2018
2018 Feb 23. pii: S0042-6822(18)30020-5. doi: 10.1016/j.virol.2018.01.014. [Epub ahead of print]
SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world.
1 Institut Pasteur, Unité Environnement et Risques Infectieux, CIBU, Infection et Epidemiologie, 75015, Paris, France; Normandie Université, EA2656, Groupe de Recherche sur l’Adaptation Microbienne, 14000, Caen, France. Electronic address: meriadeg.le-gouil@pasteur.fr.
2 Greifswald University, 17489, Greifswald, Germany; University College Dublin, Belfield, Dublin 4, Ireland; Chauves-souris Aveyron, 12310, Vimenet, France.
3 Institut Pasteur, Unité Environnement et Risques Infectieux, CIBU, Infection et Epidemiologie, 75015, Paris, France.
4 IRBIO & Departament de de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
5 French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, 22440, Ploufragan, France.
6 Ecole Nationale Vétérinaire d’Alfort, 94704, Maison-Alfort, France.
7 Normandie Université, EA2656, Groupe de Recherche sur l’Adaptation Microbienne, 14000, Caen, France.

Abstract

The emergence of SARS-CoV and MERS-CoV, triggered the discovery of a high diversity of coronaviruses in bats. Studies from Europe have shown that coronaviruses circulate in bats in France but this reflects only a fraction of the whole diversity. In the current study the diversity of coronaviruses circulating in western Europe was extensively explored. Ten alphacoronaviruses in eleven bat species belonging to the Miniopteridae, Vespertilionidae and Rhinolophidae families and, a SARS-CoV-related Betacoronavirus in Rhinolophus ferrumequinum were identified. The diversity and prevalence of bat coronaviruses presently reported from western Europe is much higher than previously described and includes a SARS-CoV sister group. This diversity demonstrates the dynamic evolution and circulation of coronaviruses in this species. That said, the identified coronaviruses were consistently associated with a particular bat species or genus, and these relationships were maintained no matter the geographic location. The observed phylogenetic grouping of coronaviruses from the same species in Europe and Asia, emphasizes the role of host/pathogen coevolution in this group.

More details here : https://www.sciencedirect.com/science/article/pii/S0042682218300205?via%3Dihub

Full text : https://www.researchgate.net/publication/323370121_SARS-CoV_related_Betacoronavirus_and_diverse_Alphacoronavirus_members_found_in_western_old-world

 

KEYWORDS:

Bats; Chiroptera; Coronavirus; Diversity; Emergence; Europe; Evolution; MERS-CoV; Phylogenetics; SARS-CoV

PMID:
29482919
DOI:
10.1016/j.virol.2018.01.014

2017
2017 Nov 29;9(12). pii: E364. doi: 10.3390/v9120364.
Identification of Alpha and Beta Coronavirus in Wildlife Species in France: Bats, Rodents, Rabbits, and Hedgehogs.
1 ANSES, Laboratoire de la rage et de la faune sauvage, 54220 Nancy, France. elodie.monchatre-leroy@anses.fr.
2 ANSES, Laboratoire de la rage et de la faune sauvage, 54220 Nancy, France. franck.boue@anses.fr.
3 ANSES, Laboratoire de la rage et de la faune sauvage, 54220 Nancy, France. jean-marc.boucher@anses.fr.
4 ANSES, Laboratoire de la rage et de la faune sauvage, 54220 Nancy, France. camille.renault20@gmail.com.
5 ANSES, ENVA, 94701 Maisons-Alfort, France. francoismoutou@orange.fr.
6 Université de Normandie, EA 2656, GRAM-Groupe de Recherche sur l’Adaptation Microbienne, UNICAEN/UNIROUEN, 14000 Caen, France. meriadeg.legouil@normandie-univ.fr.
7 Institut Pasteur, Infection et Epidemiologie, Unité Environnement et Risques Infectieux, 75015 Paris, France. meriadeg.legouil@normandie-univ.fr.
8 ANSES, Laboratoire de la rage et de la faune sauvage, 54220 Nancy, France. gerald.umhang@anses.fr.
ABSTRACT: 

Coronaviruses are closely monitored in the context of emerging diseases and, as illustrated with Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome-coronavirus (MERS-CoV), are known to cross the species barrier and eventually to move from wildlife to humans. Knowledge of the diversity of coronaviruses in wildlife is therefore essential to better understand and prevent emergence events. This study explored the presence of coronaviruses in four wild mammal orders in France: Bats, rodents, lagomorphs, and hedgehogs. Betacoronavirus and Alphacoronavirus genera were identified. The results obtained suggest the circulation of potentially evolving virus strains, with the potential to cross the species barrier.

KEYWORDS:

France; bats; coronavirus; genetic diversity; hedgehogs; rodents; wild rabbits; wildlife

PMID:
29186061
PMCID:
PMC5744139
DOI:
10.3390/v9120364

2017 May 25;5(21). pii: e00319-17. doi: 10.1128/genomeA.00319-17.
First Complete Genome Sequence of a French Bovine coronavirus Strain.
1 Normandie Université, Caen, France nathalie.kin@unicaen.fr.
2 UNICAEN, UNIROUEN, GRAM, Caen, France.
3 Normandie Université, Caen, France.
4 Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, Paris, France.
5 Department of Virology, University Hospital of Caen, Caen, France.
ABSTRACT:

We sequenced the first Bovine coronavirus (BCoV) complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014.


2016
Infect Genet Evol. 2016 Jun;40:186-91. doi: 10.1016/j.meegid.2016.03.006. Epub 2016 Mar 9.
Comparative molecular epidemiology of two closely related coronaviruses, bovine coronavirus (BCoV) and human coronavirus OC43 (HCoV-OC43), reveals a different evolutionary pattern.

1 Normandie Université, 14032 Caen, France; Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. Electronic address: nathalie.kin@unicaen.fr.
2 Normandie Université, 14032 Caen, France; Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; Laboratoire de Virologie, Centre Hospitalo-Universitaire de Caen, F-14033 Caen, France.
3 Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France.
4 ANSES, Boulogne Billancourt, F-92012, France.
5 Normandie Université, 14032 Caen, France; Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France.

ABSTRACT:

Bovine coronaviruses (BCoVs) are widespread around the world and cause enteric or respiratory infections among cattle. The current study includes 13 samples from BCoVs collected in Normandy during an 11-year period (from 2003 to 2014), 16 French HCoV-OC43s, and 113 BCoVs or BCoVs-like sequence data derived from partial or complete genome sequences available on GenBank. According to a genotyping method developed previously for HCoV-OC43, BCoVs and BCoVs-like are distributed on three main sub-clusters named C1, C2, and C3. Sub-cluster C1 includes BCoVs and BCoVs-like from America and Asia. Sub-cluster C2 includes BCoVs from Europe. Sub-cluster C3 includes prototype, vaccine, or attenuated BCoV strains. The phylogenetic analyses revealed the monophyletic status of the BCoVs from France reported here for the first time. Moreover, BCoV exhibits a relative genetic stability when compared to HCoV-OC43 we previously described from the same region. The numerous recombination detected between HCoV-OC43 were much less frequent for BCoV. The analysis points thus to the influence of different evolutive constraints in these two close groups.

KEYWORDS:

Bovine coronavirus; Epidemiology; Evolution; Genotyping; Human coronavirus OC43; Recombination; Respiratory infection


2016 Jan;97(1):110-20. doi: 10.1099/jgv.0.000338. Epub 2015 Nov 19.
1 EPICOREM Consortium, Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France 1​ VIPAC Unit, Agence Nationale de Sécurité Sanitaire (ANSES), Laboratoire de Ploufragan-Plouzané, Université Européenne de Bretagne, BP 53-22440 Ploufragan, France.
2 VB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané, Université Européenne de Bretagne, G, BP 53-22440 Ploufragan, France.
3 VIPAC Unit, Agence Nationale de Sécurité Sanitaire (ANSES), Laboratoire de Ploufragan-Plouzané, Université Européenne de Bretagne, BP 53-22440 Ploufragan, France 2​ EPICOREM Consortium, Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France.
4 EPICOREM Consortium, Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France 4​ Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, 25-28 rue du Docteur Roux, F-75724 Paris Cedex 15, France 5​ Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France.
Abstract

A full-length genome sequence of 27,739  nt was determined for the only known European turkey coronavirus (TCoV) isolate. In general, the order, number and size of ORFs were consistent with other gammacoronaviruses. Three points of recombination were predicted, one towards the end of 1a, a second in 1b just upstream of S and a third in 3b. Phylogenetic analysis of the four regions defined by these three points supported the previous notion that European and American viruses do indeed have different evolutionary pathways. Very close relationships were revealed between the European TCoV and the European guinea fowl coronavirus in all regions except one, and both were shown to be closely related to the European infectious bronchitis virus (IBV) Italy 2005. None of these regions of sequence grouped European and American TCoVs. The region of sequence containing the S gene was unique in grouping all turkey and guinea fowl coronaviruses together, separating them from IBVs. Interestingly the French guinea fowl virus was more closely related to the North American viruses. These data demonstrate that European turkey and guinea fowl coronaviruses share a common genetic backbone (most likely an ancestor of IBV Italy 2005) and suggest that this recombined in two separate events with different, yet related, unknown avian coronaviruses, acquiring their S-3a genes. The data also showed that the North American viruses do not share a common backbone with European turkey and guinea fowl viruses; however, they do share similar S-3a genes with guinea fowl virus.

PMID:
26585962
DOI:
10.1099/jgv.0.000338

2015
2015 May 7;7(5):2358-77. doi: 10.3390/v7052358.
Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes.
1 Normandie Université, 14032 Caen, France. nathalie.kin@unicaen.fr.
2 Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. nathalie.kin@unicaen.fr.
3 Normandie Université, 14032 Caen, France. fabienmzz@yahoo.fr.
4 Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. fabienmzz@yahoo.fr.
5 Department of Virology, University Hospital of Caen, F-14033 Caen, France. fabienmzz@yahoo.fr.
6 Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. wei.lin@hotmail.fr.
7 Normandie Université, 14032 Caen, France. meriadeg.le-gouil@pasteur.fr.
8 Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. meriadeg.le-gouil@pasteur.fr.
9 Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France. meriadeg.le-gouil@pasteur.fr.
10 Normandie Université, 14032 Caen, France. a-vabret@chu-caen.fr.
1 1 Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France. a-vabret@chu-caen.fr.
12 Department of Virology, University Hospital of Caen, F-14033 Caen, France. a-vabret@chu-caen.fr.
Abstract

Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.

Keywords:

genotype, sequencing, coronavirus, phylogeny, recombination, HCoV-OC43

PMID:
26008694
PMCID:
PMC4452910
DOI:
10.3390/v7052358
[Indexed for MEDLINE]

Free PMC Article