Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43

Abstract

The close genetic and antigenic relatedness among the group 2 coronaviruses human coronavirus OC43 (HCoV-OC43), bovine coronavirus (BCoV), and porcine hemagglutinating encephalomyelitis virus (PHEV) suggests that these three viruses with different host specificities diverged fairly recently. In this study, we determined the complete genomic sequence of PHEV (strain PHEV-VW572), revealing the presence of a truncated group 2-specific ns2 gene in PHEV in comparison to other group 2 coronaviruses. Using a relaxed molecular clock approach, we reconstructed the evolutionary relationships between PHEV, BCoV, and HCoV-OC43 in real-time units, which indicated relatively recent common ancestors for these species-specific coronaviruses.

FIG. 1.

Maximum-likelihood tree of coronavirus ORF1b amino acid sequences. PHEV ORF1b (GenBank accession no. DQ011855) was compared to other coronaviruses on the amino acid level. Group 1 includes human coronavirus 229E (HCoV-229E, AF304460), human coronavirus NL63 (HCoV-NL63, AY567487), porcine epidemic diarrhea virus strain CV777 (PEDV, AF353511), and porcine transmissible gastroenteritis virus Purdue strain (TGEV, AJ271965). Group 2 includes human coronavirus OC43 (HCoV-OC43, AY391777), bovine coronavirus Mebus strain (BCoV, U00735), murine hepatitis virus Penn 97-1 strain (MHV-Penn97-1, AF208066), and murine hepatitis virus A59 (MHV-A59, NC_001846). Group 3 includes avian infectious bronchitis virus Beaudette strain (IBV-Beaudette, M95169), avian infectious bronchitis virus BJ strain (IBV-BJ, AY319651) and avian infectious bronchitis virus LX4 strain (IBV-LX4, AY338732). Human coronavirus HKU1 (HCoV-HKU1, NC_006577) and SARS coronavirus Frankfurt-1 strain (SARS-CoV, AY291315) are shown. The out group includes equine Berne torovirus (EToV, X52374). The scale bar represents the genetic distance (nucleotide substitutions per site).

FIG. 2.

Linear representation of the PHEV-VW572 genome (GenBank accession no. DQ011855) and SimPlot analysis of complete genome sequence data of PHEV-VW572, BCoV-LUN (AF391542), BCoV-Mebus (U00735), HCoV-OC43 BE03 (AY903459), and HCoV-OC43 ATCC (American Type Culture Collection, AY391777). Each point plotted is the percent genetic distance within a sliding window of 400 nt wide, centered on the position plotted, with a step size of 200 nt. Each curve represents a comparison of the sequence data of PHEV-VW572, the BCoV strains, and HCoV-OC43 BE03 to the reference sequence data of the ATCC HCoV-OC43 strain. HE, hemagglutinin-esterase gene; S, spike gene; E, envelope protein gene; M, membrane protein gene; N, nucleocapsid protein gene; I, internal ORF.