ArticleBMC genomics2014
A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 84 citations in OpenAlex.
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- Universal amplification and sequencing of foot-and-mouth disease virus complete genomes using nanopore technology.BMC genomics · 2025Article
- An antigen panel to assess the regional relevance of foot and mouth disease vaccines.NPJ vaccines · 2025Article
- Longitudinal study of foot-and-mouth disease virus in Northern Nigeria: implications for the roles of small ruminants and environmental contamination in endemic settings.Veterinary research · 2025Article
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- Eastern Africa Origin of SAT2 Topotype XIV Foot-and-Mouth Disease Virus Outbreaks, Western Asia, 2023.Emerging infectious diseases · 2025Article
- Detection and genomic characterisation of foot-and-mouth disease virus serotypes circulating in Cameroon using environmental sampling.Scientific reports · 2025Article
- Detection of Long-Distance Transmission Events During the CSF Epidemic in Japan Using Whole-Genome-Sequence Data.Transboundary and emerging diseases · 2025Article
- Multiple incursions of foot-and-mouth disease virus serotype O into the Republic of Korea between 2010 and 2019.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2024Article
- Direct RNA Sequencing of Foot-and-mouth Disease Virus Genome Using a Flongle on MinION.Bio-protocol · 2024Article
- Challenges of Controlling Foot-and-Mouth Disease in Pastoral Settings in Africa.Transboundary and emerging diseases · 2024Review
- Genome Sequence of a Foot-and-Mouth Disease Virus Detected in Indonesia in 2022.Microbiology resource announcements · 2023Article
- Establishing a molecular toolbox of lineage-specific real-time RT-PCR assays for the characterization of foot-and-mouth disease viruses circulating in Asia.Frontiers in veterinary science · 2023Article
- Genome Sequences of Foot-and-Mouth Disease Virus SAT1 Strains Purified from Coinfected Cape Buffalo in Kenya.Microbiology resource announcements · 2022Article
- Foot-and-Mouth Disease Virus Serotypes O and A from Outbreaks in Pakistan 2011-2012.Microbiology resource announcements · 2022Article
- Genome Sequences of Foot-and-Mouth Disease Virus Serotype A and O Strains Obtained from Subclinically Infected Asian BuffaloMicrobiology resource announcements · 2022Article
- Multiple Genome Sequences of Foot-and-Mouth Disease Virus Asia-1 Lineage Sindh-08 from Outbreaks in Pakistan, 2011 to 2012.Microbiology resource announcements · 2022Article
- Multiple Genomes of Foot-and-Mouth Disease Virus Serotype Asia-1 Obtained from Subclinically Infected Asian Buffalo (Bubalus bubalis) in Pakistan.Microbiology resource announcements · 2022Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
backgroundNext-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 describe here 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.
resultsThe protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously 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. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region.
conclusionsWe have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.