Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins.

Coronaviruses have caused a number of major epidemics in humans and animals, including the current pandemic of COVID-19 that has brought renewed focus on evolution and interspecies transmission of coronaviruses. Swine acute diarrhea syndrome coronavirus (SADS-CoV), which was recently identified in piglets in southern China, is an alphacoronavirus that originates from the same genus of horseshoe bats as Severe Acute Respiratory Syndrome CoV (SARS-CoV), and was reported to be capable of infecting cells from broad range of species, suggesting a considerable potential for interspecies transmission. Given the importance of coronavirus spike glycoprotein (S) in host range determination and viral entry, we report a cryo-EM structure of the SADS-CoV S-trimer in prefusion conformation at 3.55 A resolution. Our structure reveals that SADS-CoV S-trimer assumes an intra-subunit quaternary packing mode in which the S1-NTD and S1-CTD of the same protomer pack together by facing each other in the "lying-down" state. SADS-CoV S has several distinctive structural features that may facilitate immune escape, such as relatively compact architecture of the S-trimer and epitope masking by glycan shielding. Comparison of SADS-CoV S with those of the other coronavirus spike proteins suggested that the structural features of SADS-CoV S are evolutionarily related to other genera rather than being that of a typical alphacoronavirus. These data provide new insights into the evolutionary relationship between spike glycoproteins of SADS-CoV and other coronaviruses and extends our understanding of their structural and functional diversity.SIGNIFICANCE In this article, we report the atomic-resolution pre-fusion structure of spike protein from swine acute diarrhea syndrome coronavirus (SADS-CoV). SADS-CoV is a pathogenic alphacoronavirus responsible for large-scale outbreak of fatal disease in pigs that was reported to be capable of interspecies transmission. We describe the overall structure of the SADS-CoV spike protein and conduct detailed analysis of its main structural elements. Our results and analyses are consistent with the previous phylogenetic studies and suggest that SADS-CoV spike protein is evolutionarily related to spike proteins of betacoronaviruses, with strong similarity in S1-NTDs and marked divergence in S1-CTDs. Moreover, we discussed possible immune evasion strategies used by SADS-CoV spike protein. Our study provides insights into structure and immune evasion strategies of SADS-CoV spike protein and broadens the understanding of evolutionary relationships between coronavirus spike proteins of different genera.