Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome

Abstract

Apart from bat-SARS-CoV, we have identified a novel group 1 coronavirus, bat-CoV HKU2, in Rhinolophus sinicus (Chinese horseshoe bats). Since it has been suggested that the receptor-binding motif (RBM) of SARS-CoV may have been acquired from a group 1 coronavirus, we conducted a surveillance study and identified bat-SARS-CoV and bat-CoV HKU2 in 8.7% and 7.5% respectively of R. sinicus in Hong Kong and Guangdong. Complete genome sequencing of four strains of bat-CoV HKU2 revealed the smallest coronavirus genome (27164 nucleotides) and a unique spike protein evolutionarily distinct from the rest of the genome. This spike protein, sharing similar deletions with other group 2 coronaviruses in its C-terminus, also contained a 15-amino acid peptide homologous to a corresponding peptide within the RBM of spike protein of SARS-CoV, which was absent in other coronaviruses except bat-SARS-CoV. These suggest a common evolutionary origin in the spike protein of bat-CoV HKU2, bat-SARS-CoV, and SARS-CoV.

Fig. 1

Map showing locations of sampling in Hong Kong. Dark circles represent locations positive for bat-CoV HKU2, squares represent locations positive for bat-SARS-CoV, and triangles represent locations positive for both bat-CoV HKU2 and bat-SARS-CoV. Blank circles represent locations negative for bat-SARS-CoV and bat-CoV HKU2. Location A was where bat-CoV HKU2/HK/33/2004 was found, location B was where bat-CoV HKU2/HK/298/2004 was found, and location C was where bat-CoV HKU2/HK/46/2006 was found.

Fig. 2

Genome organizations of bat-CoV HKU2 compared to representative coronaviruses from each group. The conserved functional domains ORF 1ab and the structural proteins are represented by gray boxes. The genome sizes (bp) are shown on the right.

Fig. 3

A short stretch of peptide within the RBM of S protein of SARS-CoV with homology to the corresponding region in the S of bat-CoV HKU2 and bat-SARS-CoV. The conserved amino acids are in bold and boxed.

Fig. 4

Phylogenetic analysis of 3CL^pro, RdRp, Hel, S, M, and N of bat-CoV HKU2. The trees were constructed by neighbor joining method using Kimura's two-parameter correction and bootstrap values calculated from 1000 trees. 306, 949, 609, 1758, 270, and 586 amino acid positions in 3CL^pro, RdRp, Hel, S, M, and N, respectively, were included in the analysis. The scale bar indicates the estimated number of substitutions per 10 amino acids. HCoV-229E, human coronavirus 229E; PEDV, porcine epidemic diarrhea virus; TGEV, porcine transmissible gastroenteritis virus; FIPV, feline infectious peritonitis virus; HCoV-NL63, human coronavirus NL63; CoV-HKU1, coronavirus HKU1; HCoV-OC43, human coronavirus OC43; MHV, murine hepatitis virus; BCoV, bovine coronavirus; PHEV, porcine hemagglutinating encephalomyelitis virus; IBV, infectious bronchitis virus; SARS-CoV, SARS coronavirus; bat-SARS-CoV HKU3, bat-SARS-like coronavirus HKU3; bat-CoV HKU4, bat coronavirus HKU4; bat-CoV HKU5, bat coronavirus HKU5; bat-CoV HKU9, bat coronavirus HKU9.