Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Wada, Yoshiko ^a,b   Wada, Kennosuke ^a   Iwasaki, Yuki ^a   Kanaya, Shigehiko ^b   Ikemura, Toshimichi ^a  

^a NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ANIMAL; EBOLAVIRUS; GENETICS; HUMAN; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NUCLEOTIDE SEQUENCE; ORTHOMYXOVIRIDAE; TIME FACTOR; VIROLOGY; VIRUS GENOME; ZOONOSIS;

ANIMALS; BASE SEQUENCE; EBOLAVIRUS; GENOME, VIRAL; HUMANS; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; OLIGONUCLEOTIDES; ORTHOMYXOVIRIDAE; TIME FACTORS; ZOONOSES;

EID: 84994316224     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep36197     Document Type: Article

References (31)

1. WHO. Ebola Response Team. Ebola virus disease in West Africa - The first 9 months of the epidemic and forward projections. N. Engl. J. Med. 371, 1481-1495 (2014).
2. Tong, Y. G. et al. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature 524, 93-96 (2015).
3. Park, D. J. et al. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell 161, 1516-1526 (2015).
4. Carroll, M. W. et al. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature 524, 97-101 (2015).
5. Nichol, S. T., Arikawa, J. & Kawaoka, Y. Emerging viral diseases. Proc. Natl Acad. Sci. USA 97, 12411-12412 (2000).
6. Karlin, S., Campbell, A. M. & Mrazek, J. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32, 185-225 (1998).
7. García-Sastre, A. Inhibition of interferon-mediated antiviral responses by influenza A viruses and other negative-strand RNA viruses. Virology 279, 375-384 (2001).
8. Voinnet, O. Induction and suppression of RNA silencing: insights from viral infections. Nat. Rev. Genet. 6, 206-220 (2005).
9. Randall, R. E. & Goodbourn, S. Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures. J. Gen. Virol. 89, 1-47 (2008).
10. Rabadan, R., Levine, A. J. & Robins, H. Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes. J. Virol. 80, 11887-11891 (2006).
11. Jimenez-Baranda, S. et al. Oligonucleotide motifs that disappear during the evolution of influenza in humans increase IFN-α secretion by plasmacytoid endritic cells. J. Virol. 85, 3893-3904 (2011).
12. Kanaya, S. et al. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM) - characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 276, 89-99 (2001).
13. Abe, T. et al. Informatics for unveiling hidden genome signatures. Genome Res. 13, 693-702 (2003).
14. Iwasaki, Y., Abe, T., Wada, K., Itoh, M. & Ikemura, T. Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case. DNA Res. 18, 125-136 (2011).
15. Iwasaki, Y., Abe, T., Wada, Y., Wada, K. & Ikemura, T. Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains. BMC Infect. Dis. 13, 386 (2013).
16. Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N. Engl. J. Med. 360, 2605-2615 (2009).
17. Neumann, G., Noda, T. & Kawaoka, Y. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459, 931-939 (2009).
18. Smith, G. J. et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459, 1122-1125 (2009).
19. Crooke, S. T. Progress toward oligonucleotide therapeutics: pharmacodynamic properties. FASEB J. 7, 533-539 (1993).
20. Kageyama, T. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41, 1548-1557 (2003).
21. Opalinska, J. B. & Gewirtz, A. M. Nucleic-acid therapeutics: basic principles and recent applications. Nat. Rev. Drug Discov. 1, 503-514 (2002).
22. Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343-349 (2004).
23. Bennett, C. F. & Swayze, E. E. RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu. Rev. Pharmacol. Toxicol. 50, 259-293 (2010).
24. Brister, J. R. et al. Virus Variation Resource - recent updates and future directions. Nucleic Acids Res. 42 (Database issue), D660-D665 (2013).
25. Azhar, E. I. et al. Evidence for camel-to-human transmission of MERS coronavirus. N. Engl. J. Med. 370, 2499-2505 (2014).
26. Ithete, N. L. et al. Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa. Emerg. Infect. Dis. 19, 1697-1699 (2013).
27. Squires, R. B. et al. Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respir. Viruses 6, 404-416 (2012).
28. Xie, Z. et al. A multiplex RT-PCR for detection of type A influenza virus and differentiation of avian H5, H7, and H9 hemagglutinin subtypes. Mol. Cell. Probes 20, 245-249 (2006).
29. Thakur, N., Qureshi, A. & Kumar, M. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res. 40 (Database issue), D230-D236 (2012).
30. Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504-507 (2013).
31. Paixão, E. S. et al. History, epidemiology, and clinical manifestations of Zika: A systematic review. Am. J. Public Health 106, 606-612 (2016).