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Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the Foot-and-Mouth Disease Virus capsid

https://doi.org/10.1101/271239
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9780470015902.a0001024.pub2openalex-snapshot
Foot‐and‐Mouth Disease
inferredcites →https://doi.org/10.1016/j.coviro.2017.11.013openalex-snapshot
Understanding the transmission of foot-and-mouth disease virus at different scales
inferredcites →https://doi.org/10.1016/j.meegid.2008.07.009openalex-snapshot
The evolution of foot-and-mouth disease virus: Impacts of recombination and selection
inferredcites →https://doi.org/10.1016/j.meegid.2013.09.009openalex-snapshot
Reconstructing the origin and transmission dynamics of the 1967–68 foot-and-mouth disease epidemic in the United Kingdom
inferredcites →https://doi.org/10.1016/j.virol.2016.03.017openalex-snapshot
Viral quasispecies complexity measures
inferredcites →https://doi.org/10.1016/s0021-9975(03)00041-0openalex-snapshot
The Pathogenesis and Diagnosis of Foot-and-Mouth Disease
inferredcites →https://doi.org/10.1016/s0168-1702(02)00257-5openalex-snapshot
Molecular basis of pathogenesis of FMDV
inferredcites →https://doi.org/10.1016/s0168-1702(02)00260-5openalex-snapshot
Molecular epidemiology of foot-and-mouth disease virus
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nature13087openalex-snapshot
A predictive fitness model for influenza
inferredcites →https://doi.org/10.1038/nmeth.2221openalex-snapshot
The GEM mapper: fast, accurate and versatile alignment by filtration
inferredcites →https://doi.org/10.1038/nrmicro2614openalex-snapshot
Why do RNA viruses recombine?
inferredcites →https://doi.org/10.1038/s41467-017-00354-5openalex-snapshot
Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses
inferredcites →https://doi.org/10.1038/srep19294openalex-snapshot
Productive Entry of Foot-and-Mouth Disease Virus via Macropinocytosis Independent of Phosphatidylinositol 3-Kinase
inferredcites →https://doi.org/10.1073/pnas.0812560106openalex-snapshot
Competition between recombination and epistasis can cause a transition from allele to genotype selection
inferredcites →https://doi.org/10.1073/pnas.1011090108openalex-snapshot
Family level phylogenies reveal modes of macroevolution in RNA viruses
inferredcites →https://doi.org/10.1073/pnas.1102036108openalex-snapshot
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/genetics/65.4.707openalex-snapshot
IS THE GENE THE UNIT OF SELECTION?
inferredcites →https://doi.org/10.1098/rstb.2009.0100openalex-snapshot
Options for control of foot-and-mouth disease: knowledge, capability and policy
inferredcites →https://doi.org/10.1099/0022-1317-35-3-555openalex-snapshot
An Extended Genetic Recombination Map for Foot-and-Mouth Disease Virus
inferredcites →https://doi.org/10.1099/0022-1317-80-10-2535openalex-snapshot
Evolutionary aspects of recombination in RNA viruses
inferredcites →https://doi.org/10.1099/0022-1317-83-10-2455openalex-snapshot
Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus
inferredcites →https://doi.org/10.1099/jgv.0.000989openalex-snapshot
Implications of segment mismatch for influenza A virus evolution
inferredcites →https://doi.org/10.1099/vir.0.029710-0openalex-snapshot
Capsid proteins from field strains of foot-and-mouth disease virus confer a pathogenic phenotype in cattle on an attenuated, cell-culture-adapted virus
inferredcites →https://doi.org/10.1099/vir.0.82555-0openalex-snapshot
Mosaic structure of foot-and-mouth disease virus genomes
inferredcites →https://doi.org/10.1111/j.1558-5646.1997.tb03949.xopenalex-snapshot
HYBRID ZONES WITH DOBZHANSKY-TYPE EPISTATIC SELECTION
inferredcites →https://doi.org/10.1126/science.aai8446openalex-snapshot
Ecological speciation of bacteriophage lambda in allopatry and sympatry
inferredcites →https://doi.org/10.1128/jvi.00166-16openalex-snapshot
Differential Persistence of Foot-and-Mouth Disease Virus in African Buffalo Is Related to Virus Virulence
inferredcites →https://doi.org/10.1128/jvi.00709-14openalex-snapshot
Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events
inferredcites →https://doi.org/10.1128/jvi.01100-06openalex-snapshot
Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses
inferredcites →https://doi.org/10.1128/jvi.01236-06openalex-snapshot
Molecular Epidemiology of the Foot-and-Mouth Disease Virus Outbreak in the United Kingdom in 2001
inferredcites →https://doi.org/10.1128/jvi.34.1.67-72.1980openalex-snapshot
Temperature-sensitive mutants of foot-and-mouth disease virus with altered structural polypeptides. II. Comparison of recombination and biochemical maps
inferredcites →https://doi.org/10.1128/jvi.62.6.2041-2049.1988openalex-snapshot
Rapid selection of genetic and antigenic variants of foot-and-mouth disease virus during persistence in cattle
inferredcites →https://doi.org/10.1128/jvi.79.10.6487-6504.2005openalex-snapshot
Comparative Genomics of Foot-and-Mouth Disease Virus
inferredcites →https://doi.org/10.1128/jvi.80.5.2472-2482.2006openalex-snapshot
Extensive Recombination among Human Immunodeficiency Virus Type 1 Quasispecies Makes an Important Contribution to Viral Diversity in Individual Patients
inferredcites →https://doi.org/10.1128/mmbr.05023-11openalex-snapshot
Viral Quasispecies Evolution
inferredcites →https://doi.org/10.1146/annurev.micro.51.1.151openalex-snapshot
RNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL
inferredcites →https://doi.org/10.1186/1471-2105-13-239openalex-snapshot
SNP calling by sequencing pooled samples
inferredcites →https://doi.org/10.1201/9781351076432-7openalex-snapshot
Genetic Recombination in Positive Strand RNA Viruses
inferredcites →https://doi.org/10.1371/journal.pbio.0030089openalex-snapshot
Recombination Every Day: Abundant Recombination in a Virus during a Single Multi-Cellular Host Infection
inferredcites →https://doi.org/10.1371/journal.pcbi.1000660openalex-snapshot
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
inferredcites →https://doi.org/10.1371/journal.pgen.0010051openalex-snapshot
The Evolutionary Value of Recombination Is Constrained by Genome Modularity
inferredcites →https://doi.org/10.1371/journal.pone.0060123openalex-snapshot
The Effect of Single Recombination Events on Coalescent Tree Height and Shape
inferredcites →https://doi.org/10.1371/journal.ppat.1001005openalex-snapshot
Quasispecies Theory and the Behavior of RNA Viruses
inferredcites →https://doi.org/10.1371/journal.ppat.1006685openalex-snapshot
Fitness cost of reassortment in human influenza
inferredcites →https://doi.org/10.1534/genetics.103.023382openalex-snapshot
Pervasive Genomic Recombination of HIV-1 in VivoSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY496645, AY496646, AY496647, AY496648, AY496649, AY496650, AY496651, AY496652, AY496653, AY496654, AY496655, AY496656, AY496657, AY496658,…
inferredcites →https://doi.org/10.1534/genetics.107.081810openalex-snapshot
Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon)
inferredcites →https://doi.org/10.3390/v10050221openalex-snapshot
Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-019-41995-4openalex-snapshot
The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa
inferred← citeshttps://doi.org/10.1128/jvi.00563-19openalex-snapshot
Persistent Infection of African Buffalo (Syncerus caffer) with Foot-and-Mouth Disease Virus: Limited Viral Evolution and No Evidence of Antibody Neutralization Escape
inferred← citeshttps://doi.org/10.1186/s13567-022-01076-3openalex-snapshot
Viral dynamics and immune responses to foot-and-mouth disease virus in African buffalo (Syncerus caffer)
inferred← citeshttps://doi.org/10.3390/v10050221openalex-snapshot
Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome
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