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

Rachel M. Palinski, Barbara Brito, Frederick R. Jaya, Abraham Sangula, Francis Gakuya, Miranda R. Bertram, Steven J. Pauszek, Ethan J. Hartwig, George R. Smoliga, Vincent Obanda, George P. Omondi, Kimberly Vanderwaal, Jonathan Arzt

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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.

Original languageEnglish (US)
Article number897
Issue number5
StatePublished - May 2022

Bibliographical note

Funding Information:
Funding: This research was supported in part by USDA-ARS CRIS 8064-32000-061-00D and USAID Prime Agreement Number AIDOAA-A-11-00012.

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.


  • foot-and-mouth disease
  • intra-host diversity
  • serotype A
  • short-read sequencing

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.


Dive into the research topics of 'Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya'. Together they form a unique fingerprint.

Cite this