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Zeng W, Yan Q, Du P, Yuan Z, Sun Y, Liu X, Zhang L, Liu X, Ding H, Yi L, Fan S, Chen J, Zhao M. Evolutionary dynamics and adaptive analysis of Seneca Valley virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105488. [PMID: 37558190 DOI: 10.1016/j.meegid.2023.105488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Over the past 20 years, the Seneca Valley virus (SVV) has emerged in various countries and regions around the world. Infected pigs display symptoms similar to foot-and-mouth disease and other vesicular diseases, causing severe economic losses to affected countries. In recent years, the number of SVV infections has been increasing in Brazil, China, and the United States. In this study, we comprehensively analyzed SVV genomic sequence data from the perspectives of evolutionary dynamics, phylogeography, and codon usage bias. We aimed to gain further insights into SVV's genetic diversity, spatiotemporal distribution patterns, and evolutionary adaptations. Phylogenetic analysis revealed that SVV has evolved into eight distinct lineages. Based on the results of phylogeographic analysis, it is speculated that the United States might have been the source of SVV, from where it subsequently spread to different countries and regions. Moreover, our analysis of positive selection sites in SVV capsid proteins suggests their potential importance in the process of receptor recognition. Finally, codon preference analysis indicates that natural selection has been a primary evolutionary driver influencing SVV codon usage bias. In conclusion, our in-depth investigation into SVV's origin, dissemination, evolution, and adaptation emphasizes the significance of SVV surveillance and control measures.
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Affiliation(s)
- Weijun Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Quanhui Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Pengfei Du
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhongmao Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yawei Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaodi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Lihong Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xueyi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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Meng H, Wang X, Wang L, Wang Q, Zhu L, Sang Y, Liu F. Identification of cis-acting replication element in VP2-encoding region of Senecavirus A genome. Vet Microbiol 2023; 280:109717. [PMID: 36893554 DOI: 10.1016/j.vetmic.2023.109717] [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: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Picornavirus possesses one positive-sense, single-stranded RNA genome, in which a cis-acting replication element (cre) is located. The cre is a stem-loop structure that harbors a conserved AAACA motif within its loop region. This motif functions as a template for adding two U residues to the viral VPg, therefore generating a VPg-pUpU that is required for viral RNA synthesis. Senecavirus A (SVA) is an emerging picornavirus. Its cre has not been identified as yet. In the present study, one putative cre containing a typical AAACA motif was computationally predicted to exist within the VP2-encoding sequence of SVA. To test the role of this putative cre, 22 SVA cDNA clones with different point mutations in their cre-formed sequences were constructed in an attempt to rescue replication-competent SVAs. A total of 11 viruses were rescued from their individual cDNA clones, implying that some mutated cres exerted lethal impacts on SVA replication. To eliminate these impacts, an intact cre was artificially inserted into those SVA cDNA clones without ability of recovering virus. The artificial cre was proven to be able of compensating for some, but not all, defects caused by mutated cres, leading to successful recovery of SVAs. These results indicated that the putative cre of SVA was functionally similar to those of other picornaviruses, perhaps involved in the uridylylation of VPg.
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Affiliation(s)
- Hailan Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoli Wang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao 266109, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010011, China
| | - Lijie Zhu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuxuan Sang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
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Wu H, Li C, Ji Y, Mou C, Chen Z, Zhao J. The Evolution and Global Spatiotemporal Dynamics of Senecavirus A. Microbiol Spectr 2022; 10:e0209022. [PMID: 36314961 PMCID: PMC9769604 DOI: 10.1128/spectrum.02090-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/08/2022] [Indexed: 12/24/2022] Open
Abstract
Recurrent outbreaks of senecavirus A (SVA)-associated vesicular disease have led to a large number of infected pigs being culled and has caused considerable economic losses to the swine industry. Although SVA was discovered 2 decades ago, knowledge about the evolutionary and transmission histories of SVA remains unclear. Herein, we performed an integrated analysis of the recombination, phylogeny, selection, and spatiotemporal dynamics of SVA. Phylogenetic analysis demonstrated that SVA diverged into two main branches, clade I (pre-2007 strains) and clade II (post-2007 strains). Importantly, analysis of selective strength showed that clade II was evolving under relaxed selection compared with clade I. Positive selection analysis identified 27 positive selective sites, most of which are located on the outer surface of capsid protomer or on the important functional domains of nonstructure proteins. Bayesian phylodynamics suggested that the estimated time to the most recent common ancestor of SVA was around 1986, and the estimated substitution rate of SVA was 3.3522 × 10-3 nucleotide substitutions/site/year. Demographic history analysis revealed that the effective population size of SVA has experienced a gradually increasing trend with slight fluctuation until 2017 followed by a sharp decline. Notably, Bayesian phylogeographic analysis inferred that Brazil might be the source of SVA's global transmission since 2015. In summary, these data illustrated that the ongoing evolution of SVA drove the lineage-specific innovation and potentially phenotypically important variation. Our study sheds new light on the fundamental understanding of SVA evolution and spread history. IMPORTANCE Recurrent outbreaks and global epidemics of senecavirus A-associated vesicular disease have caused heavy economic losses and have threatened the development of the pig industry. However, the question of where the virus comes from has been one of the biggest puzzles due to the stealthy nature of the virus. Consequently, tracing the source, evolution, and transmission pattern of SVA is a very challenging task. Based on the most comprehensive analysis, we revealed the origin time, rapid evolution, epidemic dynamics, and selection of SVA. We observed two main genetic branches, clade I (pre-2007 strains) and clade II (post-2007 strains), and described the epidemiological patterns of SVA in different countries. We also first identified Brazil as the source of SVA's global transmission since 2015. Findings in this study provide important implications for the control and prevention of the virus.
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Affiliation(s)
- Huiguang Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chen Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yongchen Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Jingwen Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, China
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Hawko S, Burrai GP, Polinas M, Angioi PP, Dei Giudici S, Oggiano A, Alberti A, Hosri C, Antuofermo E. A Review on Pathological and Diagnostic Aspects of Emerging Viruses—Senecavirus A, Torque teno sus virus and Linda Virus—In Swine. Vet Sci 2022; 9:vetsci9090495. [PMID: 36136710 PMCID: PMC9502770 DOI: 10.3390/vetsci9090495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Worldwide demand for food is expected to increase due to population growth and swine accounts for more than one-third of meat produced worldwide. Several factors affect the success of livestock production systems, including animal disease control. Despite the importance of infectious diseases to animal health and the productivity of the global swine industry, pathogens of swine, in particular emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, have gained limited interest. We performed a systematic analysis of the literature, with a focus on the main macroscopical and histological findings related to those viruses to fill the gap and highpoint these potentially hazardous pathogens. Abstract Swine production represents a significant component in agricultural economies as it occupies over 30% of global meat demand. Infectious diseases could constrain the swine health and productivity of the global swine industry. In particular, emerging swine viral diseases are omnipresent in swine populations, but the limited knowledge of the pathogenesis and the scarce information related to associated lesions restrict the development of data-based control strategies aimed to reduce the potentially great impact on the swine industry. In this paper, we reviewed and summarized the main pathological findings related to emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, suggesting a call for further multidisciplinary studies aimed to fill this lack of knowledge and better clarify the potential role of those viral diseases in swine pathology.
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Affiliation(s)
- Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giovanni P. Burrai
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-229440
| | - Marta Polinas
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Alberto Alberti
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chadi Hosri
- Department of Veterinary Medicine, Faculty of Agronomy and Veterinary Sciences, Lebanese University, Beirut 14/6573, Lebanon
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