Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Zhou, Ling; Sun, Yuan; Lan, Tian; Wu, Ruizhu; Chen, Junwei; Wu, Zhengguang; Xie, Qingmei; Zhang, Xiangbin; Ma, Jingyun

doi:10.1111/tbed.13008

Cited by 64 publications

(60 citation statements)

References 22 publications

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“…4, five strains (SD01 , SD03-2018, SD05-2018, SD06-2018and SD08-2018 W. Sun, et al Virus Research 278 (2020) 197869 Swine acute diarrhea syndrome coronavirus (SADS-CoV), also named as Swine enteric alphacoronavirus (SeACoV) (Fu et al, 2018;Zhou et al, 2018) and PDCoV. Outbreaks of these enteric coronaviruses have been reported in China, causing substantial economic losses in the swine industry (Qing et al, 2016;Zeng et al, 2015;Zhou et al, 2019). In 2014, PDCoV was first detected in China, causing tremendous financial losses in the swine industry, and the virus has rapidly spread nationwide Liu et al, 2018;Mai et al, 2018a;Song et al, 2015;Wang et al, 2018b).…”

Section: Novel Amino Acid Deletions or Insertions Were Detected In Thmentioning

confidence: 99%

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

et al. 2020

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Porcine deltacoronavirus (PDCoV) is the etiological agent of acute diarrhoea and vomiting in pigs, threatening the swine industry worldwide. Although several PDCoV studies have been conducted in China, more sequence information is needed to understand the molecular characterization of PDCoV. In this study, the partial ORF1a, spike protein (S) and nucleocapsid protein (N) were sequenced from Shandong Province between 2017 and 2018. The sequencing results for the S protein from 10 PDCoV strains showed 96.7 %-99.7 % nucleotide sequence identity with the China lineage strains, while sharing a lower level of nucleotide sequence identity, ranging from 95.7 to 96.8%, with the Vietnam/Laos/Thailand lineage strains. N protein sequencing analysis showed that these strains showed nucleotide homologies of 97.3%-99.3% with the reference strains. Phylogenetic analyses based on S protein sequences showed that these PDCoV strains were classified into the China lineage. The discontinuous 2 + 3 aa deletions at 400-401 and 758-760 were found in the Nsp2 and Nsp3 coding region in five strains, respectively, with similar deletions having been identified in Vietnam, Thailand, and Laos. Three novel patterns of deletion were observed for the first time in the Nsp2 and Nsp3 regions. Importantly, those findings suggest that PDCoV may have undergone a high degree of variation since PDCoV was first detected in China.

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Section: Novel Amino Acid Deletions or Insertions Were Detected In Thmentioning

confidence: 99%

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

et al. 2020

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“…These large, industrial swine farms, commonly known as confined animal feeding operations (CAFOs), are thought to be sites for novel pathogen emergence and transmission. In recent years, swine pathogen epizootics in China have included porcine reproductive and respiratory syndrome virus [4], porcine epidemic diarrhea virus [5], swine acute diarrhea syndrome coronavirus [6], and, most recently, a 2018-19 massive outbreak of African Swine Fever [2].…”

mentioning

confidence: 99%

High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China

Borkenhagen

Wang

Simmons

et al. 2019

Clinical Infectious Diseases

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Background.China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections.Methods. We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans.Results. Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants' microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55-358.65) and swine H3N2 (OR 2.97, 95% CI 1.16-8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure.Conclusions. While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses.

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“…The phylogenetic analysis based on the whole genome and N gene of eight SADS-CoVs and other CoVs showed that all the sequences of SADS-CoVs clustered with bat coronavirus HKU2 to form a well-defined branch and belong to the α-genera [25]. However, surprisingly/interestingly, the phylogenetic analysis of the S genes showed that the S gene cluster can be divided into two groups: α-CoV-1 and α-CoV-2.…”

Section: Resultsmentioning

confidence: 99%

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

Guan

Wang

Saeed

et al. 2020

Preprint

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27The current outbreak of Coronavirus Disease 2019 (COVID-19) by a novel 28 betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-29 CoV-2) has aroused great public health concern. Coronavirus has a history of 30 causing epidemics in human and animals. In 2017 an outbreak in piglets by a 31 novel coronavirus was emerged designated as swine acute diarrhea 32 syndrome coronavirus (SADS-CoV) which is originated from the same genus 33 of horseshoe bats (Rhinolophus) as Severe Acute Respiratory Syndrome CoV 34 (SARS-CoV) having a broad species tropism. In addition to human cells, it 35 can also infect cell lines from diverse species. Coronavirus host range is 36 determined by its spike glycoprotein (S). Given the importance of S protein in 37 viral entry to cells and host immune responses, here we report the cryo-EM 38 structure of the SADS-CoV S in the prefusion conformation at a resolution of 39 3.55 Å. Our study reveals that SADS-CoV S structure takes an intra-subunit 40 quaternary packing mode where the NTD and CTD from the same subunit 41 pack together by facing each other. The comparison of NTD and CTD with 42 that of the other four genera suggests the evolutionary process of the SADS-43 CoV S. Moreover, SADS-CoV S has several characteristic structural features, 44 such as more compact architecture of S trimer, and masking of epitopes by 45 glycan shielding, which may facilitate viral immune evasion. These data 46 provide new insights into the evolutionary relationships of SADS-CoV S and 47 would extend our understanding of structural and functional diversity, which 48 .

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Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Cited by 64 publications

References 22 publications

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China

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

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