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Title: Bioinformatics and molecular analysis of the evolutionary relationship between bovine rhinitis A viruses and foot-and-mouth disease virus

item RAI, DEVENDRA - University Of Connecticut
item Lawrence, Paul
item Pauszek, Steven
item PICCONE, MARIA - University Of Connecticut
item KNOWLES, NICK - Institute Of Animal Health - United Kingdom
item Rieder, Aida - Elizabeth

Submitted to: Bioinformatics and Biology Insights
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2015
Publication Date: 4/9/2016
Citation: Rai, D., Lawrence, P.J., Pauszek, S.J., Piccone, M.E., Knowles, N., Rieder, A.E. 2016. Bioinformatics and molecular analysis of the evolutionary relationship between bovine rhinitis A viruses and foot-and-mouth disease virus. Bioinformatics and Biology Insights. 9:43-58. doi: 10.4137/BBI.S37223.

Interpretive Summary: Bovine rhinitis virus type 1 (BRV1) is a pathogen associated with common cold in bovines. Like many other respiratory viruses, BRV1 targets the upper respiratory tract and grows well at 33 degrees Celsius. In 2010, we were the first to genetically and biologically describe bovine rhinitis viruses (BRV). Of significance, our discovery has led to the re-classification of bovine rhinitis viruses as new members of the aphthovirus genus, a group of viruses, which includes Foot-and-Mouth Disease Virus (FMDV). In the current study, we have extended our analysis to include a field isolate of BRV of type 1, including determining a nearly full-length genetic sequence of the virus. This information allowed us to compare with other members of the same family of viruses. Importantly, we concluded that the likelihood of detecting recombination events between FMDV and BRV are highly remote. Based on these results, we propose that BRV1 strain RS3X be classified as a bovine rhinitis A virus in the aphthovirus genus along with FMDV, bovine rhinitis B and equine rhinitis viruses. These findings are important to development of diagnostic and vaccines to FMDV.

Technical Abstract: Bovine rhinitis viruses (BRV) cause mild respiratory disease of cattle. In this study, a near full length genome sequence of a virus named RS3X, formerly classified as bovine rhinovirus type 1, isolated from infected cattle from the United Kingdom in the 1960s, was obtained and analyzed. Phylogenetic analysis revealed that RS3X was a member of the species Bovine rhinitis A virus (BRAV). Using different codon-based and branch-site selection models for aphthoviruses including BRAV RS3X, we observed no clear evidence for genomic regions undergoing positive selection, however, within each of the BRV species multiple sites under positive selection were detected. The results also suggest that the probability, determined by RDP, for recombination events between BRVs and other aphthoviruses were not significant. In contrast, within BRVs the probability of recombination increases. The data reported here provides genetic information to assist on the identification of diagnostic signatures and research tools for BRAV.