Viral population diversity during co-infection of foot-and-mouth disease virus serotypes SAT1 and SAT2 in African buffalo in Kenya

Authors: PALINSKI, RACHEL - Kansas State University; BRITO, BARBARA - University Of Technology Sydney; JAYA, FREDERICK - University Of Technology Sydney; SANGULA, ABRAHAM - Ministry Of Agriculture, Livestock And Fisheries, State Department Of Livestock; GAKUYA, FRANCIS - Kenya Wildlife Service; Bertram, Miranda; PAUSZEK, STEVEN - Animal And Plant Health Inspection Service (APHIS); Hartwig, Ethan; Smoliga, George; OBANDA, VINCENT - Canadian Wildlife Service; OMONDI, GEORGE - University Of Minnesota; VANDERWAAL, KIMBERLY - University Of Minnesota; Arzt, Jonathan

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2022
Publication Date: 4/25/2022
Citation: Palinski, R., Brito, B., Jaya, F., Sangula, A., Gakuya, F., Bertram, M.R., Pauszek, S.J., Hartwig, E.J., Smoliga, G.R., Obanda, V., Omondi, G., Vanderwaal, K., Arzt, J. 2022. Viral population diversity during co-infection of foot-and-mouth disease virus serotypes SAT1 and SAT2 in African buffalo in Kenya. Viruses. https://doi.org/10.3390/v14050897.
DOI: https://doi.org/10.3390/v14050897

Interpretive Summary: Foot-and-mouth disease (FMD), caused by FMD virus (FMDV), is an important livestock disease in many countries in Africa and Asia, including Kenya. Many different strains of the virus exist in different countries, and it is important to know which strains are in a country to select appropriate vaccines. In African buffalo, it is well-known that natural infection sometimes occurs with multiple strains at the same time in the same animal. The purpose of this study was to try to isolate and purify multiple viruses from samples from buffalo in Kenya. Five buffalo were found to have infections with strains of both FMDV SAT1 and SAT2. Additionally within those five buffalo multiple viruses were found that had recombinant viruses, meaning that different strains had swapped genetic material to create new viruses. This information is important to understanding the evolution of this important virus and to improve preparedness and protection for agriculture interests in USA and Kenya.

Technical Abstract: African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffaloes 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, five were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffaloes, we obtained 89 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 buffaloes 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.