The Characteristics of Spike Glycoprotein Gene of Swine Acute Diarrhea Syndrome Coronavirus Strain CH/FJWT/2018 Isolated in China

Guo, Yanyan; Wang, Peihua; Pan, Yuanqing; Shi, Rui-Zhu; Li, Yaqian; Guo, Fan; Xing, Li

doi:10.3389/fvets.2021.687079

Cited by 4 publications

(7 citation statements)

References 43 publications

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“…At the same time, some strains of SADSr‐CoV and SADS‐CoV showed topological inconsistencies in the evolutionary trees, suggesting the occurrence of recombination as well as cross‐species transmission. We also found that among the many SADS‐CoV isolates, CH/FJWT/2018 (MH615810) from Fujian in 2018 showed the closest evolutionary relationship to SADSr‐CoV, consistent with previous findings that the S gene of this virus is less similar to other SADS‐CoVs 10 . Therefore, to a certain extent, MH615810 is an unusual strain, which was also reflected in the recombination, as analyzed below.…”

Section: Discussionsupporting

confidence: 89%

“…After this, the virus was silent for some time in Guangdong, with no related reports until 2019, when the virus broke out again, in an area close to where the original outbreak occurred in 2017 9 . There were reports of reemergence in Fujian in 2018 10 . In 2021, SADS‐CoV re‐emerged in Guangxi.…”

Section: Introductionmentioning

confidence: 99%

“…9 There were reports of reemergence in Fujian in 2018. 10 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.…”

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confidence: 99%

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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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Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

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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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“…SADS-CoV is a highly pathogenic CoV that infects pigs and has a unique cleavage site (R-Y-V-R | I) in the S1 domain (region 1 in Figure 3) that is essential for cell fusion and may have an impact in the pathogenicity of this virus and its observed broad cell range (67). Comparative genetic analyses have shown that bat CoV HKU2 is closely related to SADS-CoV, suggesting that bat CoVs may also be involved in the emergence of pathogenic CoVs of veterinary importance (55).…”

Section: Discussionmentioning

confidence: 99%

Detection and characterization of novel luchacoviruses, genusAlphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States

Olarte‐Castillo

Plimpton

McQueary

et al. 2023

Preprint

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Small to mid-sized carnivores, known as meso-carnivores, comprise a group of highly diverse mammals, many of which can easily adapt to anthropogenically disturbed environments. Due to commonly inhabiting urban landscapes, high population densities, and wide home ranges, wild meso-carnivores may get exposed to or spread pathogens to other species. To date, several coronaviruses (family Coronaviridae) have been detected and characterized in domesticated and farmed meso-carnivores, but knowledge of the role of meso-carnivores in the epidemiology of coronaviruses (CoVs) remains limited. To increase our understanding of CoVs circulating in wild meso-carnivores, we screened 300 samples, including feces and tissues, from 9 species of free-ranging wild meso-carnivores in the northeastern United States collected between 2016 and 2022. Using a pan-CoV nested PCR approach, we detected CoVs in fecal samples of animals in three species: fisher (Pekania pennanti), bobcat (Lynx rufus) and red fox (Vulpes vulpes). Next generation sequencing revealed that all the detected viruses belonged to the Luchacovirus subgenus within the Alphacoronavirus genus, previously reported only in rodents and lagomorphs (i.e., rabbits and pikas). Genetic comparison of the 3 prime-end of the genome (~12,000 bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct to luchacoviruses from rodents and lagomorphs. Genetic characterization of the spike (S) protein revealed that these luchacoviruses do not have an identifiable S1/S2 cleavage site but do have highly variable structural loops within S1 that comprise protease cleavage motifs or very similar cleavage motifs to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the S protein from CoVs in various wild animal species to target specific regions for further experimental analysis and epidemiologic monitoring.

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“…It is characterized by acute diarrhea, vomiting, dehydration and high mortality in neonatal piglets, resulting in enormous economic losses (1)(2)(3). The pathogens associated with viral diarrhea disease in piglets are mainly coronaviruses, including TGEV, PEDV, PDCoV, and SADS-CoV (4)(5)(6)(7)(8)(9). These swine enteric viruses cause similar clinical symptoms in infected pigs, leading to difficulties in diagnosing diarrhea (10).…”

Section: Introductionmentioning

confidence: 99%

Development of a multiplex RT-PCR method for the detection of four porcine enteric coronaviruses

Niu

Guan

et al. 2022

Front. Vet. Sci.

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Porcine enteric coronaviruses are pathogens that cause viral diarrhea in pigs and are widely prevalent worldwide. Moreover, studies have shown that some porcine enteric coronaviruses can infect humans and poultry. In order to effectively monitor these viruses, it is necessary to establish a multiple detection method to understand their prevalence and conduct in-depth research. Common porcine enteric coronaviruses include Porcine epidemic diarrhea virus (PEDV), Porcine transmissible gastroenteritis virus (TGEV), Porcine delta coronavirus (PDCoV), and Swine acute diarrhea syndrome coronavirus (SADS-CoV). Pigs infected with these viruses have the common clinical symptoms that are difficult to distinguish. A quadruplex RT-PCR (reverse transcription-polymerase chain reaction) method for the simultaneous detection of PEDV, PDCoV, TGEV and SADS-CoV was developed. Four pairs of specific primers were designed for the PEDV M gene, PDCoV N gene, TGEV S gene and SADS-CoV RdRp gene. Multiplex RT-PCR results showed that the target fragments of PDCoV, SADS-CoV, PEDV and TGEV could be amplified by this method. and the specific fragments with sizes of 250 bp, 368 bp, 616 bp and 801 bp were amplified, respectively. This method cannot amplify any fragment of nucleic acids of Seneca Valley virus (SVV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Atypical Porcine Pestivirus (APPV), and has good specificity. The lowest detection limits of PDCoV, PEDV, TGEV and SADS-CoV were 5.66 × 105 copies/μL, 6.48 × 105 copies/μL, 8.54 × 105 copies/μL and 7.79 × 106 copies/μL, respectively. A total of 94 samples were collected from pig farms were analyzed using this method. There were 15 positive samples for PEDV, 3 positive samples for mixed infection of PEDV and PDCoV, 2 positive samples for mixed infection of PEDV and TGEV, and 1 positive sample for mixed infection of PEDV, TGEV, and PDCoV. Multiplex RT-PCR method could detect four intestinal coronaviruses (PEDV, PDCoV, TGEV, and SADS-CoV) in pigs efficiently, cheaply and accurately, which can be used for clinical large-scale epidemiological investigation and diagnosis.

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The Characteristics of Spike Glycoprotein Gene of Swine Acute Diarrhea Syndrome Coronavirus Strain CH/FJWT/2018 Isolated in China

Cited by 4 publications

References 43 publications

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

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

Detection and characterization of novel luchacoviruses, genusAlphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States

Development of a multiplex RT-PCR method for the detection of four porcine enteric coronaviruses

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