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Wang D, Yin Y, Zhang X, Ye J. An Interspecies Recombinant Sida Yellow Mosaic China Virus Isolate and Betasatellite Cause a Leaf Curl Disease in Tobacco in Hainan, China. PLANT DISEASE 2024; 108:877-886. [PMID: 37743589 DOI: 10.1094/pdis-07-23-1346-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Tobacco (Nicotiana tabacum) is an herbaceous crop. Cigar tobacco, a group of tobacco cultivars, has recently been planted in a few provinces in China. Since its introduction, symptoms such as leaf curling and vein thickening have appeared. Here we report a begomovirus, Sida yellow mosaic China virus-Hainan isolate (designated SiYMCNV-HN), associated with the betasatellite (designated SiYMCNB-HN) as the causal agent of a leaf curl disease in cigar tobacco (N. tabacum cv. Haiyan101) in Hainan Province, China. Phylogenetic and recombination analyses indicate that SiYMCNV-HN is an interspecies recombinant with a SiYMCNV isolate as the major parent and a Sida yellow vein Vietnam virus isolate as the minor parent. Full-length infectious clones of SiYMCNV-HN and SiYMCNB-HN were generated, which were highly infectious and induced high pathogenicity through agroinfiltration in Nicotiana benthamiana and N. tabacum. This newly reported recombinant begomovirus poses potential threats to tobacco plantations in the region.
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Affiliation(s)
- Duan Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuteng Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Li J, Song J, Zhou S, Li S, Liu J, Li T, Zhang Z, Zhang X, He X, Chen W, Zheng J, Zhao D, Bu Z, Huang L, Weng C. Development of a new effective African swine fever virus vaccine candidate by deletion of the H240R and MGF505-7R genes results in protective immunity against the Eurasia strain. J Virol 2023; 97:e0070423. [PMID: 37768081 PMCID: PMC10617561 DOI: 10.1128/jvi.00704-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/07/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE African swine fever (ASF) caused by ASF virus (ASFV) is a highly contagious and acute hemorrhagic viral disease in domestic pigs. Until now, no effective commercial vaccine and antiviral drugs are available for ASF control. Here, we generated a new live-attenuated vaccine candidate (ASFV-ΔH240R-Δ7R) by deleting H240R and MGF505-7R genes from the highly pathogenic ASFV HLJ/18 genome. Piglets immunized with ASFV-ΔH240R-Δ7R were safe without any ASF-related signs and produced specific antibodies against p30. Challenged with a virulent ASFV HLJ/18, the piglets immunized with high-dose group (105 HAD50) exhibited 100% protection without clinical symptoms, showing that low levels of virus replication with no observed pathogenicity by postmortem and histological analysis. Overall, our results provided a new strategy by designing live-attenuated vaccine candidate, resulting in protection against ASFV infection.
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Affiliation(s)
- Jiangnan Li
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Jie Song
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Shijun Zhou
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Shuai Li
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Jia Liu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Tingting Li
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Zhaoxia Zhang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Xianfeng Zhang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Xijun He
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Weiye Chen
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jun Zheng
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Dongming Zhao
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Zhigao Bu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Li Huang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
| | - Changjiang Weng
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, Heilongjiang, China
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Zhang Y, Wang Q, Zhu Z, Wang S, Tu S, Zhang Y, Zou Y, Liu Y, Liu C, Ren W, Zheng D, Zhao Y, Hu Y, Li L, Shi C, Ge S, Lin P, Xu F, Ma J, Wu X, Ma H, Wang Z, Bao J. Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/4820809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.
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Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
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Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
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A Naturally Occurring Microhomology-Mediated Deletion of Three Genes in African Swine Fever Virus Isolated from Two Sardinian Wild Boars. Viruses 2022; 14:v14112524. [PMID: 36423133 PMCID: PMC9693351 DOI: 10.3390/v14112524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is the etiological agent of a lethal disease of domestic pigs and wild boars. ASF threatens the pig industry worldwide due to the lack of a licensed vaccine or treatment. The disease has been endemic for more than 40 years in Sardinia (Italy), but an intense campaign pushed it close to eradication; virus circulation was last detected in wild boars in 2019. In this study, we present a genomic analysis of two ASFV strains isolated in Sardinia from two wild boars during the 2019 hunting season. Both isolates presented a deletion of 4342 base pairs near the 5' end of the genome, encompassing the genes MGF 360-6L, X69R, and MGF 300-1L. The phylogenetic evidence suggests that the deletion recently originated within the Sardinia ecosystem and that it is most likely the result of a non-allelic homologous recombination driven by a microhomology present in most Sardinian ASFV genomes. These results represent a striking example of a genomic feature promoting the rapid evolution of structural variations and plasticity in the ASFV genome. They also raise interesting questions about the functions of the deleted genes and the potential link between the evolutionary timing of the deletion appearance and the eradication campaign.
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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.
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Fiori MS, Sanna D, Scarpa F, Floris M, Di Nardo A, Ferretti L, Loi F, Cappai S, Sechi AM, Angioi PP, Zinellu S, Sirica R, Evangelista E, Casu M, Franzoni G, Oggiano A, Dei Giudici S. A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing. Viruses 2021; 13:1994. [PMID: 34696424 PMCID: PMC8539718 DOI: 10.3390/v13101994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 10/01/2021] [Indexed: 12/31/2022] Open
Abstract
African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economic losses. On the Italian island of Sardinia, the disease has been endemic since 1978, although the last control measures put in place achieved a significant reduction in ASF, and the virus has been absent from circulation since April 2019. Like many large DNA viruses, ASFV mutates at a relatively slow rate. However, the limited availability of whole-genome sequences from spatial-localized outbreaks makes it difficult to explore the small-scale genetic structure of these ASFV outbreaks. It is also unclear if the genetic variability within outbreaks can be captured in a handful of sequences, or if larger sequencing efforts can improve phylogenetic reconstruction and evolutionary or epidemiological inference. The aim of this study was to investigate the phylogenetic patterns of ASFV outbreaks between 1978 and 2018 in Sardinia, in order to characterize the epidemiological dynamics of the viral strains circulating in this Mediterranean island. To reach this goal, 58 new whole genomes of ASFV isolates were obtained, which represents the largest ASFV whole-genome sequencing effort to date. We provided a complete description of the genomic diversity of ASFV in terms of nucleotide mutations and small and large indels among the isolates collected during the outbreaks. The new sequences capture more than twice the genomic and phylogenetic diversity of all the previously published Sardinian sequences. The extra genomic diversity increases the resolution of the phylogenetic reconstruction, enabling us to dissect, for the first time, the genetic substructure of the outbreak. We found multiple ASFV subclusters within the phylogeny of the Sardinian epidemic, some of which coexisted in space and time.
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Affiliation(s)
- Mariangela Stefania Fiori
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (M.F.)
| | - Fabio Scarpa
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (F.S.); (M.C.)
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (M.F.)
| | | | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX1 4BH, UK;
| | - Federica Loi
- Osservatorio Epidemiologico Veterinario Regionale, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Stefano Cappai
- Osservatorio Epidemiologico Veterinario Regionale, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Anna Maria Sechi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Susanna Zinellu
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Roberto Sirica
- Ames Polydiagnostic Group Center SRL, 80013 Napoli, Italy; (R.S.); (E.E.)
| | - Eloisa Evangelista
- Ames Polydiagnostic Group Center SRL, 80013 Napoli, Italy; (R.S.); (E.E.)
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (F.S.); (M.C.)
| | - Giulia Franzoni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
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Bao YJ, Qiu J, Luo Y, Rodríguez F, Qiu HJ. The genetic variation landscape of African swine fever virus reveals frequent positive selection and adaptive flexibility. Transbound Emerg Dis 2021; 68:2703-2721. [PMID: 33751854 DOI: 10.1111/tbed.14018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022]
Abstract
African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the gap in knowledge concerning genetic variation of ASFV and the genetic factors involved in host adaptation and virus-host interactions. In this study, we performed a meta-genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to host adaptation. Our data reveal a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes, highlighting strong signals of adaptive evolution of ASFV. Further examination of the sequence properties reveals the link of the selection signatures with virus-host interactions and adaptive flexibility. Specifically, we discovered a site at 157th of the key antigen protein EP402R under diversifying selection, which is located in the cytotoxic T-cell epitope related to the low level of cross-reaction in T-cell response. Importantly, two multigene families MGF360 and MGF505, the host range factors of ASFV, exhibit divergent selection among the paralogous members, conferring sequence pools for genetic diversification and adaptive capability. By integrating the genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that the genes are involved in multiple processes of host immune interaction and virus life cycles, and may play crucial roles in circumventing host defence systems and enhancing adaptive fitness. Our findings will allow enhanced understanding of genetic basis of rapid spreading and adaptation of ASFV among the hosts.
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Affiliation(s)
- Yun-Juan Bao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Junhui Qiu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuzi Luo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Fernando Rodríguez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Universitat Autonòma de Barcelona, Bellaterra, 08193, Spain
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
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