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Si HR, Wu K, Su J, Dong TY, Zhu Y, Li B, Chen Y, Li Y, Shi ZL, Zhou P. Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats. Virol Sin 2024; 39:565-573. [PMID: 38945213 PMCID: PMC11401474 DOI: 10.1016/j.virs.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024] Open
Abstract
Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.
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Affiliation(s)
- Hao-Rui Si
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ke Wu
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia Su
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Tian-Yi Dong
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yan Zhu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Bei Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Ying Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Yang Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Peng Zhou
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China; State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical School, Guangzhou 510005, China.
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Hassanin A, Tu VT, Pham PV, Ngon LQ, Chabane T, Moulin L, Wurtzer S. Bat Rhinacoviruses Related to Swine Acute Diarrhoea Syndrome Coronavirus Evolve under Strong Host and Geographic Constraints in China and Vietnam. Viruses 2024; 16:1114. [PMID: 39066276 PMCID: PMC11281452 DOI: 10.3390/v16071114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Swine acute diarrhoea syndrome coronavirus (SADS-CoV; Coronaviridae, Rhinacovirus) was detected in 2017 in Guangdong Province (China), where it caused high mortality rates in piglets. According to previous studies, SADS-CoV evolved from horseshoe bat reservoirs. Here, we report the first five Rhinacovirus genomes sequenced in horseshoe bats from Vietnam and their comparisons with data published in China. Our phylogenetic analyses provided evidence for four groups: rhinacoviruses from Rhinolphus pusillus bats, including one from Vietnam; bat rhinacoviruses from Hainan; bat rhinacoviruses from Yunnan showing a divergent synonymous nucleotide composition; and SADS-CoV and related bat viruses, including four rhinacoviruses from Vietnam sampled in Rhinolophus affinis and Rhinolophus thomasi. Our phylogeographic analyses showed that bat rhinacoviruses from Dien Bien (Vietnam) share more affinities with those from Yunnan (China) and that the ancestor of SADS-CoVs arose in Rhinolophus affinis circulating in Guangdong. We detected sequencing errors and artificial chimeric genomes in published data. The two SADS-CoV genomes previously identified as recombinant could also be problematic. The reliable data currently available, therefore, suggests that all SADS-CoV strains originate from a single bat source and that the virus has been spreading in pig farms in several provinces of China for at least seven years since the first outbreak in August 2016.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), SU, MNHN, CNRS, EPHE, UA, Sorbonne Université, 75005 Paris, France;
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam; (V.T.T.); (P.V.P.); (L.Q.N.)
| | - Phu Van Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam; (V.T.T.); (P.V.P.); (L.Q.N.)
| | - Lam Quang Ngon
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam; (V.T.T.); (P.V.P.); (L.Q.N.)
| | - Thanina Chabane
- Institut de Systématique, Évolution, Biodiversité (ISYEB), SU, MNHN, CNRS, EPHE, UA, Sorbonne Université, 75005 Paris, France;
| | - Laurent Moulin
- Eau de Paris, R&D Laboratory, Direction Recherche, Développement et Qualité de l’Eau, 94200 Ivry-sur-Seine, France; (L.M.); (S.W.)
| | - Sébastien Wurtzer
- Eau de Paris, R&D Laboratory, Direction Recherche, Développement et Qualité de l’Eau, 94200 Ivry-sur-Seine, France; (L.M.); (S.W.)
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3
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Yang YL, Wang B, Li W, Cai HL, Qian QY, Qin Y, Shi FS, Bosch BJ, Huang YW. Functional dissection of the spike glycoprotein S1 subunit and identification of cellular cofactors for regulation of swine acute diarrhea syndrome coronavirus entry. J Virol 2024; 98:e0013924. [PMID: 38501663 PMCID: PMC11019839 DOI: 10.1128/jvi.00139-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine enteric coronavirus, and the broad interspecies infection of SADS-CoV poses a potential threat to human health. This study provides experimental evidence to dissect the roles of distinct domains within the SADS-CoV spike S1 subunit in cellular entry. Specifically, we expressed the S1 and its subdomains, S1A and S1B. Cell binding and invasion inhibition assays revealed a preference for the S1B subdomain in binding to the receptors on the cell surface, and this unknown receptor is not utilized by the porcine epidemic diarrhea virus. Nanoparticle display demonstrated hemagglutination of erythrocytes from pigs, humans, and mice, linking the S1A subdomain to the binding of sialic acid (Sia) involved in virus attachment. We successfully rescued GFP-labeled SADS-CoV (rSADS-GFP) from a recombinant cDNA clone to track viral infection. Antisera raised against S1, S1A, or S1B contained highly potent neutralizing antibodies, with anti-S1B showing better efficiency in neutralizing rSADS-GFP infection compared to anti-S1A. Furthermore, depletion of heparan sulfate (HS) by heparinase treatment or pre-incubation of rSADS-GFP with HS or constituent monosaccharides could inhibit SADS-CoV entry. Finally, we demonstrated that active furin cleavage of S glycoprotein and the presence of type II transmembrane serine protease (TMPRSS2) are essential for SADS-CoV infection. These combined observations suggest that the wide cell tropism of SADS-CoV may be related to the distribution of Sia or HS on the cell surface, whereas the S1B contains the main protein receptor binding site. Specific host proteases also play important roles in facilitating SADS-CoV entry.IMPORTANCESwine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel pathogen infecting piglet, and its unique genetic evolution characteristics and broad species tropism suggest the potential for cross-species transmission. The virus enters cells through its spike (S) glycoprotein. In this study, we identify the receptor binding domain on the C-terminal part of the S1 subunit (S1B) of SADS-CoV, whereas the sugar-binding domain located at the S1 N-terminal part of S1 (S1A). Sialic acid, heparan sulfate, and specific host proteases play essential roles in viral attachment and entry. The dissection of SADS-CoV S1 subunit's functional domains and identification of cellular entry cofactors will help to explore the receptors used by SADS-CoV, which may contribute to exploring the mechanisms behind cross-species transmission and host tropism.
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Affiliation(s)
- Yong-Le Yang
- Xianghu Laboratory, Hangzhou, China
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Wentao Li
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Yu Qian
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu Qin
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Yao-Wei Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
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4
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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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5
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Guo M, Zhao K, Peng X, He X, Deng J, Wang B, Yang X, Zhang L. Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China. Virol Sin 2023; 38:868-876. [PMID: 37967719 PMCID: PMC10786669 DOI: 10.1016/j.virs.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023] Open
Abstract
Coronavirus (CoV) spillover originating from game animals, particularly pangolins, is currently a significant concern. Meanwhile, vigilance is urgently needed for coronaviruses carried by bats, which are known as natural reservoirs of many coronaviruses. In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats. Using RT-PCR, we identified 58 (8.0%) bat CoVs in nine bat species from six locations. Furthermore, using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province, whereas TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province. Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV. To the best of our knowledge, this is the first report of a bat HKU4r-CoV strain containing a furin protease cleavage site. These findings expand our understanding of coronavirus geographic and host distributions.
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Affiliation(s)
- Min Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Kai Zhao
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China
| | - Xingwen Peng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Jin Deng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China; Hubei Jiangxia Lab, Wuhan, 430071, China.
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
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6
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Li KSM, Lau SKP, Woo PCY. Bats-The Magnificent Virus Player: SARS, MERS, COVID-19 and Beyond. Viruses 2023; 15:2342. [PMID: 38140583 PMCID: PMC10747191 DOI: 10.3390/v15122342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Irrespective of whether COVID-19 originated from a natural or a genetically engineered virus, the ultimate source of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is bats [...].
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Affiliation(s)
- Kenneth S. M. Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
| | - Susanna K. P. Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
| | - Patrick C. Y. Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan
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7
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Chen Y, Liu X, Zheng JN, Yang LJ, Luo Y, Yao YL, Liu MQ, Xie TT, Lin HF, He YT, Zhou P, Hu B, Tian RJ, Shi ZL. N-linked glycoproteins and host proteases are involved in swine acute diarrhea syndrome coronavirus entry. J Virol 2023; 97:e0091623. [PMID: 37772826 PMCID: PMC10617469 DOI: 10.1128/jvi.00916-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Gaining insight into the cell-entry mechanisms of swine acute diarrhea syndrome coronavirus (SADS-CoV) is critical for investigating potential cross-species infections. Here, we demonstrated that pretreatment of host cells with tunicamycin decreased SADS-CoV attachment efficiency, indicating that N-linked glycosylation of host cells was involved in SADS-CoV entry. Common N-linked sugars Neu5Gc and Neu5Ac did not interact with the SADS-CoV S1 protein, suggesting that these molecules were not involved in SADS-CoV entry. Additionally, various host proteases participated in SADS-CoV entry into diverse cells with different efficiencies. Our findings suggested that SADS-CoV may exploit multiple pathways to enter cells, providing insights into intervention strategies targeting the cell entry of this virus.
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Affiliation(s)
- Ying Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiang-Nan Zheng
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Li-Jun Yang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Yun Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Lin Yao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ting-ting Xie
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Tong He
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Rui-Jun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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8
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Zhou L, Li C, Zhang R, Li Q, Sun Y, Feng Y, Lan T, Ma J. Identification of a receptor tyrosine kinase inhibitor CP-724714 inhibits SADS-CoV related swine diarrhea coronaviruses infection in vitro. Virol Sin 2023; 38:778-786. [PMID: 37406816 PMCID: PMC10590692 DOI: 10.1016/j.virs.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023] Open
Abstract
The outbreak of the COVID-19 epidemic in 2020 has caused unprecedented panic among all mankind, pointing the major importance of effective treatment. Since the emergence of the swine acute diarrhea syndrome coronavirus (SADS-CoV) at the end of 2017, multiple reports have indicated that the bat-related SADS-CoV possesses a potential threat for cross-species transmission. Vaccines and antiviral drugs development deserve more attention. In this study, we found that the HER2 phosphorylation inhibitor (CP-724714) inhibited SADS-CoV infection in a dose-dependent manner. Further validation demonstrated that CP-724714 affected at the post-entry stage of SADS-CoV infection cycle. Also, efficient SADS-CoV infection required the activation of HER2 and its cascade Ras-Raf-Mek-Erk signaling pathway. In addition, CP-724714 has a broad-spectrum anti-swine diarrhea coronaviruses activity, and can dose-dependently combat SADS-CoV, porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV) and transmissible gastroenteritis virus (TGEV) infection in vitro with a specificity index of greater than 21.98, 9.38, 95.23 and 31.62, respectively. These results highlight the potential utility of CP-724714 or antiviral drugs targeting with HER2 and its cascade Ras-Raf-Mek-Erk signaling pathway as host-targeted SADS-CoV and other related coronaviruses therapeutics.
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Affiliation(s)
- Ling Zhou
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Cheng Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ruiyu Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qianniu Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yuan Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yaoyu Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Tian Lan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Jingyun Ma
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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9
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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10
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Cohen LE, Fagre AC, Chen B, Carlson CJ, Becker DJ. Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis. Nat Microbiol 2023; 8:1176-1186. [PMID: 37231088 PMCID: PMC10234814 DOI: 10.1038/s41564-023-01375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.
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Affiliation(s)
- Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
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11
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Cai X, Lan T, Ping P, Oliver B, Li J. Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search. Viruses 2023; 15:v15051065. [PMID: 37243151 DOI: 10.3390/v15051065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.
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Affiliation(s)
- Xinhui Cai
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tian Lan
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Pengyao Ping
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Brian Oliver
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Data Science Institute and School of Computer Science, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China
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12
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Zarei A, Ramazani A, Rezaei A, Moradi S. Screening of honey bee pollen constituents against COVID-19: an emerging hot spot in targeting SARS-CoV-2-ACE-2 interaction. Nat Prod Res 2023; 37:974-980. [PMID: 35758279 DOI: 10.1080/14786419.2022.2092865] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The attachment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike to angiotensin-converting enzyme 2 (ACE-2) leads the cell fusion process, so spike blockade may be a promising therapy combating COVID-19. Bee pollen bioflavonoids with intrinsic bioactivities are of outmost importance to block SARS-CoV-2-ACE-2 interaction. Herein, we conducted a molecular docking assessment through natural phenolics/non-phenolics of pollen to investigate their affinity against SARS-CoV-2 spike. Finally, kaempferol 3-neohesperidoside 7-O-rhamnoside (compound a), quercetin 7-rhamnoside (compound b), delphinidin-3-O-(6-p-coumaroyl) glucoside (compound c), and luteolin-7-O-6″-malonylglucoside (compound d) showed the lowest binding affinity of -8.1, -7.7, -7.3 and -6.7 kcal/mol. The docking procedure was validated using protein-protein interactions between ACE-2 and SARS-CoV-2 RBD via HADDOCK webserver. MD simulations were fulfilled to investigate different ligands' effects on protein movements. Collectively, compound a may possess the potency to disturb the binding of SARS-CoV-2 spike-ACE-2, which can be on the call for further in vitro and in vivo study to investigate its antiviral potential against SARS-CoV-2.
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Affiliation(s)
- Armin Zarei
- Department of Chemistry, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Ali Ramazani
- Department of Chemistry, Faculty of Science, University of Zanjan, Zanjan, Iran.,Department of Biotechnology, Research Institute of Modern Biological Techniques (RIMBT), University of Zanjan, Zanjan, Iran
| | - Aram Rezaei
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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13
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Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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14
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Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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15
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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Affiliation(s)
- Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 Haping Road, Harbin 150069, China.
| | - Jiumeng Sun
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Dongyan Li
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Ningning Wang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Lifang Wang
- College of Veterinary Medicine, China Agricultural University, No. 17 Qinghua Donglu, Beijing 100083, China
| | - Chang Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Xiaorong Meng
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St., Charles Avenue, New Orleans, LA 70118, USA
| | - Marc A Suchard
- Departments of Biomathematics, Human Genetics and Biostatistics, David Geffen School of Medicine and Fielding School of Public Health, University of California, Los Angeles, Geffen Hall 885 Tiverton Drive, Los Angeles, CA 90095, USA
| | - Xu Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, 400 East Main St., Frankfort, KY 40601, USA
| | - Shuo Su
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany.
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16
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Zmasek CM, Lefkowitz EJ, Niewiadomska A, Scheuermann RH. Genomic evolution of the Coronaviridae family. Virology 2022; 570:123-133. [PMID: 35398776 PMCID: PMC8965632 DOI: 10.1016/j.virol.2022.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 01/03/2023]
Abstract
The current outbreak of coronavirus disease-2019 (COVID-19) caused by SARS-CoV-2 poses unparalleled challenges to global public health. SARS-CoV-2 is a Betacoronavirus, one of four genera belonging to the Coronaviridae subfamily Orthocoronavirinae. Coronaviridae, in turn, are members of the order Nidovirales, a group of enveloped, positive-stranded RNA viruses. Here we present a systematic phylogenetic and evolutionary study based on protein domain architecture, encompassing the entire proteomes of all Orthocoronavirinae, as well as other Nidovirales. This analysis has revealed that the genomic evolution of Nidovirales is associated with extensive gains and losses of protein domains. In Orthocoronavirinae, the sections of the genomes that show the largest divergence in protein domains are found in the proteins encoded in the amino-terminal end of the polyprotein (PP1ab), the spike protein (S), and many of the accessory proteins. The diversity among the accessory proteins is particularly striking, as each subgenus possesses a set of accessory proteins that is almost entirely specific to that subgenus. The only notable exception to this is ORF3b, which is present and orthologous over all Alphacoronaviruses. In contrast, the membrane protein (M), envelope small membrane protein (E), nucleoprotein (N), as well as proteins encoded in the central and carboxy-terminal end of PP1ab (such as the 3C-like protease, RNA-dependent RNA polymerase, and Helicase) show stable domain architectures across all Orthocoronavirinae. This comprehensive analysis of the Coronaviridae domain architecture has important implication for efforts to develop broadly cross-protective coronavirus vaccines.
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Affiliation(s)
- Christian M Zmasek
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, UAB School of Medicine, Birmingham, AL, 35294, USA
| | - Anna Niewiadomska
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA; Department of Pathology, University of California, San Diego, CA, 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA; Global Virus Network, Baltimore MD, 21201, USA.
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17
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McKendry R, Lemm NM, Papargyris L, Chiu C. Human Challenge Studies with Coronaviruses Old and New. Curr Top Microbiol Immunol 2022. [PMID: 35181805 DOI: 10.1007/82_2021_247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coronavirus infections have been known to cause disease in animals since as early as the 1920s. However, only seven coronaviruses capable of causing human disease have been identified thus far. These Human Coronaviruses (HCoVs) include the causes of the common cold, but more recent coronaviruses that have emerged (i.e. SARS-CoV, MERS-CoV and SARS-CoV-2) are associated with much greater morbidity and mortality. HCoVs have been relatively under-studied compared to other common respiratory infections, as historically they have presented with mild symptoms. This has led to a relatively limited understanding of their animal reservoirs, transmission and determinants of immune protection. To address this, human infection challenge studies with HCoVs have been performed that enable a detailed clinical and immunological analysis of the host response at specific time points under controlled conditions with standardised viral inocula. Until recently, all such human challenge studies were conducted with common cold HCoVs, with the study of SARS-CoV and MERS-CoV unacceptable due to their greater pathogenicity. However, with the emergence of SARS-CoV-2 and the COVID-19 pandemic during which severe outcomes in young healthy adults have been rare, human challenge studies with SARS-CoV-2 are now being developed. Two SARS-CoV-2 human challenge studies in the UK studying individuals with and without pre-existing immunity are underway. As well as providing a platform for testing of antivirals and vaccines, such studies will be critical for understanding the factors associated with susceptibility to SARS-CoV-2 infection and thus developing improved strategies to tackle the current as well as future HCoV pandemics. Here, we summarise the major questions about protection and pathogenesis in HCoV infection that human infection challenge studies have attempted to answer historically, as well as the knowledge gaps that aim to be addressed with contemporary models.
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Affiliation(s)
- Richard McKendry
- Department of Infectious Disease, Imperial College London, London, UK
| | - Nana-Marie Lemm
- Department of Infectious Disease, Imperial College London, London, UK
| | - Loukas Papargyris
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK.
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18
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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19
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Yin C, Yau SST. Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events. J Theor Biol 2021; 530:110885. [PMID: 34478743 PMCID: PMC8406619 DOI: 10.1016/j.jtbi.2021.110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022]
Abstract
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of zoonotic infections of new coronaviruses. Of particular interest are genomic elements Inverse Repeats (IRs), which maintain genome stability, regulate gene expressions, and are the targets of mutations. However, little research attention is given to the IR content analysis in the SARS-CoV-2 genome. In this study, we propose a geometric analysis method and using the method to investigate the distributions of IRs in SARS-CoV-2 and its related coronavirus genomes. The method represents each genomic IR sequence pair as a single point and constructs the geometric shape of the genome using the IRs. Thus, the IR shape can be considered as the signature of the genome. The genomes of different coronaviruses are then compared using the constructed IR shapes. The results demonstrate that SARS-CoV-2 genome, specifically, has an abundance of IRs, and the IRs in coronavirus genomes show an increase during evolution events.
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Affiliation(s)
- Changchuan Yin
- Department of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL 60607-7045, USA.
| | - Stephen S-T Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China.
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20
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Stout AE, Millet JK, Stanhope MJ, Whittaker GR. Furin cleavage sites in the spike proteins of bat and rodent coronaviruses: Implications for virus evolution and zoonotic transfer from rodent species. One Health 2021; 13:100282. [PMID: 34179330 PMCID: PMC8216856 DOI: 10.1016/j.onehlt.2021.100282] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/02/2022] Open
Abstract
Bats and rodents comprise two of the world's largest orders of mammals and the order Chiroptera (bats) has been implicated as a major reservoir of coronaviruses in nature and a source of zoonotic transfer to humans. However, the order Rodentia (rodents) also harbors coronaviruses, with two human coronaviruses (HCoV-OC43 and HCoV-HKU1) considered to have rodent origins. The coronavirus spike protein mediates viral entry and is a major determinant of viral tropism; importantly, the spike protein is activated by host cell proteases at two distinct sites, designated as S1/S2 and S2'. SARS-CoV-2, which is considered to be of bat origin, contains a cleavage site for the protease furin at S1/S2, absent from the rest of the currently known betacoronavirus lineage 2b coronaviruses (Sarbecoviruses). This cleavage site is thought to be critical to its replication and pathogenesis, with a notable link to virus transmission. Here, we examine the spike protein across coronaviruses identified in both bat and rodent species and address the role of furin as an activating protease. Utilizing two publicly available furin prediction algorithms (ProP and PiTou) and based on spike sequences reported in GenBank, we show that the S1/S2 furin cleavage site is typically not present in bat virus spike proteins but is common in rodent-associated sequences, and suggest this may have implications for zoonotic transfer. We provide a phylogenetic history of the Embecoviruses (betacoronavirus lineage 2a), including context for the use of furin as an activating protease for the viral spike protein. From a One Health perspective, continued rodent surveillance should be an important consideration in uncovering novel circulating coronaviruses.
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Affiliation(s)
- Alison E. Stout
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jean K. Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352, Jouy-en-Josas, France
| | - Michael J. Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, USA
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21
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Khandker SS, Godman B, Jawad MI, Meghla BA, Tisha TA, Khondoker MU, Haq MA, Charan J, Talukder AA, Azmuda N, Sharmin S, Jamiruddin MR, Haque M, Adnan N. A Systematic Review on COVID-19 Vaccine Strategies, Their Effectiveness, and Issues. Vaccines (Basel) 2021; 9:1387. [PMID: 34960133 PMCID: PMC8708628 DOI: 10.3390/vaccines9121387] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
COVID-19 vaccines are indispensable, with the number of cases and mortality still rising, and currently no medicines are routinely available for reducing morbidity and mortality, apart from dexamethasone, although others are being trialed and launched. To date, only a limited number of vaccines have been given emergency use authorization by the US Food and Drug Administration and the European Medicines Agency. There is a need to systematically review the existing vaccine candidates and investigate their safety, efficacy, immunogenicity, unwanted events, and limitations. The review was undertaken by searching online databases, i.e., Google Scholar, PubMed, and ScienceDirect, with finally 59 studies selected. Our findings showed several types of vaccine candidates with different strategies against SARS-CoV-2, including inactivated, mRNA-based, recombinant, and nanoparticle-based vaccines, are being developed and launched. We have compared these vaccines in terms of their efficacy, side effects, and seroconversion based on data reported in the literature. We found mRNA vaccines appeared to have better efficacy, and inactivated ones had fewer side effects and similar seroconversion in all types of vaccines. Overall, global variant surveillance and systematic tweaking of vaccines, coupled with the evaluation and administering vaccines with the same or different technology in successive doses along with homologous and heterologous prime-booster strategy, have become essential to impede the pandemic. Their effectiveness appreciably outweighs any concerns with any adverse events.
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Affiliation(s)
- Shahad Saif Khandker
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
| | - Brian Godman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G1 1XQ, UK;
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Md. Irfan Jawad
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Bushra Ayat Meghla
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Taslima Akter Tisha
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Mohib Ullah Khondoker
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Community Medicine, Gonoshasthaya Samaj Vittik Medical College, Savar 1344, Bangladesh
| | - Md. Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
| | - Jaykaran Charan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur 342005, India;
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
| | - Shahana Sharmin
- Department of Pharmacy, BRAC University, Dhaka 1212, Bangladesh;
| | - Mohd. Raeed Jamiruddin
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Pharmacy, BRAC University, Dhaka 1212, Bangladesh;
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kem Perdana Sugai Besi, Kuala Lumpur 57000, Malaysia
| | - Nihad Adnan
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.U.K.); (M.A.H.); (M.R.J.)
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh; (M.I.J.); (B.A.M.); (T.A.T.); (A.A.T.); (N.A.)
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22
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Zhou Z, Qiu Y, Ge X. The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order. ANIMAL DISEASES 2021; 1:5. [PMID: 34778878 PMCID: PMC8062217 DOI: 10.1186/s44149-021-00005-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The frequent emergence of coronavirus (CoV) epidemics has seriously threatened public health and stock farming. The major hosts for CoVs are birds and mammals. Although most CoVs inhabit their specific natural hosts, some may occasionally cross the host barrier to infect livestock and even people, causing a variety of diseases. Since the beginning of the new century, increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics, including the recent COVID-19 pandemic. CoVs belong to the Coronaviridae family of the Nidovirales order. Recently, advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature. Here, we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range, genetic variation, genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses. This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses, including epidemic CoVs, which will benefit virological research and viral disease control.
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Affiliation(s)
- Zhijian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Xingyi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
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23
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Wong ACP, Lau SKP, Woo PCY. Interspecies Jumping of Bat Coronaviruses. Viruses 2021; 13:2188. [PMID: 34834994 PMCID: PMC8620431 DOI: 10.3390/v13112188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.
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Affiliation(s)
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
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24
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Ahmad I, Pawara R, Surana S, Patel H. The Repurposed ACE2 Inhibitors: SARS-CoV-2 Entry Blockers of Covid-19. Top Curr Chem (Cham) 2021; 379:40. [PMID: 34623536 PMCID: PMC8498772 DOI: 10.1007/s41061-021-00353-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/14/2021] [Indexed: 12/17/2022]
Abstract
The highly infectious disease COVID-19 is induced by SARS-coronavirus 2 (SARS-CoV-2), which has spread rapidly around the globe and was announced as a pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 binds to the host cell's angiotensin converting enzyme 2 (ACE2) receptor through the viral surface spike glycoprotein (S-protein). ACE2 is expressed in the oral mucosa and can therefore constitute an essential route for entry of SARS-CoV-2 into hosts through the tongue and lung epithelial cells. At present, no effective treatments for SARS-CoV-2 are yet in place. Blocking entry of the virus by inhibiting ACE2 is more advantageous than inhibiting the subsequent stages of the SARS-CoV-2 life cycle. Based on current published evidence, we have summarized the different in silico based studies and repurposing of anti-viral drugs to target ACE2, SARS-CoV-2 S-Protein: ACE2 and SARS-CoV-2 S-RBD: ACE2. This review will be useful to researchers looking to effectively recognize and deal with SARS-CoV-2, and in the development of repurposed ACE2 inhibitors against COVID-19.
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Affiliation(s)
- Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Rahul Pawara
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Sanjay Surana
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, 425405, India.
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25
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Drzewnioková P, Festa F, Panzarin V, Lelli D, Moreno A, Zecchin B, De Benedictis P, Leopardi S. Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison. Viruses 2021; 13:1975. [PMID: 34696405 PMCID: PMC8538982 DOI: 10.3390/v13101975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/28/2022] Open
Abstract
Coronaviruses (CoVs) are widespread and highly diversified in wildlife and domestic mammals and can emerge as zoonotic or epizootic pathogens and consequently host shift from these reservoirs, highlighting the importance of veterinary surveillance. All genera can be found in mammals, with α and β showing the highest frequency and diversification. The aims of this study were to review the literature for features of CoV surveillance in animals, to test widely used molecular protocols, and to identify the most effective one in terms of spectrum and sensitivity. We combined a literature review with analyses in silico and in vitro using viral strains and archive field samples. We found that most protocols defined as pan-coronavirus are strongly biased towards α- and β-CoVs and show medium-low sensitivity. The best results were observed using our new protocol, showing LoD 100 PFU/mL for SARS-CoV-2, 50 TCID50/mL for CaCoV, 0.39 TCID50/mL for BoCoV, and 9 ± 1 log2 ×10-5 HA for IBV. The protocol successfully confirmed the positivity for a broad range of CoVs in 30/30 field samples. Our study points out that pan-CoV surveillance in mammals could be strongly improved in sensitivity and spectrum and propose the application of a new RT-PCR assay, which is able to detect CoVs from all four genera, with an optimal sensitivity for α-, β-, and γ-.
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Affiliation(s)
- Petra Drzewnioková
- Laboratory of Emerging Viral Zoonoses, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (F.F.); (B.Z.); (P.D.B.)
| | - Francesca Festa
- Laboratory of Emerging Viral Zoonoses, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (F.F.); (B.Z.); (P.D.B.)
| | - Valentina Panzarin
- Innovative Virology Laboratory, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
| | - Davide Lelli
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (D.L.); (A.M.)
| | - Ana Moreno
- Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (D.L.); (A.M.)
| | - Barbara Zecchin
- Laboratory of Emerging Viral Zoonoses, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (F.F.); (B.Z.); (P.D.B.)
| | - Paola De Benedictis
- Laboratory of Emerging Viral Zoonoses, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (F.F.); (B.Z.); (P.D.B.)
| | - Stefania Leopardi
- Laboratory of Emerging Viral Zoonoses, Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (F.F.); (B.Z.); (P.D.B.)
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26
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Zhu Z, Meng K, Liu G, Meng G. A database resource and online analysis tools for coronaviruses on a historical and global scale. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5909701. [PMID: 33009914 PMCID: PMC7665380 DOI: 10.1093/database/baaa070] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/26/2020] [Accepted: 07/30/2020] [Indexed: 01/07/2023]
Abstract
The recent outbreak of COVID-19 caused by a new zoonotic origin coronavirus (SARS-CoV-2 or 2019-nCoV) has sound the alarm for the potential spread of epidemic coronavirus crossing species. With the urgent needs to assist disease control and to provide invaluable scientific information, we developed the coronavirus database (CoVdb), an online genomic, proteomic and evolutionary analysis platform. CoVdb has brought together genomes of more than 5000 coronavirus strains, which were collected from 1941 to 2020, in more than 60 countries and in hosts belonging to more than 30 species, ranging from fish to human. CoVdb presents comprehensive genomic information, such as gene function, subcellular localization, topology and protein structure. To facilitate coronavirus research, CoVdb also provides flexible search approaches and online tools to view and analyze protein structure, to perform multiple alignments, to automatically build phylogenetic trees and to carry on evolutionary analyses. CoVdb can be accessed freely at http://covdb.popgenetics.net. Hopefully, it will accelerate the progress to develop medicines or vaccines to control the pandemic of COVID-19.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Kaiwen Meng
- College of Veterinary Medicine, China Agricultural University, HaiDian District, Beijing, 100094, China
| | - Gexin Liu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, HaiDian District, Beijing, 100094, China
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27
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Guo YY, Wang PH, Pan YQ, Shi RZ, Li YQ, Guo F, Xing L. The Characteristics of Spike Glycoprotein Gene of Swine Acute Diarrhea Syndrome Coronavirus Strain CH/FJWT/2018 Isolated in China. Front Vet Sci 2021; 8:687079. [PMID: 34368275 PMCID: PMC8339410 DOI: 10.3389/fvets.2021.687079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
Swine acute diarrhea syndrome (SADS) is a highly contagious infectious disease characterized by acute vomiting and watery diarrhea in neonatal piglets. The causative agent for SADS is the swine acute diarrhea syndrome coronavirus (SADS-CoV), an alphacoronavirus in the family Coronaviridae. Currently, SADS-CoV was identified only in Guangdong and Fujian provinces of China, not in any other regions or countries in the world. To explore the genetic diversity of SADS-CoV isolates, herein we comparatively analyzed 44 full-length genomes of viruses isolated in Guangdong and Fujian provinces during 2017-2019. The spike glycoprotein gene of SADS-CoV strain CH/FJWT/2018 isolated in Fujian province is distinct from that of other viral isolates in either spike glycoprotein gene-based phylogenetic analysis or whole genome-based gene similarity analysis. Moreover, at least 7 predicted linear B cell epitopes in the spike glycoprotein of CH/FJWT/2018 would be affected by amino acid variations when compared with a representative virus isolated in Guangdong province. The spike glycoprotein of coronaviruses determines viral host range and tissue tropism during virus infection via specific interactions with the cellular receptor and also plays critical roles in eliciting the production of neutralizing antibodies. Since SADS-CoVs have a broad cell tropism, the results in this report further emphasize that the spike glycoprotein gene is a pivotal target in the surveillance of SADS-CoV.
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Affiliation(s)
- Yan-Yan Guo
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Pei-Hua Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Yuan-Qing Pan
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Rui-Zhu Shi
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Ya-Qian Li
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Fan Guo
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.,Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, China.,Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
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28
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429646. [PMID: 33564759 PMCID: PMC7872347 DOI: 10.1101/2021.02.03.429646] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
| | - Joe Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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29
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Millet JK, Jaimes JA, Whittaker GR. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol Rev 2021; 45:fuaa057. [PMID: 33118022 PMCID: PMC7665467 DOI: 10.1093/femsre/fuaa057] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
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Affiliation(s)
- Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
- Cornell Feline Health Center, Ithaca, NY 14853, USA
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30
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Hedman HD, Krawczyk E, Helmy YA, Zhang L, Varga C. Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface. Pathogens 2021; 10:180. [PMID: 33567598 PMCID: PMC7915269 DOI: 10.3390/pathogens10020180] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging infectious diseases present great risks to public health. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has become an urgent public health issue of global concern. It is speculated that the virus first emerged through a zoonotic spillover. Basic research studies have suggested that bats are likely the ancestral reservoir host. Nonetheless, the evolutionary history and host susceptibility of SARS-CoV-2 remains unclear as a multitude of animals has been proposed as potential intermediate or dead-end hosts. SARS-CoV-2 has been isolated from domestic animals, both companion and livestock, as well as in captive wildlife that were in close contact with human COVID-19 cases. Currently, domestic mink is the only known animal that is susceptible to a natural infection, develop severe illness, and can also transmit SARS-CoV-2 to other minks and humans. To improve foundational knowledge of SARS-CoV-2, we are conducting a synthesis review of its host diversity and transmission pathways. To mitigate this COVID-19 pandemic, we strongly advocate for a systems-oriented scientific approach that comprehensively evaluates the transmission of SARS-CoV-2 at the human and animal interface.
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Affiliation(s)
- Hayden D. Hedman
- Summit County Local Public Health Agency, Summit County, Frisco, CO 80443, USA;
| | - Eric Krawczyk
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Yosra A. Helmy
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA;
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
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31
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Perveen N, Muzaffar SB, Al-Deeb MA. Exploring human-animal host interactions and emergence of COVID-19: Evolutionary and ecological dynamics. Saudi J Biol Sci 2021; 28:1417-1425. [PMID: 33281479 PMCID: PMC7708805 DOI: 10.1016/j.sjbs.2020.11.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease (COVID-19) that emerged in December 2019 had caused substantial morbidity and mortality at the global level within few months. It affected economies, stopped travel, and isolated individuals and populations around the world. Wildlife, especially bats, serve as reservoirs of coronaviruses from which the variant Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged that causes COVID-19. In this review, we describe the current knowledge on COVID-19 and the significance of wildlife hosts in its emergence. Mammalian and avian coronaviruses have diverse host ranges with distinct lineages of coronaviruses. Recombination and reassortments occur more frequently in mixed-animal markets where diverse viral genotypes intermingle. Human coronaviruses have evolved through gene gains and losses primarily in interfaces where wildlife and humans come in frequent contact. There is a gap in our understanding of bats as reservoirs of coronaviruses and there is a misconception that bats periodically transmit coronaviruses to humans. Future research should investigate bat viral diversity and loads at interfaces between humans and bats. Furthermore, there is an urgent need to evaluate viral strains circulating in mixed animal markets, where the coronaviruses circulated before becoming adapted to humans. We propose and discuss a management intervention plan for COVID-19 and raise questions on the suitability of current containment plans. We anticipate that more virulent coronaviruses could emerge unless proper measures are taken to limit interactions between diverse wildlife and humans in wild animal markets.
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Affiliation(s)
- Nighat Perveen
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Sabir Bin Muzaffar
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Mohammad Ali Al-Deeb
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
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32
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Biodiversity loss and COVID-19 pandemic: The role of bats in the origin and the spreading of the disease. Biochem Biophys Res Commun 2021; 538:2-13. [PMID: 33092787 PMCID: PMC7566801 DOI: 10.1016/j.bbrc.2020.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
The loss of biodiversity in the ecosystems has created the general conditions that have favored and, in fact, made possible, the insurgence of the COVID-19 pandemic. A lot of factors have contributed to it: deforestation, changes in forest habitats, poorly regulated agricultural surfaces, mismanaged urban growth. They have altered the composition of wildlife communities, greatly increased the contacts of humans with wildlife, and altered niches that harbor pathogens, increasing their chances to come in contact with humans. Among the wildlife, bats have adapted easily to anthropized environments such as houses, barns, cultivated fields, orchards, where they found the suitable ecosystem to prosper. Bats are major hosts for αCoV and βCoV: evolution has shaped their peculiar physiology and their immune system in a way that makes them resistant to viral pathogens that would instead successfully attack other species, including humans. In time, the coronaviruses that bats host as reservoirs have undergone recombination and other modifications that have increased their ability for inter-species transmission: one modification of particular importance has been the development of the ability to use ACE2 as a receptor in host cells. This particular development in CoVs has been responsible for the serious outbreaks in the last two decades, and for the present COVID-19 pandemic.
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33
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Abstract
Among the animal superfamily Musteloidea, which includes those commonly known as mustelids, naturally occurring and species-specific alphacoronavirus infections have been observed in both mink (Mustela vison/Neovison vison) and domestic ferrets (Mustela putorius furo). Ferret systemic coronavirus (FRSCV), in particular, has been associated with a rare but fatal systemic disease. In recent months, it has become apparent that both minks and ferrets are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus and the cause of the coronavirus disease 2019 (COVID-19) pandemic. Several mink farms have experienced SARS-CoV-2 outbreaks, and experimental models have demonstrated susceptibility of ferrets to SARS-CoV-2. The potential for pet ferrets to become infected with SARS-CoV-2, however, remains elusive. During the 2002-2003 SARS epidemic, it was also apparent that ferrets were susceptible to SARS-CoV and could be utilized in vaccine development. From a comparative standpoint, understanding the relationships between different infections and disease pathogenesis in the animal superfamily Musteloidea may help elucidate viral infection and transmission mechanisms, as well as treatment and prevention strategies for coronaviruses.
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Affiliation(s)
- Alison E Stout
- Department of Microbiology & Immunology, Cornell University, Ithaca, New York, USA
| | - Qinghua Guo
- Master of Public Health Program, Cornell University, Ithaca, New York, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Ricardo de Matos
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R Whittaker
- Department of Microbiology & Immunology, Cornell University, Ithaca, New York, USA
- Master of Public Health Program, Cornell University, Ithaca, New York, USA
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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35
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Isolation of MERS-related coronavirus from lesser bamboo bats that uses DPP4 and infects human-DPP4-transgenic mice. Nat Commun 2021; 12:216. [PMID: 33431849 PMCID: PMC7801609 DOI: 10.1038/s41467-020-20458-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
While a number of human coronaviruses are believed to be originated from ancestral viruses in bats, it remains unclear if bat coronaviruses are ready to cause direct bat-to-human transmission. Here, we report the isolation of a MERS-related coronavirus, Tylonycteris-bat-CoV-HKU4, from lesser bamboo bats. Tylonycteris-bat-CoV-HKU4 replicates efficiently in human colorectal adenocarcinoma and hepatocarcinoma cells with cytopathic effects, and can utilize human-dipeptidyl-peptidase-4 and dromedary camel-dipeptidyl-peptidase-4 as the receptors for cell entry. Flow cytometry, co-immunoprecipitation and surface plasmon resonance assays show that Tylonycteris-bat-CoV-HKU4-receptor-binding-domain can bind human-dipeptidyl-peptidase-4, dromedary camel-dipeptidyl-peptidase-4, and Tylonycteris pachypus-dipeptidyl-peptidase-4. Tylonycteris-bat-CoV-HKU4 can infect human-dipeptidyl-peptidase-4-transgenic mice by intranasal inoculation with self-limiting disease. Positive virus and inflammatory changes were detected in lungs and brains of infected mice, associated with suppression of antiviral cytokines and activation of proinflammatory cytokines and chemokines. The results suggest that MERS-related bat coronaviruses may overcome species barrier by utilizing dipeptidyl-peptidase-4 and potentially emerge in humans by direct bat-to-human transmission. Several human coronaviruses (CoV) have been proposed to emerge from bats but evidence of direct bat-to-human transmission is slim. In this work, the authors isolate a MERS-related CoV strain directly from bats and show that it infects target cells in vitro and engineered mice through the human DDP4 receptor.
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Porcine enteric coronaviruses: an updated overview of the pathogenesis, prevalence, and diagnosis. Vet Res Commun 2021; 45:75-86. [PMID: 34251560 PMCID: PMC8273569 DOI: 10.1007/s11259-021-09808-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
The recent prevalence of coronavirus (CoV) poses a serious threat to animal and human health. Currently, porcine enteric coronaviruses (PECs), including the transmissible gastroenteritis virus (TGEV), the novel emerging swine acute diarrhoea syndrome coronavirus (SADS-CoV), porcine delta coronavirus (PDCoV), and re-emerging porcine epidemic diarrhoea virus (PEDV), which infect pigs of different ages, have caused more frequent occurrences of diarrhoea, vomiting, and dehydration with high morbidity and mortality in piglets. PECs have the potential for cross-species transmission and are causing huge economic losses in the pig industry in China and the world, which therefore needs to be urgently addressed. Accordingly, this article summarises the pathogenicity, prevalence, and diagnostic methods of PECs and provides an important reference for their improved diagnosis, prevention, and control.
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37
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Cuéllar-Cruz M. The histo-blood group antigens of the host cell may determine the binding of different viruses such as SARS-CoV-2. Future Microbiol 2021; 16:107-118. [PMID: 33459559 PMCID: PMC7842250 DOI: 10.2217/fmb-2020-0158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/05/2021] [Indexed: 12/18/2022] Open
Abstract
Viruses have caused the death of millions of people worldwide. Specifically, human viruses are grouped into 21 families, including the family of coronaviruses (CoVs). In December 2019, in Wuhan, China, a new human CoV was identified, SARS-CoV-2. The first step of the infection mechanism of the SARS-CoV-2 in the human host is adhesion, which occurs through the S glycoprotein that is found in diverse human organs. Another way through which SARS-CoV-2 could possibly attach to the host's cells is by means of the histo-blood group antigens. In this work, we have reviewed the mechanisms by which some viruses bind to the histo-blood group antigens, which could be related to the susceptibility of the individual and are dependent on the histo-blood group.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, C.P. 36050, Guanajuato, Guanajuato, México
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38
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Zhu Z, Meng K, Meng G. Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2. Sci Rep 2020; 10:21617. [PMID: 33303849 PMCID: PMC7728743 DOI: 10.1038/s41598-020-78703-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Road, Shapingba, Chongqing, 401331, China.
| | - Kaiwen Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
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39
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Bobay LM, O’Donnell AC, Ochman H. Recombination events are concentrated in the spike protein region of Betacoronaviruses. PLoS Genet 2020; 16:e1009272. [PMID: 33332358 PMCID: PMC7775116 DOI: 10.1371/journal.pgen.1009272] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/31/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022] Open
Abstract
The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
| | - Angela C. O’Donnell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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40
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Xu Z, Zhang Y, Cao Y. The Roles of Apoptosis in Swine Response to Viral Infection and Pathogenesis of Swine Enteropathogenic Coronaviruses. Front Vet Sci 2020; 7:572425. [PMID: 33324698 PMCID: PMC7725767 DOI: 10.3389/fvets.2020.572425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/28/2020] [Indexed: 01/18/2023] Open
Abstract
Apoptosis is a tightly regulated mechanism of cell death that plays important roles in various biological processes including biological evolution, multiple system development, anticancer, and viral infections. Swine enteropathogenic coronaviruses invade and damage villous epithelial cells of the small intestine causing severe diarrhea with high mortality rate in suckling piglets. Transmissible gastroenteritis virus (TGEV), Porcine epidemic diarrhea virus (PEDV), Porcine deltacoronavirus (PDCoV), and Swine acute diarrhea syndrome coronavirus (SADS-CoV) are on the top list of commonly-seen swine coronaviruses with a feature of diarrhea, resulting in significant economic losses to the swine industry worldwide. Apoptosis has been shown to be involved in the pathogenesis process of animal virus infectious diseases. Understanding the roles of apoptosis in host responses against swine enteropathogenic coronaviruses infection contribute to disease prevention and control. Here we summarize the recent findings that focus on the apoptosis during swine coronaviruses infection, in particular, TGEV, PEDV, PDCoV, and SADS-CoV.
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Affiliation(s)
- Zhichao Xu
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Yun Zhang
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
- Higher Education Mega Center, School of Life Science, Sun Yat-sen University, Guangzhou, China
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41
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Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins. J Virol 2020; 94:JVI.01301-20. [PMID: 32817223 DOI: 10.1128/jvi.01301-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/14/2020] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses (CoV) have caused a number of major epidemics in humans and animals, including the current pandemic of coronavirus disease 2019 (COVID-19), which has brought a renewed focus on the 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 that was reported to be capable of infecting cells from a broad range of species, suggesting a considerable potential for interspecies transmission. Given the importance of the coronavirus spike (S) glycoprotein in host range determination and viral entry, we report a cryo-electron microscopy (cryo-EM) structure of the SADS-CoV S trimer in the prefusion conformation at a 3.55-Å resolution. Our structure reveals that the SADS-CoV S trimer assumes an intrasubunit quaternary packing mode in which the S1 subunit N-terminal domain (S1-NTD) and the S1 subunit C-terminal domain (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 a relatively compact architecture of the S trimer and epitope masking by glycan shielding. Comparison of SADS-CoV S with the spike proteins of the other coronavirus genera suggested that the structural features of SADS-CoV S are evolutionarily related to those of the spike proteins of the other genera rather than to the spike protein of a typical alphacoronavirus. These data provide new insights into the evolutionary relationship between spike glycoproteins of SADS-CoV and those of other coronaviruses and extend our understanding of their structural and functional diversity.IMPORTANCE In this article, we report the atomic-resolution prefusion structure of the spike protein from swine acute diarrhea syndrome coronavirus (SADS-CoV). SADS-CoV is a pathogenic alphacoronavirus that was responsible for a large-scale outbreak of fatal disease in pigs and that was reported to be capable of interspecies transmission. We describe the overall structure of the SADS-CoV spike protein and conducted a detailed analysis of its main structural elements. Our results and analyses are consistent with those of previous phylogenetic studies and suggest that the SADS-CoV spike protein is evolutionarily related to the spike proteins of betacoronaviruses, with a strong similarity in S1-NTDs and a marked divergence in S1-CTDs. Moreover, we discuss the possible immune evasion strategies used by the SADS-CoV spike protein. Our study provides insights into the structure and immune evasion strategies of the SADS-CoV spike protein and broadens the understanding of the evolutionary relationships between coronavirus spike proteins of different genera.
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42
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020. [PMID: 32580969 DOI: 10.1128/cmr.00028-20/asset/32473ce7-130a–42a6-b589-0dd2f00518eb/assets/graphic/cmr.00028-20-f0007.jpeg] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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43
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020. [PMID: 32580969 DOI: 10.20944/preprints202003.0001.v1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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44
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Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. Coronavirus Disease 2019-COVID-19. Clin Microbiol Rev 2020; 33:e00028-20. [PMID: 32580969 PMCID: PMC7405836 DOI: 10.1128/cmr.00028-20] [Citation(s) in RCA: 549] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sharun Khan
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - D Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia
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Dhama K, Patel SK, Sharun K, Pathak M, Tiwari R, Yatoo MI, Malik YS, Sah R, Rabaan AA, Panwar PK, Singh KP, Michalak I, Chaicumpa W, Martinez-Pulgarin DF, Bonilla-Aldana DK, Rodriguez-Morales AJ. SARS-CoV-2 jumping the species barrier: Zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus. Travel Med Infect Dis 2020; 37:101830. [PMID: 32755673 PMCID: PMC7396141 DOI: 10.1016/j.tmaid.2020.101830] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome - Coronavirus-2) of the family Coronaviridae, appeared in China in December 2019. This disease was declared as posing Public Health International Emergency by World Health Organization on January 30, 2020, attained the status of a very high-risk category on February 29, and now having a pandemic status (March 11). COVID-19 has presently spread to more than 215 countries/territories while killing nearly 0.75 million humans out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost 20.5 million as of August 12, 2020, within a short period of just a few months. Researchers worldwide are pacing with high efforts to counter the spread of this virus and to design effective vaccines and therapeutics/drugs. Few of the studies have shown the potential of the animal-human interface and zoonotic links in the origin of SARS-CoV-2. Exploring the possible zoonosis and revealing the factors responsible for its initial transmission from animals to humans will pave ways to design and implement effective preventive and control strategies to counter the COVID-19. The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARS- and MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India.
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243 122, Uttar Pradesh, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd Iqbal Yatoo
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, 190025, Srinagar, Jammu and Kashmir, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243 122, Uttar Pradesh, India
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | | | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, 50-370, Poland
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Dayron F Martinez-Pulgarin
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - D Katterine Bonilla-Aldana
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia; Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de Las Américas, Sede Pereira, Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia; Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de Las Americas, Pereira, Risaralda, Colombia; School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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46
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Gupta A, Kumar S, Kumar R, Choudhary AK, Kumari K, Singh P, Kumar V. COVID-19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives. ChemistrySelect 2020; 5:7521-7533. [PMID: 32835089 PMCID: PMC7361534 DOI: 10.1002/slct.202001709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023]
Abstract
Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease-2019 (COVID-19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID-19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS-CoV-2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present-day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding.
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Affiliation(s)
- Akanksha Gupta
- Department of ChemistrySri Venkateswara CollegeUniversity of DelhiIndia.
| | - Sanjay Kumar
- Department of ChemistryDeshbandhu CollegeUniversity of DelhiIndia.
| | - Ravinder Kumar
- Department of Chemistry, Gurukula Kangri VishwavidyalayaHaridwarIndia.
| | | | - Kamlesh Kumari
- Department of ZoologyDeen Dayal Upadhyaya CollegeDelhiIndia.
| | - Prashant Singh
- Department of ChemistryAtma Ram Sanatan Dharma CollegeDelhi UniversityNew DelhiIndia.
| | - Vinod Kumar
- Department of ChemistryKirori Mal CollegeUniversity of DelhiIndia
- Special Centre for Nano SciencesJawaharlal Nehru UniversityDelhiIndia
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47
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Xu Z, Gong L, Peng P, Liu Y, Xue C, Cao Y. Porcine enteric alphacoronavirus Inhibits IFN-α, IFN-β, OAS, Mx1, and PKR mRNA Expression in Infected Peyer's Patches in vivo. Front Vet Sci 2020; 7:449. [PMID: 32719818 PMCID: PMC7347908 DOI: 10.3389/fvets.2020.00449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
Porcine enteric alphacoronavirus (PEAV) is a newly identified swine enteropathogenic coronavirus that causes watery diarrhea in neonatal piglets. The pathogenesis and host immune responses of PEAV infection are not fully characterized. The reason lies in the stomach environment, which would degrade cell-cultured live viruses via oral infection, making it difficult to establish an effective infection model to study the pathogenesis and host immune responses in pigs with a mature immune system. To solve this problem, in this study, coated PEAV-loaded microspheres were developed by centrifugal granulation-fluidized bed coating and demonstrated as an effective oral delivery system/animal infection model to protect PEAV virion against the complex gastrointestinal environment in vitro and to cause infection in weaned piglets in vivo. Weaned piglets orally inoculated with coated PEAV-loaded microspheres developed diarrhea and virus RNA was detected in rectal swabs from one to seven days post inoculation. In addition, microscopic lesions in the small intestine were observed, and viral antigens were also detected in the small intestines with PEAV immunohistochemical staining. Importantly, PEAV significantly inhibited mRNA expression of IFN-α, IFN-β, OAS, Mx1, and PKR, the genes involved in modulation of the host immune responses, in infected Peyer's patches, indicating that PEAV can overcome the antiviral response to cause damage when infection occurs. Collectively, our research successfully established a PEAV animal infection model in weaned piglets and suggested that the observed gene expression profile might help explain immunological changes associated with PEAV infection.
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Affiliation(s)
- Zhichao Xu
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Lang Gong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Peng Peng
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Yufang Liu
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
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48
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Yu J, Qiao S, Guo R, Wang X. Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution. Nat Commun 2020; 11:3070. [PMID: 32555182 PMCID: PMC7300015 DOI: 10.1038/s41467-020-16876-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/29/2020] [Indexed: 12/31/2022] Open
Abstract
Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, suggesting that SADS-CoV may have emerged from a natural reservoir in bats. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike (S) glycoprotein trimers at 2.38 Å and 2.83 Å resolution, respectively. We systematically compare the domains of HKU2 spike with those of α-, β-, γ-, and δ-coronavirus spikes, showing that the S1 subunit N- and C-terminal domains of HKU2/SADS-CoV are ancestral domains in the evolution of coronavirus spike proteins. The connecting region after the fusion peptide in the S2 subunit of HKU2/SADS-CoV adopts a unique conformation. These results structurally demonstrate a close evolutionary relationship between HKU2/SADS-CoV and β-coronavirus spikes and provide insights into the evolution and cross-species transmission of coronaviruses.
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Affiliation(s)
- Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuyuan Qiao
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Runyu Guo
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
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49
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Yang YL, Yu JQ, Huang YW. Swine enteric alphacoronavirus (swine acute diarrhea syndrome coronavirus): An update three years after its discovery. Virus Res 2020; 285:198024. [PMID: 32482591 PMCID: PMC7229464 DOI: 10.1016/j.virusres.2020.198024] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022]
Abstract
A summary of the research progress in SeACoV (SADS-CoV) from 2017 to 2020. Bat-derived SeACoV was most recently recognized prior to SARS-CoV-2 associated with COVID-19. Focusing on the etiology, epidemiology, evolutionary perspective, potential for interspecies transmission, pathogenesis and diagnosis.
Discovered in 2017, swine enteric alphacoronavirus (SeACoV), also known as swine acute diarrhea syndrome coronavirus (SADS-CoV) or porcine enteric alphacoronavirus (PEAV), is the fifth porcine CoV identified in diarrheal piglets. The presumed name “SADS-CoV” may not be appropriate since current studies have not provided strong evidence for high pathogenicity of the virus. SeACoV was the most recently recognized CoV of potential bat origin prior to the novel human severe acute respiratory syndrome CoV 2 (SARS-CoV-2), associated with the pandemic CoV disease 2019 (COVID-19). Although SeACoV is recognized as a regional epizootic virus currently, it possesses the most extensive cell species tropism in vitro among known CoVs. This review summarizes the emergence of SeACoV and updates the research progress made from 2017 to early 2020, mainly focusing on the etiology, epidemiology, evolutionary perspective, potential for interspecies transmission, pathogenesis and diagnosis.
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Affiliation(s)
- Yong-Le Yang
- Key Laboratory of Animal Virology of Ministry of Agriculture, Institute of Preventive Veterinary Medicine, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Qi Yu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Institute of Preventive Veterinary Medicine, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yao-Wei Huang
- Key Laboratory of Animal Virology of Ministry of Agriculture, Institute of Preventive Veterinary Medicine, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
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50
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Shneider A, Kudriavtsev A, Vakhrusheva A. Can melatonin reduce the severity of COVID-19 pandemic? Int Rev Immunol 2020; 39:153-162. [PMID: 32347747 DOI: 10.1080/08830185.2020.1756284] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The current COVID-19 pandemic is one of the most devastating events in recent history. The virus causes relatively minor damage to young, healthy populations, imposing life-threatening danger to the elderly and people with diseases of chronic inflammation. Therefore, if we could reduce the risk for vulnerable populations, it would make the COVID-19 pandemic more similar to other typical outbreaks. Children don't suffer from COVID-19 as much as their grandparents and have a much higher melatonin level. Bats are nocturnal animals possessing high levels of melatonin, which may contribute to their high anti-viral resistance. Viruses induce an explosion of inflammatory cytokines and reactive oxygen species, and melatonin is the best natural antioxidant that is lost with age. The programmed cell death coronaviruses cause, which can result in significant lung damage, is also inhibited by melatonin. Coronavirus causes inflammation in the lungs which requires inflammasome activity. Melatonin blocks these inflammasomes. General immunity is impaired by anxiety and sleep deprivation. Melatonin improves sleep habits, reduces anxiety and stimulates immunity. Fibrosis may be the most dangerous complication after COVID-19. Melatonin is known to prevent fibrosis. Mechanical ventilation may be necessary but yet imposes risks due to oxidative stress, which can be reduced by melatonin. Thus, by using the safe over-the-counter drug melatonin, we may be immediately able to prevent the development of severe disease symptoms in coronavirus patients, reduce the severity of their symptoms, and/or reduce the immuno-pathology of coronavirus infection on patients' health after the active phase of the infection is over.
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Affiliation(s)
- Alex Shneider
- CureLab Oncology, Inc, Dedham, Massachusetts, USA.,Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Aleksandr Kudriavtsev
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Phisics, RAS, Moscow, Russia
| | - Anna Vakhrusheva
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
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