Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya

Abstract

African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural proteins. Despite the high divergence in the capsid phylogeny between SAT1 and SAT2 serotypes, viruses from different serotypes that were collected from the same host had a high genetic similarity in non-structural protein-coding regions P2 and P3, suggesting interserotypic recombination. In two of the SAT1 and SAT2 co-infected buffalo identified at the first passage of viral isolation, the plaque-derived SAT2 genomes were distinctly grouped in two different genotypes. These genotypes were not initially detected with the NGS from the first passage (non-purified) virus isolation sample. In one animal with two SAT2 haplotypes, one plaque-derived chimeric sequence was found. These findings demonstrate within-host evolution through recombination and point mutation contributing to broad viral diversity in the wildlife reservoir. These mechanisms may be critical to FMDV persistence at the individual animal and population levels, and may contribute to the emergence of new viruses that have the ability to spill-over to livestock and other wildlife species.

Foot-and-Mouth Disease Virus Interserotypic Recombination in Superinfected Carrier Cattle

“…These animals thereby represent a distinct category as they were both persistently and acutely infected, regardless of their clinical status. Coinfection is not uncommon in FMD-endemic regions where multiple serotypes are in circulation [1][2][3][4] and superinfection of FMDV carriers comprises a subset of these dual infections. However, there are infinite permutations of the timing and strain involvement which could affect superinfection under natural conditions.…”

“…Currently, there are six antigenically distinct serotypes in circulation defined by the VP1 capsid-encoding region of the genome: A, O, Asia1, SAT 1, SAT 2, and SAT 3. Multiple serotypes regularly co-circulate in endemic regions and animals have been found to be naturally coinfected with multiple serotypes [1][2][3][4]. Further, FMDV has a high rate of mutation which contributes to a need for continuous development of updated vaccines and genomic surveillance.…”

Kinetics of foot-and-mouth disease vaccine-induced antibody responses in buffaloes (Bubalus bubalis): avidity ELISA as an alternative to the virus neutralization test

“…Based on this background, several papers studied the epidemiological role of buffalo's populations in the emergence and persistence of FMDV in the field (31), as well as the pathogenesis of the FMDV infection in these species, focusing on the transmission (32), disease symptoms (33, 34), persistence (30,35,36) and viral dynamics (37). However, few reports informed about the FMDVspecific antibody responses in buffaloes, basically studying the In this regard, there is gap in the knowledge on how serological assays that measure antibodies against capsid proteins perform with buffalo samples and which would be the most reliable test to substitute VNT for field surveillance.…”

Evaluation of Potential In Vitro Recombination Events in Codon Deoptimized FMDV Strains

“…The mechanism of Picornavirus recombination is believed to take place by way of template switching during genome replication; this involves the movement of the RdRp from one parental RNA genome (donor) to another genome (acceptor) midway through negative strand synthesis, thereby yielding a hybrid product [ 27 , 28 ]. Recombination hotspots have been identified throughout the genome with a substantial number in the conserved regions encoding NS genes [ 26 , 29 , 30 , 31 , 32 , 33 ]. More recently, both intra- and inter-serotypic recombination was observed after experimental infection of natural hosts [ 34 , 35 , 36 ].…”