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Moura P, Kihm U, Schudel A, Bergmann I, Buholzer P. Why Foot-and-Mouth Disease-Free with Vaccination Should Be Equivalent to Foot-and-Mouth Disease-Free without Vaccination. Vet Sci 2024; 11:281. [PMID: 38922028 PMCID: PMC11209047 DOI: 10.3390/vetsci11060281] [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: 05/22/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Foot-and-Mouth Disease (FMD) is still one of the most relevant animal diseases and remains of global concern. The World Organization for Animal Health (WOAH) has specified two sanitary statuses that assure freedom from FMD: a country or zone can be free from FMD either with or without vaccination. To obtain either of the two statuses, absence of virus circulation must be shown. The standards set by WOAH are used for trade negotiations. During recent decades, different tools and approaches were developed to control FMD, including vaccines, diagnostics, and the Progressive Control Pathway for FMD. These tools improved over time, and nowadays high-quality, reliable vaccines and specific diagnostics are available to efficiently control and detect the infection, even in vaccinated populations. Due to these improvements, it is no longer justifiable to treat the two FMD-free statuses differently. The distinction between the statuses provides wrong incentives and tempts countries to take increased risks by stopping vaccination to improve their trade conditions, which can have potentially devastating consequences. The decision to stop vaccination should only be made on the basis of a careful and comprehensive analysis of the local and regional epidemiological situation. This paper presents the perspective that member countries and WOAH should recognize the two FMD-free statuses as equivalent.
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Affiliation(s)
| | - Ulrich Kihm
- SAFOSO AG, CH-3097 Liebefeld, Switzerland
- TAFS Forum, CH-3097 Liebefeld, Switzerland
| | | | - Ingrid Bergmann
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Abierta Interamericana (UAI), Buenos Aires C1287, Argentina
| | - Patrik Buholzer
- SAFOSO AG, CH-3097 Liebefeld, Switzerland
- TAFS Forum, CH-3097 Liebefeld, Switzerland
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2
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Mushtaq H, Shah SS, Zarlashat Y, Iqbal M, Abbas W. Cell Culture Adaptive Amino Acid Substitutions in FMDV Structural Proteins: A Key Mechanism for Altered Receptor Tropism. Viruses 2024; 16:512. [PMID: 38675855 PMCID: PMC11054764 DOI: 10.3390/v16040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 04/28/2024] Open
Abstract
The foot-and-mouth disease virus is a highly contagious and economically devastating virus of cloven-hooved animals, including cattle, buffalo, sheep, and goats, causing reduced animal productivity and posing international trade restrictions. For decades, chemically inactivated vaccines have been serving as the most effective strategy for the management of foot-and-mouth disease. Inactivated vaccines are commercially produced in cell culture systems, which require successful propagation and adaptation of field isolates, demanding a high cost and laborious time. Cell culture adaptation is chiefly indebted to amino acid substitutions in surface-exposed capsid proteins, altering the necessity of RGD-dependent receptors to heparan sulfate macromolecules for virus binding. Several amino acid substations in VP1, VP2, and VP3 capsid proteins of FMDV, both at structural and functional levels, have been characterized previously. This literature review combines frequently reported amino acid substitutions in virus capsid proteins, their critical roles in virus adaptation, and functional characterization of the substitutions. Furthermore, this data can facilitate molecular virologists to develop new vaccine strains against the foot-and-mouth disease virus, revolutionizing vaccinology via reverse genetic engineering and synthetic biology.
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Affiliation(s)
- Hassan Mushtaq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-C (NIBGE), Faisalabad 38000, Pakistan; (H.M.); (M.I.)
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan
| | - Syed Salman Shah
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 21300, Pakistan
| | - Yusra Zarlashat
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-C (NIBGE), Faisalabad 38000, Pakistan; (H.M.); (M.I.)
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-C (NIBGE), Faisalabad 38000, Pakistan; (H.M.); (M.I.)
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan
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3
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Carson J, Keeling M, Wyllie D, Ribeca P, Didelot X. Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host. Mol Biol Evol 2024; 41:msad288. [PMID: 38168711 PMCID: PMC10798190 DOI: 10.1093/molbev/msad288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024] Open
Abstract
In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here, we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. Furthermore, we remove the need for the assumption of a complete transmission bottleneck. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number, and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.
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Affiliation(s)
- Jake Carson
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK
| | - Matt Keeling
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK
| | | | | | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
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4
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Sala JM, Mansilla FC, Miraglia MC, Caspe SG, Perez-Filgueira DM, Capozzo AV. Kinetics of foot-and-mouth disease vaccine-induced antibody responses in buffaloes ( Bubalus bubalis): avidity ELISA as an alternative to the virus neutralization test. Front Vet Sci 2023; 10:1162477. [PMID: 38026657 PMCID: PMC10661941 DOI: 10.3389/fvets.2023.1162477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
The role of water buffaloes in foot-and-mouth disease (FMD) epidemiology as one of the major hosts of the virus that can develop persistent asymptomatic infection highlights the importance of sustaining surveillance on the antibody response elicited by vaccination in these animals. There is gap in the knowledge on how serological assays that measure antibodies against capsid proteins perform with buffalo samples and which would be the most reliable test to substitute the virus neutralization test (VNT) a cumbersome and low-throughput tool for field surveillance. Alternatively, the liquid-phase blocking sandwich ELISA (LPBE) is commonly used. Previous data from our laboratory demonstrated that the vaccine-induced antibodies assessed by the LPBE yielded low specificity with buffaloes' samples. In contrast, a single-dilution avidity ELISA (AE) aimed to detect high-avidity antibodies against exposed epitopes, combined with an indirect ELISA (IE) to assess IgG levels, produced more reliable results. Here we analyzed for the first time the kinetics of the antibodies induced by vaccination in two different buffalo herds (n = 91) over 120 days using AE, IE, LPBE, and the VNT. Kinetics were similar in the different assays, with an increase of antibodies between 0- and 14-days post-vaccination (dpv) which were maintained thereafter. VNT and AE results were concordant (Kappa value = 0.76), and both assays revealed a decay in the antibody response in calves with maternal antibodies at 90 and 120 dpv, which was not evidenced by the LPBE. These results show that kinetics of antibody responses to FMD vaccination are similar in buffalo and cattle, and support the use of indirect ELISA assays, in particular Avidity ELISA, as alternatives to the VNT for vaccine-immunity monitoring irrespectively of the animal's passive or active immune status.
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Affiliation(s)
- Juan Manuel Sala
- Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria (INTA), Mercedes, Corrientes, Argentina
| | - Florencia Celeste Mansilla
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Consejo Nacional de Investigaciones Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - María Cruz Miraglia
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Consejo Nacional de Investigaciones Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Sergio Gastón Caspe
- Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria (INTA), Mercedes, Corrientes, Argentina
| | - Daniel Mariano Perez-Filgueira
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Consejo Nacional de Investigaciones Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Alejandra Victoria Capozzo
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Consejo Nacional de Investigaciones Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
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Stenfeldt C, Fish I, Meek HC, Arzt J. Heterogeneity and Recombination of Foot-and-Mouth Disease Virus during Multi-Strain Coinfection of Cattle. mSphere 2023:e0064322. [PMID: 37093054 DOI: 10.1128/msphere.00643-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Superinfection of cattle persistently infected with foot-and-mouth disease virus (FMDV), with a heterologous FMDV strain has been shown to generate novel recombinant viruses. In this study, we investigated the pathogenesis events within specific tissues associated with FMDV coinfections in cattle subjected to either simultaneous or serial exposure to two distinct strains of FMDV. Both strains of FMDV (one each of serotypes O and A) were similarly localized to the nasopharyngeal mucosa during the early stages of infection. However, while no recombinant FMDV genomes were recovered from simultaneously coinfected cattle, interserotypic recombinants were isolated from nasopharyngeal tissue samples obtained at 48 h after heterologous superinfection of a persistently infected FMDV carrier. Additionally, analysis of FMDV genomes obtained from replicate nasopharyngeal tissue samples demonstrated that adjacent segments of the mucosa were sometimes infected by distinct viruses, demonstrating a multifocal and heterogeneous distribution of FMDV infection during primary and persistent phases of infection. This work indicates that superinfection of FMDV carriers may be an important source of emergent recombinant strains of FMDV in areas where multiple strains are co-circulating. IMPORTANCE Foot-and-mouth disease (FMD) is a socioeconomically impactful livestock disease with a complex epidemiology and ecology. Although recombinant viruses have been identified in field samples, the mechanisms of emergence of those viruses have never been elucidated. This current study demonstrates how serial infection of cattle with two distinct serotypes of FMD virus (FMDV) leads to rapid generation of recombinant viruses in the upper respiratory tracts of infected animals. This finding is particularly relevant in relation to the management of persistently infected FMDV carrier cattle that can maintain subclinical FMDV infection for months to years after an initial infection. Such carrier animals may function as mixing vessels that facilitate the emergence of novel recombinant FMDV strains in areas where multiple virus strains are in circulation.
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Affiliation(s)
- Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Research Center, Greenport, New York, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Ian Fish
- Foreign Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Research Center, Greenport, New York, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Haillie C Meek
- Foreign Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Research Center, Greenport, New York, USA
- PIADC Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Plum Island Animal Disease Research Center, Greenport, New York, USA
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Woldemariyam FT, Kariuki CK, Kamau J, De Vleeschauwer A, De Clercq K, Lefebvre DJ, Paeshuyse J. Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement. Viruses 2023; 15:v15040969. [PMID: 37112947 PMCID: PMC10143177 DOI: 10.3390/v15040969] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The Horn of Africa is a large area of arid and semi-arid land, holding about 10% of the global and 40% of the entire African livestock population. The region's livestock production system is mainly extensive and pastoralist. It faces countless problems, such as a shortage of pastures and watering points, poor access to veterinary services, and multiple endemic diseases like foot-and-mouth disease (FMD). Foot-and-mouth disease is one of the most economically important livestock diseases worldwide and is endemic in most developing countries. Within Africa, five of the seven serotypes of the FMD virus (FMDV) are described, but serotype C is not circulating anymore, a burden unseen anywhere in the world. The enormous genetic diversity of FMDV is favored by an error-prone RNA-dependent RNA polymerase, intra-typic and inter-typic recombination, as well as the quasi-species nature of the virus. This paper describes the epidemiological dynamics of foot-and-mouth disease in the Horn of Africa with regard to the serotypes and topotypes distribution of FMDV, the livestock production systems practiced, animal movement, the role of wildlife, and the epidemiological complexity of FMD. Within this review, outbreak investigation data and serological studies confirm the endemicity of the disease in the Horn of Africa. Multiple topotypes of FMDV are described in the literature as circulating in the region, with further evolution of virus diversity predicted. A large susceptible livestock population and the presence of wild ungulates are described as complicating the epidemiology of the disease. Further, the husbandry practices and legal and illegal trading of livestock and their products, coupled with poor biosecurity practices, are also reported to impact the spread of FMDV within and between countries in the region. The porosity of borders for pastoralist herders fuels the unregulated transboundary livestock trade. There are no systematic control strategies in the region except for sporadic vaccination with locally produced vaccines, while literature indicates that effective control measures should also consider virus diversity, livestock movements/biosecurity, transboundary trade, and the reduction of contact with wild, susceptible ungulates.
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Affiliation(s)
- Fanos Tadesse Woldemariyam
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- College of Veterinary Medicine, Addis Ababa University, Bishoftu P.O. Box 34, Ethiopia
| | - Christopher Kinyanjui Kariuki
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- Institute of Primate Research, Karen, Nairobi P.O. Box 24481-00502, Kenya
| | - Joseph Kamau
- Institute of Primate Research, Karen, Nairobi P.O. Box 24481-00502, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi P.O. Box 30197, Kenya
| | | | - Kris De Clercq
- Sciensano, Service for Exotic and Vector-Borne Diseases, 1050 Brussels, Belgium
| | - David J Lefebvre
- Sciensano, Service for Exotic and Vector-Borne Diseases, 1050 Brussels, Belgium
| | - Jan Paeshuyse
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
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7
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Han L, Yuan Y, Hu J, Li J, Zhu S, Yang P, Cheng A, Li X, Shen C. Next-generation sequencing sheds light on the interaction between virus and cell during foot-and-mouth disease virus persistent infection. Vet Microbiol 2021; 263:109247. [PMID: 34649012 DOI: 10.1016/j.vetmic.2021.109247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease virus (FMDV) infection can be either persistent or acute in susceptible animals. The mechanisms involved in FMDV replication and clearance during persistent infection remain unclear. To identify host factors that are critical for FMDV replication during persistent infection, we used RNA-seq to compare the transcriptomes of infected (BHK-Op) cells and bystander (BHK-VEC) cells, which are exposed to FMDV but not infected. In total, 1917 genes were differentially expressed between BHK-Op cells and BHK-VEC cells, which were involved in ribosome biogenesis, cell cycle, and dilated cardiomyopathy. We further identified host genes potentially involved in viral clearance during persistent FMDV infection by comprehensive crossover analysis of differentially expressed genes in ancestral host cells, evolved infected host cells, and evolved bystander cells, which are resistant to infection by wild-type FMDV and FMDV-Op that co-evolved with host cells during persistent infection. Among the identified genes were Cav1 and Ccnd1. Subsequent experiments showed that knockdown of Cav1 and Ccnd1 in host cells significantly promoted and inhibited FMDV replication, respectively, confirming that the overexpression of Cav1 and the downregulation of Ccnd1 contribute to virus clearance during persistent FMDV infection. In addition, we found that BHK-Op cells contained mixtures of multiple genotypes of FMDV viruses, shedding light on the diversity of FMDV genotypes during persistent infection. Our findings provide a detailed overview of the responses of infected cells and bystander cells to persistent FMDV infection.
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Affiliation(s)
- Lingling Han
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuncong Yuan
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jianjun Hu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiadai Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shumin Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Pu Yang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Andi Cheng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinmei Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chao Shen
- College of Life Sciences, Wuhan University, Wuhan 430072, China; China Center for Type Culture Collection, Wuhan University, Wuhan 430072, China.
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8
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Simmonds P, Cuypers L, Irving WL, McLauchlan J, Cooke GS, Barnes E, Ansari MA. Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus. RNA (NEW YORK, N.Y.) 2020; 26:1541-1556. [PMID: 32747607 PMCID: PMC7566573 DOI: 10.1261/rna.075465.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/29/2020] [Indexed: 05/03/2023]
Abstract
Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute previously associated with formation of large-scale RNA structure in their genomic RNA. We developed novel methods to analyze and visualize genome-scale ordered RNA structure (GORS) predicted from the increasingly large data sets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localized exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally poorly conserved, even between subtypes 1a and 1b. Dynamic remodeling was further evident from comparison of HCV strains in different host genetic backgrounds. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies, and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in the IFNL4 gene compared to the CC (nonexpressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represent an important new element in RNA virus evolution and the adaptive interplay between virus and host.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
| | - Lize Cuypers
- University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Research, BE 3000, Leuven, Belgium
| | - Will L Irving
- Faculty of Medicine and Health Sciences, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, United Kingdom
| | | | - Ellie Barnes
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
| | - M Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
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9
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Pascall DJ, Nomikou K, Bréard E, Zientara S, Filipe ADS, Hoffmann B, Jacquot M, Singer JB, De Clercq K, Bøtner A, Sailleau C, Viarouge C, Batten C, Puggioni G, Ligios C, Savini G, van Rijn PA, Mertens PPC, Biek R, Palmarini M. "Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence. PLoS Biol 2020; 18:e3000673. [PMID: 32343693 PMCID: PMC7188197 DOI: 10.1371/journal.pbio.3000673] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. Bluetongue virus serotype 8 (BTV-8), an arthropod-borne virus of ruminants, emerged in livestock in northern Europe in 2006, spreading to most European countries by 2009 and causing losses of billions of euros. Although the outbreak was successfully controlled through vaccination by early 2010, puzzlingly, a closely related BTV-8 strain re-emerged in France in 2015, triggering a second outbreak that is still ongoing. The origin of this virus and the mechanisms underlying its re-emergence are unknown. Here, we performed phylogenetic analyses of 164 whole BTV-8 genomes sampled throughout the two outbreaks. We demonstrate consistent clock-like virus evolution during both epizootics but found negligible evolutionary change between them. We estimate that the ancestor of the second outbreak dates from the height of the first outbreak in 2008. This implies that the virus had not been replicating for multiple years prior to its re-emergence in 2015. Given the absence of any known natural mechanism that could explain BTV-8 persistence over this long period without replication, we hypothesise that the second outbreak could have been initiated by accidental exposure of livestock to frozen material contaminated with virus from approximately 2008. Our work highlights new targets for pathogen surveillance programmes in livestock and illustrates the power of genomic epidemiology to identify pathways of infectious disease emergence.
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Affiliation(s)
- David J. Pascall
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Emmanuel Bréard
- UMR Virologie, INRA, École Nationale Vétérinaire d’Alfort, Laboratoire de Santé Animale d’Alfort, ANSES, Université Paris-Est, Maisons-Alfort, France
| | - Stephan Zientara
- UMR Virologie, INRA, École Nationale Vétérinaire d’Alfort, Laboratoire de Santé Animale d’Alfort, ANSES, Université Paris-Est, Maisons-Alfort, France
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Maude Jacquot
- Spatial Epidemiology Lab (SpELL), University of Brussels, Brussels, Belgium
- INRAE-VetAgro Sup, UMR Epidemiology of Animal and Zoonotic Diseases, Saint Genès-Champanelle, France
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Kris De Clercq
- Infectious Diseases in Animals, Exotic and Particular Diseases, Sciensano, Brussels, Belgium
| | - Anette Bøtner
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Corinne Sailleau
- UMR Virologie, INRA, École Nationale Vétérinaire d’Alfort, Laboratoire de Santé Animale d’Alfort, ANSES, Université Paris-Est, Maisons-Alfort, France
| | - Cyril Viarouge
- UMR Virologie, INRA, École Nationale Vétérinaire d’Alfort, Laboratoire de Santé Animale d’Alfort, ANSES, Université Paris-Est, Maisons-Alfort, France
| | - Carrie Batten
- The Pirbright Institute, Pirbright, Woking, Surrey, United Kingdom
| | - Giantonella Puggioni
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Duca degli Abruzzi, Sassari, Italy
| | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Duca degli Abruzzi, Sassari, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - Piet A. van Rijn
- Department of Virology, Wageningen Bioveterinary Research (WBVR), Lelystad, the Netherlands
- Department of Biochemistry, Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Peter P. C. Mertens
- The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- The Pirbright Institute, Pirbright, Woking, Surrey, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Fish I, Stenfeldt C, Palinski RM, Pauszek SJ, Arzt J. Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle. Pathogens 2020; 9:pathogens9030208. [PMID: 32178297 PMCID: PMC7157448 DOI: 10.3390/pathogens9030208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) infects hosts as a population of closely related viruses referred to as a quasispecies. The behavior of this quasispecies has not been described in detail in natural host species. In this study, virus samples collected from vaccinated and non-vaccinated cattle up to 35 days post-experimental infection with FMDV A24-Cruzeiro were analyzed by deep-sequencing. Vaccination induced significant differences compared to viruses from non-vaccinated cattle in substitution rates, entropy, and evidence for adaptation. Genomic variation detected during early infection reflected the diversity inherited from the source virus (inoculum), whereas by 12 days post infection, dominant viruses were defined by newly acquired mutations. Mutations conferring recognized fitness gain occurred and were associated with selective sweeps. Persistent infections always included multiple FMDV subpopulations, suggesting distinct foci of infection within the nasopharyngeal mucosa. Subclinical infection in vaccinated cattle included very early bottlenecks associated with reduced diversity within virus populations. Viruses from both animal cohorts contained putative antigenic escape mutations. However, these mutations occurred during later stages of infection, at which time transmission is less likely to occur. This study improves upon previously published work by analyzing deep sequences of samples, allowing for detailed characterization of FMDV populations over time within multiple hosts.
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Affiliation(s)
- Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN 37830, USA
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M. Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Steven J. Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Correspondence:
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11
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Stenfeldt C, Arzt J. The Carrier Conundrum; A Review of Recent Advances and Persistent Gaps Regarding the Carrier State of Foot-and-Mouth Disease Virus. Pathogens 2020; 9:E167. [PMID: 32121072 PMCID: PMC7157498 DOI: 10.3390/pathogens9030167] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The existence of a prolonged, subclinical phase of foot-and-mouth disease virus (FMDV) infection in cattle was first recognized in the 1950s. Since then, the FMDV carrier state has been a subject of controversy amongst scientists and policymakers. A fundamental conundrum remains in the discordance between the detection of infectious FMDV in carriers and the apparent lack of contagiousness to in-contact animals. Although substantial progress has been made in elucidating the causal mechanisms of persistent FMDV infection, there are still critical knowledge gaps that need to be addressed in order to elucidate, predict, prevent, and model the risks associated with the carrier state. This is further complicated by the occurrence of a distinct form of neoteric subclinical infection, which is indistinguishable from the carrier state in field scenarios, but may have substantially different epidemiological properties. This review summarizes the current state of knowledge of the FMDV carrier state and identifies specific areas of research in need of further attention. Findings from experimental investigations of FMDV pathogenesis are discussed in relation to experience gained from field studies of foot-and-mouth disease.
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Affiliation(s)
- Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Plum Island animal Disease Center, Orient, NY 11957, USA
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Plum Island animal Disease Center, Orient, NY 11957, USA
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12
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Zhou Z, Zhang P, Cui Y, Zhang Y, Qin X, Li R, Liu P, Dou Y, Wang L, Zhao Y. Experiments Investigating the Competitive Growth Advantage of Two Different Genotypes of Human Metapneumovirus: Implications for the Alternation of Genotype Prevalence. Sci Rep 2020; 10:2852. [PMID: 32071381 PMCID: PMC7029021 DOI: 10.1038/s41598-020-59150-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/23/2020] [Indexed: 12/03/2022] Open
Abstract
Human metapneumovirus (hMPV) is an important pathogen that causes upper and lower respiratory tract infections in children worldwide. hMPV has two major genotypes, hMPV-A and hMPV-B. Epidemiological studies have shown that the two hMPV genotypes alternate in predominance worldwide in recent years. Co-circulation of the two genotypes of hMPV was usually observed and there is no study about the interaction between them, such as competitive replication, which maybe the possible mechanisms for alternating prevalence of subtypes. Our present study have used two different genotypes of hMPV (genotype A: NL/1/00; B: NL/1/99) in different proportions in animal model (BALB/c mice) and cell model (Vero-E6) separately. The result showed that the competitive growth does exist in BALB/c mice, genotype B had a strong competitive advantage. However, genotype B did not cause more severe disease than non-predominant (genotype A) or mixed strains in the study, which were evaluated by the body weight, airway hyperresponsiveness and lung pathology of mouse. In cell model, competitive growth and the two genotypes alternately prevalence were observed. In summary, we confirmed that there was a competitive replication between hMPV genotype A and B, and no difference in disease severity caused by the two subtypes. This study shows a new insight to understand the alternation of hMPV genotype prevalence through genotype competition and provide experimental evidence for disease control and vaccine design.
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Affiliation(s)
- Zhen Zhou
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Pan Zhang
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Yuxia Cui
- Department of Pediatrics, Guizhou Provincial People's Hospital, Guizhou, 550002, China
| | - Yongbo Zhang
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Xian Qin
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Rongpei Li
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Ping Liu
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Ying Dou
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Lijia Wang
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China
| | - Yao Zhao
- Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China. .,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, 400014, China.
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13
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Ferretti L, Pérez-Martín E, Zhang F, Maree F, de Klerk-Lorist LM, van Schalkwykc L, Juleff ND, Charleston B, Ribeca P. Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid. PLoS Pathog 2020; 16:e1008235. [PMID: 31905219 PMCID: PMC6964909 DOI: 10.1371/journal.ppat.1008235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/16/2020] [Accepted: 11/23/2019] [Indexed: 02/05/2023] Open
Abstract
Although recombination is known to occur in foot-and-mouth disease virus (FMDV), it is considered only a minor determinant of virus sequence diversity. Analysis at phylogenetic scales shows inter-serotypic recombination events are rare, whereby recombination occurs almost exclusively in non-structural proteins. In this study we have estimated recombination rates within a natural host in an experimental setting. African buffaloes were inoculated with a SAT-1 FMDV strain containing two major viral sub-populations differing in their capsid sequence. This population structure enabled the detection of extensive within-host recombination in the genomic region coding for structural proteins and allowed recombination rates between the two sub-populations to be estimated. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Using a high-resolution map of effective within-host recombination in the capsid-coding region, we identified a linkage disequilibrium pattern in VP1 that is consistent with a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although these intra-host results are not immediately translatable to a phylogenetic setting, recombination and epistasis must play a major and so far underappreciated role in the molecular evolution of the virus at all scales. There are 7 serotypes of Foot-and-Mouth Disease Virus and multiple strains of each serotype. The emergence of new strains can result in widespread outbreaks of disease and requires new vaccines to be developed. The major mechanisms driving variation are thought to be substitutions in the viral genome. Recombination in the capsid-coding region of the virus genome has been described at phylogenetic scales but not thought to play a major role in generating variants. In the current experiment, a co-infection of African buffaloes with closely related sub-populations of viruses allowed us to detect recombination events. For structural protein-coding sequences, the genetic composition of the population is driven by extensive within-host recombination. During the acute infection phase the intra-host recombination rates of 0.1 per base per year are comparable to the typical mutation rates of the virus. The recombination map reveals two strongly linked regions within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between the two regions. Our findings in this experimental setting support a major role for recombination and epistasis in the intra-host evolution of FMDV.
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Affiliation(s)
- Luca Ferretti
- The Pirbright Institute, Woking, Surrey, United Kingdom
- Current address: Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail: ,
| | | | - Fuquan Zhang
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - François Maree
- South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Onderstepoort Veterinary Institute-Transboundary Animal Diseases Programme (OVI-TADP), Onderstepoort, Gauteng, South Africa
| | - Lin-Mari de Klerk-Lorist
- South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Louis van Schalkwykc
- South Africa Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | | | | | - Paolo Ribeca
- The Pirbright Institute, Woking, Surrey, United Kingdom
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14
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Garabed RB, Jolles A, Garira W, Lanzas C, Gutierrez J, Rempala G. Multi-scale dynamics of infectious diseases. Interface Focus 2019. [DOI: 10.1098/rsfs.2019.0118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To address the challenge of multiscale dynamics of infectious diseases, the Mathematical Biosciences Institute organized a workshop at The Ohio State University to bring together scientists from a variety of disciplines to share expertise gained through looking at infectious diseases across different scales. The researchers at the workshop, held in April 2018, were specifically looking at three model systems: foot-and-mouth disease, vector-borne diseases and enteric diseases. Although every multiscale model must be necessarily derived from a multiscale system, not every multiscale system has to lead to multiscale models. These three model systems seem to have produced a variety of both multiscale and integrated single-scale mechanistic models that have developed their own strengths and particular challenges. Here, we present papers from some of the workshop participants to show the breadth of the field.
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Affiliation(s)
- Rebecca B. Garabed
- College of Veterinary Medicine–Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Anna Jolles
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Winston Garira
- Mathematics and Applied Mathematics, University of Venda, Thohoyandou, Limpopo, South Africa
| | | | - Juan Gutierrez
- Department of Mathematics, University of Texas at San Antonio, San Antonio, TX, USA
| | - Grzegorz Rempala
- College of Public Health–Biostatistics, The Ohio State University, Columbus, OH, USA
- College of Arts and Sciences–Mathematics, The Ohio State University, Columbus, OH, USA
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Foot-and-Mouth Disease Virus: Immunobiology, Advances in Vaccines and Vaccination Strategies Addressing Vaccine Failures-An Indian Perspective. Vaccines (Basel) 2019; 7:vaccines7030090. [PMID: 31426368 PMCID: PMC6789522 DOI: 10.3390/vaccines7030090] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
A mass vaccination campaign in India seeks to control and eventually eradicate foot-and-mouth disease (FMD). Biosanitary measures along with FMD monitoring are being conducted along with vaccination. The implementation of the FMD control program has drastically reduced the incidence of FMD. However, cases are still reported, even in regions where vaccination is carried out regularly. Control of FMD outbreaks is difficult when the virus remains in circulation in the vaccinated population. Various FMD risk factors have been identified that are responsible for FMD in vaccinated areas. The factors are discussed along with strategies to address these challenges. The current chemically inactivated trivalent vaccine formulation containing strains of serotype O, A, and Asia 1 has limitations including thermolability and induction of only short-term immunity. Advantages and disadvantages of several new-generation alternate vaccine formulations are discussed. It is unfeasible to study every incidence of FMD in vaccinated animals/areas in such a big country as India with its huge livestock population. However, at the same time, it is absolutely necessary to identify the precise reason for vaccination failure. Failure to vaccinate is one reason for the occurrence of FMD in vaccinated areas. FMD epidemiology, emerging and re-emerging virus strains, and serological status over the past 10 years are discussed to understand the impact of vaccination and incidences of vaccination failure in India. Other factors that are important in vaccination failure that we discuss include disrupted herd immunity, health status of animals, FMD carrier status, and FMD prevalence in other species. Recommendations to boost the search of alternate vaccine formulation, strengthen the veterinary infrastructure, bolster the real-time monitoring of FMD, as well as a detailed investigation and documentation of every case of vaccination failure are provided with the goal of refining the control program.
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