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1. Exposure of cattle to tick-borne encephalitis virus in the historical endemic zone in north-eastern France

Author

Laure Mathews-Martin, Gaëlle Gonzalez, Nolwenn M. Dheilly, Rayane Amaral-Moraes, Marine Dumarest, Teheipuaura Helle, Camille Migne, Christophe Caillot, Sandrine A. Lacour, Sylvie Pérelle, Cécile Beck, Raphaëlle Metras, and Laure Bournez

Subjects
Tick-borne encephalitis virus, cELISA, Cattle, Seroprevalence, Veterinary medicine, SF600-1100
Abstract

Abstract Background Tick-borne encephalitis (TBE) is a severe human neuroinfection caused by TBE virus (TBEV). TBEV is transmitted by tick bites and by the consumption of unpasteurized dairy products from infected asymptomatic ruminants. In France, several food-borne transmission events have been reported since 2020, raising the question of the level of exposure of domestic ungulates to TBEV. In this study, our objectives were (i) to estimate TBEV seroprevalence and quantify antibodies titres in cattle in the historical endemic area of TBEV in France using the micro virus neutralisation test (MNT) and (ii) to compare the performance of two veterinary cELISA kits with MNT for detecting anti-TBEV antibodies in cattle in various epidemiological contexts. A total of 344 cattle sera from four grid cells of 100 km² in Alsace-Lorraine (endemic region) and 84 from western France, assumed to be TBEV-free, were investigated. Results In Alsace-Lorraine, cattle were exposed to the virus with an overall estimated seroprevalence of 57.6% (95% CI: 52.1–62.8%, n = 344), varying locally from 29.9% (95% CI: 21.0–40.0%) to 92.1% (95% CI: 84.5–96.8%). Seroprevalence did not increase with age, with one- to three-year-old cattle being as highly exposed as older ones, suggesting a short-life duration of antibodies. The proportion of sera with MNT titres lower than 1:40 per grid cell decreased with increased seroprevalence. Both cELISA kits showed high specificity (> 90%) and low sensitivity (less than 78.1%) compared with MNT. Sensitivity was lower for sera with neutralising antibodies titres below 1:40, suggesting that sensitivity of these tests varied with local virus circulation intensity. Conclusions Our results highlight that cattle were highly exposed to TBEV. Screening strategy and serological tests should be carefully chosen according to the purpose of the serological study and with regard to the limitations of each method.

Published
2024
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2. Different viral genes modulate virulence in model mammal hosts and Culex pipiens vector competence in Mediterranean basin lineage 1 West Nile virus strains

Author

Lise Fiacre, Antoine Nougairède, Camille Migné, Maëlle Bayet, Maxime Cochin, Marine Dumarest, Teheipuaura Helle, Antoni Exbrayat, Nonito Pagès, Damien Vitour, Jennifer P. Richardson, Anna-Bella Failloux, Marie Vazeille, Emmanuel Albina, Sylvie Lecollinet, and Gaëlle Gonzalez

Subjects
Culex pipiens, host virulence, Mediterranean basin, reverse genetics, vector competence, West Nile virus lineage 1, Microbiology, QR1-502
Abstract

West Nile virus (WNV) is a single-stranded positive-sense RNA virus (+ssRNA) belonging to the genus Orthoflavivirus. Its enzootic cycle involves mosquito vectors, mainly Culex, and wild birds as reservoir hosts, while mammals, such as humans and equids, are incidental dead-end hosts. It was first discovered in 1934 in Uganda, and since 1999 has been responsible for frequent outbreaks in humans, horses and wild birds, mostly in America and in Europe. Virus spread, as well as outbreak severity, can be influenced by many ecological factors, such as reservoir host availability, biodiversity, movements and competence, mosquito abundance, distribution and vector competence, by environmental factors such as temperature, land use and precipitation, as well as by virus genetic factors influencing virulence or transmission. Former studies have investigated WNV factors of virulence, but few have compared viral genetic determinants of pathogenicity in different host species, and even fewer have considered the genetic drivers of virus invasiveness and excretion in Culex vector. In this study, we characterized WNV genetic factors implicated in the difference in virulence observed in two lineage 1 WNV strains from the Mediterranean Basin, the first isolated during a significant outbreak reported in Israel in 1998, and the second from a milder outbreak in Italy in 2008. We used an innovative and powerful reverse genetic tool, e.g., ISA (infectious subgenomic amplicons) to generate chimeras between Israel 1998 and Italy 2008 strains, focusing on non-structural (NS) proteins and the 3′UTR non-coding region. We analyzed the replication of these chimeras and their progenitors in mammals, in BALB/cByJ mice, and vector competence in Culex (Cx.) pipiens mosquitoes. Results obtained in BALB/cByJ mice suggest a role of the NS2B/NS3/NS4B/NS5 genomic region in viral attenuation in mammals, while NS4B/NS5/3′UTR regions are important in Cx. pipiens infection and possibly in vector competence.

Published
2024
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3. Evaluation of NS4A, NS4B, NS5 and 3′UTR Genetic Determinants of WNV Lineage 1 Virulence in Birds and Mammals

Author

Lise Fiacre, Steeve Lowenski, Céline Bahuon, Marine Dumarest, Bénédicte Lambrecht, Maha Dridi, Emmanuel Albina, Jennifer Richardson, Stéphan Zientara, Miguel-Ángel Jiménez-Clavero, Nathalie Pardigon, Gaëlle Gonzalez, and Sylvie Lecollinet

Subjects
West Nile virus, molecular determinants, virulence, reverse genetics, Microbiology, QR1-502
Abstract

West Nile virus (WNV) is amplified in an enzootic cycle involving birds as amplifying hosts. Because they do not develop high levels of viremia, humans and horses are considered to be dead-end hosts. Mosquitoes, especially from the Culex genus, are vectors responsible for transmission between hosts. Consequently, understanding WNV epidemiology and infection requires comparative and integrated analyses in bird, mammalian, and insect hosts. So far, markers of WNV virulence have mainly been determined in mammalian model organisms (essentially mice), while data in avian models are still missing. WNV Israel 1998 (IS98) is a highly virulent strain that is closely genetically related to the strain introduced into North America in 1999, NY99 (genomic sequence homology > 99%). The latter probably entered the continent at New York City, generating the most impactful WNV outbreak ever documented in wild birds, horses, and humans. In contrast, the WNV Italy 2008 strain (IT08) induced only limited mortality in birds and mammals in Europe during the summer of 2008. To test whether genetic polymorphism between IS98 and IT08 could account for differences in disease spread and burden, we generated chimeric viruses between IS98 and IT08, focusing on the 3′ end of the genome (NS4A, NS4B, NS5, and 3′UTR regions) where most of the non-synonymous mutations were detected. In vitro and in vivo comparative analyses of parental and chimeric viruses demonstrated a role for NS4A/NS4B/5′NS5 in the decreased virulence of IT08 in SPF chickens, possibly due to the NS4B-E249D mutation. Additionally, significant differences between the highly virulent strain IS98 and the other three viruses were observed in mice, implying the existence of additional molecular determinants of virulence in mammals, such as the amino acid changes NS5-V258A, NS5-N280K, NS5-A372V, and NS5-R422K. As previously shown, our work also suggests that genetic determinants of WNV virulence can be host-dependent.

Published
2023
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4. Myocarditis and Subclinical-Like Infection Associated With SARS-CoV-2 in Two Cats Living in the Same Household in France: A Case Report With Literature Review

Author

Valérie Chetboul, Pierre Foulex, Kahina Kartout, Anne Marie Klein, Corinne Sailleau, Marine Dumarest, Manon Delaplace, Meriadeg Ar Gouilh, Jeremy Mortier, and Sophie Le Poder

Subjects
cat, COVID-19, echocardiography, heart failure, myocarditis, SARS-CoV-2, Veterinary medicine, SF600-1100
Abstract

This report provides the first clinical, radiographic, echocardiographic, and biological description of SARS-CoV-2-associated myocarditis with a 6-month follow-up in a 5-year-old obese male domestic shorthair cat (Cat-1) presented for refractory congestive heart failure, with high cardiac troponin-I level (5.24 ng/ml), and a large lingual ulcer. The animal was SARS-CoV-2 positive on serology. The other cat living in the same household (Cat-2) never showed any clinical sign but was also confirmed SARS-CoV-2 positive on serology. Both cats were SARS-CoV-2 PCR negative. Cat-1 had closer contact than Cat-2 with their owner, who had been in close contact with a coworker tested PCR positive for COVID-19 (Alpha (B.1.1.7) variant) 4 weeks before Cat-1's first episode of congestive heart failure. A focused point-of-care echocardiography at presentation revealed for Cat-1 numerous B-lines, pleural effusion, severe left atrial dilation and dysfunction, and hypertrophic cardiomyopathy phenotype associated with focal pulmonary consolidations. Both myocarditis and pneumonia were suspected, leading to the prescription of cardiac medications and antibiotics. One month later, Cat-1 recovered, with normalization of left atrial size and function, and radiographic and echocardiography disappearance of heart failure signs and pulmonary lesions. An extensive literature review of SARS-CoV-2-related cardiac injury in pets in comparison with human pathology is discussed.

Published
2021
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5. Insights into the Host Range, Genetic Diversity, and Geographical Distribution of Jingmenviruses

Author

Sarah Temmam, Thomas Bigot, Delphine Chrétien, Mathilde Gondard, Philippe Pérot, Virginie Pommelet, Evelyne Dufour, Stéphane Petres, Elodie Devillers, Thavry Hoem, Valérie Pinarello, Vibol Hul, Khamsing Vongphayloth, Jeffrey C. Hertz, Irène Loiseau, Marine Dumarest, Veasna Duong, Muriel Vayssier-Taussat, Marc Grandadam, Emmanuel Albina, Philippe Dussart, Sara Moutailler, Julien Cappelle, Paul T. Brey, and Marc Eloit

Subjects
Jingmenvirus, LIPS, emergence, evolution, Microbiology, QR1-502
Abstract

ABSTRACT Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae-related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure.

Published
2019
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6. Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand

Author

Sarah Temmam, Delphine Chrétien, Thomas Bigot, Evelyne Dufour, Stéphane Petres, Marc Desquesnes, Elodie Devillers, Marine Dumarest, Léna Yousfi, Sathaporn Jittapalapong, Anamika Karnchanabanthoeng, Kittipong Chaisiri, Léa Gagnieur, Jean-François Cosson, Muriel Vayssier-Taussat, Serge Morand, Sara Moutailler, and Marc Eloit

Subjects
virome, tick, emergence, spillover, LIPS, Microbiology, QR1-502
Abstract

Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because of their inherent inability to be predictable, conversely to emergences caused by previously known agents that could be targeted by routine surveillance programs. Emerging zoonotic infections either originate from increasing contacts between wildlife and human populations, or from the geographical expansion of hematophagous arthropods that act as vectors, this latter being more capable to impact large-scale human populations. While characterizing the viral communities from candidate vectors in high-risk geographical areas is a necessary initial step, the need to identify which viruses are able to spill over and those restricted to their hosts has recently emerged. We hypothesized that currently unknown tick-borne arboviruses could silently circulate in specific biotopes where mammals are highly exposed to tick bites, and implemented a strategy that combined high-throughput sequencing with broad-range serological techniques to both identify novel arboviruses and tick-specific viruses in a ticks/mammals interface in Thailand. The virome of Thai ticks belonging to the Rhipicephalus, Amblyomma, Dermacentor, Hyalomma, and Haemaphysalis genera identified numerous viruses, among which several viruses could be candidates for future emergence as regards to their phylogenetic relatedness with known tick-borne arboviruses. Luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Orthomyxoviridae, Phenuiviridae, Flaviviridae, Rhabdoviridae, and Chuviridae families was used to screen human and cattle Thai populations highly exposed to tick bites. Although no positive serum was detected for any of the six viruses selected, suggesting that these viruses are not infecting these vertebrates, or at very low prevalence (upper estimate 0.017% and 0.047% in humans and cattle, respectively), the virome of Thai ticks presents an extremely rich viral diversity, among which novel tick-borne arboviruses are probably hidden and could pose a public health concern if they emerge. The strategy developed in this pilot study, starting from the inventory of viral communities of hematophagous arthropods to end by the identification of viruses able (or likely unable) to infect vertebrates, is the first step in the prediction of putative new emergences and could easily be transposed to other reservoirs/vectors/susceptible hosts interfaces.

Published
2019
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7. Serological evidence of infection with dengue and Zika viruses in horses on French Pacific Islands.

Author

Cécile Beck, Isabelle Leparc-Goffart, Denise Desoutter, Estelle Debergé, Hervé Bichet, Steeve Lowenski, Marine Dumarest, Gaelle Gonzalez, Camille Migné, Jessica Vanhomwegen, Stéphan Zientara, Benoit Durand, and Sylvie Lecollinet

Subjects
Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract

New Caledonia and French Polynesia are areas in which arboviruses circulate extensively. A large serological survey among horses from New Caledonia and French Polynesia was carried out to investigate the seroprevalence of flaviviruses in the horse population. Here, 293 equine sera samples were screened for flaviviruses using a competitive enzyme-linked immunosorbent assay (cELISA). The positive sera were then confirmed using a flavivirus-specific microsphere immunoassay (MIA) and seroneutralization tests. This serosurvey showed that 16.6% (27/163) and 30.8% (40/130) of horses were positive for cELISA tests in New Caledonia and French Polynesia, respectively, but the MIA technique, targeting only flaviviruses causing neuro-invasive infections in humans and horses (i.e. West Nile virus [WNV], Japanese encephalitis virus [JEV] and tick-borne encephalitis virus [TBEV]), showed negative results for more than 85% (57/67) of the cELISA-positive animals. Seroneutralization tests with the main flaviviruses circulating in the South Pacific revealed that 6.1% (10/163; confidence interval [95% CI] 3.0%-11.0%) of sera in New Caledonia and 7.7% (10/130; 95% CI 3.8%-13.7%) in French Polynesia were positive for dengue virus serotype 1 (DENV1) and 4.3% (7/163; 95% CI 1.7%-8.6%) in New Caledonia and 15.4% (20/130, 95% CI 9.7%-22.8%) in French Polynesia were found positive for Zika virus (ZIKV). Seroprevalence of the JEV and WNV flaviviruses on the 293 samples from both island groups were comparatively much lower (less than 2%). This seroprevalence study in the horse population shows that horses can be infected with dengue and Zika viruses and that these infections lead to seroconversions in horses. The consequences of these infections in horses and their role in ZIKV and DENV epidemiological cycles are two issues that deserve further investigation.

Published
2019
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8. Contrasted Epidemiological Patterns of West Nile Virus Lineages 1 and 2 Infections in France from 2015 to 2019

Author

Cécile Beck, Isabelle Leparc Goffart, Florian Franke, Gaelle Gonzalez, Marine Dumarest, Steeve Lowenski, Yannick Blanchard, Pierrick Lucas, Xavier de Lamballerie, Gilda Grard, Guillaume André Durand, Stéphan Zientara, Jackie Tapprest, Grégory L’Ambert, Benoit Durand, Stéphanie Desvaux, and Sylvie Lecollinet

Subjects
arbovirus, emerging infectious diseases, zoonotic, West Nile, lineages 1 and 2, France, Medicine
Abstract

Since 2015, annual West Nile virus (WNV) outbreaks of varying intensities have been reported in France. Recent intensification of enzootic WNV circulation was observed in the South of France with most horse cases detected in 2015 (n = 49), 2018 (n = 13), and 2019 (n = 13). A WNV lineage 1 strain was isolated from a horse suffering from West Nile neuro-invasive disease (WNND) during the 2015 episode in the Camargue area. A breaking point in WNV epidemiology was achieved in 2018, when WNV lineage 2 emerged in Southeastern areas. This virus most probably originated from WNV spread from Northern Italy and caused WNND in humans and the death of diurnal raptors. WNV lineage 2 emergence was associated with the most important human WNV epidemics identified so far in France (n = 26, including seven WNND cases and two infections in blood and organ donors). Two other major findings were the detection of WNV in areas with no or limited history of WNV circulation (Alpes-Maritimes in 2018, Corsica in 2018–2019, and Var in 2019) and distinct spatial distribution of human and horse WNV cases. These new data reinforce the necessity to enhance French WNV surveillance to better anticipate future WNV epidemics and epizootics and to improve the safety of blood and organ donations.

Published
2020
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10. A One-Health Approach to Investigating an Outbreak of Alimentary Tick-Borne Encephalitis in a Non-endemic Area in France (Ain, Eastern France): A Longitudinal Serological Study in Livestock, Detection in Ticks, and the First Tick-Borne Encephalitis Virus Isolation and Molecular Characterisation

Author

Gonzalez, Gaëlle, primary, Bournez, Laure, additional, Moraes, Rayane Amaral, additional, Marine, Dumarest, additional, Galon, Clémence, additional, Vorimore, Fabien, additional, Cochin, Maxime, additional, Nougairède, Antoine, additional, Hennechart-Collette, Catherine, additional, Perelle, Sylvie, additional, Leparc-Goffart, Isabelle, additional, Durand, Guillaume André, additional, Grard, Gilda, additional, Bénet, Thomas, additional, Danjou, Nathalie, additional, Blanchin, Martine, additional, Lacour, Sandrine A., additional, Franck, Boué, additional, Chenut, Guillaume, additional, Mainguet, Catherine, additional, Simon, Catherine, additional, Brémont, Laurence, additional, Zientara, Stephan, additional, Moutailler, Sara, additional, Martin-Latil, Sandra, additional, Dheilly, Nolwenn M., additional, Beck, Cécile, additional, and Lecollinet, Sylvie, additional

Published
2022
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11. A one health approach to investigating an outbreak of alimentary tick-borne encephalitis in a non-endemic area in France (Ain, Eastern France): a longitudinal serological study in livestock, detection in ticks, and the first TBE virus isolation and molecular characterization

Author

Gaëlle Gonzalez, Laure Bournez, Rayane Amaral Moraes, Marine Dumarest, Clémence Galon, Fabien Vorimore, Maxime Cochin, Antoine Nougairède, Catherine Hennechart-Collette, Sylvie Perelle, Isabelle Leparc-Goffart, Guillaume André Durand, Gilda Grard, Thomas Bénet, Nathalie Danjou, Martine Blanchin, Sandrine A Lacour, Franck Boué, Guillaume Chenut, Catherine Mainguet, Catherine Simon, Laurence Brémont, Stephan Zientara, Sara Moutailler, Sandra Martin-Latil, Nolwenn M Dheilly, Cécile Beck, and Sylvie Lecollinet

Abstract

Tick borne encephalitis virus geographic range and human incidence is increasing throughout Europe, putting a number of non-endemic regions and countries at risk of outbreaks. In spring 2020, there was an outbreak of TBE in Ain, Eastern France, where the virus had never been detected before. All patients but one had consumed traditional unpasteurized raw goat cheese from a local producer. We conducted an investigation in the suspected farm using an integrative One Health approach. Our methodology included (i) the detection of virus in cheese and milk products, (ii) serological testing of all animals in the suspected farm and surrounding farms, (iii) an analysis of the landscape and localisation of wooded area, (iv) the capture of questing ticks and small mammals for virus detection and estimating enzootic hazard, and (v) virus isolation and genome sequencing. This approach allowed us to confirm the alimentary origin of the TBE outbreak and to witness in real time the seroconversion of recently exposed individuals and the excretion of virus in goat milk. In addition, we identified a wooded focus area where and around which there is a risk of TBEV exposure. We provide the first TBEV isolate responsible for as a source of dietary contamination in France, obtained its full-length genome sequence, and found that it does not cluster very closely neither with the isolate circulating in Alsace nor with any other isolate within the European lineage. TBEV is now a notifiable human disease in France, which should facilitate surveillance of TBEV incidence and distribution throughout France.

Published
2021

12. Contributors

Author

Quinn H. Abram, Marcelo Addas-Carvalho, Sergio P. Alpuche-Lazcano, Maria João Alves, Soniza Vieira Alves-Leon, Fátima Amaro, Josélio Maria Galvão de Araújo, Mariana Araujo-Pereira, Maíra Cardoso Aspahan, Maria Helena de M. Barbosa, Trisha R. Barnard, Cécile Beck, Bruno Deltreggia Benites, Walter Orlando Beys-da-Silva, Marshall E. Bloom, Guy Boivin, Aaron C. Brault, Otavio Cabral-Marques, Luiz Carlos de Caires Junior, Cynthia Chester Cardoso, Marlen Yelitza Carrillo-Hernández, Leila Chimelli, Paulo Pereira Christo, Dinh-Toi Chu, Kevin M. Coombs, Fabio T.M. Costa, Lucia Maria Costa Monteiro, Juan Cristina, Marielton Dos Passos Cunha, Lia Giraldo da Silva Augusto, Philippe Desprès, Adrián Diaz, Finn Diderichsen, Alberto José da Silva Duarte, Marine Dumarest, Nadia El Khawanky, José Veríssimo Fernandes, Simone G. Fonseca, Fabrícia Lima Fontes-Dantas, Gilles Gadea, Luciana Guerra Gallo, Anne Gatignol, David Alejandro Cabrera Gaytán, Gaelle Gonzalez, Ernesto Goulart, Ernesto R. Gregorio, Paulo Marcos Matta Guedes, Rodolphe Hamel, Cristina Barroso Hofer, Amni Adilah Ismail, Anne J. Jääskeläinen, Soe Hui Jen, Carla Judice, Carolini Kaid, Jun Kobayashi, Sylvie Lecollinet, Marcio Leyser, Maria Clara de Magalhães-Barbosa, Rishya Manikam, Fernanda J.P. Marques, Marlen Martínez-Gutiérrez, Felipe Martins, António Pedro Alves de Matos, Erin M. McDonald, Eyal Meltzer, Teresita Rojas Mendoza, Thiago Mitsugi, Luwanika Mlera, Concepción Grajales Muñiz, Helder I. Nakaya, Andrezza Nascimento, Gilmara Lima Nascimento, Manuela Sales Lima Nascimento, Osvaldo J.M. Nascimento, Tiep Tien Nguyen, Lumumba Arriaga Nieto, Maria Regina Fernandes de Oliveira, Katarzyna Owczarek, Alfonso Vallejos Parás, Vinood B. Patel, Henry Maia Peixoto, Marianoel Pereira-Gómez, Irmtraut Araci H. Pfrimer, Atchara Phumee, Jocelyne Piret, Arnaldo Prata-Barbosa, Victor R. Preedy, Krzysztof Pyrć, Rajkumar Rajendram, Chandramathi Samudi Raju, Átila Duque Rossi, Fernanda Cristina Rueda-Lopes, Julian Ruiz-Saenz, Selena M. Sagan, Amanda Costa Ayres Salmeron, Sabri Saeed Sanabani, Lucélia Santi, Wilo Victor dos Santos, Viviane Schuch, Shamala Devi Sekaran, Matt Sherwood, Prateek Saurabh Shrivastava, Saurabh RamBihariLal Shrivastava, Padet Siriyasatien, Nguyen Thai Son, Juliana Miranda Tatara, Felipe Ten Caten, Ho Huu Tho, Wildriss Viranaicken, Daniela Pires Ferreira Vivacqua, Dan Xu, Zhiheng Xu, Mayana Zatz, and Libia Zé-Zé

Published
2021

13. Nonhuman occurrence of Zika virus infection : implications for control

Author

Sylvie Lecollinet, Rodolphe Hamel, Marine Dumarest, Cécile Beck, Gaelle Gonzalez, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Martin, C.R. (ed.), Hollins-Martin, C.J. (ed.), Preedy, V.R. (ed.), and Rajendram, R. (ed.)

Subjects
ETHIOPIE, ZAMBIE, [SDV]Life Sciences [q-bio], 030231 tropical medicine, BORNEO, INDONESIE, PAKISTAN, Zika virus, 03 medical and health sciences, 0302 clinical medicine, OUGANDA, NIGERIA, CENTRAFRIQUE, 030304 developmental biology, MALAISIE, 0303 health sciences, biology, GAMBIE, THAILANDE, GABON, biology.organism_classification, Virology, BRESIL, POLYNESIE FRANCAISE, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, NOUVELLE CALEDONIE, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, KENYA, TANZANIE, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Published
2021

15. First detection and genome sequencing of SARS‐CoV‐2 in an infected cat in France

Author

Loic Comtet, Bernard Klonjkowski, Marine Dumarest, Valérie Caro, Stéphan Zientara, Philippe Pourquier, Jessica Vanhomwegen, Manon Delaplace, Aurélia Kwasiborski, Corinne Sailleau, Jean-Claude Manuguerra, Véronique Hourdel, Sophie Le Poder, Alix Barbarino, Patrick Chevaillier, Virologie UMR1161 (VIRO), École nationale vétérinaire - 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), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP), Centre Collaborateur de l'OIE de Détection et identification chez l’homme des pathogènes animaux émergents et développement d’outils pour leur diagnostic / Collaborating Center for the Detection and identification in humans of emerging animal pathogens and development of tools for their diagnoses (CCOIE-OIECC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé Animale / World Organisation Animal Health [Paris] (OIE), Clinique Vétérinaire de la place Davout [Savigny-sur-Orge], Centre Hospitalier Universitaire Vétérinaire d'Alfort [Maison Alfort] (CHUVA), École nationale vétérinaire - Alfort (ENVA)-PRES Université Paris-Est, IDvet [Grabels], Manon Delaplace is supported by a PhD fellowship from the DIM 1Health (Region Ile de France) and the Direction Générale de l’Enseignement et la Recherche from the French ministry of Agriculture (DGER)., The authors thank the veterinary practitioners for contributing to this study, the AFVAC (Association Française des Animaux de Compagnie) and the SNVEL of region Ile de France for their help. We are also grateful to Dr Meriadeg Le Gouil and Pr Astrid Vabret for helpful discussions. We thank Damien Hoinard for the technical support provided for the serological analysis., 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), Institut Pasteur [Paris], Organisation Mondiale de la Santé Animale / World Animal Health Information System (OIE-WAHIS)-Institut Pasteur [Paris], École nationale vétérinaire d'Alfort (ENVA)-PRES Université Paris-Est, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA), Cellule d'Intervention Biologique d'Urgence (CIBU), Université Pierre et Marie Curie - Paris 6 (UPMC), Spectrométrie de Masse structurale et protéomique, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), IDvet, Signalisation et Mecanismes Moleculaires de l'Apoptose, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Coronavirus disease 2019 (COVID-19), 040301 veterinary sciences, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viruses, next‐generation sequencing, Cat Diseases, DNA sequencing, SARS‐CoV‐2, Serology, 0403 veterinary science, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Clade, skin and connective tissue diseases, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, CATS, biology, General Veterinary, General Immunology and Microbiology, SARS-CoV-2, fungi, cats, COVID-19, virus diseases, 04 agricultural and veterinary sciences, General Medicine, Virology, 3. Good health, body regions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, luminex, Female, ELISA, next-generation sequencing, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, Antibody, pets, Rapid Communication
Abstract

International audience; After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection by SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2. For each animal, rectal, nasopharyngeal swabs and serum were taken. Swabs were submitted to RT-qPCR assays targeting 2 genes of SARS-CoV-2. All dogs were tested SARS-CoV-2 negative. One cat was tested positive by RT-qPCR on rectal swab. Nasopharyngeal swabs from this animal were tested negative. This cat showed mild respiratory and digestive signs. Serological analysis confirms the presence of antibodies against the SARS-CoV-2 in both serum samples taken 10 days apart. Genome sequence analysis revealed that the cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon their pets or compromise their welfare.

Published
2020
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16. First detection and genome sequencing of SARS-CoV-2 in an infected cat in France

Author

Jean-Claude Manuguerra, Manon Delaplace, Sophie Lepoder, Jessica Vanhomwegen, Loic Comtet, Stéphan Zientara, Bernard Klonjkowski, Alix Barbarino, Valérie Caro, Patrick Chevaillier, Marine Dumarest, Véronique Hourdel, Philippe Pourquier, Aurélia Kwasiborski, and Corinne Sailleau

Subjects
CATS, biology, viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), fungi, virus diseases, Serum samples, Virology, DNA sequencing, Serology, body regions, biology.protein, Antibody, skin and connective tissue diseases, Clade, Gene
Abstract

After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection of SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2. For each animal, rectal, nasopharyngeal swabs and serum were taken. Swabs were submitted to RT-qPCR assays targeting 2 genes of SARS-CoV-2. All dogs were tested SARS-CoV-2 negative. One cat was tested positive by RT-qPCR on rectal swab. Nasopharyngeal swabs from this animal were tested negative. This cat showed mild respiratory and digestive signs. Serological analysis confirm the presence of antibodies against the SARS-CoV-2 in the two serum samples taken 10 days apart. Genome sequence analysis revealed that the cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon their pets or compromise their welfare.

Published
2020

17. Infestation of small seabirds by Ornithodoros maritimus ticks: Effects on chick body condition, reproduction and associated infectious agents

Author

José Manuel Igual, Marine Dumarest, Ana Payo-Payo, Lena Yousfi, Andreu Rotger, Cécile Beck, Miguel Ángel Miranda, Virginia Picorelli, Thierry Boulinier, Ana Sanz-Aguilar, Amandine Gamble, Sara Moutailler, Mariana Viñas Torres, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virologie UMR1161 (VIRO), 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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Govern Balear (Acciones Especiales) AAEE031/2017, Spanish Ministry of Innovation and Universities (RESET) CGL2017-85210-P, Spanish Ministry of Innovation and Universities Innovation and Universities, Agencia Estatal de Investigacion, European Social Fund (ESF) RYC-2017-22796, Govern de les Illes Balears, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, École nationale vétérinaire - 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), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0301 basic medicine, Tick infestation, relapsing fever, 030231 tropical medicine, Population, Zoology, Tick, medicine.disease_cause, Microbiology, Parasite load, Birds, 03 medical and health sciences, 0302 clinical medicine, WNV, Storm petrels, biology.animal, Borrelia, Infestation, parasitic diseases, medicine, Prevalence, Soft ticks, Animals, 14. Life underwater, Mortality, education, Ornithodoros, education.field_of_study, Tick-borne pathogens, biology, Bird Diseases, Coinfection, Reproduction, biology.organism_classification, medicine.disease, bacterial infections and mycoses, 3. Good health, Tick Infestations, 030104 developmental biology, Infectious Diseases, Spain, Insect Science, [SDE]Environmental Sciences, Body Composition, Parasitology, Seabird, West Nile virus
Abstract

Ticks can negatively affect their host by direct effects as blood feeding causing anaemia or discomfort, or by pathogen transmission. Consequently, ticks can have an important role in the population dynamics of their hosts. However, specific studies on the demographic effects of tick infestation on seabirds are still scarce. Seabird ticks have also the potential to be responsible for the circulation of little known tick-borne agents, which could have implications for non-seabird species. Here, we report the results of investigations on potential associations between soft tick Ornithodoros maritimus load and reproductive parameters of storm petrels Hydrobates pelagicus breeding in a large colony in a cave of Espartar Island, in the Balearic archipelago. We also investigated by molecular analyses the potential viral and bacterial pathogens associated with O. maritimus ticks present at the colony. Lower nestling survival was recorded in the most infested area, deep in the cave, compared to the area near the entrance. The parasite load was negatively associated with the body condition of the nestlings. One pool of ticks tested positive for West Nile virus and 4 pools tested positive for a Borrelia species which was determined by targeted nested PCR to have a 99% sequence identity with B. turicatae, a relapsing fever Borrelia. Overall, these results show that further investigations are needed to better understand the ecology and epidemiology of the interactions between ticks, pathogens and Procellariiform species., This Project was partially funded by the Govern Balear (Acciones Especiales, AAEE031/2017) and the Spanish Ministry of Innovation and Universities (RESET, ref: CGL2017-85210-P). ASA was funded by the Spanish Ministry of Innovation and Universities Innovation and Universities, the Agencia Estatal de Investigación and the European Social Found (RYC-2017- 22796).

Published
2019

18. Serological evidence of infection with dengue and Zika viruses in horses on French Pacific Islands

Author

Estelle Debergé, Camille Migné, Steeve Lowenski, Hervé Bichet, Jessica Vanhomwegen, Benoit Durand, Stéphan Zientara, Cécile Beck, Sylvie Lecollinet, Isabelle Leparc-Goffart, Denise Desoutter, Gaelle Gonzalez, Marine Dumarest, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), EURL for equine diseases [Maisons-Alfort], Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, 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), Centre National de Référence des Arbovirus [Marseille] (CNR Arbovirus - laboratoire associé), Unité de Virologie [Marseille], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA)-Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service des Laboratoires Officiels Vétérinaires Agroalimentaires et Phytosanitaires de Nouvelle-Calédonie [Païta, Nouvelle-Calédonie], Direction des Affaires Vétérinaires Alimentaires et Rurales de Nouvelle-Calédonie [Païta, Nouvelle-Calédonie], Service du développement rural [Papeete, Polynésie française], Présidence de la Polynésie française [Papeete, Polynésie française], Environment and Infectious Risks Research and Expertise Unit [Paris], Département Infection et Epidémiologie - Department of Infection and Epidemiology, Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP), Epidémiologie (EPI), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Centre National de Référence des Arbovirus [Marseille] (CNR Arbovirus), Institut Pasteur [Paris]-Institut Pasteur [Paris], Institut Pasteur [Paris], Epidemiology unit [Maisons-Alfort], 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)-Université Paris-Est (UPE), Bodescot, Myriam, Beck, Cecile, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est (UPE)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Centre National de Référence des Arbovirus [Marseille], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA)-Unité d'Arbovirologie [Marseille], Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées-Service de Santé des Armées-Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées-Service de Santé des Armées, École pratique des hautes études (EPHE), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellule d'Intervention Biologique d'Urgence (CIBU), and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
Serotype, Topography, RC955-962, French Polynesia, Dengue virus, Geographical locations, Zika virus, 0302 clinical medicine, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Arctic medicine. Tropical medicine, MESH: Dengue/veterinary, MESH: Animals, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Mammals, Islands, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Zika Virus Infection, transmission, Eukaryota, virus diseases, 3. Good health, arboviruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Public aspects of medicine, West Nile virus, Encephalitis, [SDV.IMM] Life Sciences [q-bio]/Immunology, diptera-culicidae, Equines, MESH: Dengue/epidemiology, Microbiology, 03 medical and health sciences, aedes-aegypti, MESH: Horse Diseases/blood, Horses, education, MESH: Horses, Medicine and health sciences, MESH: Seroepidemiologic Studies, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, MESH: Dengue/blood, MESH: New Caledonia/epidemiology, Public Health, Environmental and Occupational Health, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Organisms, Biology and Life Sciences, Japanese encephalitis, Dengue Virus, medicine.disease, Virology, 030104 developmental biology, People and places, flaviviruses, 0301 basic medicine, RNA viruses, viruses, MESH: Zika Virus Infection/veterinary, MESH: Zika Virus Infection/blood, medicine.disease_cause, MESH: Horse Diseases/virology, Dengue fever, west-nile, Dengue, MESH: Zika Virus Infection/epidemiology, MESH: Polynesia/epidemiology, Pathology and laboratory medicine, polynesia, biology, seroprevalence, Medical microbiology, Infectious Diseases, Vertebrates, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, japanese encephalitis, [SDV.IMM]Life Sciences [q-bio]/Immunology, RA1-1270, Pathogens, Research Article, 030231 tropical medicine, Population, Oceania, antibdies, New Caledonia, medicine, Seroprevalence, Animals, Landforms, Viral pathogens, Geomorphology, Zika Virus, biology.organism_classification, Microbial pathogens, Amniotes, Earth Sciences, Horse Diseases
Abstract

New Caledonia and French Polynesia are areas in which arboviruses circulate extensively. A large serological survey among horses from New Caledonia and French Polynesia was carried out to investigate the seroprevalence of flaviviruses in the horse population. Here, 293 equine sera samples were screened for flaviviruses using a competitive enzyme-linked immunosorbent assay (cELISA). The positive sera were then confirmed using a flavivirus-specific microsphere immunoassay (MIA) and seroneutralization tests. This serosurvey showed that 16.6% (27/163) and 30.8% (40/130) of horses were positive for cELISA tests in New Caledonia and French Polynesia, respectively, but the MIA technique, targeting only flaviviruses causing neuro-invasive infections in humans and horses (i.e. West Nile virus [WNV], Japanese encephalitis virus [JEV] and tick-borne encephalitis virus [TBEV]), showed negative results for more than 85% (57/67) of the cELISA-positive animals. Seroneutralization tests with the main flaviviruses circulating in the South Pacific revealed that 6.1% (10/163; confidence interval [95% CI] 3.0%-11.0%) of sera in New Caledonia and 7.7% (10/130; 95% CI 3.8%-13.7%) in French Polynesia were positive for dengue virus serotype 1 (DENV1) and 4.3% (7/163; 95% CI 1.7%-8.6%) in New Caledonia and 15.4% (20/130, 95% CI 9.7%-22.8%) in French Polynesia were found positive for Zika virus (ZIKV). Seroprevalence of the JEV and WNV flaviviruses on the 293 samples from both island groups were comparatively much lower (less than 2%). This seroprevalence study in the horse population shows that horses can be infected with dengue and Zika viruses and that these infections lead to seroconversions in horses. The consequences of these infections in horses and their role in ZIKV and DENV epidemiological cycles are two issues that deserve further investigation., Author summary New Caledonia and French Polynesia, located in the South Pacific, are facing circulation of dengue virus (DENV) for a long time and emergence of Zika virus (ZIKV) since 2013. A large serosurvey among horses’ population from these two islands was carried out to investigate the seroprevalence of the main flaviviruses circulating in the South Pacific. We find out that 6 to 7% of equine sera tested were positive for DENV serotype 1 in the two islands and 4% and 15% were positive for ZIKV in New Caledonia and French Polynesia respectively. Our study highlighted serological evidence of DENV serotype 1 and ZIKV infections of horses leading to meaningful seroconversion. Seroprevalence of other mosquito-borne flaviviruses (i.e. Japanese encephalitis and West-Nile viruses) were comparatively much lower (less than 2%) in New Caledonia and French Polynesia groups suggesting the absence of past active circulation of these viruses in both islands. This finding emphasized the need to investigate the consequences of such infections in the horse population and to determine the role of domestic animals in ZIKV and DENV epidemiological cycles.

Published
2019

19. Insights into the host range, genetic diversity, and geographical distribution of jingmenviruses

Author

Paul T. Brey, Veasna Duong, Vibol Hul, Stéphane Petres, Philippe Pérot, Delphine Chrétien, Evelyne Dufour, Valérie Pinarello, Muriel Vayssier-Taussat, Sarah Temmam, Emmanuel Albina, Elodie Devillers, Marine Dumarest, Thomas Bigot, Marc Grandadam, Thavry Hoem, Virginie Pommelet, Irène Loiseau, Jeffrey C. Hertz, Sara Moutailler, Khamsing Vongphayloth, Philippe Dussart, Julien Cappelle, Marc Eloit, Mathilde Gondard, Découverte de Pathogènes - Pathogen Discovery, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Pasteur du Laos, Réseau International des Instituts Pasteur (RIIP), Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Institut Pasteur du Cambodge, US Naval Medical Research Unit n°2, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), École nationale vétérinaire d'Alfort (ENVA), Université Paris-Est (UPE), This work was supported by Laboratoire d’Excellence (Integrative Biology of Emerging Infectious Diseases, grant no. ANR-10-LABX-62-IBEID) and by the Direction Internationale de l'Institut Pasteur., We thank Jacques Bellalou and his team at the Production and Purification of Recombinant Proteins Technological Platform of Institut Pasteur for their help in expression of recombinant proteins, Yves Jacob and Mélanie Dos Santos for their technical assistance with the luminometer, the staff members at the ICAReB Platform of Institut Pasteur for access to human control sera, and all the people involved in the sampling of ticks, bats, and cattle in France, French Antilles, Lao PDR, and Cambodia., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Eloit, Marc, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform, Institut Pasteur [Paris], Naval Medical Research Unit Two [Cambodge] (NAMRU-2), Naval Medical Research Center [Silver Spring, USA] (NMRC), Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (EPIA), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, École nationale vétérinaire - Alfort (ENVA), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé

Subjects
0301 basic medicine, lcsh:QR1-502, jingmenvirus, Global Health, L73 - Maladies des animaux, lips, lcsh:Microbiology, Ticks, Blood serum, Chiroptera, Tick-borne disease, biology, Microbiology and Parasitology, Amblyomma testudinarium, Jingmenvirus, LIPS, emergence, evolution, QR1-502, Microbiologie et Parasitologie, 3. Good health, Phylogeography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Rhipicephalus microplus, Martinique, L72 - Organismes nuisibles des animaux, Research Article, Autre (Sciences du Vivant), Ixodes ricinus, Distribution géographique, 030106 microbiology, Zoology, Ecological and Evolutionary Science, Relation hôte pathogène, Tick, Microbiology, Arbovirus, Host Specificity, Virus des animaux, 03 medical and health sciences, Variation génétique, parasitic diseases, Filoviridae Infections, medicine, Animals, Humans, Molecular Biology, Maladie transmissible par tiques, Flaviviridae, Genetic Variation, biology.organism_classification, medicine.disease, 030104 developmental biology, Cattle
Abstract

Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae-related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure., Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae-related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure.

Published
2019

20. Natural viral co-infections in pig herds affect hepatitis e virus (hev) infection dynamics and increase the risk of contaminated livers at slaughter

Author

Nicolas Rose, Maelan Cineux, Béatrice Grasland, Eric Eveno, Sophie Mahé, Olivier Bourry, V. Dorenlor, Nicole Pavio, Mathieu Andraud, Marine Dumarest, Morgane Salines, F. Eono, Elodie Barnaud, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Bretagne Loire (COMUE) (UBL), Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
Circovirus, Male, infection dynamics, Swine, viruses, animal diseases, [SDV]Life Sciences [q-bio], Porcine Reproductive and Respiratory Syndrome, medicine.disease_cause, Serology, 03 medical and health sciences, hepatitis e virus, Hepatitis E virus, Genotype, medicine, Animals, risk factors, Porcine respiratory and reproductive syndrome virus, Circoviridae Infections, Seroconversion, 030304 developmental biology, Swine Diseases, 2. Zero hunger, 0303 health sciences, General Veterinary, General Immunology and Microbiology, biology, Coinfection, 030306 microbiology, public health, virus diseases, General Medicine, biology.organism_classification, Porcine reproductive and respiratory syndrome virus, Virology, Hepatitis E, Porcine circovirus, Liver, biology.protein, Herd, Female, Antibody, Abattoirs
Abstract

International audience; Hepatitis E virus (HEV) is a zoonotic pathogen, in particular genotype 3 HEV is mainly transmitted to humans through the consumption of contaminated pork products. This study aimed at describing HEV infection patterns in pig farms and at assessing the impact of immunomodulating co-infections namely Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), as well as other individual factors such as piglets' immunity and litters' characteristics on HEV dynamics. A longitudinal follow-up was conducted in three farrow-to-finish farms known to be HEV infected. Overall, 360 piglets were individually monitored from birth to slaughter with regular blood and faecal sampling as well as blood and liver samples collected at slaughterhouse. Virological and serological analyses were performed to detect HEV, PCV2 and PRRSV genome and antibodies. The links between 12 explanatory variables and four outcomes describing HEV dynamics were assessed using cox-proportional hazard models and logistic regression. HEV infection dynamics was found highly variable between farms and in a lower magnitude between batches. HEV positive livers were more likely related to short time-intervals between HEV infection and slaughter time (

Published
2019

21. High load of hepatitis E viral RNA in pork livers but absence in pork muscle at French slaughterhouses

Author

E. Barnaud, A. Le Roux, P. Garry, Nicole Pavio, C. Feurer, R. Rossel, Marine Dumarest, Institut du Porc (IFIP), Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and FranceAgrimer (SIVAL) [2010-0947]

Subjects
Adult, 0301 basic medicine, Genotype, Swine, [SDV]Life Sciences [q-bio], Sus scrofa, 030106 microbiology, Pork muscles, Viremia, Biology, medicine.disease_cause, Microbiology, Serology, Food safety, 03 medical and health sciences, Hepatitis E virus, Seroepidemiologic Studies, medicine, Animals, Humans, Seroprevalence, Viral rna, Swine Diseases, 2. Zero hunger, Muscles, virus diseases, food and beverages, General Medicine, Viral Load, Hepatitis E, medicine.disease, Virology, 3. Good health, Red Meat, Liver, RNA, Viral, High load, France, Abattoirs, Food Science
Abstract

International audience; Pork ham muscle can be contaminated with HEV via blood vessels during viremia and represents a possible source of human contamination via the consumption of dried ham. This study evaluated the prevalence of HEV ENA in pork ham muscles and pork livers at slaughterhouses. Serology was determined on the corresponding serum samples. The apparent individual seroprevalence rate in the 49 pig farms studied was 59% [55.5%-61.4%]. None of the 1134 ham muscles tested was positive for the presence of HEV. HEV prevalence in paired liver samples was 2.8% with a level of contamination of up to 1.46 10(8) copies/g. Sequences of viral strains isolated from positive livers belonged to genotype 3 and subtypes 3c, 3e, 3f and 3j. Our results confirmed that raw pork liver food products are a source of risk for humans but they also showed that there is a limited risk of human infection by HEV through the consumption of ham muscle.

Published
2018

22. Encéphalite causée par un rotavirus aviaire chez un jeune cheval avec troubles neurologiques d’étiologie inconnue

Author

Sylvie Lecollinet, Huet, H., Marine Dumarest, Philippe Lucas, Hélène Quenault, Vandekerkhove, J., Lepault, J., cécile Beck, Leblond, A., Pierre Tritz, Stéphane Pronost, Deniau, V., Stéphan Zientara, Cordonnier, N., Poncet, D., Yannick Blanchard, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Laboratoire de Ploufragan - Plouzané, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Clinique Vétérinaire, LABÉO, Pôle d’analyses et de recherche de Normandie (LABÉO), Biologie, génétique et thérapies ostéoarticulaires et respiratoires (BIOTARGEN), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

23. Case investigation of unexplained infectious meningoencephalitis in animals - a new rotavirus in horses?

Author

Sylvie Lecollinet, Huet, H., Marine Dumarest, Philippe Lucas, Hélène Quenault, Vandekerkhove, J., Lepault, J., cécile Beck, Leblond, A., Pierre Tritz, Stéphane Pronost, Deniau, V., Stephan Zientara, Cordonnier, N., Poncet, D., Yannick Blanchard, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan - Plouzané, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Clinique Vétérinaire, LABÉO, Pôle d’analyses et de recherche de Normandie (LABÉO), Biologie, génétique et thérapies ostéoarticulaires et respiratoires (BIOTARGEN), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

24. Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing

Author

Marine Dumarest, Marlène Gratigny, Justine Cheval, Léa Gagnieur, Erika Muth, Charles Hebert, Marc Eloit, Découverte de Pathogenes, Institut Pasteur [Paris], PathoQuest, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), BioSecure Foundation, Paris Virus-Biol-HTS Labex IBEID, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
PCV, porcine circovirus, Swine, [SDV]Life Sciences [q-bio], Applied Microbiology and Biotechnology, PPV7, putative porcine parvovirus 7, MULTIPLE, Anelloviridae, PIGS, Gut, PRV-A, porcine group A rotavirus, 0303 health sciences, High-throughput sequencing, Gc/mL, genome copies/mL, biology, PBoV, porcine bocavirus, PPV1-6, porcine parvovirus 1 to 6, General Medicine, 3. Good health, Virus, Intestines, INFECTIONS, Viruses, Circoviridae, Viral load, Biotechnology, Birnaviridae, GENETICS, Picornaviridae, RT-PCR, PAV B, porcine adenovirus B, Reoviridae, Bioengineering, PCV1, porcine circovirus type 1, Real-Time Polymerase Chain Reaction, Article, Microbiology, 03 medical and health sciences, HIGH PREVALENCE, Animals, HTS, high-throughput sequencing, 030304 developmental biology, DNA Primers, Pharmacology, Parvoviridae, Pig, General Immunology and Microbiology, IDENTIFICATION, Base Sequence, 030306 microbiology, Heparin, biology.organism_classification, Virology, Caliciviridae, High-Throughput Screening Assays, Mucus, DISCOVERY, PCV2, porcine circovirus type 2, Metagenomics, PAV A, porcine adenovirus A, GENERATION
Abstract

International audience; Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picomaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination.

Published
2014

25. Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture

Author

Marine Dumarest, Erika Muth, Justine Cheval, Charles Hebert, Léa Gagnieur, Marlène Gratigny, Marc Eloit, Découverte de Pathogènes - Pathogen Discovery, Biologie des Infections - Biology of Infection, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], PathoQuest, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), foundation Biosecure, Paris, Labex IBEID, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
Fetal bovine serum, [SDV]Life Sciences [q-bio], viruses, Pegivirus, Bioengineering, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Virus, Parvovirus, medicine, Animals, Trypsin, High throughput sequencing, Cells, Cultured, Pharmacology, Diarrhea Viruses, Bovine Viral, General Immunology and Microbiology, biology, High-Throughput Nucleotide Sequencing, General Medicine, Bovine parvovirus, biology.organism_classification, Virology, Porcine circovirus, Nucleic acid, Cattle, Polyomavirus, Biotechnology, medicine.drug
Abstract

International audience; Fetal bovine serum (FBS) and trypsin are reagents used in cell culture and have been the source of viral contamination of pharmaceutical products. We performed high throughput sequencing (HTS) of two pools of commercial batches of FBS and three commercial batches of trypsin. Taxonomies were assigned by comparing sequences of contigs and singletons to the entire NCBI nucleic acid and protein databases. The same major viral species were evidenced between batches of a given reagent but the proportion of viral reads among total reads varied markedly between samples (from 0.002% to 22.7%). In FBS, the sequences found were mainly from bovine viral diarrhea virus (BVDV) 1 to 3 and bovine parvovirus 3 (BPV3). The BVDV sequences derived from FBS showed only minor discrepancies with primers generally used for the screening of BVDV. Viral sequences in trypsin were mainly from porcine circovirus type 2. Other known viral sequences at lower read counts and potential new viral species (bovine parvovirus and bovine pegivirus) were evidenced. The load of some known and new viruses detected by FITS could be quantified by qPCR. Results of HTS provide a framework for evaluating the pertinence of control measures including the design of PCRs, bioassays and inactivation procedures.

Published
2014

26. No Viral Transcripts Associated with Folliculotropic Mycosis Fungoides Using a High Throughput Sequencing Approach

Author

Marc Eloit, Liza Al-Shikhley, Bernard Guillot, Céline Girard, Justine Cheval, Olivier Dereure, Marine Dumarest, Aurélie Du-Thanh, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Laboratoire d'Excellence [ANR-10-LABX-62-IBEID], and Du-Thanh, Aurelie

Subjects
Adult, Male, Biopsy, [SDV]Life Sciences [q-bio], Dermatology, viruses, cell, lymphoma, samples, Mycosis Fungoides, Medicine, Humans, Viral, Throughput (business), ComputingMilieux_MISCELLANEOUS, Skin, Aged, Mycosis fungoides, Hardware_MEMORYSTRUCTURES, medicine.diagnostic_test, business.industry, High-Throughput Nucleotide Sequencing, General Medicine, Middle Aged, medicine.disease, Folliculotropic Mycosis Fungoides, Virology, 3. Good health, RL1-803, RNA, Viral, RNA, business
Abstract

is missing (Short communication)

Published
2017

27. Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis

Author

Nizar Mahlaoui, Marie-Louise Frémond, Marine Dumarest, Capucine Picard, C. Hébert, Philippe Pérot, Guilhem Cros, Nicole Corre-Catelin, Isabelle Desguerre, Marc Eloit, Stéphane Blanche, Danielle Seilhean, Marc Lecuit, E. Muth, Bénédicte Neven, CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5), Institut des Maladies Génétiques Imagine [Paris], Découverte de Pathogènes - Pathogen Discovery, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), PathoQuest, Centre de Référence Déficits Immunitaires Héréditaires (CEREDIH), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Génétique Humaine des Maladies Infectieuses (Inserm U980), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), CHU Pitié-Salpêtrière [APHP], Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Institut Pasteur [Paris], Service des Maladies infectieuses et tropicales [CHU Necker], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris], Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was funded by the French Government's Investissement d'Avenir program, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (Grant Number ANR-10-LABX-62-IBEID), and Institut National de la Santé et de la Recherche Médicale., We thank the platform Investigation Clinique et Accès aux Ressources Biologiques (Institut Pasteur, Paris) for help in the management of biological samples., ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Pasteur [Paris] (IP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Male, encephalitis, [SDV]Life Sciences [q-bio], Anti-Inflammatory Agents, X-linked agammaglobulinemia, law.invention, Epilepsy, astrovirus, Cerebrospinal fluid, MESH: Astroviridae Infections, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Astroviridae Infections, MESH: Sequence Analysis, RNA, Encephalitis, Viral, MESH: High-Throughput Nucleotide Sequencing, Polymerase chain reaction, medicine.diagnostic_test, biology, High-Throughput Nucleotide Sequencing, Genetic Diseases, X-Linked, General Medicine, 3. Good health, MESH: Encephalitis, Viral, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Epilepsy, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Genome, Viral, Encephalitis, MESH: Astroviridae, MESH: Antiviral Agents, Adolescent, Bruton, Genome, Viral, Antiviral Agents, DNA sequencing, Astrovirus, Cerebellar Diseases, medicine, MESH: Genetic Diseases, X-Linked, Humans, MESH: Agammaglobulinemia, MESH: Adolescent, MESH: Humans, Sequence Analysis, RNA, business.industry, Brain biopsy, MESH: Cerebellar Diseases, medicine.disease, biology.organism_classification, Virology, MESH: Male, agammaglobulinemia, MESH: Anti-Inflammatory Agents, Pediatrics, Perinatology and Child Health, Astroviridae, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; A boy with X-linked agammaglobulinemia experienced progressive global motor decline, cerebellar syndrome, and epilepsy. All standard polymerase chain reactions for neurotropic viruses were negative on cerebrospinal fluid and brain biopsy. Next-generation sequencing allowed fast identification of a new astrovirus strain (HAstV-VA1/HMO-C-PA), which led to tailor the patient's treatment, with encouraging clinical monitoring over 1 year.

Published
2015

28. Antibodies to VP1 of swine pasivirus in humans without evidence of transmission from a pig source

Author

Marc Eloit, Famara Sane, Marine Dumarest, Jacques Bellalou, Mireille Nowakowsjki, Emma Rigaud, Didier Hober, Hélène Chaussade, Pierre Coursaget, Rachel Desailloud, Françoise Arnold, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Université de Tours (UT), Pathogenèse virale du diabète de type 1 - ULR 3610 (Laboratoire de Virologie), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service des Maladies Infectieuses, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Production de Protéines Recombinantes (Plate-Forme) (PRPF), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Mutualité Sociale Agricole (MSA), Université de Picardie Jules Verne (UPJV), PathoQuest, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°.ANR-10-LABX-62-IBEID) and EU PF6 Integrated Project EUROTHYMAIDE (contract LSHB-CT-2003-503410), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Université de Tours, Pathogenèse virale du diabète 1-EA 3610, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Institut National de la Recherche Agronomique (INRA)-Université de Tours, and Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)

Subjects
Adult, Male, China, Picornavirus, Adolescent, Swine, viruses, Parechovirus, Enzyme-Linked Immunosorbent Assay, Picornaviridae, Cross Reactions, Antibodies, Viral, Virus, Young Adult, Zoonosis, Antigen, Risk Factors, Seroepidemiologic Studies, Virology, medicine, Seroprevalence, Animals, Humans, Risk factor, Child, Swine Diseases, Viral Structural Proteins, Picornaviridae Infections, biology, Middle Aged, medicine.disease, biology.organism_classification, 3. Good health, Europe, Infectious Diseases, Diabetes Mellitus, Type 1, Child, Preschool, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, Female, Antibody, Pasivirus, Human
Abstract

Background Swine pasivirus (SPaV1) is a recently described enteric virus close to human parechoviruses and highly prevalent in pigs. Antibodies to Escherichia coli -expressed VP1 of SpaV1 have been found in a majority of humans in China. Objectives The objectives were to estimate the antibody prevalence in a European country, to test if exposure to the virus was linked to pig products and if this exposure was a risk factor for the development of diabetes type 1. Study design An ELISA test was developed and used to screen 842 healthy subjects with known exposure to pig products, 39 patients with diabetes type 1 and 20 controls. Results We identified a high seroprevalence (15.6%) reacting to VP1 of SPaV1 among healthy human subjects. Analysis of risk factors argues against cross-species transmission from pigs as the source of infection. Data also indicate that the presence of SPaV1 VP1-binding antibodies is not associated with diabetes type 1 in humans. Conclusion Our results suggest that the seroreactivity frequently found in humans against SpaV1 is due to cross-reactivity with related antigen, perhaps a picornavirus, and that SpaV1 is not a zoonotic virus.

Published
2015

29. Chicken skin virome analyzed by high throughput sequencing shows a composition highly different from human skin

Author

Marine Dumarest, Sylvie Rémy, Caroline Denesvre, Marc Eloit, David Gourichon, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Pôle d'Expérimentation Avicole de Tours (UE PEAT), Institut National de la Recherche Agronomique (INRA), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), PathoQuest, UR Infectiologie animale et Santé publique (UR IASP), Pôle d'Expérimentation Avicole de Tours (PEAT), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
medicine.medical_specialty, Herpesviruses, animal structures, Mardivirus, viruses, Population, Human skin, DNA sequencing, Virus, Medical microbiology, Virology, Genetics, medicine, Animals, Human virome, education, Molecular Biology, Skin, education.field_of_study, biology, integumentary system, High-Throughput Nucleotide Sequencing, General Medicine, Biodiversity, biology.organism_classification, Chicken, Metagenomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA viruses, Chickens
Abstract

Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

Published
2015

30. Hepatitis E Virus Exposure is Increased in Pork Butchers from Burkina Faso

Author

Nicole Pavio, Nicolas Barro, Nicolas Huot, Pierre Roques, Jean Bienvenue Ouoba, Alfred S. Traoré, Kuan Abdoulaye Traore, Marine Dumarest, Sophie Rogée, Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), École nationale vétérinaire - Alfort (ENVA), French Government through the 3rd cycle university scholarship program, University Paris-Sud, and École nationale vétérinaire d'Alfort (ENVA)

Subjects
Male, Swine, viruses, [SDV]Life Sciences [q-bio], Antibodies, Viral, medicine.disease_cause, West africa, Hepatitis E virus, Seroepidemiologic Studies, Zoonoses, Genotype, Medicine, Phylogeny, 2. Zero hunger, 0303 health sciences, education.field_of_study, virus diseases, food and beverages, Articles, Hepatitis E, 3. Good health, Occupational Diseases, Infectious Diseases, Liver, Female, Pigs, Abattoirs, Adult, Meat, Population, Professional activity, Young Adult, 03 medical and health sciences, Virology, Burkina Faso, parasitic diseases, Animals, Humans, Seroprevalence, Transmission, education, 030304 developmental biology, 030306 microbiology, business.industry, Odds ratio, medicine.disease, digestive system diseases, Parasitology, business
Abstract

International audience; We conducted the first survey of zoonotic risk of Hepatitis E virus (REV) transmissions in Ouagadougou, Burkina Faso, through the direct contact with pork meat during professional activity. Anti-REV antibodies were more prevalent in pork butchers, 76% than in the general population, which was 47.8% in 2013 (odds ratio = 3.46, 95% CI = 2.85-4.21, P < 0.001). Among slaughter-aged swine, REV seroprevalence was of 80%, and REV RNA was detected in 1% of pork livers. Phylogenetic analysis pointed out HEV genotype 3. Thus, in addition to possible HEV contamination through the water source, as in endemic region, zoonotic transmissions of REV probably occur in west Africa.

Published
2015

31. Analysis by high throughput sequencing of Specific Pathogen Free eggs

Author

Charles Hebert, Muriel Coulpier, Léa Gagnieur, Marc Eloit, Erika Muth, Cyril Viarouge, Marlène Gratigny, Marielle Cochet, Justine Cheval, Marine Dumarest, Emmanuel Bréard, Découverte de Pathogenes, Institut Pasteur [Paris], PathoQuest, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), foundation Biosecure, Paris, Labex IBEID, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), ANR-10-LABX-0062/10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)

Subjects
Eggs, viruses, [SDV]Life Sciences [q-bio], Endogenous retrovirus, Bioengineering, Chick Embryo, Avian leukosis, Biology, Applied Microbiology and Biotechnology, DNA sequencing, Virus, Specific Pathogen Free, Animals, High throughput sequencing, Specific-pathogen-free, Pharmacology, Vaccines, Avian Leukosis Virus, General Immunology and Microbiology, Endogenous Retroviruses, Embryonated, High-Throughput Nucleotide Sequencing, Embryo, General Medicine, Virology, Specific Pathogen-Free Organisms, 3. Good health, Viral genomes, DNA, Viral, embryonic structures, RNA, Viral, Chickens, Biotechnology
Abstract

Specific Pathogen Free (SPF) embryonated eggs are used for the production of many veterinary and human vaccines. We have used High Throughput Sequencing to screen allantoic fluids and embryos for the presence of encapsidated viral genomes and viral transcripts, respectively. SPF eggs from two different producers were tested. We evidenced sequences corresponding to known endogenous retroviruses and sequences of Avian Leukosis Virus, but no sequence that might suggest a productive infection of eggs with a virus even distant from known viruses. Our results strongly suggest that SPF eggs such as those used for this study represent a safe substrate for the production of vaccines.

Published
2014

32. Direct contact and environmental contaminations are responsible for HEV transmission in pigs

Author

Mathieu Andraud, Elodie Barnaud, Nicole Pavio, Nicolas Rose, Roland Cariolet, F. Eono, Marine Dumarest, Bouchra Aylaj, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Bretagne Occidentale, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Université Hassan II [Casablanca] (UH2MC), French Research Agency (ANR) as part of the research project called 'HEVECODYN, and École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
Veterinary medicine, Swine, [SDV]Life Sciences [q-bio], Population, Biology, medicine.disease_cause, Persistence (computer science), law.invention, 03 medical and health sciences, Feces, Random Allocation, Hepatitis E virus, law, medicine, Animals, education, 030304 developmental biology, Hepatitis, Swine Diseases, 0303 health sciences, education.field_of_study, General Veterinary, 030306 microbiology, Research, medicine.disease, Hepatitis E, Infectious period, Virology, veterinary(all), 3. Good health, Transmission (mechanics), Herd
Abstract

International audience; Hepatitis E virus (HEV) can cause enterically-transmitted hepatitis in humans. The zoonotic nature of Hepatitis E infections has been established in industrialized areas and domestic pigs are considered as the main reservoir. The dynamics of transmission in pig herds therefore needs to be understood to reduce the prevalence of viremic pigs at slaughter and prevent contaminated pig products from entering the food chain. An experimental trial was carried out to study the main characteristics of HEV transmission between orally inoculated pigs and naive animals. A mathematical model was used to investigate three transmission routes, namely direct contact between pigs and two environmental components to represent within-and between-group oro-fecal transmission. A large inter-individual variability was observed in response to infection with an average latent period lasting 6.9 days (5.8; 7.9) in inoculated animals and an average infectious period of 9.7 days (8.2; 11.2). Our results show that direct transmission alone, with a partial reproduction number of 1.41 (0.21; 3.02), can be considered as a factor of persistence of infection within a population. However, the quantity of virus present in the environment was found to play an essential role in the transmission process strongly influencing the probability of infection with a within pen transmission rate estimated to 2 . 10(-6)g ge(-1)d(-1)(1 . 10(-7); 7 . 10(-6)). Between-pen environmental transmission occurred to a lesser extent (transmission rate: 7 . 10(-8)g ge(-1)d(-1)(5 . 10(-9); 3 . 10(-7)) but could further generate a within-group process. The combination of these transmission routes could explain the persistence and high prevalence of HEV in pig populations.

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