Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

Theocharis Tsoleridis, Joseph G. Chappell, Okechukwu Onianwa, Denise A. Marston, Anthony R. Fooks, Elodie Monchatre-Leroy, Gérald Umhang, Marcel A. Müller, Jan F. Drexler, Christian Drosten, Rachael E. Tarlinton, Charles P. McClure, Edward C. Holmes, Jonathan K. Ball

The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) sampled worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of rodent CoVs in more detail, particularly the relative frequencies of virus-host co-divergence and cross-species transmission, we recovered longer fragments of CoV genomes from previously discovered European rodent alpha-CoVs using a combination of PCR and high-throughput sequencing. Accordingly, the full genome sequence was retrieved from the UK rat coronavirus, along with partial genome sequences from the UK field vole and Poland-resident bank vole CoVs, and a short conserved ORF1b fragment from the French rabbit CoV. Genome and phylogenetic analysis showed that despite their diverse geographic origins, all rodent alpha-CoVs formed a single monophyletic group and shared similar features, such as the same gene constellations, a recombinant beta-CoV spike gene, and similar core transcriptional regulatory sequences (TRS). These data suggest that all rodent alpha CoVs sampled so far originate from a single common ancestor, and that there has likely been a long-term association between alpha CoVs and rodents. Despite this likely antiquity, the phylogenetic pattern of the alpha-CoVs was also suggestive of relatively frequent host-jumping among the different rodent species.

2019

coronavirus, alphacoronavirus, Rodents, ancestry, recombination, evolution

DOI: 10.3390/v11020125

Viruses

MDPI AG

Microbiology

EN