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Genome-wide transcriptomic analysis of highly virulent African swine fever virus infection reveals complex and unique virus host interaction. Vet Microbiol 2021; 261:109211. [PMID: 34481273 DOI: 10.1016/j.vetmic.2021.109211] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/15/2021] [Indexed: 01/08/2023]
Abstract
African swine fever virus (ASFV), one of the most devastating emerging swine pathogens in China, causes nearly 100 % mortality in naive herds. Here, whole-transcriptome RNA-seq analysis was conducted in porcine alveolar macrophages (PAMs) infected with Pig/Heilongjiang/2018 (Pig/HLJ/18) ASFV at different time points. Our data suggested that ASFV genes expression demonstrated a time-depended pattern and ASFV early genes were involved in antagonizing host innate immunity. Moreover, viral small RNA (vsRNA) was generated as well. Meanwhile, transcriptome analysis of host genes suggested a strong inhibition host immunity-related genes by ASFV infection in PAMs, while enhanced chemokine-mediated signaling pathways and neutrophil chemotaxis were observed in ASFV infected PAMs. Furthermore, ASFV infection also down-regulated host microRNAs (miRNAs) that putatively targeted viral genes, while also triggering dysregulation of host metabolism that promoted virus replication at transcription level. Most importantly, infection of PAMs with ASFV induced a different transcriptome pattern from that of highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV), which is known to trigger a host cytokine storm. In conclusion, our transcriptome data implied that ASFV infection in PAMs appeared to be associated with strong inhibition of host immune responses, dysregulation of host chemokine axis and metabolic pathways.
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52
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Yang J, Tang K, Cao Z, Pfeiffer DU, Zhao K, Zhang Q, Zeng DD. Demand-driven spreading patterns of African swine fever in China. CHAOS (WOODBURY, N.Y.) 2021; 31:061102. [PMID: 34241307 DOI: 10.1063/5.0053601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs. ASF has led to major economic losses and adverse impacts on livelihoods of stakeholders involved in the pork food system in many European and Asian countries. While the epidemiology of ASF virus (ASFV) is fairly well understood, there is neither any effective treatment nor vaccine. In this paper, we propose a novel method to model the spread of ASFV in China by integrating the data of pork import/export, transportation networks, and pork distribution centers. We first empirically analyze the overall spatiotemporal patterns of ASFV spread and conduct extensive experiments to evaluate the efficacy of a number of geographic distance measures. These empirical analyses of ASFV spread within China indicate that the first occurrence of ASFV has not been purely dependent on the geographical distance from existing infected regions. Instead, the pork supply-demand patterns have played an important role. Predictions based on a new distance measure achieve better performance in predicting ASFV spread among Chinese provinces and thus have the potential to enable the design of more effective control interventions.
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Affiliation(s)
- Jiannan Yang
- School of Data Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kaichen Tang
- School of Data Science, City University of Hong Kong, Hong Kong 999077, China
| | - Zhidong Cao
- The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Dirk U Pfeiffer
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong 999077, China
| | - Kang Zhao
- Tippie College of Business, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Qingpeng Zhang
- School of Data Science, City University of Hong Kong, Hong Kong 999077, China
| | - Daniel Dajun Zeng
- The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
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53
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Liu K, Meng Y, Chai Y, Li L, Sun H, Gao GF, Tan S, Qi J. Crystal structure of the African swine fever virus core shell protein p15. BIOSAFETY AND HEALTH 2021. [DOI: 10.1016/j.bsheal.2020.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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54
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Li G, Fu D, Zhang G, Zhao D, Li M, Geng X, Sun D, Wang Y, Chen C, Jiao P, Cao L, Guo Y, Rao Z. Crystal structure of the African swine fever virus structural protein p35 reveals its role for core shell assembly. Protein Cell 2021; 11:600-605. [PMID: 32519301 PMCID: PMC7381542 DOI: 10.1007/s13238-020-00730-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Guobang Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Dan Fu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Guangshun Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Dongming Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Mingyu Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Xue Geng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Dongdong Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Yuhui Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, 300071, China
| | - Peng Jiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China.
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
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55
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Jia R, Zhang G, Liu H, Chen Y, Zhou J, Liu Y, Ding P, Wang Y, Zang W, Wang A. Novel Application of Nanofluidic Chip Digital PCR for Detection of African Swine Fever Virus. Front Vet Sci 2021; 7:621840. [PMID: 33614757 PMCID: PMC7894257 DOI: 10.3389/fvets.2020.621840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 01/06/2023] Open
Abstract
African swine fever virus (ASFV) gives rise to a grievous transboundary and infectious disease, African swine fever (ASF), which has caused a great economic loss in the swine industry. To prevent and control ASF, once suspicious symptoms have presented, the movement of animal and pork products should be stopped, and then, laboratory testing should be adopted to diagnose ASF. A method for ASFV DNA quantification is presented in this research, which utilizes the next-generation PCR platform, nanofluidic chip digital PCR (cdPCR). The cdPCR detection showed good linearity and repeatability. The limit of detection for cdPCR is 30.1995 copies per reaction, whereas no non-specific amplification curve was found with other swine viruses. In the detection of 69 clinical samples, the cdPCR showed significant consistency [91.30% (63/69)] to the Office International des Epizooties-approved quantitative PCR. Compared with the commercial quantitative PCR kit, the sensitivity of the cdPCR assay was 86.27% (44/50), and the specificity was 94.44% (17/18). The positive coincidence rate of the cdPCR assay was 88% (44/50). The total coincidence rate of the cdPCR and kit was 89.86% (62/69), and the kappa value reached 0.800 (P < 0.0001). This is the first time that cdPCR has been applied to detecting ASFV successfully.
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Affiliation(s)
- Rui Jia
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongliang Liu
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.,Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Jingming Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yankai Liu
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanwei Wang
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Weimin Zang
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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56
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Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens 2020; 9:pathogens9121078. [PMID: 33371523 PMCID: PMC7767518 DOI: 10.3390/pathogens9121078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/12/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.
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57
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Ravantti JJ, Martinez-Castillo A, Abrescia NG. Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses. Viruses 2020; 12:v12101146. [PMID: 33050291 PMCID: PMC7600307 DOI: 10.3390/v12101146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate “self”. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate “self”) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural “self” traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses
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Affiliation(s)
- Janne J. Ravantti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Ane Martinez-Castillo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain;
| | - Nicola G.A. Abrescia
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain;
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-946572502
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58
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Xian Y, Xiao C. Current capsid assembly models of icosahedral nucleocytoviricota viruses. Adv Virus Res 2020; 108:275-313. [PMID: 33837719 PMCID: PMC8328511 DOI: 10.1016/bs.aivir.2020.09.006] [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] [Indexed: 10/23/2022]
Abstract
Nucleocytoviricota viruses (NCVs) belong to a newly established phylum originally grouped as Nucleocytoplasmic large DNA viruses. NCVs are unique because of their large and complicated genomes that contain cellular genes with homologs from all kingdoms of life, raising intensive debates on their evolutional origins. Many NCVs pack their genomes inside massive icosahedral capsids assembled from thousands of proteins. Studying the assembly mechanism of such capsids has been challenging until breakthroughs from structural studies. Subsequently, several models of the capsid assembly were proposed, which provided some interesting insights on this elaborate process. In this review, we discuss three of the most recent assembly models as well as supporting experimental observations. Furthermore, we propose a new model that combines research developments from multiple sources. Investigation of the assembly process of these vast NCV capsids will facilitate future deciphering of the molecular mechanisms driving the formation of similar supramolecular complexes.
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Affiliation(s)
- Yuejiao Xian
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, United States.
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59
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Blome S, Franzke K, Beer M. African swine fever – A review of current knowledge. Virus Res 2020; 287:198099. [DOI: 10.1016/j.virusres.2020.198099] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
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60
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Tao D, Liu J, Nie X, Xu B, Tran-Thi TN, Niu L, Liu X, Ruan J, Lan X, Peng G, Sun L, Ma Y, Li X, Li C, Zhao S, Xie S. Application of CRISPR-Cas12a Enhanced Fluorescence Assay Coupled with Nucleic Acid Amplification for the Sensitive Detection of African Swine Fever Virus. ACS Synth Biol 2020; 9:2339-2350. [PMID: 32786346 DOI: 10.1021/acssynbio.0c00057] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
African swine fever (ASF) is one of the most severe diseases of pigs. In this study, a CRISPR-Cas12a (also known as Cpf1) system coupled with nucleic acid amplification was optimized for the detection of ASF virus (ASFV). Two novel single-stranded DNA-fluorophore-quencher (ssDNA-FQ) reporters were developed to increase the brightness of the fluorescent signal for the visualization of nucleic acid detection. The CRISPR-Cas12a system was used to simultaneously cleave the polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP) amplicons and the newly developed ssDNA-FQ reporter, resulting in fluorescence that could be easily detected in multiple platforms, especially on cheap and portable blue or UV light transilluminators. This specific cleavage with fluorescence reveals the presence of the amplicon and confirms its identity, thereby preventing false-positive test results from nonspecific amplicons. This method is also uninterfered by the presence of large amounts of irrelevant background DNA and displays no cross-reactivity with other porcine DNA or RNA viruses. When coupled with LAMP, the Cas12a platform can detect a plasmid containing p72 with as few as 2 copies/μL reaction. Our results indicate that the CRISPR-Cas12a enhanced fluorescence assay coupled with nucleic acid amplification is robust, convenient, specific, confirmatory, affordable, and potentially adaptable for ASF diagnosis.
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Affiliation(s)
- Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jiajia Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Xiongwei Nie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Thuy-Nhien Tran-Thi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Xiangdong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiaochen Lan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Guiqing Peng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Limeng Sun
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Congcong Li
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, P. R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
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61
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Goatley LC, Reis AL, Portugal R, Goldswain H, Shimmon GL, Hargreaves Z, Ho CS, Montoya M, Sánchez-Cordón PJ, Taylor G, Dixon LK, Netherton CL. A Pool of Eight Virally Vectored African Swine Fever Antigens Protect Pigs Against Fatal Disease. Vaccines (Basel) 2020; 8:E234. [PMID: 32443536 PMCID: PMC7349991 DOI: 10.3390/vaccines8020234] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
Classical approaches to African swine fever virus (ASFV) vaccine development have not been successful; inactivated virus does not provide protection and use of live attenuated viruses generated by passage in tissue culture had a poor safety profile. Current African swine fever (ASF) vaccine research focuses on the development of modified live viruses by targeted gene deletion or subunit vaccines. The latter approach would be differentiation of vaccinated from infected animals (DIVA)-compliant, but information on which viral proteins to include in a subunit vaccine is lacking. Our previous work used DNA-prime/vaccinia-virus boost to screen 40 ASFV genes for immunogenicity, however this immunization regime did not protect animals after challenge. Here we describe the induction of both antigen and ASFV-specific antibody and cellular immune responses by different viral-vectored pools of antigens selected based on their immunogenicity in pigs. Immunization with one of these pools, comprising eight viral-vectored ASFV genes, protected 100% of pigs from fatal disease after challenge with a normally lethal dose of virulent ASFV. This data provide the basis for the further development of a subunit vaccine against this devastating disease.
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Affiliation(s)
- Lynnette C. Goatley
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Ana Luisa Reis
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Raquel Portugal
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Hannah Goldswain
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Gareth L. Shimmon
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Zoe Hargreaves
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Chak-Sum Ho
- Gift of Hope Organ and Tissue Donor Network, Itasca, IL 60143, USA;
| | - María Montoya
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Pedro J. Sánchez-Cordón
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Geraldine Taylor
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Linda K. Dixon
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Christopher L. Netherton
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
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62
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Xian Y, Xiao C. The Structure of ASFV Advances the Fight against the Disease. Trends Biochem Sci 2020; 45:276-278. [PMID: 32169172 DOI: 10.1016/j.tibs.2020.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/25/2022]
Abstract
African swine fever virus (ASFV) is the causative pathogen of the recent African swine fever epidemic, with devastating impacts on economy. A recent study by Wang et al. reveals the multilayer structural details of ASFV at near-atomic resolution, which provides interesting insights about giant virus assembly and paves the way for vaccine development.
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Affiliation(s)
- Yuejiao Xian
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX 79968, USA.
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63
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Andrés G, Charro D, Matamoros T, Dillard RS, Abrescia NGA. The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes. J Biol Chem 2020; 295:1-12. [PMID: 31649031 PMCID: PMC6952596 DOI: 10.1074/jbc.ac119.011196] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/22/2019] [Indexed: 11/06/2022] Open
Abstract
African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. Despite intense research efforts, relevant gaps in the architecture of the infectious virus particle remain. Here, we used single-particle cryo-EM to analyze the three-dimensional structure of the mature ASFV particle. Our results show that the ASFV virion, with a radial diameter of ∼2,080 Å, encloses a genome-containing nucleoid surrounded by two distinct icosahedral protein capsids and two lipoprotein membranes. The outer capsid forms a hexagonal lattice (triangulation number T = 277) composed of 8,280 copies of the double jelly-roll major capsid protein (MCP) p72, arranged in trimers displaying a pseudo-hexameric morphology, and of 60 copies of a penton protein at the vertices. The inner protein layer, organized as a T = 19 capsid, confines the core shell, and it is composed of the mature products derived from the ASFV polyproteins pp220 and pp62. Also, an icosahedral membrane lies between the two protein layers, whereas a pleomorphic envelope wraps the outer capsid. This high-level organization confers to ASFV a unique architecture among the NCLDVs that likely reflects the complexity of its infection process and may help explain current challenges in controlling it.
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Affiliation(s)
- German Andrés
- Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Diego Charro
- Molecular Recognition and Host-Pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tania Matamoros
- Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Rebecca S Dillard
- NeCEN, Institute of Biology Leiden, Leiden University, 2333_CC Leiden, Netherlands
| | - Nicola G A Abrescia
- Molecular Recognition and Host-Pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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64
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Liang X, Li R, Shen X, Xiao K, Li X, Irwin DM, Shen Y. Two newly identified genotypes for African swine fever virus are incorrect. J Infect 2019; 80:469-496. [PMID: 31790708 DOI: 10.1016/j.jinf.2019.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 12/09/2022]
Affiliation(s)
- Xianghui Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Kangpeng Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaobing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto, M5S 1A8, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China.
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65
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Liu S, Luo Y, Wang Y, Li S, Zhao Z, Bi Y, Sun J, Peng R, Song H, Zhu D, Sun Y, Li S, Zhang L, Wang W, Sun Y, Qi J, Yan J, Shi Y, Zhang X, Wang P, Qiu HJ, Gao GF. Cryo-EM Structure of the African Swine Fever Virus. Cell Host Microbe 2019; 26:836-843.e3. [PMID: 31787524 DOI: 10.1016/j.chom.2019.11.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 11/18/2022]
Abstract
African swine fever virus (ASFV) is a large double-stranded DNA virus with an icosahedral multilayered structure. ASFV causes a lethal swine hemorrhagic disease and is currently responsible for widespread damage to the pork industry in Asia. Neither vaccines nor antivirals are available and the molecular characterization of the ASFV particle is outstanding. Here, we describe the cryogenic electron microscopy (cryo-EM) structure of the icosahedral capsid of ASFV at 4.6-Å. The ASFV particle consists of 8,280 copies of the major capsid protein p72, 60 copies of the penton protein, and at least 8,340 minor capsid proteins, of which there might be 3 different types. Like other nucleocytoplasmic large DNA viruses, the minor capsid proteins form a hexagonal network below the outer capsid shell, functioning as stabilizers by "gluing" neighboring capsomers together. Our findings provide a comprehensive molecular model of the ASFV capsid architecture that will contribute to the future development of countermeasures, including vaccines.
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Affiliation(s)
- Sheng Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuzi Luo
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yajuan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shihua Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Junqing Sun
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongjie Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Su Li
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Li Zhang
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wei Wang
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinghua Yan
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Peiyi Wang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China; SUSTech Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology and National High-Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - George F Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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