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Vet. Sci. 2018, 5(3), 76; https://doi.org/10.3390/vetsci5030076

Analysis of the Variability in the Non-Coding Regions of Influenza A Viruses

1
Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
2
Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce St., Mount Pearl, NL A1N 4T3, Canada
*
Author to whom correspondence should be addressed.
Received: 4 July 2018 / Revised: 14 August 2018 / Accepted: 22 August 2018 / Published: 25 August 2018
(This article belongs to the Collection Human and Animal Influenzas: A Shared Public Health Concern)
Full-Text   |   PDF [5866 KB, uploaded 25 August 2018]   |  

Abstract

The genomes of influenza A viruses (IAVs) comprise eight negative-sense single-stranded RNA segments. In addition to the protein-coding region, each segment possesses 5′ and 3′ non-coding regions (NCR) that are important for transcription, replication and packaging. The NCRs contain both conserved and segment-specific sequences, and the impacts of variability in the NCRs are not completely understood. Full NCRs have been determined from some viruses, but a detailed analysis of potential variability in these regions among viruses from different host groups and locations has not been performed. To evaluate the degree of conservation in NCRs among different viruses, we sequenced the NCRs of IAVs isolated from different wild bird host groups (ducks, gulls and seabirds). We then extended our study to include NCRs available from the National Center for Biotechnology Information (NCBI) Influenza Virus Database, which allowed us to analyze a wider variety of host species and more HA and NA subtypes. We found that the amount of variability within the NCRs varies among segments, with the greatest variation found in the HA and NA and the least in the M and NS segments. Overall, variability in NCR sequences was correlated with the coding region phylogeny, suggesting vertical coevolution of the (coding sequence) CDS and NCR regions. View Full-Text
Keywords: viral evolution; phylogeny; avian influenza viral evolution; phylogeny; avian influenza
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Benkaroun, J.; Robertson, G.J.; Whitney, H.; Lang, A.S. Analysis of the Variability in the Non-Coding Regions of Influenza A Viruses. Vet. Sci. 2018, 5, 76.

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