1
|
Abd-Ellatieff HA, Hegazy AA, AbouRawash ARA, Tohamy HG, Al-Shehri M, Bazh EK, Hassan H, Essa BH. Pathological and genetic characterization of foot and mouth disease viruses collected from cattle and water buffalo in Egypt. PLoS One 2023; 18:e0291970. [PMID: 37819946 PMCID: PMC10566709 DOI: 10.1371/journal.pone.0291970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/08/2023] [Indexed: 10/13/2023] Open
Abstract
Foot-and-mouth disease (FMD), a highly contagious viral disease caused by FMD virus (FMDV) that threatens Egypt's livestock industry. FMDV causes severe economic losses in the livestock, with restriction of international trade from endemic regions. Surveillance for FMDV serotypes circulating in Egypt is urgently needed to assess the epidemiological situation in the country. FMD outbreaks reported in Egypt in between December 2016 and January-March 2017. A cross-sectional study was conducted to identify the FMDV serotypes responsible for the outbreaks and to collect information on the virus's morphopathological effects. Postmortem tissue and clinical samples (oral swabs, vesicular fluids from ruptured vesicles, and blood) were collected from recently deceased and infected animals. Pathological examination revealed classical FMD lesions as vesicular and erosive lesions on epithelial tissues with non-suppurative lymphoplasmacytic myocarditis. Phylogenetic and sequencing analyses demonstrated that FMDV serotype O, EA-3 topotype, VP1 is the prevalent serotype responsible for the pathological alterations and the high mortality in young calves, adult cattle, and water buffalo. The outcomes indicate continuous mutations in the circulating FMDV, which result in the occasional failure of vaccination. Based on these findings, extensive continuous monitoring and serotyping of the existing circulating FMDV isolates and regular vaccination with reevaluation of the currently used vaccine in Egypt are recommended to prevent the recurrence of such outbreaks.
Collapse
Affiliation(s)
- Hoda A. Abd-Ellatieff
- Department of Pathology, Faculty of Veterinary Medicine, Damanhour University, Abadiyyat Damanhur, El-Beheira, Egypt
| | - Asmaa A. Hegazy
- Department of Pathology, Faculty of Veterinary Medicine, Damanhour University, Abadiyyat Damanhur, El-Beheira, Egypt
| | - Abdel-Rahman A. AbouRawash
- Department of Pathology, Faculty of Veterinary Medicine, Damanhour University, Abadiyyat Damanhur, El-Beheira, Egypt
| | - Hossam G. Tohamy
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Mohammed Al-Shehri
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Eman K. Bazh
- Department of Parasitology, Faculty of Veterinary Medicine, Menoufia University, Shebin Al-Kom, Egypt
| | - Hesham Hassan
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Bothaina H. Essa
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Damanhour University, Abadiyyat Damanhur, El-Beheira, Egypt
| |
Collapse
|
2
|
Woldemariyam F, Paeshuyse J. Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015. VETERINARY MEDICINE (AUCKLAND, N.Z.) 2023; 14:91-101. [PMID: 37256222 PMCID: PMC10226516 DOI: 10.2147/vmrr.s408352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/19/2023] [Indexed: 06/01/2023]
Abstract
Introduction Pathogen molecular epidemiology determines the origin of specific outbreaks locality of foot-and-mouth disease virus serotype South African Territories-2 sequence-based analysis of highly variable Viral Protein 1 (VP1), which helps to identify the evolution of this virus through time and space. The objective of this study was to compare the differences between SAT-2 VP1 sequences of FMDV circulated in Ethiopia from 1990 to 2015 at the genetic level. Methods The nucleotide and amino acid sequences were analyzed using Basic Local Alignment Search Tools (BLAST), Multiple sequence alignment and sequence editing and Phylogenetic tree reconstruction. The nucleotide and amino acid sequences alignment, distance matrix, and phylogenetic tree constructions were done using the MEGA 6.0 software package. Result and Discussion In this analysis, we found 76% nucleotide identities and amino acid similarities among the sequences. The overall group mean distance at nucleotide level was 19% with a mean intra-population diversity of 2%. The lowest sequence variation was observed among sequences obtained from the years 2007/09/10, 2014/15, and 1990/91 which was less than 5% among them. This analysis revealed that in the last 25 years, four different topotypes of the FMDV SAT-2 were circulating in Ethiopia. The Arg-Gly-Asp (RGD) amino acid (AA) motif at AA position 144-146 within the G-H loop of the VP1 protein of FMDV is conserved, but up- and downstream hyper-variable AA sequences are identified. In this study, it was observed that four topotypes (IV, XIV, XIII, and VII) were circulating in Ethiopia for 25 years. Further, compared with sequences from neighboring countries (Sudan, Kenya) confirmed the presence of these topotypes. Conclusion Pertinent to this genetic diversity control strategies in Ethiopia should be based on having regular antigenic and genetic vaccine matching tests with the circulating strain within a defined period, space, transboundary nature of the disease and applying biosecurity measures.
Collapse
Affiliation(s)
- Fanos Woldemariyam
- Laboratory of Host-Pathogen Interaction, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Leuven, Belgium
- Department of Biomedical Sciences, College of Veterinary Medicine, Addis Ababa University, Bishoftu, Ethiopia
| | - Jan Paeshuyse
- Laboratory of Host-Pathogen Interaction, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, Leuven, Belgium
| |
Collapse
|
3
|
Establishing an In Vitro System to Assess How Specific Antibodies Drive the Evolution of Foot-and-Mouth Disease Virus. Viruses 2022; 14:v14081820. [PMID: 36016442 PMCID: PMC9412381 DOI: 10.3390/v14081820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Viruses can evolve to respond to immune pressures conferred by specific antibodies generated after vaccination and/or infection. In this study, an in vitro system was developed to investigate the impact of serum-neutralising antibodies upon the evolution of a foot-and-mouth disease virus (FMDV) isolate. The presence of sub-neutralising dilutions of specific antisera delayed the onset of virus-induced cytopathic effect (CPE) by up to 44 h compared to the untreated control cultures. Continued virus passage with sub-neutralising dilutions of these sera resulted in a decrease in time to complete CPE, suggesting that FMDV in these cultures adapted to escape immune pressure. These phenotypic changes were associated with three separate consensus-level non-synonymous mutations that accrued in the viral RNA-encoding amino acids at positions VP266, VP280 and VP1155, corresponding to known epitope sites. High-throughput sequencing also identified further nucleotide substitutions within the regions encoding the leader (Lpro), VP4, VP2 and VP3 proteins. While association of the later mutations with the adaptation to immune pressure must be further verified, these results highlight the multiple routes by which FMDV populations can escape neutralising antibodies and support the application of a simple in vitro approach to assess the impact of the humoral immune system on the evolution of FMDV and potentially other viruses.
Collapse
|
4
|
Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan. Viruses 2022; 14:v14081634. [PMID: 35893699 PMCID: PMC9331208 DOI: 10.3390/v14081634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.
Collapse
|
5
|
Yang B, Zhang X, Zhang D, Hou J, Xu G, Sheng C, Choudhury SM, Zhu Z, Li D, Zhang K, Zheng H, Liu X. Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus. Pathogens 2020; 9:pathogens9090729. [PMID: 32899635 PMCID: PMC7558374 DOI: 10.3390/pathogens9090729] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious vesicular disease in cloven-hoofed livestock that results in severe consequences for international trade, posing a great economic threat to agriculture. The FMDV infection antagonizes the host immune responses via different signaling pathways to achieve immune escape. Strategies to escape the cell immune system are key to effective infection and pathogenesis. This review is focused on summarizing the recent advances to understand how the proteins encoded by FMDV antagonize the host innate and adaptive immune responses.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Keshan Zhang
- Correspondence: (K.Z.); (H.Z.); Tel.: +86-15214078335 (K.Z.)
| | - Haixue Zheng
- Correspondence: (K.Z.); (H.Z.); Tel.: +86-15214078335 (K.Z.)
| | | |
Collapse
|
6
|
King DJ, Freimanis GL, Orton RJ, Waters RA, Haydon DT, King DP. Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 44:286-292. [PMID: 27421209 PMCID: PMC5036933 DOI: 10.1016/j.meegid.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022]
Abstract
Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT-PCR method was developed to amplify a 7.6kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.
Collapse
Affiliation(s)
- David J King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Graham L Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK; MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, 464 Bearsden Road, G61 1QH, UK
| | - Ryan A Waters
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| |
Collapse
|
7
|
Gao Y, Sun SQ, Guo HC. Biological function of Foot-and-mouth disease virus non-structural proteins and non-coding elements. Virol J 2016; 13:107. [PMID: 27334704 PMCID: PMC4917953 DOI: 10.1186/s12985-016-0561-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) represses host translation machinery, blocks protein secretion, and cleaves cellular proteins associated with signal transduction and the innate immune response to infection. Non-structural proteins (NSPs) and non-coding elements (NCEs) of FMDV play a critical role in these biological processes. The FMDV virion consists of capsid and nucleic acid. The virus genome is a positive single stranded RNA and encodes a single long open reading frame (ORF) flanked by a long structured 5ʹ-untranslated region (5ʹ-UTR) and a short 3ʹ-UTR. The ORF is translated into a polypeptide chain and processed into four structural proteins (VP1, VP2, VP3, and VP4), 10 NSPs (Lpro, 2A, 2B, 2C, 3A, 3B1–3, 3Cpro, and 3Dpol), and some cleavage intermediates. In the past decade, an increasing number of studies have begun to focus on the molecular pathogenesis of FMDV NSPs and NCEs. This review collected recent research progress on the biological functions of these NSPs and NCEs on the replication and host cellular regulation of FMDV to understand the molecular mechanism of host–FMDV interactions and provide perspectives for antiviral strategy and development of novel vaccines.
Collapse
Affiliation(s)
- Yuan Gao
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Shi-Qi Sun
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Hui-Chen Guo
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China.
| |
Collapse
|
8
|
Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 2015; 28:541-63. [PMID: 25876885 PMCID: PMC4399107 DOI: 10.1128/cmr.00075-13] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed.
Collapse
Affiliation(s)
- Carol A Gilchrist
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen D Turner
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret F Riley
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA School of Law, University of Virginia, Charlottesville, Virginia, USA Batten School of Leadership and Public Policy, University of Virginia, Charlottesville, Virginia, USA
| | - William A Petri
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Erik L Hewlett
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
9
|
Hu S, Qiao J, Fu Q, Chen C, Ni W, Wujiafu S, Ma S, Zhang H, Sheng J, Wang P, Wang D, Huang J, Cao L, Ouyang H. Transgenic shRNA pigs reduce susceptibility to foot and mouth disease virus infection. eLife 2015; 4:e06951. [PMID: 26090904 PMCID: PMC4502569 DOI: 10.7554/elife.06951] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/18/2015] [Indexed: 11/13/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) is an economically devastating viral disease leading to a substantial loss to the swine industry worldwide. A novel alternative strategy is to develop pigs that are genetically resistant to infection. Here, we produce transgenic (TG) pigs that constitutively expressed FMDV-specific short interfering RNA (siRNA) derived from small hairpin RNA (shRNA). In vitro challenge of TG fibroblasts showed the shRNA suppressed viral growth. TG and non-TG pigs were challenged by intramuscular injection with 100 LD50 of FMDV. High fever, severe clinical signs of foot-and-mouth disease and typical histopathological changes were observed in all of the non-TG pigs but in none of the high-siRNA pigs. Our results show that TG shRNA can provide a viable tool for producing animals with enhanced resistance to FMDV. DOI:http://dx.doi.org/10.7554/eLife.06951.001 Foot-and-mouth disease regularly causes serious outbreaks in livestock. The virus that causes the disease can infect cattle, pigs, sheep, goats, and many species of wild animals; the disease is also highly contagious and spreads very quickly and easily. To control the spread of foot-and-mouth disease, farmers must often kill entire herds of animals that have been exposed. Wild animals that can spread the virus may also be killed in an effort to stop the spread of the disease. Vaccines that protect against foot-and-mouth disease are available and are often used to help prevent the spread of the disease. However, once an outbreak of foot-and-mouth disease begins it may be too late for vaccines to stop its spread. This is because the vaccines can take about a week to provide protection, and by that time an exposed animal may already be very ill. Previous work conducted in 2010 reported that mice could be genetically engineered to produce short stretches of RNA molecules that can switch off genes from the foot-and-mouth disease virus. Compared with normal mice infected with the foot-and-mouth disease virus, the genetically engineered mice showed little sign of the disease in their bodies. Now, Hu, Qiao, Fu et al.—including some of the researchers involved in the 2010 work—have genetically engineered pigs in the same way. The experiments show that when cells from these pigs are exposed to the foot-and-mouth disease virus in the laboratory, the virus grows much less than normal. Next, Hu, Qiao, Fu et al. injected genetically engineered pigs and non-genetically engineered pigs with the virus. All of the normal pigs developed severe symptoms very quickly, including the disease's characteristic mouth and foot sores. Additionally, examinations of these pigs' cells showed signs of the disease. But the genetically engineered pigs did not become seriously ill and their cells showed little sign of the disease. Some of the genetically engineered pigs developed a few sores but these sores appeared much later than normal. So far, the results suggest that it may be possible to develop pigs that are resistant to foot-and-mouth disease. Hu, Qiao, Fu et al. will next determine whether or not the genetically engineered pigs can pass the foot-and-mouth virus on to other pigs and livestock. DOI:http://dx.doi.org/10.7554/eLife.06951.002
Collapse
Affiliation(s)
- Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jun Qiao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Qiang Fu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Chuangfu Chen
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Animal Sciences, Shihezi University, Shihezi, China
| | - Sai Wujiafu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Shiwei Ma
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Hui Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jingliang Sheng
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Pengyan Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jiong Huang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Lijuan Cao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Hongsheng Ouyang
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
10
|
Maree FF, Kasanga CJ, Scott KA, Opperman PA, Melanie C, Sangula AK, Raphael S, Yona S, Wambura PN, King DP, Paton DJ, Rweyemamu MM. Challenges and prospects for the control of foot-and-mouth disease: an African perspective. VETERINARY MEDICINE-RESEARCH AND REPORTS 2014; 5:119-138. [PMID: 32670853 PMCID: PMC7337166 DOI: 10.2147/vmrr.s62607] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/23/2014] [Indexed: 11/23/2022]
Abstract
The epidemiology of foot-and-mouth disease (FMD) in Africa is unique in the sense that six of the seven serotypes of FMD viruses (Southern African Territories [SAT] 1, SAT2, SAT3, A, O, and C), with the exception of Asia-1, have occurred in the last decade. Due to underreporting of FMD, the current strains circulating throughout sub-Saharan Africa are in many cases unknown. For SAT1, SAT2, and serotype A viruses, the genetic diversity is reflected in antigenic variation, and indications are that vaccine strains may be needed for each topotype. This has serious implications for control using vaccines and for choice of strains to include in regional antigen banks. The epidemiology is further complicated by the fact that SAT1, SAT2, and SAT3 viruses are maintained and spread by wildlife, persistently infecting African buffalo in particular. Although the precise mechanism of transmission of FMD from buffalo to cattle is not well understood, it is facilitated by direct contact between these two species. Once cattle are infected they may maintain SAT infections without the further involvement of buffalo. No single strategy for control of FMD in Africa is applicable. Decision on the most effective regional control strategy should focus on an ecosystem approach, identification of primary endemic areas, animal husbandry practices, climate, and animal movement. Within each ecosystem, human behavior could be integrated in disease control planning. Different regions in sub-Saharan Africa are at different developmental stages and are thus facing unique challenges and priorities in terms of veterinary disease control. Many science-based options targeting improved vaccinology, diagnostics, and other control measures have been described. This review therefore aims to emphasize, on one hand, the progress that has been achieved in the development of new technologies, including research towards improved tailored vaccines, appropriate vaccine strain selection, vaccine potency, and diagnostics, and how it relates to the conditions in Africa. On the other hand, we focus on the unique epidemiological, ecological, livestock farming and marketing, socioeconomic, and governance issues that constrain effective FMD control. Any such new technologies should have the availability of safe livestock products for trade as the ultimate goal.
Collapse
Affiliation(s)
- Francois F Maree
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | - Christopher J Kasanga
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Katherine A Scott
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa
| | - Pamela A Opperman
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | - Chitray Melanie
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Sallu Raphael
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sinkala Yona
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Philemon N Wambura
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | | | - Mark M Rweyemamu
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| |
Collapse
|
11
|
Ludi AB, Horton DL, Li Y, Mahapatra M, King DP, Knowles NJ, Russell CA, Paton DJ, Wood JLN, Smith DJ, Hammond JM. Antigenic variation of foot-and-mouth disease virus serotype A. J Gen Virol 2013; 95:384-392. [PMID: 24187014 DOI: 10.1099/vir.0.057521-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The current measures to control foot-and-mouth disease (FMD) include vaccination, movement control and slaughter of infected or susceptible animals. One of the difficulties in controlling FMD by vaccination arises due to the substantial diversity found among the seven serotypes of FMD virus (FMDV) and the strains within these serotypes. Therefore, vaccination using a single vaccine strain may not fully cross-protect against all strains within that serotype, and therefore selection of appropriate vaccines requires serological comparison of the field virus and potential vaccine viruses using relationship coefficients (r1 values). Limitations of this approach are that antigenic relationships among field viruses are not addressed, as comparisons are only with potential vaccine virus. Furthermore, inherent variation among vaccine sera may impair reproducibility of one-way relationship scores. Here, we used antigenic cartography to quantify and visualize the antigenic relationships among FMD serotype A viruses, aiming to improve the understanding of FMDV antigenic evolution and the scope and reliability of vaccine matching. Our results suggest that predicting antigenic difference using genetic sequence alone or by geographical location is not currently reliable. We found co-circulating lineages in one region that were genetically similar but antigenically distinct. Nevertheless, by comparing antigenic distances measured from the antigenic maps with the full capsid (P1) sequence, we identified a specific amino acid substitution associated with an antigenic mismatch among field viruses and a commonly used prototype vaccine strain, A22/IRQ/24/64.
Collapse
Affiliation(s)
- A B Ludi
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.,The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - D L Horton
- Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Y Li
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - M Mahapatra
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - D P King
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - N J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - C A Russell
- WHO Collaborating Centre for Modelling, Evolution and Control of Emerging Infectious Diseases, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - D J Paton
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - J L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - D J Smith
- WHO Collaborating Centre for Modelling, Evolution and Control of Emerging Infectious Diseases, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Department of Virology, Erasmus Medical Centre, 3000 CA, Rotterdam, The Netherlands.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - J M Hammond
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| |
Collapse
|
12
|
Wright CF, Knowles NJ, Di Nardo A, Paton DJ, Haydon DT, King DP. Reconstructing the origin and transmission dynamics of the 1967-68 foot-and-mouth disease epidemic in the United Kingdom. INFECTION GENETICS AND EVOLUTION 2013; 20:230-8. [PMID: 24035793 PMCID: PMC3898989 DOI: 10.1016/j.meegid.2013.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/25/2013] [Accepted: 09/05/2013] [Indexed: 12/03/2022]
Abstract
A large epidemic of foot-and-mouth disease (FMD) occurred in the United Kingdom (UK) over a seven month period in Northwest England from late 1967 to the summer of 1968. This was preceded by a number of smaller FMD outbreaks in the country, two in 1967, in Hampshire and Warwickshire and one in Northumberland during 1966. The causative agent of all four events was identified as FMD virus (FMDV) serotype O and the source of the large epidemic was attributed to infected bone marrow in lamb products imported from Argentina. However, the diagnostic tools available at the time were unable to entirely rule out connections with the earlier UK FMD outbreaks, as well as other potential sources from Europe. The aim of this study was to apply molecular sequencing to investigate the likely source of this epidemic using VP1 region and full genome (FG) sequences determined directly from clinical epithelium samples (n = 13) or cell culture isolates (n = 6), from this and contemporary outbreaks in the UK, Europe and South America. Analysis of the VP1 sequences provided evidence for at least three separate incursions of FMDV into the UK including one independent introduction that was responsible for the main 1967/68 epidemic. Analysis of FG sequences from the main 1967/68 outbreak (n = 10) revealed nucleotide substitutions at 94 genomic sites providing evidence for the linear accumulation of nucleotide substitutions (rate = 2.42 × 10−5 nt substitutions/site/day). However, there were five samples where this linear relationship was absent, indicating evolutional dormancy of the virus, presumably outside a host. These results help define the evolutionary dynamics of FMDV during an epidemic and contribute to the knowledge and understanding from which to base future outbreak control strategies.
Collapse
Affiliation(s)
- Caroline F Wright
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | | | | |
Collapse
|
13
|
Juleff N, Valdazo-González B, Wadsworth J, Wright CF, Charleston B, Paton DJ, King DP, Knowles NJ. Accumulation of nucleotide substitutions occurring during experimental transmission of foot-and-mouth disease virus. J Gen Virol 2012; 94:108-119. [PMID: 23034594 PMCID: PMC3542721 DOI: 10.1099/vir.0.046029-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of full-genome sequences was previously used to trace the origin and transmission pathways of foot-and-mouth disease virus (FMDV) outbreaks in the UK in 2001 and 2007. Interpretation of these data was sometimes at variance with conventional epidemiological tracing, and was also used to predict the presence of undisclosed infected premises that were later discovered during serological surveillance. Here we report the genome changes associated with sequential passage of a highly BHK-21-cell-adapted (heparan sulphate-binding) strain of FMDV arising from two independent transmission chains in cattle. In vivo virus replication rapidly selected for a wild-type variant with an amino acid substitution at VP3(56). Full-genome sequence analysis clearly demonstrated sequence divergence during parallel passage. The genetic diversity generated over the course of infection and the rate at which these changes became fixed and were transmitted between cattle occurred at a rate sufficient to enable reliable tracing of transmission pathways at the level of the individual animal. However, tracing of transmission pathways was only clear when sequences from epithelial lesions were compared. Sequences derived from oesophageal-pharyngeal scrapings were problematic to interpret, with a varying number of ambiguities suggestive of a more diverse virus population. These findings will help to correctly interpret full-genome sequence analyses to resolve transmission pathways within future FMDV epidemics.
Collapse
Affiliation(s)
- Nicholas Juleff
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | | | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Caroline F Wright
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Bryan Charleston
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - David J Paton
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| |
Collapse
|
14
|
Wang H, Wu J, Liu X, He H, Ding F, Yang H, Cheng L, Liu W, Zhong J, Dai Y, Li G, He C, Yu L, Li J. Identification of short hairpin RNA targeting foot-and-mouth disease virus with transgenic bovine fetal epithelium cells. PLoS One 2012; 7:e42356. [PMID: 22905125 PMCID: PMC3414509 DOI: 10.1371/journal.pone.0042356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/04/2012] [Indexed: 12/28/2022] Open
Abstract
Background Although it is known that RNA interference (RNAi) targeting viral genes protects experimental animals, such as mice, from the challenge of Foot-and-mouth disease virus (FMDV), it has not been previously investigated whether shRNAs targeting FMDV in transgenic dairy cattle or primary transgenic bovine epithelium cells will confer resistance against FMDV challenge. Principal Finding Here we constructed three recombinant lentiviral vectors containing shRNA against VP2 (RNAi-VP2), VP3 (RNAi-VP3), or VP4 (RNAi-VP4) of FMDV, and found that all of them strongly suppressed the transient expression of a FLAG-tagged viral gene fusion protein in 293T cells. In BHK-21 cells, RNAi-VP4 was found to be more potent in inhibition of viral replication than the others with over 98% inhibition of viral replication. Therefore, recombinant lentiviral vector RNAi-VP4 was transfected into bovine fetal fibroblast cells to generate transgenic nuclear donor cells. With subsequent somatic cell cloning, we generated forty transgenic blastocysts, and then transferred them to 20 synchronized recipient cows. Three transgenic bovine fetuses were obtained after pregnant period of 4 months, and integration into chromosome in cloned fetuses was confirmed by Southern hybridization. The primary tongue epithelium cells of transgenic fetuses were isolated and inoculated with 100 TCID50 of FMDV, and it was observed that shRNA significantly suppressed viral RNA synthesis and inhibited over 91% of viral replication after inoculation of FMDV for 48 h. Conclusion RNAi-VP4 targeting viral VP4 gene appears to prevent primary epithelium cells of transgenic bovine fetus from FMDV infection, and it could be a candidate shRNA used for cultivation of transgenic cattle against FMDV.
Collapse
Affiliation(s)
- Hongmei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Jianming Wu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Xiao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Hongbin He
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
- * E-mail: (HH); (GL)
| | - Fangrong Ding
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Hongjun Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Lei Cheng
- College of Life Science, Inner Mongolia University, Huhehaote, People's Republic of China
| | - Wenhao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Yunping Dai
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Guangpeng Li
- College of Life Science, Inner Mongolia University, Huhehaote, People's Republic of China
- * E-mail: (HH); (GL)
| | - Chengqiang He
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, People's Republic of China
| | - Jianbin Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| |
Collapse
|
15
|
Ahn I, Bae SE, Son HS. Comparative study of codon substitution patterns in foot-and-mouth disease virus (serotype O). Exp Mol Med 2012; 43:587-95. [PMID: 21825834 DOI: 10.3858/emm.2011.43.10.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We compared genetic variations in the VP1 gene of foot-and-mouth disease viruses (FMDVs) isolated since 2000 from various region of the world. We analyzed relative synonymous codon usage (RSCU) and phylogenetic relationship between geographical regions, and calculated the genetic substitution patterns between Korean isolate and those from other countries. We calculated the ratios of synonymously substituted codons (SSC) to all observed substitutions and developed a new analytical parameter, EMC (the ratio of exact matching codons within each synonymous substitution group) to investigate more detailed substitution patterns within each synonymous codon group. We observed that FMDVs showed distinct RSCU patterns according to phylogenetic relationships in the same serotype (serotype O). Moreover, while the SSC and EMC values of FMDVs decreased according to phylogenetic distance, G + C composition at the third codon position was strictly conserved. Although there was little variation among the SSC values of 18 amino acids, more dynamic differences were observed in EMC values. The EMC values of 4- and 6-fold degenerate amino acids showed significantly lower values while most 2-fold degenerate amino acids showed no significant difference. Our findings suggest that different EMC patterns among the 18 amino acids might be an important factor in determining the direction of evolution in FMDV.
Collapse
Affiliation(s)
- Insung Ahn
- Supercomputing Center,Korea Institute of Science and Technology Information,Daejon, Korea
| | | | | |
Collapse
|
16
|
León EA. Foot-and-mouth disease in pigs: current epidemiological situation and control methods. Transbound Emerg Dis 2012; 59 Suppl 1:36-49. [PMID: 22225815 DOI: 10.1111/j.1865-1682.2011.01290.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Foot-and-mouth disease (FMD) is the paradigm of a transboundary animal disease. Beyond any doubt, it is the most serious challenge for livestock's health. Official Veterinary Services from free countries invest considerable amount of money to prevent its introduction, whereas those from endemic countries invest most of their resources in the control of the disease. A very important volume of scientific production is developed every year in different aspects of FMD, and for that reason, the current knowledge makes the diagnosis of the disease easier to a great extent. However, FMD is still endemic in about two-thirds of the countries, and periodically re-emergent in several countries. This paper is a review of recent publications, focusing mainly on control measures and current world epidemiological situation, emphasizing primarily pigs.
Collapse
Affiliation(s)
- Emilio A León
- Instituto de Patobiología, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Castelar, Argentina.
| |
Collapse
|
17
|
Jaworski JP, Compaired D, Trotta M, Perez M, Trono K, Fondevila N. Validation of an r3AB1-FMDV-NSP ELISA to distinguish between cattle infected and vaccinated with foot-and-mouth disease virus. J Virol Methods 2011; 178:191-200. [DOI: 10.1016/j.jviromet.2011.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 06/20/2011] [Accepted: 09/14/2011] [Indexed: 11/25/2022]
|
18
|
Borca MV, Pacheco JM, Holinka LG, Carrillo C, Hartwig E, Garriga D, Kramer E, Rodriguez L, Piccone ME. Role of arginine-56 within the structural protein VP3 of foot-and-mouth disease virus (FMDV) O1 Campos in virus virulence. Virology 2011; 422:37-45. [PMID: 22036313 DOI: 10.1016/j.virol.2011.09.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 07/12/2011] [Accepted: 09/13/2011] [Indexed: 11/25/2022]
Abstract
FMDV O1 subtype undergoes antigenic variation under diverse growth conditions. Of particular interest is the amino acid variation observed at position 56 within the structural protein VP3. Selective pressures influence whether histidine (H) or arginine (R) is present at this position, ultimately influencing in vitro plaque morphology and in vivo pathogenesis in cattle. Using reverse genetics techniques, we have constructed FMDV type O1 Campos variants differing only at VP3 position 56, possessing either an H or R (O1Ca-VP3-56H and O1Ca-VP3-56R, respectively), and characterized their in vitro phenotype and virulence in the natural host. Both viruses showed similar growth kinetics in vitro. Conversely, they had distinct temperature-sensitivity (ts) and displayed significantly different pathogenic profiles in cattle and swine. O1Ca-VP3-56H was thermo stable and induced typical clinical signs of FMD, whereas O1Ca-VP3-56R presented a ts phenotype and was nonpathogenic unless VP3 position 56 reverted in vivo to either H or cysteine (C).
Collapse
Affiliation(s)
- Manuel V Borca
- Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, New York 11944-0848, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Muellner P, Zadoks RN, Perez AM, Spencer SEF, Schukken YH, French NP. The integration of molecular tools into veterinary and spatial epidemiology. Spat Spatiotemporal Epidemiol 2011; 2:159-71. [PMID: 22748175 DOI: 10.1016/j.sste.2011.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
At the interface of molecular biology and epidemiology, the emerging discipline of molecular epidemiology offers unique opportunities to advance the study of diseases through the investigation of infectious agents at the molecular level. Molecular tools can increase our understanding of the factors that shape the spatial and temporal distribution of pathogens and disease. Both spatial and molecular aspects have always been important to the field of infectious disease epidemiology, but recently news tools have been developed which increase our ability to consider both elements within a common framework. This enables the epidemiologist to make inferences about disease patterns in space and time. This paper introduces some basic concepts of molecular epidemiology in a veterinary context and illustrates the application of molecular tools at a range of spatio-temporal scales. Case studies - a multi-state outbreak of Serratia mastitis, a national control program for campylobacteriosis, and evolution of foot-and-mouth-disease viruses - are used to demonstrate the importance of considering molecular aspects in modern epidemiological studies. The discipline of molecular epidemiology is in its infancy and our contribution aims to promote awareness, understanding and uptake of molecular epidemiology in veterinary science.
Collapse
Affiliation(s)
- Petra Muellner
- Epi-interactive, 8a Darlington Road, Miramar, Wellington 6022, New Zealand.
| | | | | | | | | | | |
Collapse
|
20
|
Bayissa B, Ayelet G, Kyule M, Jibril Y, Gelaye E. Study on seroprevalence, risk factors, and economic impact of foot-and-mouth disease in Borena pastoral and agro-pastoral system, southern Ethiopia. Trop Anim Health Prod 2011; 43:759-66. [DOI: 10.1007/s11250-010-9728-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2010] [Indexed: 10/18/2022]
|
21
|
Direct typing and molecular evolutionary analysis of field samples of foot-and-mouth disease virus collected in Viet Nam between 2006 and 2007. Vet Microbiol 2011; 147:244-52. [DOI: 10.1016/j.vetmic.2010.06.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 06/25/2010] [Accepted: 06/29/2010] [Indexed: 11/18/2022]
|
22
|
Sangula AK, Belsham GJ, Muwanika VB, Heller R, Balinda SN, Masembe C, Siegismund HR. Evolutionary analysis of foot-and-mouth disease virus serotype SAT 1 isolates from east Africa suggests two independent introductions from southern Africa. BMC Evol Biol 2010; 10:371. [PMID: 21118525 PMCID: PMC3004922 DOI: 10.1186/1471-2148-10-371] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 11/30/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In East Africa, foot-and-mouth disease virus serotype SAT 1 is responsible for occasional severe outbreaks in livestock and is known to be maintained within the buffalo populations. Little is known about the evolutionary forces underlying its epidemiology in the region. To enhance our appreciation of the epidemiological status of serotype SAT 1 virus in the region, we inferred its evolutionary and phylogeographic history by means of genealogy-based coalescent methods using 53 VP1 coding sequences covering a sampling period from 1948-2007. RESULTS The VP1 coding sequence of 11 serotype SAT 1 FMD viruses from East Africa has been determined and compared with known sequences derived from other SAT 1 viruses from sub-Saharan Africa. Purifying (negative) selection and low substitution rates characterized the SAT 1 virus isolates in East Africa. Two virus groups with probable independent introductions from southern Africa were identified from a maximum clade credibility tree. One group was exclusive to Uganda while the other was present within Kenya and Tanzania. CONCLUSIONS Our results provide a baseline characterization of the inter-regional spread of SAT 1 in sub-Saharan Africa and highlight the importance of a regional approach to trans-boundary animal disease control in order to monitor circulating strains and apply appropriate vaccines.
Collapse
Affiliation(s)
- Abraham K Sangula
- Makerere University, Institute of Environment and Natural Resources, Molecular Biology Laboratory, P, O, Box 7298, Kampala, Uganda.
| | | | | | | | | | | | | |
Collapse
|
23
|
Shim E, Chapman GB, Galvani AP. Decision making with regard to antiviral intervention during an influenza pandemic. Med Decis Making 2010; 30:E64-81. [PMID: 20634545 DOI: 10.1177/0272989x10374112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Antiviral coverage is defined by the proportion of the population that takes antiviral prophylaxis or treatment. High coverage of an antiviral drug has epidemiological and evolutionary repercussions. Antivirals select for drug resistance within the population, and individuals may experience adverse effects. To determine optimal antiviral coverage in the context of an influenza outbreak, we compared 2 perspectives: 1) the individual level (the Nash perspective), and 2) the population level (utilitarian perspective). METHODS We developed an epidemiological game-theoretic model of an influenza pandemic. The data sources were published literature and a national survey. The target population was the US population. The time horizon was 6 months. The perspective was individuals and the population overall. The interventions were antiviral prophylaxis and treatment. The outcome measures were the optimal coverage of antivirals in an influenza pandemic. RESULTS At current antiviral pricing, the optimal Nash strategy is 0% coverage for prophylaxis and 30% coverage for treatment, whereas the optimal utilitarian strategy is 19% coverage for prophylaxis and 100% coverage for treatment. Subsidizing prophylaxis by $440 and treatment by $85 would bring the Nash and utilitarian strategies into alignment. For both prophylaxis and treatment, the optimal antiviral coverage decreases as pricing of antivirals increases. Our study does not incorporate the possibility of an effective vaccine and lacks probabilistic sensitivity analysis. Our survey also does not completely represent the US population. Because our model assumes a homogeneous population and homogeneous antiviral pricing, it does not incorporate heterogeneity of preference. CONCLUSIONS The optimal antiviral coverage from the population perspective and individual perspectives differs widely for both prophylaxis and treatment strategies. Optimal population and individual strategies for prophylaxis and treatment might be aligned through subsidization.
Collapse
Affiliation(s)
- Eunha Shim
- Department of Epidemiology & Public Health, Yale School of Public Health, New Haven, CT 06520, USA.
| | | | | |
Collapse
|
24
|
Zhou JH, Zhang J, Chen HT, Ma LN, Liu YS. Analysis of synonymous codon usage in foot-and-mouth disease virus. Vet Res Commun 2010; 34:393-404. [PMID: 20425142 DOI: 10.1007/s11259-010-9359-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2010] [Indexed: 10/19/2022]
Abstract
In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C & O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.
Collapse
Affiliation(s)
- Jian-Hua Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | | | | | | | | |
Collapse
|
25
|
Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field. Epidemiol Infect 2010; 139:189-96. [DOI: 10.1017/s0950268810000580] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYMost viruses are maintained by complex processes of evolution that enable them to survive but also complicate efforts to achieve their control. In this paper, we study patterns of evolution in foot-and-mouth disease (FMD) serotype C virus isolates from Kenya, one of the few places in the world where serotype C has been endemic and is suspected to remain. The nucleotide sequences encoding the capsid protein VP1 from eight isolates collected between 1967 and 2004 were analysed for patterns of sequence divergence and evolution. Very low nucleotide diversity (π=0·0025) and remarkably little change (only five segregating sites and three amino-acid changes) were observed in these isolates collected over a period of almost 40 years. We interpret these results as being suggestive of re-introductions of the vaccine strain into the field. The implications of these results for the maintenance of serotype C FMD virus and the use of vaccination as a control measure in Kenya are discussed.
Collapse
|
26
|
Garabed RB, Johnson WO, Thurmond MC. Analytical Epidemiology of Genomic Variation among Pan Asia Strains of Foot-and-Mouth Disease Virus. Transbound Emerg Dis 2009; 56:142-56. [DOI: 10.1111/j.1865-1682.2009.01068.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
27
|
Lee KN, Oem JK, Park JH, Kim SM, Lee SY, Tserendorj S, Sodnomdarjaa R, Joo YS, Kim H. Evidence of recombination in a new isolate of foot-and-mouth disease virus serotype Asia 1. Virus Res 2009; 139:117-21. [DOI: 10.1016/j.virusres.2008.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 09/22/2008] [Accepted: 09/26/2008] [Indexed: 11/30/2022]
|
28
|
Wee SH, Yoon H, More SJ, Nam HM, Moon OK, Jung JM, Kim SJ, Kim CH, Lee ES, Park CK, Hwang IJ. Epidemiological Characteristics of the 2002 Outbreak of Foot-and-Mouth Disease in The Republic of Korea. Transbound Emerg Dis 2008; 55:360-8. [DOI: 10.1111/j.1865-1682.2008.01045.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Hughes AL, Piontkivska H. Nucleotide sequence polymorphism in circoviruses. INFECTION GENETICS AND EVOLUTION 2007; 8:130-8. [PMID: 18093882 DOI: 10.1016/j.meegid.2007.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 11/02/2007] [Accepted: 11/07/2007] [Indexed: 12/24/2022]
Abstract
Analysis of nucleotide diversity within six species of circovirus showed consistently stronger purifying selection at nonsynonymous sites in the rep gene than on those in the cap gene. In addition, synonymous nucleotide diversity in the rep gene was significantly lower than that in the cap gene, suggesting functional constraint even at synonymous sites in rep, which was associated in all six species with strongly negative AT-skew. Of the six virus species examined, four species showed evidence of ongoing purifying selection at nonsynonymous polymorphic sites in the rep gene, indicating the presence of slightly deterious nonsynonymous variants in these populations. The rep gene of porcine circovirus 2 (PCV2) was unique, however, in showing a strong excess of rare nonsynonymous polymorphisms. The excess of rare nonsynonymous polymorphisms suggests a prolonged population bottleneck in PCV2, allowing slightly deleterious mutations to accumulate, followed by a population expansion during which selection to remove these variants has increased in effectiveness. Such a population history is consistent with the epidemiological evidence of a recent worldwide spread of PCV2.
Collapse
Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States.
| | | |
Collapse
|
30
|
Vosloo W, de Klerk LM, Boshoff CI, Botha B, Dwarka RM, Keet D, Haydon DT. Characterisation of a SAT-1 outbreak of foot-and-mouth disease in captive African buffalo (Syncerus caffer): Clinical symptoms, genetic characterisation and phylogenetic comparison of outbreak isolates. Vet Microbiol 2007; 120:226-40. [PMID: 17194552 DOI: 10.1016/j.vetmic.2006.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 10/27/2006] [Accepted: 11/02/2006] [Indexed: 10/23/2022]
Abstract
African buffalo (Syncerus caffer) play an important role in the maintenance of the SAT types of foot-and-mouth disease (FMD) in southern Africa. These long-term carriers mostly become sub-clinically infected, maintaining the disease and posing a threat to other susceptible wildlife and domestic species. During an unrelated bovine tuberculosis experiment using captive buffalo in the Kruger National Park (KNP), an outbreak of SAT-1 occurred and was further investigated. The clinical signs were recorded and all animals demonstrated significant weight loss and lymphopenia that lasted 100 days. In addition, the mean cell volume and mean cell haemoglobin values were significantly higher than before the outbreak started. Virus was isolated from several buffalo over a period of 167 days post infection and the molecular clock estimated to be 3 x 10(-5) nucleotide substitutions per site per day. Seven amino acid changes occurred of which four occurred in hypervariable regions previously described for SAT-1. The genetic relationship of the outbreak virus was compared to buffalo viruses previously obtained from the KNP but the phylogeny was largely unresolved, therefore the relationship of this outbreak strain to others isolated from the KNP remains unclear.
Collapse
Affiliation(s)
- W Vosloo
- Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, South Africa.
| | | | | | | | | | | | | |
Collapse
|
31
|
Cottam EM, Haydon DT, Paton DJ, Gloster J, Wilesmith JW, Ferris NP, Hutchings GH, King DP. Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. J Virol 2006; 80:11274-82. [PMID: 16971422 PMCID: PMC1642183 DOI: 10.1128/jvi.01236-06] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to quantify the extent to which the genetic diversity of foot-and-mouth disease virus (FMDV) arising over the course of infection of an individual animal becomes fixed, is transmitted to other animals, and thereby accumulates over the course of an outbreak. Complete consensus sequences of 23 genomes (each of 8,200 nucleotides) of FMDV were recovered directly from epithelium tissue acquired from 21 farms infected over a nearly 7-month period during the 2001 FMDV outbreak in the United Kingdom. An analysis of these consensus sequences revealed very few apparently ambiguous sites but clear evidence of 197 nucleotide substitutions at 191 different sites. We estimated the rate of nucleotide substitution to be 2.26 x 10(-5) per site per day (95% confidence interval [CI], 1.75 x 10(-5) to 2.80 x 10(-5)) and nucleotide substitutions to accrue in the consensus sequence at an average rate of 1.5 substitutions per farm infection. This is a sufficiently high rate showing that detailed histories of the transmission pathways can be reliably reconstructed. Coalescent methods indicated that the date at which FMDV first infected livestock in the United Kingdom was 7 February 2001 (95% CI, 20 January to 19 February 2001), which was identical to estimates obtained on the basis of purely clinical evidence. Nucleotide changes appeared to have occurred evenly across the genome, and within the open reading frame, the ratio of nonsynonymous-to-synonymous change was 0.09. The ability to recover particular transmission pathways of acutely acting RNA pathogens from genetic data will help resolve uncertainties about how virus is spread and could help in the control of future epidemics.
Collapse
Affiliation(s)
- Eleanor M Cottam
- Institute for Animal Health, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Haydon DT, Kao RR, Kitching RP. The UK foot-and-mouth disease outbreak - the aftermath. Nat Rev Microbiol 2004; 2:675-81. [PMID: 15263902 DOI: 10.1038/nrmicro960] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel T Haydon
- Division of Environmental and Evolutionary Biology, University of Glasgow, UK.
| | | | | |
Collapse
|
33
|
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals. The disease was initially described in the 16th century and was the first animal pathogen identified as a virus. Recent FMD outbreaks in developed countries and their significant economic impact have increased the concern of governments worldwide. This review describes the reemergence of FMD in developed countries that had been disease free for many years and the effect that this has had on disease control strategies. The etiologic agent, FMD virus (FMDV), a member of the Picornaviridae family, is examined in detail at the genetic, structural, and biochemical levels and in terms of its antigenic diversity. The virus replication cycle, including virus-receptor interactions as well as unique aspects of virus translation and shutoff of host macromolecular synthesis, is discussed. This information has been the basis for the development of improved protocols to rapidly identify disease outbreaks, to differentiate vaccinated from infected animals, and to begin to identify and test novel vaccine candidates. Furthermore, this knowledge, coupled with the ability to manipulate FMDV genomes at the molecular level, has provided the framework for examination of disease pathogenesis and the development of a more complete understanding of the virus and host factors involved.
Collapse
Affiliation(s)
- Marvin J Grubman
- Plum Island Animal Disease Center, USDA, Agricultural Research Service, North Atlantic Area, Greenport, New York 11944, USA.
| | | |
Collapse
|
34
|
|
35
|
Bastos ADS, Haydon DT, Sangaré O, Boshoff CI, Edrich JL, Thomson GR. The implications of virus diversity within the SAT 2 serotype for control of foot-and-mouth disease in sub-Saharan Africa. J Gen Virol 2003; 84:1595-1606. [PMID: 12771430 DOI: 10.1099/vir.0.18859-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SAT 2 is the serotype most often associated with outbreaks of foot-and-mouth disease (FMD) in livestock in southern and western Africa and is the only SAT type to have been recorded outside the African continent in the last decade. Its epidemiology is complicated by the presence of African buffalo (Syncerus caffer), which play an important role in virus maintenance and transmission. To assess the level of genetic complexity of this serotype among viruses associated with both domestic livestock and wildlife, complete VP1 gene sequences of 53 viruses from 17 countries and three different host species were analysed. Phylogenetic analysis revealed eleven virus lineages, differing from each other by at least 20 % in pairwise nucleotide comparisons, four of which fall within the southern African region, two in West Africa and the remaining five in central and East Africa. No evidence of recombination between these lineages was detected, and thus we conclude that these are independently evolving virus lineages which occur primarily in discrete geographical localities in accordance with the FMD virus topotype concept. Applied to the whole phylogeny, rates of nucleotide substitution are significantly different between topotypes, but most individual topotypes evolve in accordance with a molecular clock at an average rate of approximately 0.002 substitutions per site per year. This study provides an indication of the intratypic complexity of the SAT 2 serotype at the continental level and emphasizes the value of molecular characterization of diverse FMD field strains for tracing the origin of outbreaks.
Collapse
Affiliation(s)
- A D S Bastos
- ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria 0002, South Africa
| | - D T Haydon
- Centre for Tropical Veterinary Medicine, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - O Sangaré
- Laboratoire Central Veterinaire, BP 2295, Bamako, Mali
- ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa
| | - C I Boshoff
- ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa
| | - J L Edrich
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria 0002, South Africa
| | - G R Thomson
- Organization of African Unity/Inter-African Bureau for Animal Resources (OAU-IBR), PO Box 30786, Nairobi, Kenya
- ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa
| |
Collapse
|