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.2014 Feb;159(2):249-55.
doi: 10.1007/s00705-013-1815-3. Epub 2013 Aug 13.

Genomic and evolutionary characterization of a novel influenza-C-like virus from swine

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Genomic and evolutionary characterization of a novel influenza-C-like virus from swine

Zizhang Sheng et al. Arch Virol.2014 Feb.

Abstract

We recently described the isolation of a novel influenza virus from swine exhibiting respiratory disease in the United States that is distantly related to human influenza C virus. Based on genetic, biochemical and morphological analysis, the virus was provisionally classified as C/swine/Oklahoma/1334/2011 (C/OK). To further understand the genetics and evolution of this novel pathogen, we performed a comprehensive analysis of its sequence and phylogeny. The results demonstrated that C/OK and human influenza C viruses share a conserved array of predicted functional domains in the viral RNA genome replication and viral entry machinery but vary at key functional sites. Furthermore, our evolutionary analysis showed that homologous genes of C/OK and human influenza C viruses diverged from each other an estimated several hundred to several thousand years ago. Taken together, the findings described in this study support and extend our previous observations that C/OK is a genetically and evolutionarily distinct influenza virus in the family Orthomyxoviridae.

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Figures

Fig. 1
Fig. 1
Schematic diagram of positional similarity and modeled structures of viral polymerase proteins. For the position similarity, the colored bar below in each plot shows domains and known functional sites. Domain regions and functional sites were predicted according to previous studies on human ICV and IAV [8, 10, 11, 26, 30]. Positions are numbered according to C/OK proteins. Virus strains: influenza A (H1N1/1918/Brevig Mission and H5N1/1996/GuangDong), influenza B (B/Brisbane/2008), influenza C (C/1966/Johannesburg), infectious salmon anemia virus (ISAV/1990/Glesvaer) and Thogoto virus (Dhori/1313/61). For the modeled structures, the side chains of active-site residues of C/OK and IAV P3 or PA are colored gray and magenta, respectively. Magnesium is shown as a green ball. Hydrogen bonds and salt bridges are shown with dashed yellow lines. Residues of C/OK and IAV PB2 are colored gray and magenta, respectively. The guanosine-binding residues are conserved, but the phosphate-binding resides (underlined) are different between C/OK virus and IAV. The structures were modeled using Modeller [5] with the structures of the endonuclease domain and cap-binding domain of influenza A virus as template (PDBID: 3HW5 and 2VQZ, respectively) [8]. The quality of the modeled structure was verified by Verify_3D [4]
Fig. 2
Fig. 2
Schematic diagram of positional similarity and modeled structures of the viral HE protein. (A) Sequence position similarity between human ICV and C/OK. The F′ and TM regions of the C/OK HE protein were predicted using TMHMM [14]. The alignment of the TM region is colored according to sequence similarity (conserved residue: blue). S, signal peptide; F1, fusion domain 1; F2, fusion domain 2; F3, fusion domain 3; R, receptor-binding domain; E1, esterase domain 1; E2, esterase domain 2; C, cleavage site; F′, fusion peptide; TM, transmembrane region. (B) Modeled structure. Transparent cartoon and surface view of predicted glycosylation sites in human ICV and C/OK HE proteins. The modeled structure of C/OK HE is from our previous study [10]. Glycan (β-D-Manp-(1-4)- β-D-GlcpNAc, orange) and modified asparagine (magenta) are shown in stick mode. Sialic acid (cyan) is added to the receptor-binding pocket and esterase active site
Fig. 3
Fig. 3
Estimated divergence time to the most recent common ancestor of C/OK and human ICV using the Bayesian probability method. The mean time is marked by a dot. The upper and lower lines are the 95 % highest posterior density (HPD) limits
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