Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

Ramirez-Carvajal, Lisbeth; Pauszek, Steven J.; Ahmed, Zaheer; Farooq, Umer; Naeem, Khalid; Shabman, Reed S.; Stockwell, Timothy B.; Rodriguez, Luis L.

doi:10.1371/journal.pone.0190977

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

Journal Article · Thu Feb 01 00:00:00 EST 2018 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0190977· OSTI ID:1627849

Ramirez-Carvajal, Lisbeth ^[1]; Pauszek, Steven J. ^[2]; Ahmed, Zaheer ^[3]; Farooq, Umer ^[4]; Naeem, Khalid ^[4]; Shabman, Reed S. ^[5]; Stockwell, Timothy B. ^[5]; Rodriguez, Luis L. ^[2]

Plum Island Animal Disease Center, Greenport, NY (United States); Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); DOE/OSTI
Plum Island Animal Disease Center, Greenport, NY (United States)
Plum Island Animal Disease Center, Greenport, NY (United States); Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
National Agricultural Research Center, Isamabad (Pakistan). Animal Health Program
J. Craig Venter Inst., Rockville, MD (United States)

Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-andmouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo. Using next-generation sequencing (NGS) we obtained 21 near complete FMDV genome sequences from 12 sub-clinically infected buffalo over a period of one year. Four animals yielded only one virus isolate and one yielded two isolates of different serotype suggesting a serial infection. Seven persistently infected animals yielded more than one virus of the same serotype showing a longterm intra-host viral genetic divergence at the consensus level of less than 2.5%. Quasi-species analysis showed few nucleotide variants and non-synonymous substitutions of progeny virus despite intra-host persistence of up to 152 days. Phylogenetic analyses of serotype Asia-1 VP1 sequences clustered all viruses from persistent animals with Group VII viruses circulating in Pakistan in 2011, but distinct from those circulating on 2008–2009. Furthermore, signature amino acid (aa) substitutions were found in the antigenically relevant VP1 of persistent viruses compared with viruses from 2008–2009. Intra-host purifying selective pressure was observed, with few codons in structural proteins undergoing positive selection. However, FMD persistent viruses did not show a clear pattern of antigenic selection. Our findings provide insight into the evolutionary dynamics of FMDV populations within naturally occurring subclinical and persistent infections that may have implications to vaccination strategies in the region.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Associated Univ., Oak Ridge, TN (United States)

Sponsoring Organization:: Agricultural Research Service (ARS); Plum Island Animal Disease Center Research Participation Program; US Department of Homeland Security; US Department of State; USDA; USDOE

Grant/Contract Number:: SC0014664

OSTI ID:: 1627849

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 2 Vol. 13; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

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