Comparative molecular epidemiology of two closely related coronaviruses, bovine coronavirus (BCoV) and human coronavirus OC43 (HCoV-OC43), reveals a different evolutionary pattern

Abstract

Bovine coronaviruses (BCoVs) are widespread around the world and cause enteric or respiratory infections among cattle. The current study includes 13 samples from BCoVs collected in Normandy during an 11-year period (from 2003 to 2014), 16 French HCoV-OC43s, and 113 BCoVs or BCoVs-like sequence data derived from partial or complete genome sequences available on GenBank. According to a genotyping method developed previously for HCoV-OC43, BCoVs and BCoVs-like are distributed on three main sub-clusters named C1, C2, and C3. Sub-cluster C1 includes BCoVs and BCoVs-like from America and Asia. Sub-cluster C2 includes BCoVs from Europe. Sub-cluster C3 includes prototype, vaccine, or attenuated BCoV strains. The phylogenetic analyses revealed the monophyletic status of the BCoVs from France reported here for the first time. Moreover, BCoV exhibits a relative genetic stability when compared to HCoV-OC43 we previously described from the same region. The numerous recombination detected between HCoV-OC43 were much less frequent for BCoV. The analysis points thus to the influence of different evolutive constraints in these two close groups.

Keywords: Bovine coronavirus; Epidemiology; Evolution; Genotyping; Human coronavirus OC43; Recombination; Respiratory infection.

Graphical abstract

Fig. 1

Location of the livestock where nine of our samples were collected. The name of sample was indicated above each farm of origin as follows: Caen/year of sampling/specimen number. The nine corresponding farms were named F1 to F9.

Fig. 2

Phylogenetic analysis of the complete nsp12, S, and N genes of 29 BCoVs, 16 HCoV-OC43s, 17 bovine-like CoVs. The phylogenetic trees were constructed by the maximum likelihood method. Bootstrap values were calculated from 1000 replicates. Bootstrap values over 70% are shown. The evolutionary distances were computed using the Tamura Nei model and units are the number of base substitutions per site.