Published February 16, 2022 | Version v1
Journal article Open

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

  • 1. Institut Pasteur, Université de Paris, Pathogen Discovery Laboratory, Paris, France & Institut Pasteur, Université de Paris, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France
  • 2. Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
  • 3. Institut Pasteur, Université de Paris, CNRS UMR 3569, Structural Virology Unit, Paris, France
  • 4. Institut Pasteur, Université de Paris, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France
  • 5. Institut Pasteur, Université de Paris, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
  • 6. Faculty of Environmental Sciences, National University of Laos, Vientiane, Lao People's Democratic Republi
  • 7. Faculty of Environmental Sciences, National University of Laos, Vientiane, Lao People's Democratic Republic
  • 8. Institut Pasteur, Université de Paris, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France & Institut Pasteur, Université de Paris, National Reference Center for Respiratory Viruses, Paris, France
  • 9. Institut Pasteur, Université de Paris, Pathogen Discovery Laboratory, Paris, France & Institut Pasteur, Université de Paris, Bioinformatic and Biostatistic Hub - Computational Biology Department, Paris, France
  • 10. Institut Pasteur, Université de Paris, Pathogen Discovery Laboratory, Paris, France & Institut Pasteur, Université de Paris, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France & Ecole Nationale Vétérinaire d'Alfort, University of Paris-Est, Maisons-Alfort, France

Description

Temmam, Sarah, Vongphayloth, Khamsing, Baquero, Eduard, Munier, Sandie, Bonomi, Massimiliano, Regnault, Béatrice, Douangboubpha, Bounsavane, Karami, Yasaman, Chrétien, Delphine, Sanamxay, Daosavanh, Xayaphet, Vilakhan, Paphaphanh, Phetphoumin, Lacoste, Vincent, Somlor, Somphavanh, Lakeomany, Khaithong, Phommavanh, Nothasin, Pérot, Philippe, Dehan, Océane, Amara, Faustine, Donati, Flora, Bigot, Thomas, Nilges, Michael, Rey, Félix A., Werf, Sylvie van der, Brey, Paul T., Eloit, Marc (2022): Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature 604: 330-336, DOI: 10.1038/s41586-022-04532-4

Files

source.pdf

Files (18.3 MB)

Name Size Download all
md5:03aa03911e43d104d64275380095065b
18.3 MB Preview Download

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FFAAFF911E43D104D6427538FF95065B

References

  • 1. Delaune,D. etal. AnovelSARS-CoV-2 relatedcoronavirusinbatsfromCambodia.Nat. Commun. 12, 6563 (2021).
  • 2. Zhou, H. etal. Identificationofnovelbatcoronavirusesshedslightontheevolutionary originsof SARS-CoV-2 and related viruses.Cell 184, 4380-4391 (2021).
  • 3. Wacharapluesadee,S.etal.EvidenceforSARS-CoV-2 relatedcoronavirusescirculatingin bats and pangolins in Southeast Asia.Nat. Commun. 12, 972 (2021).
  • 4. Murakami,S.etal. Detectionandcharacterizationofbatsarbecovirusphylogenetically relatedto SARS-CoV-2,Japan.Emerg. Infect.Dis.26, 3025-3029 (2020).
  • 5. Zhou, P.etal. Apneumoniaoutbreakassociatedwithanewcoronavirusofprobablebat origin.Nature 579, 270-273 (2020).
  • 6. Rahalkar,M. C.& Bahulikar,R. A.LethalpneumoniacasesinMojiangminers (2012) and the mineshaftcould provide important clues to the origin of SARS-CoV-2.Front.Public Health https://doi.org/10.3389/fpubh.2020.581569 (2020).
  • 7. Liu, P. etal. Arepangolinstheintermediatehostofthe 2019 novelcoronavirus (SARS-CoV-2)? PLoS Pathog.16, e1008421 (2020).
  • 8. Xiao,K.etal. IsolationofSARS-CoV-2-relatedcoronavirusfromMalayanpangolins. Nature 583, 286-289 (2020).
  • 9. Wahba,L. etal. Anextensivemeta-metagenomicsearchidentifiesSARS-CoV- 2-homologous sequences in pangolin lung viromes.mSphere 5, e00160-20 (2020).
  • 10. Letko,M., Marzi,A. & Munster,V.Functionalassessmentofcellentryandreceptorusage for SARS-CoV-2 and other lineage B betacoronaviruses.Nat.Microbiol. 5, 562-569 (2020).
  • 11. Shang,J.etal. StructuralbasisofreceptorrecognitionbySARS-CoV-2.Nature 581, 221-224 (2020).
  • 12. Wang,Q. etal. StructuralandfunctionalbasisofSARS-CoV-2 entrybyusinghuman ACE2.Cell 181, 894-904 (2020).
  • 13. Delaune,D. etal. AnovelSARS-CoV-2 relatedcoronavirusinbatsfromCambodia.Nat. Commun. 12, 6563 (2021).
  • 14. Jackson,B.etal.Generationandtransmissionofinterlineagerecombinantsinthe SARS-CoV-2 pandemic.Cell 184, 5179-5188 (2021).
  • 15. Rochman,N.D.etal.OngoingglobalandregionaladaptiveevolutionofSARS-CoV-2. Proc.NatlAcad.Sci. USA 118, e2104241118 (2021).
  • 16. Liu, K.etal. BindingandmolecularbasisofthebatcoronavirusRaTG13 virustoACE2 in humans and other species.Cell 184, 3438-3451 (2021).
  • 17. Aicher,S.-M.etal.Species-specificmolecularbarrierstoSARS-CoV-2 replicationinbat cells.Preprint at bioRxiv https://doi.org/10.1101/2021.05.31.446374 (2021).
  • 18. Johnson,B.A. etal. LossoffurincleavagesiteattenuatesSARS-CoV-2 pathogenesis. Nature 591, 293-299 (2021).
  • 19. Liu, K.etal. Cross-speciesrecognitionofSARS-CoV-2 tobatACE2.Proc.NatlAcad.Sci. USA 118, e2020216118 (2020).
  • 20. Chu,D. K.W.etal.Aviancoronavirusinwildaquaticbirds.J. Virol.85, 12815-12820 (2011).
  • 21. Rambaut,A.etal.AdynamicnomenclatureproposalforSARS-CoV-2 lineagestoassist genomicepidemiology.Nat.Microbiol. 5, 1403-1407 (2020).
  • 22. Wrapp,D.etal. Cryo-EMstructureofthe 2019-nCoVspikeintheprefusionconformation. Science 367, 1260-1263 (2020).
  • 23. Laffeber,C., deKoning,K., Kanaar,R. & Lebbink,J.H. G. Experimentalevidencefor enhanced receptor binding by rapidly spreading SARS-CoV-2 variants.J.Mol.Biol.433, 167058 (2021).
  • 24. Lei, C.etal.NeutralizationofSARS-CoV-2 spikepseudotypedvirusbyrecombinant ACE2-Ig.Nat.Commun.11, 2070 (2020).
  • 25. Walls,A.C.etal. Structure,function,andantigenicityoftheSARS-CoV-2 spike glycoprotein.Cell 181, 281-292 (2020).
  • 26. Niu,S.etal.Molecularbasisofcross-speciesACE2 interactionswithSARS-CoV-2-like viruses of pangolin origin.EMBO J.40, e107786 (2021).
  • 27. Zhang,Y.etal. SARS-CoV-2 rapidlyadaptsinagedBALB/cmiceandinducestypical pneumonia.J.Virol. 95, e02477-20 (2021).
  • 28. Huang,K.etal.Q493KandQ498HsubstitutionsinSpikepromoteadaptationof SARS-CoV-2 in mice.EBioMedicine 67, 103381 (2021).
  • 29. Zhang,S. etal. Batandpangolincoronavirusspikeglycoproteinstructuresprovide insights into SARS-CoV-2 evolution.Nat. Commun. 12, 1607 (2021).
  • 30. Lan,J.etal.StructureoftheSARS-CoV-2 spikereceptor-bindingdomainboundtothe ACE2 receptor.Nature 581, 215-220 (2020).
  • 31. Hu,B. etal. DiscoveryofarichgenepoolofbatSARS-relatedcoronavirusesprovidesnew insights into the origin of SARScoronavirus.PLoS Pathog.13, e1006698 (2017).
  • 32. Ge,X.-Y.etal. IsolationandcharacterizationofabatSARS-likecoronavirusthatusesthe ACE2 receptor.Nature 503, 535-538 (2013).
  • 33. Latinne,A.etal. Originandcross-speciestransmissionofbatcoronavirusesinChina. Nat.Commun. 11, 4235 (2020).
  • 34. Tan,Y.,Schneider,T.,Leong,M., Aravind,L.& Zhang,D. Novelimmunoglobulindomain proteins provide insightsinto evolution and pathogenesis of SARS-CoV-2-related viruses. mBio https://doi.org/10.1128/mBio.00760-20 (2020).
  • 35. Su, Y.C.F.etal.Discoveryandgenomiccharacterizationofa 382-nucleotidedeletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2.mBio 11, e01610-20 (2020).
  • 36. ChineseSARSMolecularEpidemiologyConsortium.MolecularevolutionoftheSARS coronavirus during the course of the SARS epidemic in China.Science 303, 1666-1669 (2004).
  • 37. Conceicao,C.etal.TheSARS-CoV-2 Spikeproteinhasabroadtropismformammalian ACE2 proteins.PLoS Biol. 18, e3001016 (2020).
  • 38. Damas,J. etal. BroadhostrangeofSARS-CoV-2 predictedbycomparativeandstructural analysisofACE2 invertebrates.Proc.NatlAcad.Sci.USA 117, 22311-22322 (2020).
  • 39. Cohen,J. WuhancoronavirushunterShiZhenglispeaksout.Science 369, 487-488 (2020).
  • 40. Ge,X.-Y.etal. Coexistenceofmultiplecoronavirusesinseveralbatcoloniesinan abandoned mineshaft.Virol.Sin. 31, 31-40 (2016).
  • 41. Clements,R.,Sodhi,N. S.,Schilthuizen,M. & Ng, P. K.L.LimestonekarstsofSoutheast Asia:imperiled arks of biodiversity.BioScience 56, 733-742 (2006).
  • 42. Hassanin,A., Tu,V.T.,Curaudeau,M.& Csorba,G.Inferringtheecologicalnicheofbat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species.Sci. Rep.11, 14276 (2021).
  • 43. Soisook,P.etal. Ataxonomicreviewof Rhinolophusstheno and R.malayanus (Chiroptera: Rhinolophidae) from continental Southeast Asia:an evaluation of echolocation call frequency in discriminating between cryptic species.Acta Chiropt. 10, 221-242 (2008).
  • 44. Francis,C.FieldGuidetotheMammalsofSouth-eastAsia 2ndedn (BloomsburyWildlife, 2019).
  • 45. Makarenkov,V.,Mazoure,B.,Rabusseau,G. & Legendre,P.Horizontalgenetransferand recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.BMC Ecol. Evol. 21, 5 (2021).
  • 46. Andersen,K. G., Rambaut,A.,Lipkin,W.I., Holmes,E. C.& Garry,R.F.Theproximalorigin of SARS-CoV-2.Nat.Med.26, 450-452 (2020).
  • 47. Lytras,S. TheSarbecovirusoriginofSARS-CoV-2'sfurincleavagesite.Virologicalhttps:// virological.org/t/the-sarbecovirus-origin-of-sars-cov-2-s-furin-cleavage-site/536/6 (2021).
  • 48. Puray-Chavez,M.etal.SystematicanalysisofSARS-CoV-2 infectionofanACE2-negative human airway cell.Cell Rep.36, 109364 (2021).
  • 49. Katoh,K.,Rozewicki,J. & Yamada,K.D.MAFFTonlineservice:multiplesequence alignment,interactive sequence choice and visualization.Brief.Bioinform.20, 1160-1166 (2019).
  • 50. Lemoine,F.etal.NGPhylogeny.fr:newgenerationphylogeneticservicesfor non-specialists.NucleicAcidsRes. 47, W260-W265 (2019).
  • 51. Lole,K. S. etal. Full-lengthhumanimmunodeficiencyvirustype 1 genomesfromsubtype C-infected seroconverters in India,with evidence of intersubtype recombination.J.Virol. 73, 152-160 (1999).
  • 52. PREDICTOneHealthConsortium.ProtocolforBatandRodentSamplingMethods (2013).
  • 53. Sikes,R.S.,Gannon,W.L.& theAnimalCareandUseCommitteeoftheAmericanSociety of Mammalogists.Guidelines of the American Societyof Mammalogists for the use of wild mammals in research.J.Mammal.92, 235-253 (2011).
  • 54. Virachith,S.etal.LowseroprevalenceofCOVID-19 inLaoPDR,late 2020.LancetReg. Health West Pac. 13, 100197 (2021).
  • 55. Francis,C. Acomparisonofmistnetsandtwodesignsofharptrapsforcapturingbats. J.Mammal.70, 865-870.
  • 56. Corbet,G.B.& Hill,J. E.MammalsoftheIndomalayanRegion: aSystematicReview (Oxford Univ.Press & Natural History Museum,1992).
  • 57. Csorba,G., Ujhelyi,P.& Thomas,N. HorseshoeBatsoftheWorld (Chiroptera: rhinolophidae) (Alana Books,2003).
  • 58. Deng,X.etal.Metagenomicsequencingwithspikedprimerenrichmentforviral diagnostics andgenomic surveillance.Nat.Microbiol. 5, 443-454 (2020).
  • 59. Fu, L., Niu,B., Zhu,Z., Wu,S. & Li, W.CD-HIT:acceleratedforclusteringthe next-generation sequencingdata.Bioinformatics 28, 3150-3152 (2012).
  • 60. Regnault,B. etal. Deepimpactofrandomamplificationandlibraryconstructionmethods on viral metagenomics results.Viruses 13, 253 (2021).
  • 61. Bratuleanu,B.E.etal.Theviromeof Rhipicephalus, Dermacentor and Haemaphysalis ticksfrom Eastern Romaniaincludes novel viruses with potential relevance for public health.Transbound. Emerg.Dis.https://doi.org/10.1111/tbed.14105 (2021).
  • 62. KosakovskyPond,S.L., Posada,D., Gravenor,M. B., Woelk,C.H.& Frost,S.D.W. Automatedphylogenetic detectionof recombinationusingagenetic algorithm. Mol.Biol.Evol.23, 1891-1901 (2006).
  • 63. KosakovskyPond,S.L., Posada,D., Gravenor,M. B., Woelk,C.H.& Frost,S.D.W.GARD: agenetic algorithm for recombination detection. Bioinformatics 22, 3096-3098 (2006).
  • 64. Crawford,K.H.D.etal. Protocolandreagentsforpseudotypinglentiviralparticleswith SARS-CoV-2 spike protein for neutralization assays.Viruses 12, E513 (2020).
  • 65. Anna,F. etal. Highseroprevalencebutshort-livedimmuneresponsetoSARS-CoV-2 infection in Paris.Eur.J.Immunol. 51, 180-190 (2021).
  • 66. Corman,V.M.etal.Detectionof 2019 novelcoronavirus (2019-nCoV) byreal-time RT-PCR.Euro Surveill.25, 2000045 (2020).
  • 67. Monteil, V.etal. InhibitionofSARS-CoV-2 infectionsinengineeredhumantissuesusing clinical-grade soluble human ACE2.Cell 181, 905-913 (2020).
  • 68. Kabsch,W.XDS.ActaCrystallogr.D 66, 125-132 (2010).
  • 69. McCoy,A.J.etal. Phasercrystallographicsoftware.J.Appl. Crystallogr.40, 658-674 (2007).
  • 70. Emsley,P. & Cowtan,K.Coot: model-buildingtoolsformoleculargraphics.Acta Crystallogr.D 60, 2126-2132 (2004).
  • 71. Liebschner,D. etal. MacromolecularstructuredeterminationusingX-rays,neutronsand electrons:recent developments in Phenix.Acta Crystallogr.D 75, 861-877 (2019).
  • 72. Sali,A. & Blundell, T.L.Comparativeproteinmodellingbysatisfactionofspatial restraints.J.Mol. Biol. 234, 779-815 (1993).
  • 73. Shen,M.-Y.& Sali,A.Statisticalpotentialforassessmentandpredictionofprotein structures.Protein Sci.15, 2507-2524 (2006).
  • 74. Jo,S.,Kim,T., Iyer,V.G.& Im,W.CHARMM-GUI:aweb-basedgraphicaluserinterfacefor CHARMM.J.Comput.Chem.29, 1859-1865 (2008).
  • 75. Huang,J. etal. CHARMM36m:animprovedforcefieldforfoldedandintrinsically disordered proteins.Nat.Methods 14, 71-73 (2017).
  • 76. Jorgensen,W.L., Chandrasekhar,J., Madura,J.D.,Impey,R.W.& Klein,M.L.Comparison of simple potential functions for simulating liquid water.J.Chem. Phys. 79, 926-935 (1983).
  • 77. Bussi,G., Donadio,D.& Parrinello,M.Canonicalsamplingthroughvelocityrescaling. J.Chem. Phys.126, 014101 (2007).
  • 78. Berendsen,H.J.C., Postma,J.P.M.,vanGunsteren,W.F.,DiNola,A. & Haak,J.R. Molecular dynamics with coupling to an external bath.J.Chem. Phys. 81, 3684-3690 (1984).
  • 79. Hess,B., Bekker,H.,Berendsen,H. J.C.& Fraaije,J. G.E.M.LINCS:alinearconstraint solver for molecular simulations.J.Comput.Chem.18, 1463-1472 (1997).
  • 80. Essmann,U.etal. AsmoothparticlemeshEwaldmethod.J.Chem.Phys.103, 8577-8593 (1995).
  • 81. ThePLUMEDconsortium.Promotingtransparencyandreproducibilityinenhanced molecular simulations.Nat.Methods 16, 670-673 (2019).
  • 82. Daura,X.etal.Peptidefolding:whensimulationmeetsexperiment.Angew.Chem.Int. Ed. 38, 236-240 (1999).
  • 83. Stranges,P.B. & Kuhlman,B.Acomparisonofsuccessfulandfailedproteininterface designs highlights the challenges of designing buriedhydrogen bonds.Protein Sci.22, 74-82 (2013).
  • 84. Schymkowitz,J.etal.TheFoldXwebserver:anonlineforcefield. NucleicAcidsRes.33, W382-W388 (2005).
  • 85. Humphrey,W.,Dalke,A. & Schulten,K.VMD:visualmoleculardynamics.J.Mol. Graph. 14, 33-38 (1996).
  • 86. Michaud-Agrawal,N., Denning,E. J.,Woolf,T.B.& Beckstein,O.MDAnalysis:atoolkitfor the analysis of molecular dynamics simulations.J.Comput.Chem.32, 2319-2327 (2011).