| Summary: | Avian infectious bronchitis virus (IBV) and bovine coronavirus (BCoV) are pathogens of veterinary importance that affect birds and bovine in Cuba; however, molecular characteristics and genetic diversity of these viruses are unknown. This study was aimed at determining the molecular characteristics and genetic diversity of both agents, based in the spike S gene. A molecular analysis was carried out from field strains of BCoV collected between 2009 and 2011 and phylogenetic studies were conducted using partial or complete S gene sequences as phylogenetic markers. Besides, studies of phylogenetic inference were carried out in S1 region of recent isolates of IBV. All Cuban bovine coronavirus sequences were located in a single cluster supported by 100 % bootstrap and 1.00 posterior probability values. The Cuban BCoV sequences were also clustered with the USA BCoV strains corresponding to the GenBank accession numbers EF424621 and EF424623, suggesting a common origin for these viruses. This phylogenetic cluster was also the only group of sequences in which no recombination events were detected. Of the 45 amino acid changes found in the Cuban strains, four were unique. On the other hand, two putative genotypes genetically different to the Massachusetts genotype H120 strain used in the Cuban vaccination program were found in the flocks assessed. In addition, a potential nephropathogenic IBV isolate was found by first time in Cuba. This research won the 2012 Award of the Cuban National Academy of Sciences.
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