# Coding-complete genome sequences of hedgehog coronavirus isolated from Erinaceus europaeus in France

Kevyn Beissat, Evelyne Picard-Meyer, Pascal Arné, Flavie Chanteclair, Cécile Le Barzic, Lorette Hivert, Guillaume Le Loc’h, Marie-Pierre Puech, Fanny Bastien, Jean-Luc Schereffer, et al.

<figure><img src="image_1.png" /></figure>

## ► To cite this version:

Kevyn Beissat, Evelyne Picard-Meyer, Pascal Arné, Flavie Chanteclair, Cécile Le Barzic, et al. Coding-complete genome sequences of hedgehog coronavirus isolated from Erinaceus europaeus in France. Microbiology Resource Announcements, 2025, 14 (7), pp.e00157-25. 10.1128/mra.00157-25. anses-05189673

HAL Id: anses-05189673

https://anses.hal.science/anses-05189673v1

Submitted on 28 Jul 2025

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Coding-complete genome sequences of hedgehog coronavirus isolated from *Erinaceus europaeus* in France

Kevyn Beissat,¹,² Evelyne Picard-Meyer,¹ Pascal Arné,³,⁴ Flavie Chanteclair,¹ Cécile Le Barzic,³ Lorette Hivert,⁵,⁶ Guillaume Le Loc'h,⁵,⁶ Marie-Pierre Puech,⁷ Fanny Bastien,¹ Jean-Luc Schereffer,¹ Marine Wasniewski¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 2.

**ABSTRACT** The coding-complete genome sequences of hedgehog coronavirus were retrieved from rectal swabs collected in 2022 and 2023 in France. Information on this virus is crucial to understand the pathogenicity and ecology of this *Betacoronavirus*.

**KEYWORDS** hedgehog, coronavirus, complete genome, *Erinaceus europaeus*

The hedgehog coronavirus (Coronaviridae family, Betacoronavirus genus, Merbecovirus subgenus), otherwise known as the *Erinaceus* coronavirus (EriCoV), was first detected in fecal samples of European Hedgehog (*Erinaceus europaeus*) in 2012 in Germany (1). EriCoV is capable of infecting hedgehogs exclusively and seems to be asymptomatic (2). This virus groups phylogenetically with bat coronaviruses and MERS-CoV (Middle-East Respiratory Syndrome Coronavirus), which is also known to infect humans (1, 3). To date, two hedgehog coronaviruses have been identified. The first EriCoV has been detected in *E. europaeus* in several European countries (1–7). The second EriCoV, a slightly different strain (HKU31), has been detected in the Amur Hedgehog (*Erinaceus amurensis*) in China (8, 9). Complete genomes of EriCoV have already been obtained in Europe (Germany, the United Kingdom, Poland, Italy, and Russia).

Two coding-complete genomes were retrieved from French European hedgehogs, collected in 2023 in Toulouse, Haute Garonne, and 2022 in Maisons-Alfort, Val-de-Marne.

These sequences were isolated from rectal swabs (Σ-VIROCULT) collected between 2020 and 2023 from three wildlife care centers located in Toulouse, Maisons-Alfort, and Ganges in France. Sample collection was authorized by the ANSES ethics committee (ComEth). RNA was extracted using the NucleoSpin RNA, Mini Kit (Macherey-Nagel). Following primers (PanCov Pol 15197-Forward: GGTTGGGACTATCCTAAGTGTGA and PanCov Pol 15635-Reverse: CCATCATCAGATAGAATCATCAT) (10) were used to perform RT-PCR and nested PCR targeting the RNA-dependent RNA polymerase (RdRp) gene (11) of alphacoronaviruses and betacoronaviruses.

Next-generation sequencing was performed on total RNA by Helixio, France, using a 2 × 150 bp sequencing library prepared on Illumina with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). A total of 15.9 and 15 million reads were generated for the two samples. MultiQC v.1.27 (12) was used to check the quality of all total reads. Trimmomatic v.0.39 (13) was utilized to remove adapters and perform a quality check of raw reads. Raw reads were cut from 5' and 3' extremities if quality was under 20, and reads were deleted if their length was under 90 bp.

De novo assembly was performed using RNA SPAdes v.3.14.0 (14), and quality was checked using QUAST v.5.0.2 (15). Unless otherwise indicated, default parameters were utilized. A total of 55,017 (22-3151 sample) and 74,536 (22-7137 sample) sequences were aligned with the reference sequence (NC_039207). Only four and one sequences, respectively, for the 22-3151 and 22-7137 samples uniquely mapped to the reference sequence.

Editor John J. Dennehy, Queens College
Department of Biology, Queens, New York, USA

Address correspondence to Marine Wasniewski,
marine.wasniewski@anses.fr.

The authors declare no conflict of interest.

See the funding table on p. 3.

Received 17 February 2025

Accepted 16 May 2025

Published 9 June 2025

Copyright © 2025 Beissat et al. This is an open-access
article distributed under the terms of the Creative
Commons Attribution 4.0 International license.
<figure><img src="image_3.png" /><figcaption>FIG 1 Genome organization of the EriCoV full genome sequences (samples 22-3151 and 22-7137) isolated in *Erinaceus europaeus* in France.</figcaption></figure>

The coding regions were visualized and annotated using Geneious Prime v.2022.0.2 (16) by referring to the reference sequence. The genomic organization of both EriCoV sequences was found to be similar to EriCoV isolated in Europe, with a complete coding-genome length of 30,105 nucleotides for 22-3151 (37.6% GC content) and 30,092 nucleotides for 22-7137 (37.5% GC content) (Fig. 1). Using BLAST v.2.16.0 (17), 22-3151 and 22-7137 were, respectively, 93.64% and 93.68%, similar to the reference sequence.

## ACKNOWLEDGMENTS

We would like to thank the Wildlife Hospital of the Veterinary School of Alfort, the Wildlife Care Center of the National Veterinary School of Toulouse, and the Wildlife Hospital of Ganges for the sample collection.

This study received financial support from the MUSECOV project, an ICRAD ERA-NET supported by the European Union's Horizon 2020 Research and Innovation Programme.

## AUTHOR AFFILIATIONS

## PRESENT ADDRESS

Marine Wasniewski, Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France

<footnote n="1">¹Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France</footnote>

<footnote n="2">²USC-1233 Rongeurs Sauvages Risques Sanitaires et Gestion des Populations (RS2GP), VetAgroSup, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Lyon University, Marcy-L'Etoile, France</footnote>

<footnote n="3">³Centre Hospitalier Universitaire Vétérinaire de la Faune Sauvage (Chuv-FS), Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France</footnote>

<footnote n="4">⁴UMR 1161 Virologie, INRAE-ENVA-ANSES, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, Paris, France</footnote>

<footnote n="5">⁵Wildlife Care Centre, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse, Toulouse, France</footnote>

<footnote n="6">⁶IHAP, ENVT, INRAE, Université de Toulouse, Toulouse, France</footnote>

<footnote n="7">⁷Hôpital Faune Sauvage - Goupil connexion, Ganges, France</footnote>
## AUTHOR ORCIDs

Marine Wasniewski http://orcid.org/0000-0001-5054-3634

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s) Author(s)</td></tr></thead><tbody><tr><td>European Union's Horizon 2020/ICRAD-ERA-NET/ MUSECoV</td><td>Marine Wasniewski</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Kevyn Beissat, Data curation, Formal analysis, Methodology, Software, Visualization, Writing – original draft, Writing – review and editing | Evelyne Picard-Meyer, Data curation, Formal analysis, Methodology, Project administration, Software, Supervision, Validation, Writing – original draft, Writing – review and editing | Pascal Arné, Investigation, Resources, Writing – review and editing | Flavie Chanteclair, Investigation | Cécile Le Barzic, Investigation, Resources, Writing – review and editing | Lorette Hivert, Investigation, Resources, Writing – review and editing | Guillaume Le Loc'h, Investigation, Resources, Writing – review and editing | Marie-Pierre Puech, Investigation, Resources, Writing – review and editing | Fanny Bastien, Investigation | Jean-Luc Schereffer, Investigation | Marine Wasniewski, Conceptualization, Funding acquisition, Project administration, Supervision, Validation, Writing – original draft, Writing – review and editing

## DATA AVAILABILITY

EriCoV sequences have been deposited in GenBank (PQ869634 and PQ869635). The raw sequence reads are accessible in the Sequence Read Archive (SRA) (SRR31931794 and SRR31931795).

## REFERENCES

1. Corman VM, Kallies R, Philipps H, Gönner G, Müller MA, Eckerle I, Brünink S, Drosten C, Drexler JF. 2014. Characterization of a novel betacoronavirus related to middle East respiratory syndrome coronavirus in European hedgehogs. J Virol 88:717–724. https://doi.org/10.1128/JVI.01600-13

2. Pomorska-Mól M, Ruszkowski JJ, Gogulski M, Domanska-Blicharz K. 2022. First detection of hedgehog coronavirus 1 in Poland. Sci Rep 12:2386. https://doi.org/10.1038/s41598-022-06432-z

3. Saldanha IF, Lawson B, Goharriz H, Rodriguez-Ramos Fernandez J, John SK, Fooks AR, Cunningham AA, Johnson N, Horton DL. 2019. Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host. Epidemiol Infect 147:e169. https://doi.org/10.1017/S0950268819002027

4. Monchatre-Leroy E, Boué F, Boucher J-M, Renault C, Moutou F, Ar Gouilh M, Umhang G. 2017. Identification of alpha and beta coronavirus in wildlife species in france: bats, rodents, rabbits, and hedgehogs. Viruses 9:364. https://doi.org/10.3390/v9120364

5. De Sabato L, Di Bartolo I, De Marco MA, Moreno A, Lelli D, Cotti C, Delogu M, Vaccari G. 2020. Can coronaviruses steal genes from the host as evidenced in Western European hedgehogs by EriCoV genetic characterization? Viruses 12:1471. https://doi.org/10.3390/v12121471

6. Cruz AVS, Santos-Silva S, Queirós-Reis L, Rodrigues C, Soeiro V, Tarlinton RE, Mesquita JR. 2024. Genomic characterization and cross-species transmission potential of hedgehog coronavirus. One Health 19:100940. https://doi.org/10.1016/j. onehlt.2024.100940

7. Lukina-Gronskaya AV, Chudinov IK, Korneenko EV, Mashkova SD, Semashko TA, Sinkova MA, Penkin LN, Litvinova EM, Feoktistova NY, Speranskaya AS. 2024. Novel coronaviruses and mammarenaviruses of hedgehogs from Russia including the comparison of viral communities of hibernating and active specimens. Front Vet Sci 11:1486635. https://doi.org/10.3389/fvets.2024.1486635

8. Lau SKP, Luk HKH, Wong ACP, Fan RYY, Lam CSF, Li KSM, Ahmed SS, Chow FWN, Cai J-P, Zhu X, Chan JFW, Lau TCK, Cao K, Li M, Woo PCY, Yuen K-Y. 2019. Identification of a novel betacoronavirus (Merbecovirus)

in amur hedgehogs from China. Viruses 11:980. https://doi.org/10.3390/v11110980

9. Li D, Gong X-Q, Xiao X, Han H-J, Yu H, Li Z-M, Yan L-N, Gu X-L, Duan S-H. 2021. MERS-related CoVs in hedgehogs from Hubei Province, China. One Health 13:100332. https://doi.org/10.1016/j. onehlt.2021.100332

10. Gouilh MA, Puechmaille SJ, Gonzalez JP, Teeling E, Kittayapong P, Manuguerra JC. 2011. SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory. Infect Genet Evol 11:1690–1702. https://doi.org/10.1016/j. meegid.2011.06.021

11. Wasniewski M, Boué F, Richomme C, Simon-Lorière E, der Werf SV, Donati F, Enouf V, Blanchard Y, Beven V, Leperchois E, Leterrier B, Corbet S, Le Gouilh M, Monchatre-Leroy E, Picard-Meyer E. 2023. Investigations into SARS-CoV-2 and other coronaviruses on mink farms in France late in the first year of the COVID-19 pandemic. PLoS ONE 18:e0290444. https://doi.org/10.1371/journal.pone.0290444

12. Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/bt w354

13. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

14. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70:e102. http://doi.org/10.1002/cpbi.102

15. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086

16. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence
data. Bioinformatics 28:1647–1649. https://doi.org/10.1093/bioinformati cs/bts199

17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S 0022-2836(05)80360-2