Shared common ancestry of rodent alphacoronaviruses sampled globally

Abstract

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.

• Journal Article Type: Article
• Publication Date: Jan 30, 2019
• Publisher: MDPI
• Peer Reviewed: Peer Reviewed
• Volume: 11
• Issue: 2
• Article Number: 125
• APA6 Citation: Tsoleridis, T., Chappell, J. G., Onianwa, O., Marston, D. A., Fooks, A. R., Monchatre‐leroy, E., …K 7 Ball, J. (2019). Shared common ancestry of rodent alphacoronaviruses sampled globally. Viruses, 11(2), doi:10.3390/v11020125
• DOI: https://doi.org/10.3390/v11020125
• Keywords: coronavirus; alphacoronavirus; rodents; ancestry; recombination; evolution
• Publisher URL: https://www.mdpi.com/1999-4915/11/2/125/htm