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.
Highlights
Influenza A viruses (IAVs) are most well known for their circulation in humans, causing yearly seasonal epidemics and occasional pandemics, and for outbreaks in poultry
The 30 non-coding regions (NCR) contains 12 conserved nucleotides followed by a segment-specific region of variable length
NCR sequences from previously identified and sequenced viruses originating from three different wild bird host groups were determined: A/domestic duck/Newfoundland/MW668/2010(H1N1), A/American black duck/Newfoundland/GR679/
Summary
Influenza A viruses (IAVs) are most well known for their circulation in humans, causing yearly seasonal epidemics and occasional pandemics, and for outbreaks in poultry. The viral strains responsible for these infections represent only a small portion of the total known IAV diversity, most of which is maintained in the natural wild bird reservoir. IAVs are members of the family Orthomyxoviridae and have segmented negative-sense single-stranded RNA genomes. The viral genome is composed of eight segments that encode at least 11 proteins, depending on the strain. Each segment has non-coding regions (NCRs) at both ends. The 30 NCR contains 12 conserved nucleotides followed by a segment-specific region of variable length
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