1
|
Evaluation of Potential In Vitro Recombination Events in Codon Deoptimized FMDV Strains. Viruses 2023; 15:v15030670. [PMID: 36992379 PMCID: PMC10052203 DOI: 10.3390/v15030670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Codon deoptimization (CD) has been recently used as a possible strategy to derive foot-and-mouth disease (FMD) live-attenuated vaccine (LAV) candidates containing DIVA markers. However, reversion to virulence, or loss of DIVA, from possible recombination with wild-type (WT) strains has yet to be analyzed. An in vitro assay was developed to quantitate the levels of recombination between WT and a prospective A24-P2P3 partially deoptimized LAV candidate. By using two genetically engineered non-infectious RNA templates, we demonstrate that recombination can occur within non-deoptimized viral genomic regions (i.e., 3′end of P3 region). The sequencing of single plaque recombinants revealed a variety of genome compositions, including full-length WT sequences at the consensus level and deoptimized sequences at the sub-consensus/consensus level within the 3′end of the P3 region. Notably, after further passage, two recombinants that contained deoptimized sequences evolved to WT. Overall, recombinants featuring large stretches of CD or DIVA markers were less fit than WT viruses. Our results indicate that the developed assay is a powerful tool to evaluate the recombination of FMDV genomes in vitro and should contribute to the improved design of FMDV codon deoptimized LAV candidates.
Collapse
|
2
|
Ward JC, Lasecka-Dykes L, Neil C, Adeyemi OO, Gold S, McLean-Pell N, Wright C, Herod MR, Kealy D, Warner E, Jackson T, King DP, Tuthill TJ, Rowlands DJ, Stonehouse NJ. The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication, but essential for the production of infectious virus. PLoS Pathog 2022; 18:e1010589. [PMID: 35666744 PMCID: PMC9203018 DOI: 10.1371/journal.ppat.1010589] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/16/2022] [Accepted: 05/12/2022] [Indexed: 11/22/2022] Open
Abstract
Non-coding regions of viral RNA (vRNA) genomes are critically important in the regulation of gene expression. In particular, pseudoknot (PK) structures, which are present in a wide range of RNA molecules, have a variety of roles. The 5' untranslated region (5' UTR) of foot-and-mouth disease virus (FMDV) vRNA is considerably longer than in other viruses from the picornavirus family and consists of a number of distinctive structural motifs that includes multiple (2, 3 or 4 depending on the virus strain) putative PKs linked in tandem. The role(s) of the PKs in the FMDV infection are not fully understood. Here, using bioinformatics, sub-genomic replicons and recombinant viruses we have investigated the structural conservation and importance of the PKs in the FMDV lifecycle. Our results show that despite the conservation of two or more PKs across all FMDVs, a replicon lacking PKs was replication competent, albeit at reduced levels. Furthermore, in competition experiments, GFP FMDV replicons with less than two (0 or 1) PK structures were outcompeted by a mCherry FMDV wt replicon that had 4 PKs, whereas GFP replicons with 2 or 4 PKs were not. This apparent replicative advantage offered by the additional PKs correlates with the maintenance of at least two PKs in the genomes of FMDV field isolates. Despite a replicon lacking any PKs retaining the ability to replicate, viruses completely lacking PK were not viable and at least one PK was essential for recovery of infections virus, suggesting a role for the PKs in virion assembly. Thus, our study points to roles for the PKs in both vRNA replication and virion assembly, thereby improving understanding the molecular biology of FMDV replication and the wider roles of PK in RNA functions.
Collapse
Affiliation(s)
- Joseph C. Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Chris Neil
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | - Oluwapelumi O. Adeyemi
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah Gold
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | - Niall McLean-Pell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Caroline Wright
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | - Morgan R. Herod
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - David Kealy
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Emma Warner
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Terry Jackson
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | - Donald P. King
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | | | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NJS)
| | - Nicola J. Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NJS)
| |
Collapse
|
3
|
Ecological and Anthropogenic Spatial Gradients Shape Patterns of Dispersal of Foot-and-Mouth Disease Virus in Uganda. Pathogens 2022; 11:pathogens11050524. [PMID: 35631045 PMCID: PMC9143568 DOI: 10.3390/pathogens11050524] [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: 04/01/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Using georeferenced phylogenetic trees, phylogeography allows researchers to elucidate interactions between environmental heterogeneities and patterns of infectious disease spread. Concordant with the increasing availability of pathogen genetic sequence data, there is a growing need for tools to test epidemiological hypotheses in this field. In this study, we apply tools traditionally used in ecology to elucidate the epidemiology of foot-and-mouth disease virus (FMDV) in Uganda. We analyze FMDV serotype O genetic sequences and their corresponding spatiotemporal metadata from a cross-sectional study of cattle. We apply step selection function (SSF) models, typically used to study wildlife habitat selection, to viral phylogenies to show that FMDV is more likely to be found in areas of low rainfall. Next, we use a novel approach, a resource gradient function (RGF) model, to elucidate characteristics of viral source and sink areas. An RGF model applied to our data reveals that areas of high cattle density and areas near livestock markets may serve as sources of FMDV dissemination in Uganda, and areas of low rainfall serve as viral sinks that experience frequent reintroductions. Our results may help to inform risk-based FMDV control strategies in Uganda. More broadly, these tools advance the phylogenetic toolkit, as they may help to uncover patterns of spread of other organisms for which genetic sequences and corresponding spatiotemporal metadata exist.
Collapse
|
4
|
Hassan AM, El-Mayet FS, El-Habbaa AS, Shahein MA, Zowalaty MEE, Hagag NM, Sharawi SSA. Molecular Characterization of newly emerging Foot-and-Mouth Disease Virus Serotype SAT2 of Lib-12 Lineage Isolated from Egypt. Virus Res 2021; 311:198651. [PMID: 34879242 DOI: 10.1016/j.virusres.2021.198651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/03/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
An outbreak of foot-and-mouth disease virus (FMDV) serotype SAT2 occurred in Egypt in 2018, which affected cattle and water buffalo. Previous phylogenetic studies on FMDV circulating in Egypt have mainly focused on genomic regions encoding structural proteins that determine the FMDV serotype. Still, none of them have analyzed the open reading frame (ORF) sequence of the Egyptian SAT2/Lib-12 lineage. The present study aimed to analyze and identify the ORF genome sequence of Lib-12 lineage that belongs to FMDV SAT2 topotype VII in Egypt. The protocol workflow was optimized and tested using a representative field isolate of FMDV/SAT2/Lib-12 from a bovine tongue sample collected in 2018 from Ismailia governorate (SAT2/EGY/Ismailia/2018). The protocol was based on reverse transcription polymerase chain reaction with multiple overlapping primers, amplicons sequencing, and assembly to complete the ORF consensus sequence. Alignments of the sequence fragments formed consensus genome sequence of 7219 nucleotides in length. The complete nucleotide sequence of the Egyptian isolate was related to Ethiopian, Nigerian, and Ghanaian strains, with identity not exceeding 95%. The divergence in the genetic identity of the Egyptian SAT2/Lib-12 lineage from other Egyptian strains and the neighboring Libyan isolates reached 7%, and this may be attributed to the absence of the Lib-12 lineage ORF sequence from Egypt and Libya in the database. The present study significantly advances the knowledge of the molecular analysis of FMDV SAT2 and the design of vaccine selection for FMDV SAT2 in Egypt. The study protocol could be applied to other FMDV serotypes.
Collapse
Affiliation(s)
- Ayah M Hassan
- Genome Research Unit, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Fouad S El-Mayet
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
| | - Ayman S El-Habbaa
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
| | - Momtaz A Shahein
- Virology Research Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Mohamed E El Zowalaty
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-75 123 Uppsala, Sweden
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), 12618 Giza, Egypt
| | - Saad S A Sharawi
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobyia, Egypt
| |
Collapse
|
5
|
Lasecka-Dykes L, Tulloch F, Simmonds P, Luke GA, Ribeca P, Gold S, Knowles NJ, Wright CF, Wadsworth J, Azhar M, King DP, Tuthill TJ, Jackson T, Ryan MD. Mutagenesis Mapping of RNA Structures within the Foot-and-Mouth Disease Virus Genome Reveals Functional Elements Localized in the Polymerase (3D pol)-Encoding Region. mSphere 2021; 6:e0001521. [PMID: 34259558 PMCID: PMC8386395 DOI: 10.1128/msphere.00015-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/16/2021] [Indexed: 01/24/2023] Open
Abstract
RNA structures can form functional elements that play crucial roles in the replication of positive-sense RNA viruses. While RNA structures in the untranslated regions (UTRs) of several picornaviruses have been functionally characterized, the roles of putative RNA structures predicted for protein coding sequences (or open reading frames [ORFs]) remain largely undefined. Here, we have undertaken a bioinformatic analysis of the foot-and-mouth disease virus (FMDV) genome to predict 53 conserved RNA structures within the ORF. Forty-six of these structures were located in the regions encoding the nonstructural proteins (nsps). To investigate whether structures located in the regions encoding the nsps are required for FMDV replication, we used a mutagenesis method, CDLR mapping, where sequential coding segments were shuffled to minimize RNA secondary structures while preserving protein coding, native dinucleotide frequencies, and codon usage. To examine the impact of these changes on replicative fitness, mutated sequences were inserted into an FMDV subgenomic replicon. We found that three of the RNA structures, all at the 3' termini of the FMDV ORF, were critical for replicon replication. In contrast, disruption of the other 43 conserved RNA structures that lie within the regions encoding the nsps had no effect on replicon replication, suggesting that these structures are not required for initiating translation or replication of viral RNA. Conserved RNA structures that are not essential for virus replication could provide ideal targets for the rational attenuation of a wide range of FMDV strains. IMPORTANCE Some RNA structures formed by the genomes of RNA viruses are critical for viral replication. Our study shows that of 46 conserved RNA structures located within the regions of the foot-and-mouth disease virus (FMDV) genome that encode the nonstructural proteins, only three are essential for replication of an FMDV subgenomic replicon. Replicon replication is dependent on RNA translation and synthesis; thus, our results suggest that the three RNA structures are critical for either initiation of viral RNA translation and/or viral RNA synthesis. Although further studies are required to identify whether the remaining 43 RNA structures have other roles in virus replication, they may provide targets for the rational large-scale attenuation of a wide range of FMDV strains. FMDV causes a highly contagious disease, posing a constant threat to global livestock industries. Such weakened FMDV strains could be investigated as live-attenuated vaccines or could enhance biosecurity of conventional inactivated vaccine production.
Collapse
Affiliation(s)
| | - Fiona Tulloch
- Biomedical Sciences Research Complex (BSRC), School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Garry A. Luke
- Biomedical Sciences Research Complex (BSRC), School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - Paolo Ribeca
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Sarah Gold
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | | | | | | | - Mehreen Azhar
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Donald P. King
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | | | - Terry Jackson
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Martin D. Ryan
- Biomedical Sciences Research Complex (BSRC), School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| |
Collapse
|
6
|
Nardo AD, Ferretti L, Wadsworth J, Mioulet V, Gelman B, Karniely S, Scherbakov A, Ziay G, Özyörük F, Parlak Ü, Göktuna PT, Hassanzadeh R, Khalaj M, Dastoor SM, Abdollahi D, Khan EUH, Afzal M, Hussain M, Knowles NJ, King DP. Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages. Mol Biol Evol 2021; 38:4346-4361. [PMID: 34115138 PMCID: PMC8476141 DOI: 10.1093/molbev/msab172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Livestock farming across the world is constantly threatened by evolutionary turnover of foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics of which remain to be elucidated. Here, we map the eco-evolutionary landscape of co-circulating FMDV lineages within an important endemic virus pool encompassing Western, Central and parts of Southern Asia, reconstructing the evolutionary history and spatial dynamics over the last 20 years that shapes the current epidemiological situation. We demonstrate that new FMDV variants periodically emerge from Southern Asia, precipitating waves of virus incursions that systematically travel in a westerly direction. We evidence how metapopulation dynamics drive the emergence and extinction of spatially structured virus populations, and how transmission in different host species regulates the evolutionary space of virus serotypes. Our work provides the first integrative framework that defines co-evolutionary signatures of FMDV in regional contexts to help understand the complex interplay between virus phenotypes, host characteristics, and key epidemiological determinants of transmission that drive FMDV evolution in endemic settings.
Collapse
Affiliation(s)
- Antonello Di Nardo
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Valerie Mioulet
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Boris Gelman
- Division of Virology, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Sharon Karniely
- Division of Virology, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Alexey Scherbakov
- Federal Governmental Budgetary Institution "Federal Centre for Animal Health" (FGBI "ARRIAH"), Yur'evets, Vladimir, Russia
| | - Ghulam Ziay
- Central Veterinary Diagnostic and Research Laboratory, Kabul, Afghanistan
| | - Fuat Özyörük
- Faculty of Veterinary Medicine, Harran University, Sanliurfa, Turkey
| | - Ünal Parlak
- Foot and Mouth Disease (ŞAP) Institute, Ankara, Turkey
| | | | - Reza Hassanzadeh
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | - Mehdi Khalaj
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | | | - Darab Abdollahi
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | - Ehtisham-Ul-Haq Khan
- Livestock and Dairy Development Department, Government of Punjab, Rawalpindi, Pakistan
| | - Muhammad Afzal
- Food and Agriculture Organization of the United Nations, Pakistan Office, Islamabad, Pakistan
| | - Manzoor Hussain
- Food and Agriculture Organization of the United Nations, Pakistan Office, Islamabad, Pakistan
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| |
Collapse
|
7
|
Munsey A, Mwiine FN, Ochwo S, Velazquez-Salinas L, Ahmed Z, Maree F, Rodriguez LL, Rieder E, Perez A, Dellicour S, VanderWaal K. Phylogeographic analysis of foot-and-mouth disease virus serotype O dispersal and associated drivers in East Africa. Mol Ecol 2021; 30:3815-3825. [PMID: 34008868 DOI: 10.1111/mec.15991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
The continued endemicity of foot and mouth disease virus (FMDV) in East Africa has significant implications for livestock production and poverty reduction, yet its complex epidemiology in endemic settings remains poorly understood. Identifying FMDV dispersal routes and drivers of transmission is key to improved control strategies. Environmental heterogeneity and anthropogenic drivers (e.g., demand for animal products) can impact viral spread by influencing host movements. Here, we utilized FMDV serotype O VP1 genetic sequences and corresponding spatiotemporal data in order to (i) infer the recent dispersal history, and (II) investigate the impact of external factors (cattle density, human population density, proximity to livestock markets, and drought) on dispersal velocity, location, and direction of FMDV serotype O in East Africa. We identified statistical evidence of long-distance transmission events, and we found that FMDV serotype O tends to remain circulating in areas of high cattle density, high human population density, and in close proximity to livestock markets. The latter two findings highlight the influence of anthropogenic factors on FMDV serotype O spread in this region. These findings contribute to the understanding of FMDV epidemiology in East Africa and can help guide improved control measures.
Collapse
Affiliation(s)
- Anna Munsey
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
| | - Frank Norbert Mwiine
- Makerere University College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Kampala, Uganda
| | - Sylvester Ochwo
- Makerere University College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Kampala, Uganda
| | - Lauro Velazquez-Salinas
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA.,Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Zaheer Ahmed
- Animal and Plant Health Inspection Services (APHIS), National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, United States Department of Agriculture, Greenport, NY, USA
| | - Francois Maree
- Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Andres Perez
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
| | - Simon Dellicour
- Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.,Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Kimberly VanderWaal
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
| |
Collapse
|
8
|
Campbell Z, Coleman P, Guest A, Kushwaha P, Ramuthivheli T, Osebe T, Perry B, Salt J. Prioritizing smallholder animal health needs in East Africa, West Africa, and South Asia using three approaches: Literature review, expert workshops, and practitioner surveys. Prev Vet Med 2021; 189:105279. [PMID: 33581421 PMCID: PMC8024747 DOI: 10.1016/j.prevetmed.2021.105279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022]
Abstract
Managing the health needs of livestock contributes to reducing poverty and improving the livelihoods of smallholder and pastoralist livestock keepers globally. Animal health practitioners, producers, policymakers, and researchers all must prioritize how to mobilize limited resources. This study employed three approaches to prioritize animal health needs in East and West Africa and South Asia to identify diseases and syndromes that impact livestock keepers. The approaches were a) systematic literature review, b) a series of expert workshops, and c) a practitioner survey of veterinarians and para-veterinary professionals. The top constraints that emerged from all three approaches include endo/ ectoparasites, foot and mouth disease, brucellosis, peste des petits ruminants, Newcastle disease, and avian influenza. Expert workshops additionally identified contagious caprine pleuropneumonia, contagious bovine pleuropneumonia, mastitis, and reproductive disorders as constraints not emphasized in the literature review. Practitioner survey results additionally identified nutrition as a constraint for smallholder dairy and pastoralist small ruminant production. Experts attending the workshops agreed most constraints can be managed using existing veterinary technologies and best husbandry practices, which supports a shift away from focusing on individual diseases and new technologies towards addressing systemic challenges that limit access to veterinary services and inputs. Few research studies focused on incidence/ prevalence of disease and impact, suggesting better incorporation of socio-economic impact measures in future research would better represent the interests of livestock keepers.
Collapse
Affiliation(s)
- Zoë Campbell
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, 00100, Kenya.
| | - Paul Coleman
- H20 Venture Partners, 33-35 George Street, Oxford, OX1 2AY, United Kingdom
| | - Andrea Guest
- H20 Venture Partners, 33-35 George Street, Oxford, OX1 2AY, United Kingdom
| | - Peetambar Kushwaha
- GALVmed Asia Office, Unit 118 & 120 B, Splendor Forum, Plot No 3, Jasola District Centre, Jasola, New Delhi, 110025, India
| | - Thembinkosi Ramuthivheli
- GALVmed Africa Office, International Livestock Research Institute (ILRI), Swing One, Naivasha Road, Nairobi, Kenya
| | - Tom Osebe
- GALVmed Africa Office, International Livestock Research Institute (ILRI), Swing One, Naivasha Road, Nairobi, Kenya
| | - Brian Perry
- Nuffield College of Clinical Medicine, University of Oxford, United Kingdom; College of Medicine and Veterinary Medicine, University of Edinburgh, Arthurstone House, Meigle, Blairgowrie, PH12 8QW, Scotland, United Kingdom
| | - Jeremy Salt
- GALVmed UK Office, Doherty Building, Pentlands Science Park, Bush Loan, Penicuik Edinburgh, EH26 0PZ, Scotland, United Kingdom
| |
Collapse
|
9
|
Alkhamis MA, Li C, Torremorell M. Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks. Front Vet Sci 2020; 7:176. [PMID: 32373634 PMCID: PMC7186338 DOI: 10.3389/fvets.2020.00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/16/2020] [Indexed: 11/22/2022] Open
Abstract
Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring many uncertainties and made joint conclusions from both analytical approaches. Phylodynamic methods offer a uniquely integrated platform capable of inferring complex epidemiological and evolutionary processes from the phylogeny of viruses in populations using a single Bayesian statistical framework. In this study, we reviewed and outlined basic concepts and aspects of phylodynamic methods and attempted to summarize essential components of the methodology in one analytical pipeline to facilitate the proper use of the methods by animal health researchers. Also, we challenged the robustness of the posterior evolutionary parameters, inferred by the commonly used phylodynamic models, using hemagglutinin (HA) and polymerase basic 2 (PB2) segments of the currently circulating human-like H3 swine influenza (SI) viruses isolated in the United States and multiple priors. Subsequently, we compared similarities and differences between the posterior parameters inferred from sequence data using multiple phylodynamic models. Our suggested phylodynamic approach attempts to reduce the impact of its inherent limitations to offer less biased and biologically plausible inferences about the pathogen evolutionary characteristics to properly guide intervention activities. We also pinpointed requirements and challenges for integrating phylodynamic methods in routine animal disease surveillance activities.
Collapse
Affiliation(s)
- Moh A Alkhamis
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait City, Kuwait.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Chong Li
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Montserrat Torremorell
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| |
Collapse
|
10
|
Blignaut B, van Heerden J, Reininghaus B, Fosgate GT, Heath L. Characterization of SAT2 foot-and-mouth disease 2013/2014 outbreak viruses at the wildlife-livestock interface in South Africa. Transbound Emerg Dis 2020; 67:1595-1606. [PMID: 31984622 DOI: 10.1111/tbed.13493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/12/2019] [Accepted: 01/20/2020] [Indexed: 11/30/2022]
Abstract
The Southern African Territories (SAT)-type foot-and-mouth disease viruses (FMDV) are endemic to the greater Kruger National Park (KNP) area in South Africa, where they are maintained through persistent infections in African buffalo. The occurrence of FMDV within the Greater KNP area constitutes a continual threat to the livestock industry. To expand on knowledge of FMDV diversity, the genetic and antigenic relatedness of SAT2-type viruses isolated from cattle during a FMD outbreak in Mpumalanga Province in 2013 and 2014 were investigated. Cattle from twelve diptanks tested positive on polymerase chain reaction (PCR), and molecular epidemiological relationships of the viruses were determined by VP1 sequencing. Phylogenetic analysis of the SAT2 viruses from the FMD outbreak in Mpumalanga in 2013/2014 revealed their genetic relatedness to other SAT2 isolates from topotype I (South Africa, Zimbabwe and Mozambique), albeit genetically distinct from previous South African outbreak viruses (2011 and 2012) from the same topotype. The fifteen SAT2 field isolates clustered into a novel genotype with ≥98.7% nucleotide identity. High neutralization antibody titres were observed for four 2013/2014 outbreak viruses tested against the SAT2 reference antisera representative of viruses isolated from cattle and buffalo from South Africa (topotype I) and Zimbabwe (topotype II). Comparison of the antigenic relationship (r1 values) of the outbreak viruses with reference antisera indicated a good vaccine match with 90% of r1 values > 0.3. The r1 values for the 2013/2014 outbreak viruses were 0.4 and above for the three South African vaccine/reference strains. These results confirm the presence of genetic and antigenic variability in SAT2 viruses and suggest the emergence of new variants at the wildlife-livestock interface in South Africa. Continuous characterization of field viruses should be performed to identify new virus strains as epidemiological surveillance to improve vaccination efforts.
Collapse
Affiliation(s)
- Belinda Blignaut
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Onderstepoort, South Africa.,Mpumalanga Veterinary Services, Department of Agriculture, Rural Development, Land and Environmental Affairs, Thulamahashe, South Africa
| | - Juanita van Heerden
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Onderstepoort, South Africa
| | - Björn Reininghaus
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Geoffrey T Fosgate
- Mpumalanga Veterinary Services, Department of Agriculture, Rural Development, Land and Environmental Affairs, Thulamahashe, South Africa
| | - Livio Heath
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Onderstepoort, South Africa
| |
Collapse
|
11
|
Jo HE, You SH, Choi JH, Ko MK, Shin SH, Song J, Jo H, Lee MJ, Kim SM, Kim B, Park JH. Evaluation of novel inactivated vaccines for the SAT 1, SAT 2 and SAT 3 serotypes of foot-and-mouth disease in pigs. Virol J 2019; 16:156. [PMID: 31842907 PMCID: PMC6916012 DOI: 10.1186/s12985-019-1262-1] [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: 03/06/2019] [Accepted: 11/29/2019] [Indexed: 11/14/2022] Open
Abstract
Background The foot-and-mouth disease (FMD) virus is classified into seven serotypes, of which the South African types have South African Territories (SAT)1, SAT2, and SAT3 that are prevalent in Africa. Especially SAT2 have spread to Arabian Peninsula and the Palestinian Autonomous Territories. Of these viruses, the incidence of SAT2 is the highest. It is important to prepare for the spread of the virus to other continents, even though most FMD viruses are bovine-derived. In particular, due to the high breeding density of pigs in Asia, more attention is usually paid to the immunity and protection of pigs than cattle. For this reason, this study investigated the immunity and protection of pigs against the SAT viruses. Methods Specific vaccines were developed for SAT1, SAT2, and SAT3 serotypes. These vaccine viruses were designed to be distinguished from the wild-type strain. An immunogenicity test was conducted using these vaccines in both cattle (n = 5/group) and pigs (n = 20/group). Results High virus-neutralizing titer of antibodies (> 1:100) was induced in only 2 weeks after the immunization of cattle with the individual vaccine for SAT1, SAT2 or SAT3, and a clear immune response was induced after the second immunization in pigs. When the vaccinated pigs (n = 4–5/group) were challenged by the homologous wild-type virus strain 4 weeks after immunization, all the pigs were protected from the challenge. Conclusions This study confirmed that these vaccines can be used against SAT1, SAT2, and SAT3 viruses in cattle and pigs. The vaccine strains developed in this study are expected to be used as vaccines that can protect against FMD in the event of a future FMD outbreak in pigs in consideration of the situation in Asia.
Collapse
Affiliation(s)
- Hye-Eun Jo
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Su-Hwa You
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Joo-Hyung Choi
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Mi-Kyeong Ko
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Sung Ho Shin
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Jisoo Song
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Hyundong Jo
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Min Ja Lee
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Su-Mi Kim
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Byounghan Kim
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Jong-Hyeon Park
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea.
| |
Collapse
|
12
|
Palinski RM, Sangula A, Gakuya F, Bertram MR, Pauszek SJ, Hartwig EJ, Smoliga GR, Obanda V, Omondi G, VanderWaal K, Arzt J. Foot-and-Mouth Disease Virus Serotype A Genome Sequence from Kenya in 2016. Microbiol Resour Announc 2019; 8:e00987-19. [PMID: 31537675 PMCID: PMC6753279 DOI: 10.1128/mra.00987-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 11/24/2022] Open
Abstract
We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa isolate collected from bovine vesicular epithelium from Kenya in 2016. This novel sequence updates the knowledge of FMDV diversity in eastern Africa and has important implications for FMDV epidemiology and molecular analyses.
Collapse
Affiliation(s)
- Rachel M Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
| | | | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Miranda R Bertram
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, Tennessee, USA
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
| | - Ethan J Hartwig
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
| | - George R Smoliga
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - George Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS-USDA, Orient Point, New York, USA
| |
Collapse
|
13
|
Palinski RM, Sangula A, Gakuya F, Bertram MR, Pauszek SJ, Hartwig EJ, Smoliga GR, Vierra D, Fish I, Obanda V, Omondi G, VanderWaal K, Arzt J. First Report of Near-Complete Genome Sequences of Foot-and-Mouth Disease Virus Serotype O Strains from Kenya. Microbiol Resour Announc 2019; 8:e00808-19. [PMID: 31467103 PMCID: PMC6715873 DOI: 10.1128/mra.00808-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/10/2019] [Indexed: 12/03/2022] Open
Abstract
This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (FMDV) serotype O from Kenya. The viruses were isolated from bovine epithelium collected in 2014 and 2016 from local FMD outbreaks. These full-genome sequences are critical for improving the understanding of regional FMDV molecular epidemiology.
Collapse
Affiliation(s)
- Rachel M Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
| | | | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Miranda R Bertram
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, Tennessee, USA
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
| | - Ethan J Hartwig
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
| | - George R Smoliga
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
| | - David Vierra
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas, USA
| | - Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, Tennessee, USA
| | - Vincent Obanda
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, Tennessee, USA
| | - George Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, New York, USA
| |
Collapse
|
14
|
Mwiine FN, Velazquez-Salinas L, Ahmed Z, Ochwo S, Munsey A, Kenney M, Lutwama JJ, Maree FF, Lobel L, Perez AM, Rodriguez LL, VanderWaal K, Rieder E. Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross-sectional surveillance study in cattle between 2014 and 2017. Transbound Emerg Dis 2019; 66:2011-2024. [PMID: 31127983 DOI: 10.1111/tbed.13249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 04/20/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
Here, we report the results of a cross-sectional study designed to monitor the circulation and genetic diversity of foot and mouth disease virus (FMDV) in Uganda between 2014 and 2017. In this study, 13,614 sera and 2,068 oral-pharyngeal fluid samples were collected from cattle and analysed to determine FMDV seroprevalence, circulating serotypes and their phylogenetic relationships. Circulation of FMDV was evidenced by the detection of antibodies against non-structural proteins of FMDV or viral isolations in all districts sampled in Uganda. Sequence analysis revealed the presence of FMDV serotypes A, O, SAT 1 and SAT 2. FMDVs belonging to serotype O, isolated from 21 districts, were the most prevalent and were classified into six lineages within two East African topotypes, namely EA-1 and EA-2. Serotype A viruses belonging to the Africa G-I topotype were isolated from two districts. SAT 1 viruses grouped within topotypes I and IV and SAT 2 viruses within topotypes VII, IV and X were isolated from six and four districts respectively. Phylogenetic analysis of SAT 1 and SAT 2 sequences from cattle clustered with historical sequences from African buffalo, indicating possible interspecies transmission at the wildlife-livestock interface. In some cases, Uganda viruses also shared similarities to viral strains recovered from other regions in East Africa. This 3-year study period provides knowledge about the geographical distribution of FMDV serotypes isolated in Uganda and insights into the genetic diversity of the multiple serotypes circulating in the country. Knowledge of circulating FMDV viruses will assist in antigenic matching studies to devise improved FMDV control strategies with vaccination and vaccine strain selection for Uganda.
Collapse
Affiliation(s)
- Frank Norbert Mwiine
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Lauro Velazquez-Salinas
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota.,Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Zaheer Ahmed
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Sylvester Ochwo
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Anna Munsey
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Mary Kenney
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Julius J Lutwama
- Department of Emerging and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francois F Maree
- Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, South Africa
| | - Leslie Lobel
- Department of Virology and Developmental Genetics, Ben Gurion University, Beer Sheva, Israel
| | - Andres M Perez
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Kimberly VanderWaal
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| |
Collapse
|
15
|
Senecavirus-Specific Recombination Assays Reveal the Intimate Link between Polymerase Fidelity and RNA Recombination. J Virol 2019; 93:JVI.00576-19. [PMID: 30996084 DOI: 10.1128/jvi.00576-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Senecavirus A (SVA) is a reemerging virus, and recent evidence has emphasized the importance of SVA recombination in vivo on virus evolution. In this study, we report the development of an infectious cDNA clone for the SVA/HLJ/CHA/2016 strain. We used this strain to develop a reporter virus expressing enhanced green fluorescent protein (eGFP), which we then used to screen for a recombination-deficient SVA by an eGFP retention assay. Sequencing of the virus that retained the eGFP following passage allowed us to identify the nonsynonymous mutations (S460L alone and I212V-S460L in combination) in the RNA-dependent RNA polymerase (RdRp) region of the genome. We developed a Senecavirus-specific cell culture-based recombination assay, which we used to elucidate the role of RdRp in SVA recombination. Our results demonstrate that these two polymerase variants (S460L and I212/S460L) have reduced recombination capacity. These results indicate that the RdRp plays a central role in SVA replicative recombination. Notably, our results showed that the two recombination-deficient variants have higher replication fidelity than the wild type (WT) and display decreased ribavirin sensitivity compared to the WT. In addition, these two mutants exhibited significantly increased fitness in vitro compared to the WT. These results demonstrate that recombination and mutation rates are intimately linked. Our results have important implications for understanding the crucial role of the RdRp in virus recombination and fitness, especially in the molecular mechanisms of SVA evolution and pathogenicity.IMPORTANCE Recent evidence has emphasized the importance of SVA recombination on virus evolution in vivo We describe the first assays to study Senecavirus A recombination. The results show that the RNA-dependent RNA polymerase plays a crucial role in recombination and that recombination can impact the fitness of SVA in cell culture. Further, SVA polymerase fidelity is closely related to recombination efficiency. The results provide key insights into the role of recombination in positive-strand RNA viruses.
Collapse
|
16
|
Omondi G, Alkhamis MA, Obanda V, Gakuya F, Sangula A, Pauszek S, Perez A, Ngulu S, van Aardt R, Arzt J, VanderWaal K. Phylogeographical and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa. Mol Ecol 2019; 28:2903-2916. [PMID: 31074125 DOI: 10.1111/mec.15125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.
Collapse
Affiliation(s)
- George Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Moh A Alkhamis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota.,Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait, Kuwait
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | | | - Steven Pauszek
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, USDA, Orient Point, New York
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | | | | | - Jonathan Arzt
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, USDA, Orient Point, New York
| | - Kim VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| |
Collapse
|
17
|
Viral Recombination: Ecology, Evolution, and Pathogenesis. Viruses 2018; 10:v10070358. [PMID: 29986376 PMCID: PMC6070879 DOI: 10.3390/v10070358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 12/12/2022] Open
|
18
|
Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome. Viruses 2018; 10:v10050221. [PMID: 29693634 PMCID: PMC5977214 DOI: 10.3390/v10050221] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/21/2023] Open
Abstract
Recombination is one of the determinants of genetic diversity in the foot-and-mouth disease virus (FMDV). FMDV sequences have a mosaic structure caused by extensive intra- and inter-serotype recombination, with the exception of the capsid-encoding region. While these genome-wide patterns of broad-scale recombination are well studied, not much is known about the patterns of recombination that may exist within infected hosts. In addition, detection of recombination among viruses evolving at the within-host level is challenging due to the similarity of the sequences and the limitations in differentiating recombination from point mutations. Here, we present the first analysis of recombination events between closely related FMDV sequences occurring within buffalo hosts. The detection of these events was made possible by the occurrence of co-infection of two viral swarms with about 1% nucleotide divergence. We found more than 15 recombination events, unequally distributed across eight samples from different animals. The distribution of these events along the FMDV genome was neither uniform nor related to the phylogenetic distribution of recombination breakpoints, suggesting a mismatch between within-host evolutionary pressures and long-term selection for infectivity and transmissibility.
Collapse
|