The origin and evolution of emerged swine acute diarrhea syndrome coronavirus with zoonotic potential

Abstract

Swine acute diarrhea syndrome coronavirus (SADS‐CoV) is a newly discovered alphacoronavirus with zoonotic potential that causes diarrhea and vomiting mainly in piglets. Having emerged suddenly in 2017, the prevailing opinion is that the virus originated from HKU2, an alphacoronavirus whose primary host is bats, and at some unknown point achieved interspecies transmission via some intermediate. Here, we further explore the evolutionary history and possible cross‐species transmission event for SADS‐CoV. Coevolutionary analysis demonstrated that HKU2 may have achieved host switch via SADS‐related (SADSr)‐CoV, which was isolated from the genus Rhinolophus in 2017. SADS‐CoV, HKU2, and SADSr‐CoV share similar codon usage patterns and showed a lower tendency to use CpG, which may reflect a method of immune escape. The analyses of virus‐host coevolution and recombination support SADSr‐CoV is the direct source of SADS‐CoV that may have undergone recombination events during its formation. Structure‐based spike glycoprotein variance analysis revealed a more nuanced evolutionary pathway to receptor recognition for host switch. We did not find a possible positive selection site, and the dN/dS of the S gene was only 0.29, which indicates that the current SADS‐CoV is slowly evolving. These results provide new insights that may help predict future cross‐species transmission, and possibly surveil future zoonotic outbreaks and associated public health emergencies.

Research Advances on Swine Acute Diarrhea Syndrome Coronavirus

“…Although the scale of outbreaks caused by this virus has not yet reached pandemic levels, it is still endemic to specific regions. Studies have consistently shown that SADS-CoV, with its unique structure, is at risk of evolving into a zoonotic virus [24][25][26]. The study of SADS-CoV is critical for the surveillance and control of animal diseases, while also enhancing our understanding of coronaviruses by identifying their unique characteristics.…”

Analysis of Codon Usage Bias of Thioredoxin in Apicomplexan Protozoa

“…CUB is known to have a signi cant impact on a wide range of cellular processes such as mRNA stability, transcription, translation e ciency and accuracy, as well as protein structure, folding, expression, and function. Additionally, there are various practical applications in understanding CUB that are of signi cant value, including heterologous gene expression [19], identifying species origins [6,20], designing degenerate primers [21], predicting gene expression levels [22][23], predicting gene functions [24][25], and designing synthetic genes for biotechnological applications [26]. However, most of the numerous studies on CUB have focused on bacterium, fungi, viruses, and mycoplasma [27][28][29][30][31].…”