Virus Genes

, Volume 55, Issue 1, pp 60–67 | Cite as

Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny

  • Roberta LecisEmail author
  • Mauro Mucedda
  • Ermanno Pidinchedda
  • Marco Pittau
  • Alberto Alberti


Bats may be natural reservoirs for a large variety of emerging viruses, including mammalian coronaviruses (CoV). The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) in humans, with evidence that these viruses may have their ancestry in bats, highlights the importance of virus surveillance in bat populations. Here, we report the identification and molecular characterization of a bat β-Coronavirus, detected during a viral survey carried out on different bat species in the island of Sardinia (Italy). Cutaneous, oral swabs, and faecal samples were collected from 46 bats, belonging to 15 different species, and tested for viral presence. Coronavirus RNA was detected in faecal samples from three different species: the greater horseshoe bat (Rhinolophus ferrumequinum), the brown long-eared bat (Plecotus auritus), and the European free-tailed bat (Tadarida teniotis). Phylogenetic analyses based on RNA-dependent RNA polymerase (RdRp) sequences assigned the detected CoV to clade 2b within betacoronaviruses, clustering with SARS-like bat CoVs previously reported. These findings point to the need for continued surveillance of bat CoV circulating in Sardinian bats, and extend the current knowledge on CoV ecology with novel sequences detected in bat species not previously described as β-Coronavirus hosts.


Bats Coronavirus RNA-dependent RNA polymerase Rhinolophus ferrumequinum Sardinia 



We thank Luca Montanaro, Gaetano Fichera Enrico Melis, and Manuele Bardi Lecis for their support in the field and technical support.

Author contributions

RL and AA conceived the study; RL conducted field and lab study and analyzed sequence data; MM and EP provided bat samples; RL drafted the manuscript; MP and AA reviewed the ms. All authors revised and approved the manuscript.


This research was cofunded by the University of Sassari (Italy), PhD course in Life Sciences and Biotechnologies, and Regione Sardegna.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

All international, national and institutional guidelines for the care of sampled animals were followed. Samples were collected under ethical and capture permits: “Autorizzazione Ministero Ambiente e Tutela del Territorio e del Mare 0007134 PNM (08/04/2016, DIV II)”, and “Autorizzazione Regione Autonoma della Sardegna, Assessorato Difesa dell’Ambiente, Det. 7325 Rep. N. 171 (13/04/2016)”.


  1. 1.
    Burgin CJ, Colella JP, Kahn PL, Upham NS (2018) How many species of mammals are there? J Mammal 99:1–14CrossRefGoogle Scholar
  2. 2.
    García-Pérez R, Ibáñez C, Godínez JM, Aréchiga N, Garin I, Pérez-Suárez G, de Paz O, Juste J, Echevarría JE, Bravo IG (2014) Novel Papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity, and hints for recombination. Genome Biol Evol 6:94–104CrossRefGoogle Scholar
  3. 3.
    Smith I, Wang L (2012) Bats and their virome: an important source of emerging viruses capable of infecting humans. Curr Opin Virol 3:1–8CrossRefGoogle Scholar
  4. 4.
    Lin XD, Wanga W, Haoc ZY, Wang ZX, Guoa WP, Guana XQ, Wange MR, Wang HW, Zhoua RH, Lia MH, Tang GP, Wug J, Holmesh EC, Zhanga YZ (2017) Extensive diversity of coronaviruses in bats from China. Virol 507:1–10CrossRefGoogle Scholar
  5. 5.
    Tse H, Tsang AKL, Tsoi HW, Leung ASP, Ho CC, Lau SKP, Woo PCY, Yuen KY (2012) Identification of a novel bat papillomavirus by metagenomics. PLoS ONE 7:e43986CrossRefGoogle Scholar
  6. 6.
    Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T (2006) Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev 19:531–545CrossRefGoogle Scholar
  7. 7.
    Woo PCY, Huang Y, Lau SKP, Yuen KY (2010) Coronavirus genomics and bioinformatics analysis. Viruses 2:1804–1820CrossRefGoogle Scholar
  8. 8.
    Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY (2012) Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol 86:3995–4008CrossRefGoogle Scholar
  9. 9.
    International Committee on Taxonomy of Viruses (ICTV) (2017) Taxonomy.
  10. 10.
    Lelli D, Papetti A, Sabelli C, Rosti E, Moreno A, Boniotti MB (2013) Detection of coronaviruses in bats of various species in Italy. Viruses 5:2679–2689CrossRefGoogle Scholar
  11. 11.
    Decaro N, Mari V, Campolo M, Lorusso A, Camero M, Elia G, Martella V, Cordioli P, Enjuanes L, Buonavoglia C (2009) Recombinant canine Coronaviruses related to transmissible gastroenteritis virus of swine are circulating in dogs. J Virol 83:1532–1537CrossRefGoogle Scholar
  12. 12.
    Decaro N, Mari V, Elia G, Addie DD, Camero M, Lucente MS, Martella V, Buonavoglia C (2010) Recombinant canine Coronaviruses in dogs, Europe. Emerg Infect Dis 16:41–47CrossRefGoogle Scholar
  13. 13.
    Lorusso A, Decaro N, Schellen P, Rottier PJM, Buonavoglia C, Haijema BJ, de Groot RJ (2008) Gain, preservation and loss of a group 1a Coronavirus accessory glycoprotein. J Virol 82:10312–10317CrossRefGoogle Scholar
  14. 14.
    Drexler JF, Gloza-Rausch F, Glende J, Corman VM, Muth D, Goettsche M, Seebens A, Niedrig M, Pfefferle S, Yordanov S, Zhelyazkov L, Hermanns U, Vallo P, Lukashev A, Muller MA, Deng H, Herrler G, Drosten C (2010) Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of Coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. JVirol 84:11336–11349CrossRefGoogle Scholar
  15. 15.
    Corman VM, Ithete NL, Richards LR, Schoeman MC, Preiser W, Drosten C, Drexler JF (2014) Rooting the phylogenetic tree of Middle East Respiratory Syndrome Coronavirus by characterization of a conspecific virus from an African bat. JVirol 88:11297–11303CrossRefGoogle Scholar
  16. 16.
    Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF (2005) Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676–679CrossRefGoogle Scholar
  17. 17.
    Poon LL, Chu DK, Chan KH, Wong OK, Ellis TM, Leung YH, Lau SK, Woo PC, Suen KY, Yuen KY, Guan Y, Peiris JS (2005) Identification of a novel coronavirus in bats. J Virol 79:2001–2009CrossRefGoogle Scholar
  18. 18.
    Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, Li G, Dong BQ, Liu W, Cheung CL, Xu KM, Song WJ, Vijaykrishna D, Poon LL, Peiris JS, Smith GJ, Chen H, Guan Y (2006) Prevalence and genetic diversity of coronaviruses in bats from China. J Virol 80:7481–7490CrossRefGoogle Scholar
  19. 19.
    Drexler JF, Corman VM, Drosten C (2014) Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral Res 101:45–56CrossRefGoogle Scholar
  20. 20.
    Falcón A, Vázquez-Morón S, Casas I, Aznar C, Ruiz G, Pozo F, Perez-Breña P, Juste J, Ibáñez C, Garin I, Aihartza J, Echevarría JE (2011) Detection of alpha and betacoronaviruses in multiple Iberian bat species. Arch Virol 156:1883–1890CrossRefGoogle Scholar
  21. 21.
    Gloza-Rausch F, Ipsen A, Seebens A, Göttsche M, Panning M, Drexler JF, Petersen N, Annan A, Grywna K, Müller M, Pfefferle S, Drosten C (2008) Detection and prevalence patterns of Group I Coronaviruses in bats, Northern Germany. Emerg Infect Dis 14:626–631CrossRefGoogle Scholar
  22. 22.
    Reusken CBEM, Lina PHC, Pielaat A, de Vries A, Dam-Deisz C, Adema J, Drexler JF, Drosten C, Kooi EA (2010) Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe. Vect Borne Zoonotic Dis 10:785–791CrossRefGoogle Scholar
  23. 23.
    Balboni A, Gallina L, Palladini A, Prosperi S, Battilani M (2012) A real-time PCR assay for bat SARS-like Coronavirus detection and its application to Italian greater horseshoe bat faecal sample surveys. Sci World J 2012:989514Google Scholar
  24. 24.
    De Benedictis P, Marciano S, Scaravelli D, Priori P, Zecchin B, Capua I, Monne I, Cattoli G (2014) Alpha and lineage C betaCoV infections in Italian bats. Virus Genes 48:366–371CrossRefGoogle Scholar
  25. 25.
    Moreno A, Lelli D, de Sabato L, Zaccaria G, Boni A, Sozzi E, Prosperi A, Lavazza A, Cella E, Castrucci M, Ciccozzi M, Vaccari G (2017) Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy. Virol J 14:239CrossRefGoogle Scholar
  26. 26.
    Veith M, Mucedda M, Kiefer A, Pidinchedda E (2011) On the presence of pipistrelle bats (Pipistrellus and Hypsugo; Chiroptera: Vespertilionidae) in Sardinia. Acta Chiropter 13:89–99CrossRefGoogle Scholar
  27. 27.
    VanDevanter DR, Warrener P, Bennett L, Schultz ER, Coulter S, Garber RL, Rose TM (1996) Detection and analysis of diverse herpesviral species by consensus primer PCR. J Clin Microbiol 34:1666–1671Google Scholar
  28. 28.
    Li Y, Meyer H, Zhao H, Damon IK (2010) GC content-based pan-pox universal PCR assays for Poxvirus detection. J Clin Microbiol 48:268–276CrossRefGoogle Scholar
  29. 29.
    Perez-Tris J, Williams RAJ, Abel-Fernandez E, Barreiro J, Conesa JJ, Figuerola J, Martinez-Martinez M, Ramirez A, Benitez L (2011) A multiplex PCR for detection of poxvirus and papillomavirus in cutaneous warts from live birds and museum skins. Avian Dis 55:545–553CrossRefGoogle Scholar
  30. 30.
    De Sales Lima FE, Campos FS, Kuner Filho HC, De Carvalho Ruthner Batista HB, Carnielli PJ, Cibulski SP, Spilki FR, Roehe PM, Franco AC (2013) Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil. Virus Genes 47:164–167CrossRefGoogle Scholar
  31. 31.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  32. 32.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA 6: molecular evolutionary genetics analysis Version 6.0. Mol Biol Evol 30:2725–2729CrossRefGoogle Scholar
  33. 33.
    Amoroso MG, Russo D, Lanave G, Cistrone L, Pratelli A, Martella V, Galiero G, Decaro N, Fusco G (2018) Detection and phylogenetic characterization of Astroviruses in insectivorous bats from Central-Southern Italy. Zoonoses Public Health. Google Scholar
  34. 34.
    Yuan J, Hon CC, Li Y, Wang D, Xu G, Zhang H, Zhou P, Poon LLM, Lam TTY, Leung FCCL, Shi Z (2010) Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol 91:1058–1062CrossRefGoogle Scholar
  35. 35.
    Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C, Zhang YJ, Luo CM, Tan B, Wang N, Zhu Y, Crameri G, Zhang SY, Wang LF, Daszak P, Shi ZL (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503:535–538CrossRefGoogle Scholar
  36. 36.
    Rihtaric D, Hostnik P, Steyer A, Grom J, Toplak I (2010) Identification of SARS-like coronaviruses in horseshoe bats (Rhinolophus hipposideros) in Slovenia. Arch Virol 155:507–514CrossRefGoogle Scholar
  37. 37.
    Mucedda M, Pidinchedda E (2010) Pipistrelli in Sardegna. Conoscere e tutelare i mammiferi volanti. Nuova Sampa Color, Muros: 1–46Google Scholar
  38. 38.
    Mucedda M, Kiefer A, Pidinchedda E, Veith M (2002) A new species of long-eared bat (Chiroptera, Vespertilionidae) from Sardinia, Italy. Acta Chiropterol 42:121–135CrossRefGoogle Scholar
  39. 39.
    Biollaz F, Bruyndonckx N, Beuneux G, Mucedda M, Goudet J, Christe P (2010) Genetic isolation of insular populations of the Maghrebian bat, Myotis punicus, in the Mediterranean Basin. J Biogeogr. Google Scholar
  40. 40.
    Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, Wong SS, Leung SY, Chan KH, Yuen KY (2005) Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA 102:14040–14045CrossRefGoogle Scholar
  41. 41.
    Corman VM, Baldwin HJ, Tateno AF, Zerbinati RM, Annan A, Owusu M, Nkrumah EE, Maganga GD, Oppong S, Adu-Sarkodie Y, Vallo P, Ferreira da Silva Filho LVR, Leroy EM, Thiel V, van der Hoek L, Poon LLM, Tschapka M, Drosten C, Drexler JF (2015). Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. J Virol 89:11858–11870CrossRefGoogle Scholar
  42. 42.
    Hu B, Ge X, Wang LF, Shi Z (2015) Bat origin of human coronaviruses. Virol J 12:221CrossRefGoogle Scholar
  43. 43.
    Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S (2017) Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. J Virol JVI-01953-16Google Scholar
  44. 44.
    Lòpez-Baucells A, Rocha R, Fernàndez-Llamazares A (2017) When bats go viral: negative framings in virological research imperil bat conservation. Mammal Rev. Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Roberta Lecis
    • 1
    • 2
    Email author
  • Mauro Mucedda
    • 3
  • Ermanno Pidinchedda
    • 3
  • Marco Pittau
    • 1
    • 2
  • Alberto Alberti
    • 1
    • 2
  1. 1.Department of Veterinary MedicineUniversity of SassariSassariItaly
  2. 2.Mediterranean Centre for Disease ControlUniversity of SassariSassariItaly
  3. 3.Centro Pipistrelli SardegnaSassariItaly

Personalised recommendations