1
|
Chen S, Wang T, Luo R, Lu Z, Lan J, Sun Y, Fu Q, Qiu HJ. Genetic Variations of African Swine Fever Virus: Major Challenges and Prospects. Viruses 2024; 16:913. [PMID: 38932205 PMCID: PMC11209373 DOI: 10.3390/v16060913] [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: 05/06/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
African swine fever (ASF) is a contagious viral disease affecting pigs and wild boars. It typically presents as a hemorrhagic fever but can also manifest in various forms, ranging from acute to asymptomatic. ASF has spread extensively globally, significantly impacting the swine industry. The complex and highly variable character of the ASFV genome makes vaccine development and disease surveillance extremely difficult. The overall trend in ASFV evolution is towards decreased virulence and increased transmissibility. Factors such as gene mutation, viral recombination, and the strain-specificity of virulence-associated genes facilitate viral variations. This review deeply discusses the influence of these factors on viral immune evasion, pathogenicity, and the ensuing complexities encountered in vaccine development, disease detection, and surveillance. The ultimate goal of this review is to thoroughly explore the genetic evolution patterns and variation mechanisms of ASFV, providing a theoretical foundation for advancement in vaccine and diagnostic technologies.
Collapse
Affiliation(s)
- Shengmei Chen
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Tao Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Rui Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhanhao Lu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jing Lan
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qiang Fu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Hua-Ji Qiu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
| |
Collapse
|
2
|
Xie S, Cui L, Liao Z, Zhu J, Ren S, Niu K, Li H, Jiang F, Wu J, Wang J, Wu J, Song B, Wu W, Peng C. Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism. NPJ Vaccines 2024; 9:65. [PMID: 38514651 PMCID: PMC10957905 DOI: 10.1038/s41541-024-00846-8] [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: 09/12/2023] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an 'open' pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.
Collapse
Affiliation(s)
- Shijie Xie
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Lianxin Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Zhiyi Liao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Junda Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Shuning Ren
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Kang Niu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Hua Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Fei Jiang
- China Animal Disease Control Center, Beijing, 102618, China
| | - Jiajun Wu
- China Animal Disease Control Center, Beijing, 102618, China
| | - Jie Wang
- Xinjiang Key Laboratory of Animal Infectious Diseases/Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, 830013, China
| | - Jian Wu
- Xinjiang Key Laboratory of Animal Infectious Diseases/Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, 830013, China
| | - Baifen Song
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Wenxue Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China.
| | - Chen Peng
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
3
|
Gómez-Sánchez I, Castelán-Sánchez HG, Martínez-Castilla LP, Hurtado-Ramírez JM, López-Leal G. Genetic insights into the microevolutionary dynamics and early introductions of human monkeypox virus in Mexico. Arch Virol 2023; 169:2. [PMID: 38070010 DOI: 10.1007/s00705-023-05936-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023]
Abstract
The recent global outbreak of mpox, caused by monkeypox virus (MPV) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. In this study, we analyzed 880 MPV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than single-nucleotide polymorphisms (SNPs), which do not contribute significantly to genome diversity. Although the genome contains multiple SNPs in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is amino acid position 63 of the protein encoded by the Cop-A4L gene, which is intricately related to viral maturity, which we found to be under strong positive selection. Ancestral state reconstruction indicated that the ancestral state at position 63 corresponds to the amino acid valine, which is present only in isolates of clade I. However, the isolates from the current outbreak contained threonine at position 63. Our findings contribute new information about the evolution of monkeypox virus.
Collapse
Affiliation(s)
- Israel Gómez-Sánchez
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Hugo G Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos EmergentesPrograma de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico.
| | - León P Martínez-Castilla
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos EmergentesPrograma de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
4
|
Kim G, Kim SJ, Kim WJ, Kim JH, Kim JC, Lee SG, Kim ES, Lee SH, Jheong WH. Emergence and Prevalence of an African Swine Fever Virus Variant in Wild Boar Populations in South Korea from 2019 to 2022. Viruses 2023; 15:1667. [PMID: 37632010 PMCID: PMC10459476 DOI: 10.3390/v15081667] [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: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
African swine fever (ASF), a viral disease caused by the African swine fever virus (ASFV), is associated with high mortality rates in domestic pigs and wild boars. ASF has been spreading since its discovery in wild boars in Korea in October 2019. Genomic analyses have provided insights into the genetic diversity of the ASFV isolated from various regions, enabling a better understanding of the virus origin and transmission patterns. We conducted a genome analysis to evaluate the diversity and mutations of ASFV spreading among wild boars in Korea during 2019-2022. We compared the genomes of ASFV strains isolated from Korean wild boars and publicly available ASFV genomes. Genomic analysis revealed several single-nucleotide polymorphisms within multigene families (MGFs) 360-1La and 360-4L in Korean ASFV. MGF 360-1La and 360-4L variations were not observed in other ASFV strains, including those of genotype II. Finally, we partially analyzed MGFs 360-1La and 360-4L in ASFV-positive samples between 2019 and 2022, confirming the geographical distribution of the variants. Our findings can help identify new genetic markers for epidemiological ASFV analysis and provide essential information for effective disease management.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Weon-Hwa Jheong
- Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention (NIWDC), 1 Songam-gil, Gwangsan-gu, Gwangju 62407, Republic of Korea; (G.K.); (S.-J.K.); (W.-J.K.); (J.-H.K.); (J.-C.K.); (S.-G.L.); (E.-S.K.); (S.-H.L.)
| |
Collapse
|
5
|
Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait. J Appl Genet 2023; 64:351-360. [PMID: 36892794 DOI: 10.1007/s13353-023-00752-0] [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: 09/07/2022] [Revised: 12/26/2022] [Accepted: 02/10/2023] [Indexed: 03/10/2023]
Abstract
Stenotrophomonas maltophilia is a species with immensely broad phenotypic and genotypic diversity that could widely distribute in natural and clinical environments. However, little attention has been paid to reveal their genome plasticity to diverse environments. In the present study, a comparative genomic analysis of S. maltophilia isolated from clinical and natural sources was systematically explored its genetic diversity of 42 sequenced genomes. The results showed that S. maltophilia owned an open pan-genome and had strong adaptability to different environments. A total of 1612 core genes were existed with an average of 39.43% of each genome, and the shared core genes might be necessary to maintain the basic characteristics of those S. maltophilia strains. Based on the results of the phylogenetic tree, the ANI value, and the distribution of accessory genes, genes associated with the fundamental process of those strains from the same habitat were found to be mostly conserved in evolution. Isolates from the same habitat had a high degree of similarity in COG category, and the most significant KEGG pathways were mainly involved in carbohydrate and amino acid metabolism, indicating that genes related to essential processes were mostly conserved in evolution for the clinical and environmental settings. Meanwhile, the number of resistance and efflux pump gene was significantly higher in the clinical setting than that of in the environmental setting. Collectively, this study highlights the evolutionary relationships of S. maltophilia isolated from clinical and environmental sources, shedding new light on its genomic diversity.
Collapse
|
6
|
Identification of African swine fever virus MGF505-2R as a potent inhibitor of innate immunity in vitro. Virol Sin 2023; 38:84-95. [PMID: 36442611 PMCID: PMC10006314 DOI: 10.1016/j.virs.2022.11.009] [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: 05/05/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022] Open
Abstract
African swine fever (ASF) is etiologically an acute, highly contagious and hemorrhagic disease caused by African swine fever virus (ASFV). Due to its genetic variation and phenotypic diversity, until now, no efficient commercial vaccines or therapeutic options are available. The ASFV genome contains a conserved middle region and two flexible ends that code for five multigene families (MGFs), while the biological functions of the MGFs are not fully characterized. Here, ASFV MGF505-2R-deficient mutant ASFV-Δ2R was constructed based on a highly virulent genotype II field isolate ASFV CN/GS/2018 currently circulating in China. Transcriptomic profiling demonstrated that ASFV-Δ2R was capable of inducing a larger number of differentially expressed genes (DEGs) compared with ASFV CN/GS/2018. Hierarchical clustering of up-regulated DEGs revealed that ASFV-Δ2R induced the most dramatic expression of interferon-related genes and inflammatory and innate immune genes, as further validated by RT-qPCR. The GO and KEGG pathway analysis identified significantly enriched pathways involved in pathogen recognition and innate antiviral immunity. Conversely, pharmacological activation of those antiviral immune responses by exogenous cytokines, including type I/II IFNs, TNF-α and IL-1β, exerted combinatory effects and synergized in antiviral capacity against ASFV replication. Collectively, MGF505-2R is a newly identified inhibitor of innate immunity potentially implicated in immune evasion.
Collapse
|
7
|
Sequential Deletions of Interferon Inhibitors MGF110-9L and MGF505-7R Result in Sterile Immunity against the Eurasia Strain of Africa Swine Fever. J Virol 2022; 96:e0119222. [PMID: 36197109 PMCID: PMC9599437 DOI: 10.1128/jvi.01192-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
African swine fever virus (ASFV) causes significant morbidity and mortality in pigs worldwide. The lack of vaccines or therapeutic options warrants urgent further investigation. To this aim, we developed a rationally designed live attenuated ASFV-Δ110-9L/505-7R mutant based on the highly pathogenic Genotype II ASFV CN/GS/2018 backbone by deleting 2 well-characterized interferon inhibitors MGF110-9L and MGF505-7R. The mutant was slightly attenuated in vitro compared to parental ASFV but highly tolerant to genetic modifications even after 30 successive passages in vitro. Groups of 5 pigs were intramuscularly inoculated with increasing doses of the mutant, ranging from 103 to 106 hemadsorption units (HAD50). Thirty-five days later, all groups were challenged with 102 HAD50 of virulent parental ASFV. All the animals were clinically normal and devoid of clinical signs consistent with ASFV at the period of inoculation. In the virulent challenge, 2 animals from 103 HAD50-inoculated group and 1 animal from 104 HAD50-inoculated group were unprotected with severe postmortem and histological lesions. The rest of animals survived and manifested with relatively normal clinical appearance accompanied by tangible histological improvements in the extent of tissue damage. Meanwhile, antibody response, as represented by p30-specific antibody titers was positively correlated to protective efficacy, potentializing its usage as an indicator of protection. Moreover, compared to 1 dose, 2 doses provided additional protection, proving that 2 doses were better than 1 dose. The sufficiency in effectiveness supports the claim that our attenuated mutant may be a viable vaccine option with which to fight ASF. IMPORTANCE African swine fever virus (ASFV) is a causative agent of acute viral hemorrhagic disease of domestic swine which is associated with significant economic losses in the pig industry. The lack of vaccines or treatment options requires urgent further investigation. ASFV MGF110-9L and MGF505-7R, 2 well-characterized interferon inhibitors, were associated with viral virulence, host range, and immune modulation. In this study, a recombinant two-gene deletion ASFV mutant with deletion of MGF110-9L and MGF505-7R was constructed. The result showed that the mutant was safe, and also highly resistant to genetic modification even after 30 successive passages. High doses of our mutant (105 and 106 HAD50) provided sterile immunity and complete protection in a virulent challenge. Two doses were superior to 1 dose and provided additional protection. This study develops a new ASFV-specific live attenuated vaccine and may be a viable vaccine option against ASF.
Collapse
|
8
|
Transcriptome profiling in swine macrophages infected with African swine fever virus at single-cell resolution. Proc Natl Acad Sci U S A 2022; 119:e2201288119. [PMID: 35507870 PMCID: PMC9171760 DOI: 10.1073/pnas.2201288119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
African swine fever virus (ASFV) causes a severe and highly contagious disease in pigs and wild boars, but no commercial vaccines or antivirals are available currently. Understanding the mutual antagonism between virus and host factors during ASFV infection may facilitate the development of new vaccines and antivirals. Our work profiled transcriptomes of swine macrophages infected with ASFV through single-cell RNA-sequencing technology. Identified dynamic transcriptome events of viral genes provide molecular characteristics of ASFV during infection. Moreover, virus–host interactions imply the regulation pathway of viral replication in host cells, which may guide research on antiviral strategies and dissection of ASFV pathogenesis. African swine fever virus (ASFV) is the causative agent of African swine fever, a highly contagious and usually fatal disease in pigs. The pathogenesis of ASFV infection has not been clearly elucidated. Here, we used single-cell RNA-sequencing technology to survey the transcriptomic landscape of ASFV-infected primary porcine alveolar macrophages. The temporal dynamic analysis of viral genes revealed increased expression of viral transmembrane genes. Molecular characteristics in the ASFV-exposed cells exhibited the activation of antiviral signaling pathways with increased expression levels of interferon-stimulated genes and inflammatory- and cytokine-related genes. By comparing infected cells with unexposed cells, we showed that the unfolded protein response (UPR) pathway was activated in low viral load cells, while the expression level of UPR-related genes in high viral load cells was less than that in unexposed cells. Cells infected with various viral loads showed signature transcriptomic changes at the median progression of infection. Within the infected cells, differential expression analysis and coregulated virus–host analysis both demonstrated that ASFV promoted metabolic pathways but inhibited interferon and UPR signaling, implying the regulation pathway of viral replication in host cells. Furthermore, our results revealed that the cell apoptosis pathway was activated upon ASFV infection. Mechanistically, the production of tumor necrosis factor alpha (TNF-α) induced by ASFV infection is necessary for cell apoptosis, highlighting the importance of TNF-α in ASFV pathogenesis. Collectively, the data provide insights into the comprehensive host responses and complex virus–host interactions during ASFV infection, which may instruct future research on antiviral strategies.
Collapse
|
9
|
Characterization and genomic analysis of a Demerecviridae phage SP76 with lytic multiple-serotypes of Salmonella. Arch Microbiol 2022; 204:175. [PMID: 35166928 DOI: 10.1007/s00203-022-02762-8] [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: 08/25/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/02/2022]
Abstract
With the increase in antimicrobial resistance of Salmonella, phages have been paid more attention to as an alternative to antibiotics. In this study, a phage designated as SP76 was isolated from sewage. It can lyse several serotypes of Salmonella, including S. typhimurium (21/33), S. enteritidis (7/7), S. dublin (4/4), S. pullorum (2/2) and S. choleraesuis (1/2). SP76 showed a latent time of about 10 min, and maintained good lytic activity at a pH range of 3-10 and temperatures between 4 and 37 °C. Moreover, its optimal multiplicity of infection (MOI) was 0.0001. Based on the results of genomic sequence and analysis, SP76 was found to have a genome of 111,639 bp that encoded 166 predicted ORFs and belong to the Demerecviridae family, order Caudovirales. No virulence or lysogen formation gene clusters were identified in the SP76 genome. A pan-genome analysis based on 100 phages within the subfamily Markadamsvirinae indicated that SP76 had 23 core genes and 1199 accessory genes. We grouped the subfamily Markadamsvirinae and found that the main difference was in group III. In vitro bacteriostasis, experiments showed that the phage SP76 reduced planktonic bacteria by 1.52 log10 CFU/mL, and biofilms (24 h old) by 0.372 log10 CFU/mL, respectively. Thus, we isolated a safe and efficient phage that might be a good antibacterial agent.
Collapse
|
10
|
Genetic Characterization and Variation of African Swine Fever Virus China/GD/2019 Strain in Domestic Pigs. Pathogens 2022; 11:pathogens11010097. [PMID: 35056045 PMCID: PMC8780551 DOI: 10.3390/pathogens11010097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
African swine fever (ASF) was first introduced into Northern China in 2018 and has spread through China since then. Here, we extracted the viral DNA from the blood samples from an ASF outbreak farm in Guangdong province, China and sequenced the whole genome. We assembled the full length genomic sequence of this strain, named China/GD/2019. The whole genome was 188,642 bp long (terminal inverted repeats and loops were not sequenced), encoding 175 open reading frames (ORF). The China/GD/2019 strain belonged to p72 genotype II and p54 genotype IIa. Phylogenetic analysis relationships based on single nucleotide polymorphisms (SNPs) also demonstrated that it grouped into genotype II. A certain number of ORFs mainly belonging to multigene families (MGFs) were absent in the China/GD/2019 strain in comparison to the China/ASFV/SY-18 strain. A deletion of approximately 1 kb was found in the China/GD/2019 genome which was located at the EP153R and EP402R genes in comparison to the China/2018/AnhuiXCGQ strain. We revealed a synonymous mutation site at gene F317L and a non-synonymous mutation site at gene MGF_360-6L in China/GD/2019 comparing to three known Chinese strains. Pair-wise comparison revealed 165 SNP sites in MGF_360-1L between Estonia 2014 and the China/GD/2019 strain. Comparing to China/GD/2019, we revealed a base deletion located at gene D1133L in China/Pig/HLJ/2018 and China/DB/LN/2018, which results in a frameshift mutation to alter the encoding protein. Our findings indicate that China/GD/2019 is a new variant with certain deletions and mutations. This study deepens our understanding of the genomic diversity and genetic variation of ASFV.
Collapse
|
11
|
Jiao D, Dong X, Yu Y, Wei C. Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity. Int J Biol Sci 2021; 17:3717-3727. [PMID: 34671195 PMCID: PMC8495401 DOI: 10.7150/ijbs.58220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/07/2021] [Indexed: 11/15/2022] Open
Abstract
SARS-CoV-2 belongs to the coronavirus family. Comparing genomic features of viral genomes of coronavirus family can improve our understanding about SARS-CoV-2. Here we present the first pan-genome analysis of 3,932 whole genomes of 101 species out of 4 genera from the coronavirus family. We found that a total of 181 genes in the pan-genome of coronavirus family, among which only 3 genes, the S gene, M gene and N gene, are highly conserved. We also constructed a pan-genome from 23,539 whole genomes of SARS-CoV-2. There are 13 genes in total in the SARS-CoV-2 pan-genome. All of the 13 genes are core genes for SARS-CoV-2. The pan-genome of coronaviruses shows a lower level of diversity than the pan-genomes of other RNA viruses, which contain no core gene. The three highly conserved genes in coronavirus family, which are also core genes in SARS-CoV-2 pan-genome, could be potential targets in developing nucleic acid diagnostic reagents with a decreased possibility of cross-reaction with other coronavirus species.
Collapse
Affiliation(s)
- Du Jiao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaorui Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yingyan Yu
- Department of General Surgery of Ruijin Hospital, Shanghai Institute of Digestive Surgery, and Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| |
Collapse
|
12
|
Zakharova OI, Titov IA, Gogin AE, Sevskikh TA, Korennoy FI, Kolbasov DV, Abrahamyan L, Blokhin AA. African Swine Fever in the Russian Far East (2019-2020): Spatio-Temporal Analysis and Implications for Wild Ungulates. Front Vet Sci 2021; 8:723081. [PMID: 34422950 PMCID: PMC8374597 DOI: 10.3389/fvets.2021.723081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF) is an emerging viral contagious disease affecting domestic pigs (DP) and wild boar (WB). ASF causes significant economic damage to the pig industry worldwide due to nearly 100% mortality and the absence of medical treatments. Since 2019, an intensive spread of ASF has been observed in the Russian Far East region. This spread raises concerns for epidemiologists and ecologists given the potential threat to the WB population, which is an essential member of the region's wild ungulates and provides a notable share of food resources for predatory species. This study aims to determine the genotype of ASF virus circulating in the region, reveal the spatio-temporal patterns of the ASF outbreaks' emergence, and assess the potential reduction of the regional fauna because of expected depopulation of WB. The first historical case of ASF in the study region was caused by an African swine fever virus (ASFV) isolated from DPs and belonging to Genotype 2, CVR1; IGR-2 (TRS +). Sequencing results showed no significant differences among ASFV strains currently circulating in the Russian Federation, Europe, and China. The spatiotemporal analysis with the space-time permutations model demonstrated the presence of six statistically significant clusters of ASF outbreaks with three clusters in DPs and one cluster in WBs. DP outbreaks prevail in the north-west regions of the study area, while northern regions demonstrate a mixture of DP and WB outbreaks. Colocation analysis did not reveal a statistically significant pattern of grouping of one category of outbreaks around the others. The possible damage to the region's fauna was assessed by modeling the total body mass of wild ungulates before and after the wild boars' depopulation, considering a threshold density of WB population of 0.025 head/km2, according to the currently in force National Plan on the ASF Eradication in Russia. The results suggest the total mass of ungulates of the entire study region will likely decrease by 8.4% (95% CI: 4.1-13.0%), while it may decrease by 33.6% (19.3-46.1%) in the Primorsky Krai, thereby posing an undeniable threat to the predatory species of the region.
Collapse
Affiliation(s)
- Olga I Zakharova
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ilya A Titov
- Federal Research Center for Virology and Microbiology, Pokrov, Russia
| | - Andrey E Gogin
- Federal Research Center for Virology and Microbiology, Pokrov, Russia
| | | | - Fedor I Korennoy
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, Nizhny Novgorod, Russia.,Federal Center for Animal Health (FGBI ARRIAH), Vladimir, Russia
| | - Denis V Kolbasov
- Federal Research Center for Virology and Microbiology, Pokrov, Russia
| | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center (CRIPA) and Groupe de Recherche sur les Maladies Infectieuses en Production Animale (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Andrey A Blokhin
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, Nizhny Novgorod, Russia
| |
Collapse
|
13
|
Wang T, Wang L, Han Y, Pan L, Yang J, Sun M, Zhou P, Sun Y, Bi Y, Qiu HJ. Adaptation of African swine fever virus to HEK293T cells. Transbound Emerg Dis 2021; 68:2853-2866. [PMID: 34314096 DOI: 10.1111/tbed.14242] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/19/2022]
Abstract
African swine fever (ASF), caused by African swine fever virus (ASFV), is a highly contagious disease with high morbidity and mortality in domestic pigs. Although adaptation of ASFV to Vero cells has been investigated, the phenotypic changes and the corresponding genomic variations during adaptation of ASFV to other cell lines remain unclear. To obtain a cell-adapted ASFV strain, different cell lines were tested to determine whether they support ASFV infection. Interestingly, the ASFV wild-type strain ASFV-HLJ/18 can infect HEK293T cells and replicate at a low level. After continuous passaging, the adapted ASFV strain can replicate efficiently in both HEK293T and Vero cells. However, the adapted ASFV strain displayed reduced infectivity in primary porcine alveolar macrophages compared to the corresponding wild-type strain. Furthermore, stepwise losses at the left variable end of the MGF genes and accumulative mutations were identified during passaging, indicating that the ASFV strain gradually adapted to HEK293T cells. Comparison of MGF deletions in other cell culture-adapted ASFV strains revealed that the deletions of MGF300 (1L, 2R and 4L) and MGF360 genes (8L, 9L, 10L and 11L) play an important role for the adaptation of ASFV to HEK293T cells at the early stage. The biological functions of the deletions and mutants associated with ASFV infection in HEK293T cells and pigs warrant further study. Overall, our findings provide new targets to elucidate the molecular mechanism of adaptation of ASFV to cell lines.
Collapse
Affiliation(s)
- Tao Wang
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China
| | - Yu Han
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Pan
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jing Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China
| | - Maowen Sun
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Pingping Zhou
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
14
|
Calcino AD, Kenny NJ, Gerdol M. Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200153. [PMID: 33813894 PMCID: PMC8059565 DOI: 10.1098/rstb.2020.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Collapse
Affiliation(s)
- Andrew D. Calcino
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Nathan J. Kenny
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| |
Collapse
|
15
|
Genome Sequence of a Virulent African Swine Fever Virus Isolated in 2020 from a Domestic Pig in Northern Vietnam. Microbiol Resour Announc 2021; 10:10/19/e00193-21. [PMID: 33986078 PMCID: PMC8142564 DOI: 10.1128/mra.00193-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study reports the genome sequence of an isolated African swine fever (ASF) virus (VNUA-ASFV-05L1/HaNam) obtained at the fourth passage on pulmonary alveolar macrophages. The virus was isolated during a typical acute ASF outbreak in pigs in a northern province of Vietnam in 2020.
Collapse
|
16
|
Aslanyan L, Avagyan H, Karalyan Z. Whole-genome-based phylogeny of African swine fever virus. Vet World 2020; 13:2118-2125. [PMID: 33281345 PMCID: PMC7704302 DOI: 10.14202/vetworld.2020.2118-2125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/21/2020] [Indexed: 01/18/2023] Open
Abstract
Aim A genome-scale phylogenetic analysis was used to infer the evolutionary dynamics of Asfarviridae - African swine fever virus (ASFV) - and better define its genetic diversity. Materials and Methods All complete ASFV genomes from NCBI's resource as of March 2020 were used. The phylogenetic analysis used maximum likelihood and neighbor-joining methods. The evolutionary models detection was done with the help of the package of programs MEGA-X. Algorithms were used to build phylogenetic trees for type B DNA polymerases of ASFV (n=34) and HcDNAV (n=2), as an external group. Results An expedient categorization of the Asfarviridae family uses five clades. Genotype 1 (except for LIV 5/40 virus isolate) as well genotype 7 are assigned to the alpha clade; genotype 2 to the beta clade; genotypes 8, 9, and 10 to the gamma clade; genotype 5 to the delta clade; and genotypes 3, 4, and 20, as well as genotype 22 and the LIV 5/40 isolate to the epsilon clade. Branch lengths on the phylogenetic tree are proportional to genetic distance along the branch. Branches at the phylogenetic tree of Asfarviridae are much shorter than branches for Baculoviridae. Shorter branches in ASFVs population suggest that Asfarviridae evolved relatively recently and remain more closely related. Conclusion We suggest applying more robust standards using whole genomes to ensure the correct classification of ASFV and maintain phylogeny as a useful tool.
Collapse
Affiliation(s)
- Levon Aslanyan
- Department of Mathematics, Institute for Informatics and Automation Problems of NAS RA, Yerevan, Armenia
| | - Hranush Avagyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia.,Experimental Laboratory, Yerevan State Medical University, Yerevan, Armenia
| | - Zaven Karalyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia.,Department of Medical Biology, Yerevan State Medical University, Yerevan, Armenia
| |
Collapse
|
17
|
Lu G, Pan J, Ou J, Shao R, Hu X, Wang C, Li S. African horse sickness: Its emergence in Thailand and potential threat to other Asian countries. Transbound Emerg Dis 2020; 67:1751-1753. [PMID: 32406171 DOI: 10.1111/tbed.13625] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Jialiang Pan
- General Station of Forest and Grassland Pest Management, National Forestry and Grassland Administration, Shenyang, China
| | - Jiajun Ou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Ran Shao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Xue Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Caiying Wang
- Guangdong Huangcun Sports Training Center, Guangzhou, China
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| |
Collapse
|