Whole genome characterisation of quail deltacoronavirus detected in Poland

Domańska-Blicharz, Katarzyna; Kuczkowski, Maciej; Sajewicz-Krukowska, Joanna

Quail deltacoronavirus (QdCoV) described for the first time in the United Arab Emirates in 2018 belongs to the same deltacoronavirus species as viruses discovered in swine and tree sparrows. The full-length genome of QdCoV detected in quails with enteritis in Poland has similar organization as Middle Eastern viruses although there is no NSP7c gene. The overall degree of nucleotide sequence identity was 92.4–92.6% between Polish PL/G032/2015 and Middle Eastern UAE-HKU30 QdCoV isolates. The sequences of the individual genes show similar nucleotide identities in the range of 91.4–94.7% with the exception of the S gene with lower identity of 85.6–85.7%. The most variable part of the S gene is its fragment encoding the N-terminal domain of the S protein which is responsible for receptor binding. The amino acid homology in this region between PL/G032/2015 and UAE-HKU30 QdCoVs was 74.5–74.7%. In contrast, the C-terminal domain of the S protein which is responsible for membrane fusion had an amino acid homology of 96.9%. In the phylogenetic tree, PL/G032/2015 branched separately but clustered with the UAE-HKU30 QdCoV isolates. These data suggest that PL/G032/2015 could be a new genetic/serologic variant of QdCoV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-019-01639-1) contains supplementary material, which is available to authorized users.