Molecular diversity of coronaviruses in bats

Abstract

The existence of coronaviruses in bats is unknown until the recent discovery of bat-SARS-CoV in Chinese horseshoe bats and a novel group 1 coronavirus in other bat species. Among 309 bats of 13 species captured from 20 different locations in rural areas of Hong Kong over a 16-month period, coronaviruses were amplified from anal swabs of 37 (12%) bats by RT-PCR. Phylogenetic analysis of RNA-dependent-RNA-polymerase (pol) and helicase genes revealed six novel coronaviruses from six different bat species, in addition to the two previously described coronaviruses. Among the six novel coronaviruses, four were group 1 coronaviruses (bat-CoV HKU2 from Chinese horseshoe bat, bat-CoV HKU6 from rickett's big-footed bat, bat-CoV HKU7 from greater bent-winged bat and bat-CoV HKU8 from lesser bent-winged bat) and two were group 2 coronaviruses (bat-CoV HKU4 from lesser bamboo bats and bat-CoV HKU5 from Japanese pipistrelles). An astonishing diversity of coronaviruses was observed in bats.

Fig. 1

Map of HKSAR showing locations of bat surveillance indicated by dots. Areas belonging to Shenzhen of mainland China are shaded. Solid dots represent the 10 locations with bats positive for coronaviruses. Location A is where CoV HKU4-1, bat-CoV HKU4-2 and bat-CoV HKU4-3 were found, location B is where bat-CoV HKU4-4 and bat-CoV HKU5-1 were found, and location C is where bat-CoV HKU5-2, bat-CoV HKU5-3 and bat-CoV HKU5-5 were found.

Fig. 2

Phylogenetic trees of Pol (2a) and helicase (2b) showing the relationship of the novel bat coronaviruses to known coronaviruses. The trees were inferred from amino acid sequence data (949 amino acid positions for RNA-dependent RNA polymerase and 609 amino acid positions for helicase) by the neighbor-joining method. Numbers at nodes indicated levels of bootstrap support calculated from 1000 trees. The scale bar indicates the estimated number of substitutions per 50 amino acids. Only three of the 21 strains of bat-SARS-CoV are shown. GenBank accession numbers are in brackets and names of bats from which the coronaviruses were recovered are in square brackets. The 13 strains of the six novel coronaviruses in bats are in bold. HCoV-229E, human coronavirus 229E; PEDV, porcine epidemic diarrhea virus; TGEV, porcine transmissible gastroenteritis virus; FeCoV, feline coronavirus; HCoV-NL63, human coronavirus NL63; HCoV-OC43, human coronavirus OC43; MHV, murine hepatitis virus; BCoV, bovine coronavirus; CoV-HKU1, coronavirus HKU1; SARS-CoV, SARS coronavirus; bat-SARS-CoV, SARS coronavirus-like virus found in bats; IBV, infectious bronchitis virus; MR, Myotis ricketti; RS, Rhinolophus sinicus; MP, Miniopterus pusillus; MM, Miniopterus magnater; TP, Tylonycteris pachypus; PA, Pipistrellus abramus.