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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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Expansion in host dynamics of peste des petits ruminants: Potential attribute of outbreaks in disease-endemic settings. Acta Trop 2022; 234:106609. [PMID: 35850237 DOI: 10.1016/j.actatropica.2022.106609] [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: 03/21/2022] [Revised: 06/22/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022]
Abstract
Since the first case report in 1942, the peste-des-petits-ruminants virus (PPRV) has been causing infection in a wide range of susceptible hosts, particularly in disease-endemic regions. In the last 40 years, various reports highlighted the evidence of disease and viral genome in around 46 animal species from nine diverse families, including Bovidae, Cervidae, Camelidae, Suidae, Canidae, Felidae, Muridae, and Elephantidae. This evidence of clinical and/ or subclinical infection and the presence of the virus in an extended range of susceptible hosts emphasizes the cross-species transmission that remains a significant obstacle to effective control, particularly in disease-endemic regions. Therefore, a better understanding of virus transmission, host susceptibility, and epidemiological investigation of the disease is crucial to achieving the goals of efficient disease control and eradication programs initiated by OIE and FAO in various diseases-endemic regions. Nevertheless, the propensity of PPRV to inter- and intra-transmission may be a possible constraint in disease control strategies in terms of the new outbreak with the involvement of unusual or novel hosts. Considering this aspect, we tried to summarize the scattered data on PPR in available information about the susceptibility of a wide range of wildlife species, large ruminants, camels, and unusual hosts.
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Baron MD, Bataille A. A curated dataset of peste des petits ruminants virus sequences for molecular epidemiological analyses. PLoS One 2022; 17:e0263616. [PMID: 35143560 PMCID: PMC8830648 DOI: 10.1371/journal.pone.0263616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/23/2022] [Indexed: 12/23/2022] Open
Abstract
Peste des petits ruminants (PPR) is a highly contagious and devastating viral disease infecting predominantly sheep and goats. Tracking outbreaks of disease and analysing the movement of the virus often involves sequencing part or all of the genome and comparing the sequence obtained with sequences from other outbreaks, obtained from the public databases. However, there are a very large number (>1800) of PPRV sequences in the databases, a large majority of them relatively short, and not always well-documented. There is also a strong bias in the composition of the dataset, with countries with good sequencing capabilities (e.g. China, India, Turkey) being overrepresented, and most sequences coming from isolates in the last 20 years. In order to facilitate future analyses, we have prepared sets of PPRV sequences, sets which have been filtered for sequencing errors and unnecessary duplicates, and for which date and location information has been obtained, either from the database entry or from other published sources. These sequence datasets are freely available for download, and include smaller datasets which maximise phylogenetic information from the minimum number of sequences, and which will be useful for simple lineage identification. Their utility is illustrated by uploading the data to the MicroReact platform to allow simultaneous viewing of lineage date and geographic information on all the viruses for which we have information. While preparing these datasets, we identified a significant number of public database entries which contain clear errors, and propose guidelines on checking new sequences and completing metadata before submission.
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Affiliation(s)
- Michael D. Baron
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- * E-mail:
| | - Arnaud Bataille
- CIRAD, UMR, ASTRE, Montpellier, France
- ASTRE, University of Montpellier, CIRAD, INRAE, Montpellier, France
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Miao Q, Qi R, Meng C, Zhu J, Tang A, Dong D, Guo H, van Oers MM, Pijlman GP, Liu G. Caprine MAVS Is a RIG-I Interacting Type I Interferon Inducer Downregulated by Peste des Petits Ruminants Virus Infection. Viruses 2021; 13:v13030409. [PMID: 33807534 PMCID: PMC7998690 DOI: 10.3390/v13030409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
The mitochondrial antiviral-signaling protein (MAVS, also known as VISA, IPS-1, or CARDIF) plays an essential role in the type I interferon (IFN) response and in retinoic acid-inducible gene I (RIG-I) mediated antiviral innate immunity in mammals. In this study, the caprine MAVS gene (caMAVS, 1566 bp) was identified and cloned. The caMAVS shares the highest amino acid similarity (98.1%) with the predicted sheep MAVS. Confocal microscopy analysis of partial deletion mutants of caMAVS revealed that the transmembrane and the so-called Non-Characterized domains are indispensable for intracellular localization to mitochondria. Overexpression of caMAVS in caprine endometrial epithelial cells up-regulated the mRNA levels of caprine interferon-stimulated genes. We concluded that caprine MAVS mediates the activation of the type I IFN pathway. We further demonstrated that both the CARD-like domain and the transmembrane domain of caMAVS were essential for the activation of the IFN-β promotor. The interaction between caMAVS and caprine RIG-I and the vital role of the CARD and NC domain in this interaction was demonstrated by co-immunoprecipitation. Upon infection with the Peste des Petits Ruminants Virus (PPRV, genus Morbillivirus), the level of MAVS was greatly reduced. This reduction was prevented by the addition of the proteasome inhibitor MG132. Moreover, we found that viral protein V could interact and colocalize with MAVS. Together, we identified caMAVS as a RIG-I interactive protein involved in the activation of type I IFN pathways in caprine cells and as a target for PPRV immune evasion.
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Affiliation(s)
- Qiuhong Miao
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Ruibing Qi
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Chunchun Meng
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Jie Zhu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Aoxing Tang
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Dandan Dong
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Hongyuan Guo
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
| | - Monique M. van Oers
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
- Correspondence: (G.P.P.); (G.L.)
| | - Guangqing Liu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (Q.M.); (R.Q.); (C.M.); (J.Z.); (A.T.); (D.D.); (H.G.)
- Correspondence: (G.P.P.); (G.L.)
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Peste des petits ruminants in Africa: a review of currently available molecular epidemiological data, 2020. Arch Virol 2020; 165:2147-2163. [PMID: 32653984 PMCID: PMC7497342 DOI: 10.1007/s00705-020-04732-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/11/2020] [Indexed: 12/03/2022]
Abstract
Small ruminants (e.g., sheep and goats) contribute considerably to the cash income and nutrition of small farmers in most countries in Africa and Asia. Their husbandry is threatened by the highly infectious transboundary viral disease peste des petits ruminants (PPR) caused by peste-des-petits-ruminants virus (PPRV). Given its social and economic impact, PPR is presently being targeted by international organizations for global eradication by 2030. Since its first description in Côte d’Ivoire in 1942, and particularly over the last 10 years, a large amount of molecular epidemiological data on the virus have been generated in Africa. This review aims to consolidate these data in order to have a clearer picture of the current PPR situation in Africa, which will, in turn, assist authorities in global eradication attempts.
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Dou Y, Liang Z, Prajapati M, Zhang R, Li Y, Zhang Z. Expanding Diversity of Susceptible Hosts in Peste Des Petits Ruminants Virus Infection and Its Potential Mechanism Beyond. Front Vet Sci 2020; 7:66. [PMID: 32181263 PMCID: PMC7059747 DOI: 10.3389/fvets.2020.00066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/27/2020] [Indexed: 01/12/2023] Open
Abstract
Peste des petits ruminants (PPR) is a severe respiratory and digestive tract disease of domestic small ruminants caused by PPR virus (PPRV) of the genus Morbillivirus. Although the primary hosts of PPRV are goats and sheep, the host range of PPRV has been continuously expanding and reported to infect various animal hosts over the last decades, which could bring a potential challenge to effectively control and eradicate PPR globally. In this review, we focused on current knowledge about host expansion and interspecies infection of PPRV and discussed the potential mechanisms involved.
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Affiliation(s)
- Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Zhongxiang Liang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Meera Prajapati
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,Animal Health Research Division, Nepal Agricultural Research Council, Lalitpur, Nepal
| | - Rui Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Yanmin Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Zhidong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,College of Life Science and Technology, Southwest Minzu University, Chengdu, China
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Li L, Cao X, Wu J, Dou Y, Meng X, Liu D, Liu Y, Shang Y, Liu X. Epidemic and evolutionary characteristics of peste des petits ruminants virus infecting Procapra przewalskii in Western China. INFECTION GENETICS AND EVOLUTION 2019; 75:104004. [PMID: 31415822 DOI: 10.1016/j.meegid.2019.104004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/14/2022]
Abstract
Due to the migration or transboundary spread of domestic and wild animals, peste des petits ruminants virus posed a high potential threat to them. In this study, we initially detected that a class of animal named Procapra przewalskii was infected with peste des petits ruminants virus (PPRV ChinaGS2018) in Gansu province. According to phylogenetic relationships analysis, we found that ChinaGS2018 comprised of 15,954 nucleotides and was classified into IV genotypes. In addition, indirect immunofluorescence assay (IFA) showed that ChinaGS2018 could infect isolated primary goat tracheal epithelium cells (GTC). Comparing with full-length genome sequences revealed that ChinaGS2018 strain has high identity to the reference complete genomes (87.16-99.55%) at the nucleotide level. Multiple sequence alignment showed that F protein has the highest identity of 99.8%, and H protein has the highest nucleotide substitution ratio. Our study also suggested this strain may be transmitted from Xinjiang, China. Along with the migratory of Procapraprzewalskii, this wild ruminant infected with PPRV can pose a huge threat to other wild ruminants and domestic ones. This is the first report describing infected with PPRV which will provide insights into the epidemiology and pathogenesis of this important virus.
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Affiliation(s)
- Lingxia Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Jinyan Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xuelian Meng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Dan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
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A comparative phylogenomic analysis of peste des petits ruminants virus isolated from wild and unusual hosts. Mol Biol Rep 2019; 46:5587-5593. [PMID: 31317455 DOI: 10.1007/s11033-019-04973-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Peste des petits ruminants virus (PPRV) infects a wide range of domestic and wild ruminants, and occasionally unusual hosts such as camel, cattle and pig. Given their broad host-spectrum and disease endemicity in several developing countries, it is imperative to elucidate the viral evolutionary insights for their dynamic pathobiology and differential host-selection. For this purpose, a dataset of all available (n = 37) PPRV sequences originating from wild and unusual hosts was composed and in silico analysed. Compared to domestic small ruminant strains of same geographical region, phylogenomic and residue analysis of PPRV sequences originating from wild and unusual hosts revealed a close relationship between strains. A lack of obvious difference among the studied sequences and deduced residues suggests that these are the host factors that may play a role in their susceptibility to PPRV infection, immune response, pathogenesis, excretion patterns and potential clinical signs or resistance to clinical disease. Summarizing together, the comparative analysis enhances our understanding towards molecular epidemiology of the PPRV in wild and unusual hosts for appropriate intervention strategies particularly at livestock-wildlife interface.
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Peste des petits ruminants in wild ungulates. Trop Anim Health Prod 2018; 50:1815-1819. [PMID: 29881925 DOI: 10.1007/s11250-018-1623-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/21/2018] [Indexed: 10/14/2022]
Abstract
Peste des petits ruminants (PPR) is a contagious viral disease of domestic small ruminants. It also affects wild ungulates but there are comparatively few studies of the incidence of natural infection, clinical signs and pathology, and confirmation of the virus, and in these species. In this article, we list the wild ungulates in which PPRV infection has been confirmed and summarize available information about the presentation of the disease, its identification, and impact of virus on wildlife populations. Considering recent reports of outbreaks by the World Organization for Animal Health (OIE), it is important to understand the transmission of this disease within wildlife populations in PPR endemic regions.
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