Comparison of the genome organization of toro- and coronaviruses: Evidence for two nonhomologous RNA recombination events during berne virus evolution

Snijder, Eric J.; Den Boon, Johan A.; Horzinek, Marian C.; Spaan, Willy J.M.

Abstract Recently, toroviruses and coronaviruses have been found to be ancestrally related by divergence of their polymerase and envelope proteins from common ancestors. In addition, their genome organization and expression strategy, which involves the synthesis of a 3′-coterminal nested set of mRNAs, are comparable. Nucleotide sequence analysis of the genome of the torovirus prototype, Berne virus (BEV), has now revealed the results of two independent nonhomologous RNA recombinations during torovirus evolution. Berne virus open reading frame (ORF) 4 encodes a protein with significant sequence similarity (30–35% identical residues) to a part of the hemagglutinin esterase proteins of corona-viruses and influenza virus C. The sequence of the C-terminal part of the predicted BEV polymerase ORF1a product contains 31–36% identical amino acids when compared with the sequence of a nonstructural 30 32K corona-virus protein. The cluster of coronaviruses which contains this nonstructural gene expresses it not as a part of their polymerase, but by synthesizing an additional subgenomic mRNA.