High detection rates of picobirnaviruses in free roaming rats (Rattus spp.): Molecular characterization of complete gene segment-2

We report here high rates of detection (54%, 21/39) of picobirnaviruses (PBVs) in feces/intestinal contents of free roaming, apparently healthy rats (Rattus spp.) on the Caribbean island of St. Kitts. One of the PBV strains, strain PBV/Rat/KNA/Rat9/2017, was molecularly characterized for complete gene segment-2. To determine the nucleotide (nt) sequence of full-length gene segment-2, the 5′- and 3′- portions of gene segment-2 of strain Rat9 containing an overlapping region were amplified using a non-specific primer-based amplification method with modifications. The complete gene segment-2 of PBV strain Rat9 was 1730 bp in length, encoding a putative RNA-dependent RNA polymerase (RdRp) of 535 amino acid (aa). By nt and deduced aa sequence identities and phylogenetic analysis, the complete gene segment-2 of strain Rat9 exhibited high genetic diversity with those of PBVs from other host species. On the other hand, 5′- and 3′- end nt sequences of gene segment-2, and the three domains of putative RdRp that are conserved in PBVs were retained in strain Rat9. To our knowledge, this is the first report on molecular characterization of complete gene segment-2 of a PBV strain from Rattus spp., providing important insights into the putative RdRp, and genetic diversity and evolution of PBV in rats. The high detection rates of PBV in free roaming rats on St. Kitts emphasizes the importance of further studies on epidemiology and genetic makeup of PBVs in Rattus spp.