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Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022; 9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [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: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Lei Lu
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Fei-yang Pu
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - De-rong Zhang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Fu-qiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Fu-qiang Xie
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Liu F, Wang N, Lin J, Wang Q, Huang Y, Zhang Y, Shan H. Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles. Front Cell Infect Microbiol 2021; 11:746926. [PMID: 34604118 PMCID: PMC8481889 DOI: 10.3389/fcimb.2021.746926] [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: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 02/05/2023] Open
Abstract
Due to lacking a proofreading mechanism in their RNA-dependent RNA polymerases (RdRp), RNA viruses generally possess high mutation frequencies, making them evolve rapidly to form viral quasispecies during serial passages in cells, especially treated with mutagens, like ribavirin. Canine distemper virus (CDV) belongs to the genus Morbillivirus. Its L protein functions as an RdRp during viral replication. In this study, a recombinant enhanced green fluorescence protein-tagged CDV (rCDV-eGFP) was rescued from its cDNA clone, followed by viral identification and characterization at passage-7 (P7). This recombinant was independently subjected to extra 40 serial passages (P8 to 47) in ribavirin- and non-treated cells. Two viral progenies, undergoing passages in ribavirin- and non-treated VDS cells, were named rCDV-eGFP-R and -N, respectively. Both progenies were simultaneously subjected to next-generation sequencing (NGS) at P47 for comparing their quasispecies diversities with each other. The rCDV-eGFP-R and -N showed 62 and 23 single-nucleotide mutations (SNMs) in individual antigenomes, respectively, suggesting that the ribavirin conferred a mutagenic effect on the rCDV-eGFP-R. The spectrum of 62 SNMs contained 26 missense and 36 silent mutations, and that of 23 SNMs was composed of 17 missense and 6 silent mutations. Neither the rCDV-eGFP-R nor -N exhibited nonsense mutation in individual antigenomes. We speculate that the rCDV-eGFP-R may contain at least one P47 sub-progeny characterized by high-fidelity replication in cells. If such a sub-progeny can be purified from the mutant swarm, its L protein would elucidate a molecular mechanism of CDV high-fidelity replication.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jiahui Lin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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3
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Liu F, Zou Y, Li L, Liu C, Wu X. Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells. Front Vet Sci 2021; 8:690204. [PMID: 34368277 PMCID: PMC8333274 DOI: 10.3389/fvets.2021.690204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
Small ruminant morbillivirus (SRMV), formerly known as peste-des-petits-ruminants virus, classified into the genus Morbillivirus in the family Paramyxoviridae. Its L protein functions as the RNA-dependent RNA polymerases (RdRp) during viral replication. Due to the absence of efficient proofreading activity in their RdRps, various RNA viruses reveal high mutation frequencies, making them evolve rapidly during serial passages in cells, especially treated with a certain mutagen, like ribavirin. We have previously rescued a recombinant enhanced green fluorescence protein-tagged SRMV (rSRMV-eGFP) using reverse genetics. In this study, the rSRMV-eGFP was subjected to serial passages in ribavirin-treated cells. Due to the ribavirin-exerted selective pressure, it was speculated that viral progenies would form quasispecies after dozens of passages. Viral progenies at passage-10, -20, -30, -40, and -50 were separately subjected to next-generation sequencing (NGS), consequently revealing a total of 34 single-nucleotide variations, including five synonymous, 21 missense, and one non-sense mutations. The L sequence was found to harbor eight missense mutations during serial passaging. It was speculated that at least one high-fidelity variant was present in viral quasispecies at passage-50. If purified from the population of viral progenies, this putative variant would contribute to clarifying a molecular mechanism in viral high-fidelity replication in vitro.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yanli Zou
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
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Rescue of Senecavirus A to uncover mutation profiles of its progenies during 80 serial passages in vitro. Vet Microbiol 2020; 253:108969. [PMID: 33450657 DOI: 10.1016/j.vetmic.2020.108969] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. In this study, a China SVA isolate (CH-LX-01-2016) was rescued from its cDNA clone, and then identified by RT-PCR, indirect immunofluorescence assay and mass spectrometry. The rescued SVA could separately induce typical plaque formations and cytopathic effects in cell monolayers. In order to uncover its evolutionary dynamics, the SVA was subjected to eighty serial passages in vitro. Its progenies per ten passages were analyzed by next-generation sequencing (NGS). The NGS analyses showed that neither sequence-deleting nor -inserting phenotype was detectable in eight progenies, within which a total of forty-one intra-host single-nucleotide variations (SNVs) arose with passaging. Almost all SNVs were identified as the single-nucleotide polymorphism with mixture of two nucleotides. SNVs led to eighteen nonsynonymous mutations, out of which sixteen could directly reflect their own frequencies of amino acid mutation, due to only one SNV occurring in their individual codons. Compared with its parental virus without passaging, the passage-80 SVA progeny had formed a viral quasispecies, as evidenced by a total of twenty-eight SNVs identified in it.
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Yan F, Li E, Li L, Schiffman Z, Huang P, Zhang S, Li G, Jin H, Wang H, Zhang X, Gao Y, Feng N, Zhao Y, Wang C, Xia X. Virus-Like Particles Derived From a Virulent Strain of Pest des Petits Ruminants Virus Elicit a More Vigorous Immune Response in Mice and Small Ruminants Than Those From a Vaccine Strain. Front Microbiol 2020; 11:609. [PMID: 32390966 PMCID: PMC7190788 DOI: 10.3389/fmicb.2020.00609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/19/2020] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants (PPRs) is highly contagious, acute or subacute disease of small ruminants caused by peste des petits ruminants virus (PPRV). To date, several studies have designed and evaluated PPRV-like particles (VLPs) as a vaccine candidate for the prevention and control of PPR, with the majority of these VLPs constructed using sequences derived from a PPRV vaccine strain due to its high immunogenicity. However, because of the lack of available genetic material and certain structural proteins and/or the alteration of posttranslational glycosylation modifications, the immunogenicity of VLPs derived from a vaccine strain is not always optimal. In this study, two PPRV VLP candidates, derived from either the lineage IV Tibet/30 virulent strain or the lineage II Nigeria 75/1 vaccine strain, were generated using a baculovirus system through the coexpression of the PPRV matrix (M), hemagglutinin (H), and fusion (F) proteins in the high expression level cell line High Five. These VLPs were then used to immunize mice, goats, and sheep followed by two boosts after primary immunization. Both VLPs were found to induce a potent humoral immune response as demonstrated by the high ratio of immunoglobulin G1 (IgG1) to IgG2a. In all animals, both VLPs induced high titers of virus-neutralizing antibodies (VNAs), as well as H- and F-specific antibodies, with the Tibet/30 VLPs yielding higher antibody titers by comparison to the Nigeria 75/1 VLPs. Studies in mice also demonstrated that the Tibet/30 VLPs induced a more robust interleukin 4 and interferon γ response than the Nigeria 75/1 VLPs. Goats and sheep immunized with both VLPs exhibited a robust humoral and cell-mediated immune response. Furthermore, our results demonstrated that the VLPs derived from the virulent lineage IV Tibet/30 strain were more immunogenic, inducing a more potent and robust humoral and cell-mediated immune response in vaccinated animals by comparison to the lineage II Nigeria 75/1 vaccine strain VLPs. In addition, VNA titers were significantly higher among animals vaccinated with the Tibet/30 VLPs by comparison to the Nigeria 75/1 VLPs. Taken together, these findings suggest that VLPs derived from the virulent lineage IV Tibet/30 strain are more immunogenic by comparison to those derived from the lineage II Nigeria 75/1 vaccine strain and thus represent a promising vaccine candidate for the control and eradication of PPR.
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Affiliation(s)
- Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ling Li
- National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Zachary Schiffman
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Special Pathogens Program, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Pei Huang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Shengnan Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Guohua Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hualei Wang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xinghai Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chengyu Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
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Clarke BD, Islam MR, Yusuf MA, Mahapatra M, Parida S. Molecular detection, isolation and characterization of Peste-des-petits ruminants virus from goat milk from outbreaks in Bangladesh and its implication for eradication strategy. Transbound Emerg Dis 2018; 65:1597-1604. [PMID: 29806118 PMCID: PMC6282541 DOI: 10.1111/tbed.12911] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/09/2018] [Accepted: 04/22/2018] [Indexed: 10/27/2022]
Abstract
Peste-des-petits ruminants (PPR) is a highly contagious transboundary viral disease of small ruminants, which is endemic in much of Africa, the Middle East and Asia. In South Asia, PPR is of significant concern to the Indian subcontinent including Bangladesh as more than 30% of the world's sheep and goats are farmed in this region, predominantly by small, poor and marginal farmers. PPR virus was detected and isolated from goat milk from field samples from PPR outbreaks (2012-2015) in Bangladesh and its full-length sequences obtained. Sequence analysis of the partial N gene of Bangladesh isolates showed 99.3%-100% identity whereas 98.2%-99.6% identity was observed when compared with neighbouring Indian viruses. Further analysis of the full-length genomes indicated that the Bangladesh isolates were 99.3%-99.99% identical among themselves and 98.3%-98.4% identical to neighbouring Indian viruses. These findings further support the transboundary transmission of PPR virus across the Indian and Bangladesh border. In additional, the establishment of a cross-border strategy between India and Bangladesh will be of paramount importance for the eradication of PPR in this region. Molecular detection and isolation of PPR virus from milk is of significant potential concern for spread of the disease to free areas as the major producers of goat milk globally are PPR endemic countries in particular India and Bangladesh, as well as Sudan. Milk is a noninvasive sample type and bulk goat milk sampling for the detection of PPRV would be of practical significance for regional surveillance of PPRV as progress is made towards the targeted 2030 eradication.
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Affiliation(s)
| | | | - Mohammad Abu Yusuf
- SAARC Regional Leading Diagnostic Laboratory for PPR, Bangladesh Livestock Research Institute, Savar, Bangladesh
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Liu F, Li J, Li L, Liu Y, Wu X, Wang Z. Peste des petits ruminants in China since its first outbreak in 2007: A 10-year review. Transbound Emerg Dis 2018; 65:638-648. [PMID: 29322642 DOI: 10.1111/tbed.12808] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 11/30/2022]
Abstract
Peste des petits ruminants (PPR) is a highly infectious disease of small ruminants and caused by small ruminant morbillivirus (SRMV), formerly called peste-des-petits-ruminants virus (PPRV). This disease is circulating in Africa (except most countries in southern Africa), the Arabian Peninsula, the Middle East, and Central, East and South-East Asia. Peste des petits ruminants is still regarded as an exotic disease in China, where its first outbreak was reported in the Ngari region of Tibet in 2007, but effectively controlled by slaughter, vaccination and animal movement restriction in PPR-infected areas. However, PPR re-emerged in Xinjiang of China in December 2013, rapidly spread into much of China in the first half of 2014, but since then was substantially inhibited countrywide. Phylogenetic analysis shows that SRMVs from China share the highest homology with others from its neighbouring countries, possibly indicating the transboundary transmission of SRMVs. In 2015, a national eradication program for PPR was issued and has been being implemented in China, expecting to achieve a PPR-eradicating aim countrywide by 2020. Here, we reviewed a 10-year history (2007-2017) of PPR in China, including two major outbreaks, its infection in wild species, development of diagnostics and vaccines, and implementation of the national eradication program.
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Affiliation(s)
- F Liu
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - J Li
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - L Li
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Y Liu
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - X Wu
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Z Wang
- OIE Reference Laboratory for Peste des Petits Ruminants, National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, Shandong, China
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Liu F, Wu X, Li L, Zou Y, Liu S, Wang Z. Evolutionary characteristics of morbilliviruses during serial passages in vitro: Gradual attenuation of virus virulence. Comp Immunol Microbiol Infect Dis 2016; 47:7-18. [DOI: 10.1016/j.cimid.2016.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 02/05/2023]
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