Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021

Sun, Yankuo; Xu, Zhenbo; Gao, Han; Xu, Sijia; Liu, Jing; Zhu, Di-Hua; Guo, Yifan; Yang, Bin-shuo; Chen, Xiong-nan; Zheng, Zezhong; Wang, Heng; Gong, Lang; Holmes, Edward C.; Xing, Jiabao

doi:10.1016/j.jinf.2022.08.020

Cited by 25 publications

(15 citation statements)

References 10 publications

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“…In addition, our previous report of the re-emergence of SADS-CoV in May-2021 identi ed its potential inter-group recombination history. However, in this study, we failed to obtain simultaneous recombination support collected, despite contemporaneity (30). Adding to the fact that two genomes of SADS-CoV identi ed in May-2021 and Mar-2022 respectively in this cohort showed such ample phylogenetic divergence, these combinations suggest that this virus might have evolved to be endemic and multi-lineage in Guangxi, China, since at least 2021, as well as corroborating the evidence for domestically continuous cross-regional transmission.…”

Section: Discussionmentioning

confidence: 56%

“…Strikingly, we detected the prevalence of Swine Acute Diarrhea Syndrome Coronavirus (SADS-CoV) twice in Spring 2021 and March 2022 from Guangxi, respectively (RPM: 387.75 and 58.23, respectively) (Fig. 2, Additional le1) (30). Furthermore, PRRSV was prevalent only in the mixed samples, with no virus being detected in the intestine-only samples (mean RPM: 3971).…”

Section: Total Infectome Characterizationmentioning

confidence: 93%

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Total infectome of etiology and epidemiology unravels a complex infection landscape in Chinese acute diarrheal pig herds

Sun

Xing

et al. 2023

Preprint

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Background Porcine diarrhea is predominantly caused by infectious pathogens, leading to decreased appetite, poor digestion, intestinal inflammation, dysbiosis, and weight loss. These factors significantly affect productivity and performance in modern farming systems. However, the interactions between these pathogens and their temporal-spatial dynamics, as well as their interactions with other concurrent pathogens in multiorgan complex diseases, are rarely considered. Thus, understanding the relevant etiology of these clinical manifestations is crucial. Results To address this gap, we used a meta-transcriptomics approach to jointly characterize the prevalence, abundance, evolutionary history, and natural diversity of a wide spectrum of pathogens within 122 cases of acute diarrhea from different pig farms, including 47 mixed group samples involving other pathological tissues. We categorized the samples into two groups: "intestine only" and "mixed tissue." We identified 43 species of pathogenic microbes, consisting of 37 species of viruses and six species of prokaryotes that contribute putatively to clinical manifestations. Evolutionary estimation revealed a highly divergent evolutionary dynamic of important swine pathogens that was previously unknown. Diversity analysis revealed that seasonal turnover was a significant factor affecting the structure of enteric pathogen populations. Correlation analysis performed on gut-only samples provided insight into the synergistic relationship between enteric pathogens. Comparative analysis of the infectome against both sampling categories mapped the heterogeneity of the pathogenic community underlying multiorgan complex diseases. Conclusion In summary, our meta-transcriptomics approach revealed a complex infectome of porcine diarrhea, which threatens livestock and humans. It offers valuable prior knowledge of disease interactions for veterinarians prior to clinical diagnosis. Our findings may serve as a reference for understanding microbial communities and could inform disease prevention and control strategies.

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Section: Discussionmentioning

confidence: 56%

Section: Total Infectome Characterizationmentioning

confidence: 93%

Total infectome of etiology and epidemiology unravels a complex infection landscape in Chinese acute diarrheal pig herds

Sun

Xing

et al. 2023

Preprint

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“…SADS-CoV as an emerging virus, jumping from bat to pigs, caused a huge number of piglet infections and deaths in China (Sun et al 2022 ; Wang et al 2018b ; Zhou et al 2019 , 2018b ). So far, there is no vaccine or clinically approved drugs to prevent and cure SADS-CoV, nor commercial diagnostic kits.…”

Section: Discussionmentioning

confidence: 99%

“…In 2020, epidemiology investigation showed that SADS-CoV infection had existed in other provinces, such as Shanxi, Yunnan, Guangdong, Jiangxi, Henan, Hubei, Hebei, Hunan, Qinghai, Anhui, and Shanxi in China (Peng et al 2021 ). In May 2021, a large-scale fatal swine diarrhea disease outbreak of SADS-CoV in an intensive scale pig farm in Guangxi province was reported (Sun et al 2022 ). The latest report showed that SADS-CoV had a wide range of cellular fitness in vitro, including various rodent and human cell lines, suggesting that the virus has a potential threat of cross-species transmission to humans (Yang et al 2019b ).…”

Section: Introductionmentioning

confidence: 99%

Development of a novel double-antibody sandwich quantitative ELISA for detecting SADS-CoV infection

Cao

Kong

Zhang

et al. 2023

Appl Microbiol Biotechnol

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“…In 2021, SADS‐CoV re‐emerged in Guangxi. Epidemiological investigation suggested that the virus likely originated from Fujian and was latent in Guangxi at least as early as 2019 11 . In general, the virus has sporadic outbreaks in the south of China, mainly affecting farms with frequent diarrhea, and there is no evidence of farm‐to‐farm transmission.…”

Section: Introductionmentioning

confidence: 99%

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

Zhao

Yang

et al. 2023

Journal of Medical Virology

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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.

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Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021

Cited by 25 publications

References 10 publications

Total infectome of etiology and epidemiology unravels a complex infection landscape in Chinese acute diarrheal pig herds

Total infectome of etiology and epidemiology unravels a complex infection landscape in Chinese acute diarrheal pig herds

Development of a novel double-antibody sandwich quantitative ELISA for detecting SADS-CoV infection

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

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