Comparative evolutionary biology of RNA viruses

Lead Research Organisation: The Pirbright Institute
Department Name: UNLISTED

Abstract

This core project will develop an improved understanding of the evolutionary biology of RNA viruses including those that cause important trans-boundary animal diseases. These studies will exploit the potential provided by the extensive virus archive maintained by the international Reference Laboratories at Pirbright. The principal focus of this work is the natural history of foot-and-mouth disease virus (FMDV), but comparative insights generated from genomic studies of related picornaviruses will also be included. At the finest scales, we will utilise the latest techniques for sequencing viral genomes to characterise viral genetic swarms and define the specific mechanisms that drive viral evolution within and between susceptible hosts. At broadest scales, spatial and temporal analyses will be integrated into on-going cross-sectional and longitudinal field studies in sub-Saharan Africa and Asia to provide valuable insights into the factors that are responsible for the extent of global viral variation that is generated by the circulation of FMDV in endemic regions. These data will define the relative importance of different transmission routes, and support the development of predictive models by providing data on host, viral and environmental factors that influence sequence changes that accrue during virus transmission. A key activity will be to test specific hypotheses relating to factors that influence viral evolution and transmission using controlled experiments in high containment facilities using cell cultures and appropriate experiments in natural animal hosts. These studies will link to related studies in other IAH research groups on transmission biology, immunology, field epidemiology and disease modelling. This capability will be complemented by the strong links with mathematical and evolutionary biologists at Glasgow University, and with bio-informatics expertise that is available at The Genome Analysis Centre at Norwich.
 
Description Comparative evolutionary biology of RNA viruses: the focus of this core project is to develop an improved understanding of the evolutionary biology of RNA viruses including those that cause important trans-boundary animal diseases. Since the award of this core project, we have undertaken studies in the following areas: [1] to characterise the genomes of novel picornaviruses and other related RNA viruses; and [2] to establish next-generation sequencing approaches that can be applied to study the antigenic properties and phylo-dynamics of important livestock viruses such as FMDV and SVDV.

Key outputs of this project:
1) Pioneered next-generation sequencing (NGS) protocols for complete genome sequencing of RNA viruses without the requirement for PCR amplification [1], now employed by the FMD Reference Laboratory as well as across different research groups at TPI.
2) Developed a model to understand the extent of technical error in NGS pipelines used to characterise FMD viral sequence swarms [2], and applied these methods to understand the evolution of FMDV [3].
3) Secured external collaborative funding to support complementary activities for FMDV evolutionary biology from BBSRC (sLOLA: The Molecular Biology of FMDV Replication: Towards New Methods of FMDV Control), BBSRC/DBT (An effective vaccination programme for the eradication of foot-and-mouth disease from India) and a new BBSRC CASE Studentship (David King: Impact of vaccine-induced immunity on the evolution of FMDV).
4) Used NGS to characterise Seneca Valley virus, providing an early warning to the UK of a new vesicular disease in pigs. These data were also used to rapidly develop a new diagnostic test for SVV [4], now in use in the FMD Reference Laboratory.
5) Contributed to work to determine the X-ray crystal structure of a picornavirus, Ljungan virus [5] and (in collaboration with other groups) characterised the genomes of novel picornaviruses from fish [6], birds [7], cats [8], rats [9], cattle [10], and a novel virus in seals that is closely related to human hepatitis A virus [11]. This work has also demonstrated that swine vesicular disease virus originates by the recombination of human coxsackieviruses B5 and A9 [12].

References: [1] Logan et al., (2014) BMC Genomics 15: 828; [2] Orton et al., (2015) BMC Genomics 16: 229; [3] Morelli et al., (2013) Veterinary Research 44: 12; [4] Fowler et al., (2017) J. Virol. Methods 239: 34-7; [5] Zhu et al., (2015) Nat. Commun. 6: 8316; [6] Barbknecht et al., (2014) J. Gen. Virol. 95: 601-13; [7] Boros et al., (2014) J. Virol. 88: 6434-43; [8] Ng et al., (2014) Vet. Microbiol. 171: 102-111; [9] Ng et al., (2015) Arch. Virol. 160: 2569-75; [10] Rai et al., (2015) Bioinformatics and Biology Insights 9 (Suppl 2): 43-58; [11] Anthony et al., (2015) MBio 6(4): e01180-15; [12] Bruhn et al., (2015) Evol. Med. Public Health (1): 289-303.
Exploitation Route Future work will continue to explore the comparative genomics of RNA viruses, including new work to study a range of uncharacterised vesiviruses (caliciviruses) and other FMD viruses in the Reference Laboratory collection. Although this work will continue to use the established (Sanger) sequencing platforms, we will increasingly look to develop and evaluate new unbiased protocols to sequence viruses using next-generation sequencing (NGS) approaches. Furthermore, we also plan to explore new NGS pipelines that might be used for metagenomics analyses leading to virus discovery.
Sectors Agriculture, Food and Drink,Education,Environment,Healthcare

 
Description Work to date has identified and characterised novel picornaviruses that infect a range of mammalian and non-mammalian hosts. These data contribute to our understanding of the diversity of this important RNA virus family and highlight evolutionary relationship between human and animal viruses (such as between swine vesicular disease virus and coxsackie B5 virus). As a practical example of the outputs from this project, our work to characterise novel picornaviruses has led to the development of new diagnostic tests for Seneca Valley virus (SVV) that infects pigs. This is emerging picornavirus causes vesicular disease signs in pigs, and is becoming widely distributed in swine industries globally (South America, USA and China) and now poses a threat to the pig industries in the UK (and Europe). This project has provided characterised materials that have been used to validate these new tests - and have led to the establishment of routine diagnostic capacity for this virus in the UK (and in the USA).
First Year Of Impact 2012
Sector Agriculture, Food and Drink,Education
Impact Types Economic,Policy & public services

 
Title Universal method to sequence RNA virus genomes 
Description Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We have developed a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using FMDV positive clinical samples, as well as samples that had been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment. 
Type Of Material Technology assay or reagent 
Year Produced 2013 
Provided To Others? Yes  
Impact This protocol is now being routinely applied to samples received into FMD Reference Laboratories. 
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247156/pdf/12864_2014_Article_6688.pdf
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Botswana Vaccine Institute
Country Botswana 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Department of Livestock Development
Country Thailand 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation FGBI Federal Centre for Animal Health
Country Russian Federation 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation French Agency for Food, Environmental and Occupational Health & Safety (ANSES)
Country France 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Lanzhou Veterinary Research Institute
Country China 
Sector Learned Society 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Lombardy and Emilia Romagna Experimental Zootechnic Institute (IZSLER)
Country Italy 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation National Agri-Food Quality and Health Service (SENASA)
Country Argentina 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation National Centre for Foreign Animal Diseases (NCFAD)
Country Canada 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Onderstepoort Veterinary Institute
Country South Africa 
Sector Academic/University 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Pan American Foot-and-Mouth Disease Center (Panaftosa)
Country Brazil 
Sector Charity/Non Profit 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Project Directorate on Foot and Mouth Disease
Country India 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Veterinary and Agrochemical Research Centre
Country Belgium 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description 33rd World Veterinary Congress, Incheon, South Korea, August 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Don King was an invited speaker at the 33rd World Veterinary Congress, Incheon, South Korea, August 2017. He presented a talk entitled: New tools for the detection and characterisation of transboundary diseases.
Year(s) Of Engagement Activity 2017
URL http://wvc2017korea.com/
 
Description CEEZAD BSL-3 Training/Transboundary Animal Disease Summer Program - Manhattan, Kansas, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact CEEZAD BSL-3 Training/Transboundary Animal Disease Summer Program Provides a Unique Opportunity for Future Veterinary Professionals

Ten future veterinary professionals with an interest in transboundary disease research took part in a two-week training program conducted by the Center of Excellence for Emerging Zoonotic and Animal Diseases (CEEZAD) at Kansas State University in coordination with the Kansas State University Biosecurity Research Institute (BRI).

The program involved one week of exposure to operations, safety techniques and lab principles of high-containment BSL-3 work at the Biosecurity Research Institute at Kansas State University followed by a second week of visits to institutions involved in the animal health industry and lectures. Students, representing 10 universities from around the USA, heard from prominent professionals in the area of zoonotic and transboundary disease research. The participants include students in veterinary medicine, doctoral students and post-DVM residents
Year(s) Of Engagement Activity 2016
URL http://ceezad.org/news_events/
 
Description EUROPIC 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Knowles NJ, Todd D, Bachanek-Bankowska K. (2016c). Genome sequence of avian entero-like virus 2 shows it to be a chicken megrivirus. EUROPIC 2016: IX Meeting of the European Study Group on the Molecular Biology of Picornaviruses, Diablerets, Switzerland, 4-8th September 2016.9.
Year(s) Of Engagement Activity 2016
 
Description EuFMD 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at EuFMD open session: Knowles NJ, Wadsworth J, Fowler V, Bachanek-Bankowska K. (2016e). The origin, evolution and diagnosis of Seneca valley virus, a new vesicular disease-causing picornavirus of pigs. Open Session of the EuFMD Standing Technical Committee, Cascais, Portugal, 26-28 October 2016.
Year(s) Of Engagement Activity 2016
URL https://www.opensessioneufmd.com/os-16
 
Description Keynote presentation - 3rd Global Conference of OIE Reference Laboratories. Incheon (Seoul), Republic of Korea, October 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented an Invited-Keynote talk at the 3rd Global Conference of OIE Reference Laboratories. Incheon (Seoul), Republic of Korea, October 2014. This session considered the practical applications of new genomic sequencing methods to understand the epidemiology of pathogens that infect livestock.

Talk title:
King D. P. Use of next-generation sequencing to investigate foot-and-mouth disease virus transmission.
Year(s) Of Engagement Activity 2014
URL http://www.oie.int/eng/refcentre2014/presentations.htm
 
Description Keynote presentation - 7th International Symposium on Emerging and re-emerging Pig Diseases, Kyoto, Japan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk outlining our research findings - entitled: "King D.P., Logan G., Freimanis G. L., Wright C. F., King D. J., Knowles N. J., Wadsworth J., Lasecka L., Bachanek-Bankowska K., Di Nardo A., Orton R. and Haydon D. T. Using sequence data to understand the epidemiology of foot-and-mouth disease" at the 7th International Symposium on Emerging and re-emerging Pig Diseases, Kyoto, Japan, June 2015.
Year(s) Of Engagement Activity 2015
URL http://emerging2015.com
 
Description Lecture to students - Cambridge University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Provided a lecture to undergraduate vet/med students at the University of Cambridge - on FMD and tools to control the disease
Year(s) Of Engagement Activity 2016
 
Description Webinar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Organised Webinar with US Researchers to discuss diagnostic methods for surveillance using bulk milk
Year(s) Of Engagement Activity 2017