Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

• Main Authors: 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
• Format: Article
• Language: English
• Published: MDPI AG 2019-01-01
• Series: Viruses
• Subjects: coronavirus; alphacoronavirus; rodents; ancestry; recombination; evolution
• Online Access: https://www.mdpi.com/1999-4915/11/2/125

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.