A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Abstract

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

Tracing foot-and-mouth disease virus phylogeographical patterns and transmission dynamics.

“…Following the pandemic patterns showed by serotype O, the next large-scale potential of diffusion was exhibited by serotype A. Phylogeographic analysis suggested India as the most likely center of origin of the current circulating serotype A strains. Supporting previous studies [26,60], we observed that India was also a key source of dispersal events for this serotype since most of the current strains are strongly related to India. Whole genome sequences of this serotype have been recorded in three continents, Asia, Africa, and South America, where it was reported as the causing agent of one of the biggest FMDV outbreaks, which occurred in Argentina in 2011, affecting a total of 2,126 herds [84].…”

“…The result of such improvement in disease surveillance would not only be beneficial for the targeted region, but also for all the areas that are directly connected (i.e., through geographical limits) and indirectly (i.e., through commercial networks), including countries currently considered as free zones [111]. Even though past studies have found recombination in WGS of FMDV [53,60], it is important to mention that after filtering the dataset to keep just one sequence per outbreak event, we did not found evidence of recombination on the remaining samples.…”

“…Several studies have explored the spatiotemporal evolutionary dynamics of FMDV in different parts of the world, mainly focusing on the diffusion patterns across its endemic regions: Asia and Africa [31,48,[55][56][57][58][59] However, studies considering all serotypes are only available within small geographic regions, and global studies only assessed some of the viral serotypes [55,60].…”

Foot-and-Mouth Disease Virus Serotype O/CATHAY Genome Sequences from Five Outbreaks in Vietnam, 2017 to 2019

“…The O/CATHAY topotype was responsible for a 1997 FMD outbreak in Taiwan, leading to the culling of over 4 million pigs and an economic loss of more than 6 billion dollars (6). O/CATHAY is currently endemic in Southeast Asia, including Vietnam (7,8).…”

Senecavirus-Specific Recombination Assays Reveal the Intimate Link between Polymerase Fidelity and RNA Recombination

“…For example, the live attenuated Sabin vaccine strain is known to recombine with cocirculating species C enterovirus, where subsequent infection can lead to pathogenic outcomes (20,21). Further, intrahost recombination events in the related foot-and-mouth disease virus (FMDV) play a significant role in increasing genetic diversity in FMDV quasispecies (22)(23)(24). However, much less recombination is observed when virus infection occurs in multiple wildlife species in southern Africa (25), while recombination seems to dominate when FMDV infection occurs in a very narrow host range (23).…”