Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome

Area of Science:

• Virology
• Molecular Evolution
• Genetics

Background:

• Recombination is a key driver of genetic diversity in foot-and-mouth disease virus (FMDV).
• While genome-wide recombination patterns are known, within-host FMDV recombination remains poorly understood.
• Detecting within-host recombination is difficult due to sequence similarity and challenges in distinguishing it from point mutations.

Purpose of the Study:

• To investigate recombination events between closely related FMDV sequences within buffalo hosts.
• To analyze the patterns and distribution of within-host FMDV recombination across the viral genome.

Main Methods:

• Analysis of FMDV sequences from co-infected buffalo, exhibiting approximately 1% nucleotide divergence.
• Identification and characterization of recombination events within infected host samples.
• Assessment of recombination event distribution across the FMDV genome and comparison with phylogenetic data.

Main Results:

• Over 15 recombination events were detected across eight buffalo samples.
• Recombination events were unequally distributed among the samples.
• The genomic distribution of within-host recombination was non-uniform and did not correlate with known long-term recombination breakpoint patterns.

Conclusions:

• This study provides the first evidence of recombination between closely related FMDV strains within a host.
• Within-host recombination patterns differ from those observed at broader evolutionary scales.
• A potential mismatch exists between within-host evolutionary pressures and the long-term selection pressures driving FMDV infectivity and transmissibility.