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

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 evo...

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Autores principales: Palinski, Rachel M., Brito, Barbara, Jaya, Frederick R., Sangula, Abraham, Gakuya, Francis, Bertram, Miranda R., Pauszek, Steven J., Hartwig, Ethan J., Smoliga, George R., Obanda, Vincent, Omondi, George P., VanderWaal, Kimberly, Arzt, Jonathan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145140/
https://www.ncbi.nlm.nih.gov/pubmed/35632639
http://dx.doi.org/10.3390/v14050897
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author Palinski, Rachel M.
Brito, Barbara
Jaya, Frederick R.
Sangula, Abraham
Gakuya, Francis
Bertram, Miranda R.
Pauszek, Steven J.
Hartwig, Ethan J.
Smoliga, George R.
Obanda, Vincent
Omondi, George P.
VanderWaal, Kimberly
Arzt, Jonathan
author_facet Palinski, Rachel M.
Brito, Barbara
Jaya, Frederick R.
Sangula, Abraham
Gakuya, Francis
Bertram, Miranda R.
Pauszek, Steven J.
Hartwig, Ethan J.
Smoliga, George R.
Obanda, Vincent
Omondi, George P.
VanderWaal, Kimberly
Arzt, Jonathan
author_sort Palinski, Rachel M.
collection PubMed
description 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.
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spelling pubmed-91451402022-05-29 Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya Palinski, Rachel M. Brito, Barbara Jaya, Frederick R. Sangula, Abraham Gakuya, Francis Bertram, Miranda R. Pauszek, Steven J. Hartwig, Ethan J. Smoliga, George R. Obanda, Vincent Omondi, George P. VanderWaal, Kimberly Arzt, Jonathan Viruses Article 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. MDPI 2022-04-25 /pmc/articles/PMC9145140/ /pubmed/35632639 http://dx.doi.org/10.3390/v14050897 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Palinski, Rachel M.
Brito, Barbara
Jaya, Frederick R.
Sangula, Abraham
Gakuya, Francis
Bertram, Miranda R.
Pauszek, Steven J.
Hartwig, Ethan J.
Smoliga, George R.
Obanda, Vincent
Omondi, George P.
VanderWaal, Kimberly
Arzt, Jonathan
Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title_full Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title_fullStr Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title_full_unstemmed Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title_short Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya
title_sort viral population diversity during co-infection of foot-and-mouth disease virus serotypes sat1 and sat2 in african buffalo in kenya
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145140/
https://www.ncbi.nlm.nih.gov/pubmed/35632639
http://dx.doi.org/10.3390/v14050897
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