Recent emergence of bovine coronavirus variants with mutations in the hemagglutinin-esterase receptor binding domain in U.S. cattle

Authors: Workman, Aspen; McDaneld, Tara; Harhay, Gregory; DAS, SUBHA - South Dakota State University; LOY, JOHN - University Of Nebraska; HAUSE, BENJAMIN - South Dakota State University

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2022
Publication Date: 9/27/2022
Citation: Workman, A.M., McDaneld, T.G., Harhay, G.P., Das, S., Loy, J.D., Hause, B.M. 2022. Recent emergence of bovine coronavirus variants with mutations in the hemagglutinin-esterase receptor binding domain in U.S. cattle. Viruses. 14(10). Article 2125. https://doi.org/10.3390/v14102125.
DOI: https://doi.org/10.3390/v14102125

Interpretive Summary: Bovine coronavirus (BCoV) is associated with bovine respiratory disease complex (BRDC) and calf diarrhea, which are the two most significant and costly infectious diseases of cattle worldwide. Furthermore, BCoV is a zoonotic pathogen that has been detected in multiple species, including humans. Despite this, there is a paucity of whole genome sequences available in public databases. Here, 78 complete or near complete BCoV genomes were sequenced and assembled directly from clinical samples collected between 2013 and 2022 from 27 enteric disease cases and 51 respiratory disease cases from cattle in 12 states, primarily in the Midwestern U.S. Genomic comparisons revealed a recent emergence of BCoV variants with mutations in the hemagglutinin-esterase (HE) gene. Specifically, we observed both insertions and deletions in the receptor binding domain of the HE protein. The HE protein has a receptor binding domain and an enzymatically active esterase domain responsible for receptor destruction and virus release from infected cells. Changes in the HE gene of BCoV and related coronaviruses have been associated with changes in cellular tropism or host range. Thus, we expressed isogenic HE proteins containing either the insertion or deletion in the receptor binding domain and measured receptor binding and cleavage functions. Both HE variants maintained their ability to bind and cleave the cellular receptor despite protein modeling that predicted structural changes in the HE protein. How these HE variants impact BCoV pathogenesis in cattle remains unknown. Thus, further investigation of BCoV evolution and in particular these novel HE variants is warranted.

Technical Abstract: Bovine coronavirus (BCoV) has spilled over to many species, including humans, where the host range variant coronavirus OC43 is endemic. Balance of the opposing activities of the surface spike (S) and hemagglutinin esterase (HE) glycoproteins control virion avidity which is critical for interspecies transmission and host adaptation. Here, 78 genomes were sequenced directly from clinical samples collected between 2013 and 2022 from cattle in 12 states, primarily in the Midwestern U.S. Relatively little genetic diversity was observed, with genomes having >98% nucleotide identity. Eleven isolates collected between 2020 and 2022 from four states (Nebraska, Colorado, California, and Wisconsin) contained a 12-nucleotide insertion in the receptor-binding domain (RBD) of the HE gene identical to one recently reported in China, and a single genome from Nebraska collected in 2020 contained a novel 12-nucleotide deletion in the HE gene RBD. Isogenic HE proteins containing either the insertion or deletion in the HE RBD maintained esterase activity and ability to bind bovine submaxillary mucin, a substrate enriched in the receptor 9-O-acetylated-sialic acid, despite modeling that predicted structural changes in the HE R3 loop critical for receptor binding. The emergence of BCoV with structural variants in the RBD raises the possibility of further interspecies transmission.