacoronavirus in Rhinolophus ferrumequinum were identified. The diversity and prevalence of bat coronaviruses presently reported from western Europe is much higher than previously described and includes a SARS-CoV sister group. This diversity demonstrates the dynamic evolution and circulation of coronaviruses in this species. That said, the identified coronaviruses were consistently associated with a particular bat species or genus, and these relationships were maintained no matter the geographic location. The observed phylogenetic grouping of coronaviruses from the same species in Europe and Asia, emphasizes the role of host/pathogen coevolution in this group., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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20. A four-year survey (2011-2014) of West Nile virus infection in humans, mosquitoes and birds, including the 2012 meningoencephalitis outbreak in Tunisia.
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Monastiri A, Mechri B, Vázquez-González A, Ar Gouilh M, Chakroun M, Loussaief C, Mastouri M, Dimassi N, Boughzala L, Aouni M, and Serra-Cobo J
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- Adolescent, Adult, Aged, Animals, Bird Diseases blood, Bird Diseases epidemiology, Birds, Cerebrospinal Fluid virology, Child, Child, Preschool, Disease Outbreaks, Female, Humans, Infant, Male, Meningoencephalitis blood, Meningoencephalitis epidemiology, Middle Aged, Phylogeny, Tunisia epidemiology, West Nile Fever blood, West Nile Fever epidemiology, West Nile virus classification, West Nile virus genetics, West Nile virus physiology, Young Adult, Bird Diseases virology, Culex virology, Meningoencephalitis veterinary, Meningoencephalitis virology, Mosquito Vectors virology, West Nile Fever veterinary, West Nile Fever virology, West Nile virus isolation & purification
- Abstract
A West Nile virus (WNV) outbreak occurred in Tunisia between mid-July and December 2012. To assess the epidemiological features of the WNV transmission cycle, human cerebrospinal fluid samples from patients with suspected cases (n = 79), Culex pipiens mosquitoes (n = 583) and serum specimens from domestic and migratory birds (n = 70) were collected for 4 years (2011-2014) in the Tunisian Sahel region. Viral testing was performed by polymerase chain reaction (PCR). The WNV genome was detected in 7 patients (8.8%), 4 Culex pipiens pools, and a domestic mallard (Anas platyrhynchos). All PCR-positive samples were from the Monastir region. Phylogenetic analysis revealed that two different WNV strain groups circulated, and isolates from the reservoir (bird), vector (Culex pipiens), and dead-end hosts (humans) were closely related. The Monastir region is a hot-spot for WNV infection, and the reiterative presence of WNV over the years has increased the risk of viral reemergence in Tunisia, which highlights the need for more enhanced and effective WNV surveillance in humans with public awareness campaigns strengthened by monitoring mosquitoes and maintaining avian surveillance for early detection of WNV circulation.
- Published
- 2018
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21. Identification of Alpha and Beta Coronavirus in Wildlife Species in France: Bats, Rodents, Rabbits, and Hedgehogs.
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Monchatre-Leroy E, Boué F, Boucher JM, Renault C, Moutou F, Ar Gouilh M, and Umhang G
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- Alphacoronavirus classification, Alphacoronavirus isolation & purification, Animals, Betacoronavirus classification, Betacoronavirus isolation & purification, Chiroptera virology, Coronavirus genetics, Coronavirus isolation & purification, Coronavirus Infections virology, France, Geography, Hedgehogs, Phylogeny, Rabbits, Rodentia, Coronavirus classification, Coronavirus Infections veterinary, Disease Reservoirs virology, Genetic Variation
- Abstract
Coronaviruses are closely monitored in the context of emerging diseases and, as illustrated with Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome-coronavirus (MERS-CoV), are known to cross the species barrier and eventually to move from wildlife to humans. Knowledge of the diversity of coronaviruses in wildlife is therefore essential to better understand and prevent emergence events. This study explored the presence of coronaviruses in four wild mammal orders in France: Bats, rodents, lagomorphs, and hedgehogs. Betacoronavirus and Alphacoronavirus genera were identified. The results obtained suggest the circulation of potentially evolving virus strains, with the potential to cross the species barrier., Competing Interests: The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.
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- 2017
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22. First Complete Genome Sequence of a French Bovine coronavirus Strain.
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Kin N, Guerard P, Diancourt L, Caro V, Vabret A, and Ar Gouilh M
- Abstract
We sequenced the first Bovine coronavirus (BCoV) complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014., (Copyright © 2017 Kin et al.)
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- 2017
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23. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes.
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Lequime S, Fontaine A, Ar Gouilh M, Moltini-Conclois I, and Lambrechts L
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- Aedes genetics, Animals, Base Sequence, Dengue virology, Evolution, Molecular, Female, Genetic Variation genetics, High-Throughput Nucleotide Sequencing, Insect Vectors genetics, Male, RNA, Viral genetics, Sequence Analysis, RNA, Virus Replication, Aedes virology, Dengue transmission, Dengue Virus genetics, Genetic Drift, Genome, Viral genetics, Host-Pathogen Interactions
- Abstract
Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution.
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- 2016
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24. A member of a new Picornaviridae genus is shed in pig feces.
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Sauvage V, Ar Gouilh M, Cheval J, Muth E, Pariente K, Burguiere A, Caro V, Manuguerra JC, and Eloit M
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- Amino Acid Sequence, Animals, Base Sequence, Capsid Proteins genetics, DNA, Viral genetics, Feces virology, Female, Genetic Variation, Genome, Viral, Male, Metagenome, Molecular Sequence Data, Parechovirus classification, Parechovirus genetics, Phylogeny, Picornaviridae classification, Sequence Homology, Amino Acid, Virus Shedding, Picornaviridae genetics, Picornaviridae isolation & purification, Sus scrofa virology
- Abstract
During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C(pro), and 3D(pol)). Given its particular relationship with Parechovirus, we propose to name it "Pasivirus" for Parecho sister clade virus, with "Swine pasivirus 1" (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel Picornaviridae genus related to parechoviruses.
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- 2012
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25. Human polyomavirus related to African green monkey lymphotropic polyomavirus.
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Sauvage V, Foulongne V, Cheval J, Ar Gouilh M, Pariente K, Dereure O, Manuguerra JC, Richardson J, Lecuit M, Burguière A, Caro V, and Eloit M
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- Adult, Aged, Aged, 80 and over, Animals, DNA, Viral analysis, DNA, Viral isolation & purification, Female, High-Throughput Nucleotide Sequencing, Humans, Male, Merkel Cells virology, Middle Aged, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Polyomavirus isolation & purification, Polyomavirus Infections virology, Sequence Analysis, DNA, Tumor Virus Infections virology, Young Adult, Carcinoma, Merkel Cell virology, Chlorocebus aethiops virology, Polyomavirus classification, Polyomavirus genetics, Skin virology, Skin Neoplasms virology
- Abstract
While studying the virome of the skin surface of a patient with a Merkel cell carcinoma (MCC) by using unbiased, high-throughput sequencing, we identified a human polyomavirus nearly identical to human polyomavirus 9, a virus recently reported in blood and urine of renal transplantion patients and closely related to the African green monkey lymphotropic polyomavirus. Specific PCR analysis further identified this virus in 2/8 patients with MCC but in only 1/111 controls without MCC. This virus was shed for ≥20 months by the MCC index patient and was on the skin of the spouse of the index patient. These results provide information on the viral ecology of human skin and raise new questions regarding the pathology of virus-associated skin disorders.
- Published
- 2011
- Full Text
- View/download PDF
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