Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Sarah Temmam (1, 2) , Khamsing Vongphayloth (3) , Eduard Baquero (4) , Sandie Munier (5) , Massimiliano Bonomi (6) , Béatrice Regnault (1, 2) , Bounsavane Douangboubpha (7) , Yasaman Karami (6) , Delphine Chrétien (1, 2) , Daosavanh Sanamxay (7) , Vilakhan Xayaphet (7) , Phetphoumin Paphaphanh (7) , Vincent Lacoste (3) , Somphavanh Somlor (3) , Khaithong Lakeomany (3) , Nothasin Phommavanh (3) , Philippe Pérot (1, 2) , Océane Dehan (5, 8) , Faustine Amara (5) , Flora Donati (5, 8) , Thomas Bigot (1, 9) , Michael Nilges (6) , Félix Rey (4) , Sylvie van Der Werf (5, 8) , Paul Brey (3) , Marc Eloit (1, 2, 10)

1 Découverte de pathogènes – Pathogen discovery
2 CCOIE-OIECC - 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
3 Institut Pasteur du Laos
4 Virologie Structurale - Structural Virology
5 GMV-ARN (UMR_3569 / U-Pasteur_2) - Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses
6 Bioinformatique structurale - Structural Bioinformatics
7 National University of Laos
8 CNR - laboratoire coordonnateur - Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris]
9 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
10 ENVA - École nationale vétérinaire - Alfort

The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats1-4, including the closest virus from R. affinis, RaTG13 (refs. 5,6), and pangolins7-9. SARS-CoV-2 has a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range10-12. SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 (hACE2) pathway have not yet been identified, although they would be key in understanding the origin of the epidemic. Here we show that such viruses circulate in cave bats living in the limestone karstic terrain in northern Laos, in the Indochinese peninsula. We found that the receptor-binding domains of these viruses differ from that of SARS-CoV-2 by only one or two residues at the interface with ACE2, bind more efficiently to the hACE2 protein than that of the SARS-CoV-2 strain isolated in Wuhan from early human cases, and mediate hACE2-dependent entry and replication in human cells, which is inhibited by antibodies that neutralize SARS-CoV-2. None of these bat viruses contains a furin cleavage site in the spike protein. Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula.

Domains: Virology; Populations and Evolution [q-bio.PE]

Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero, Sandie Munier, Massimiliano Bonomi, et al.. Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature, 2022, 604 (7905), pp.330-336. ⟨10.1038/s41586-022-04532-4⟩. ⟨pasteur-03661247⟩