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Том 18   Выпуск 2   Год 2023
Чалей М.Б.1, Кутыркин В.А.2

Выбор таргета в геномах прототипных штаммов для распознавания подрода коронавирусов

Математическая биология и биоинформатика. 2023;18(2):267-281.

doi: 10.17537/2023.18.267.

Список литературы

  1. Sprindzuk M.V., Bernik V.I., Kalosha N.I., Batgerel B. Automation and mathematical apparatus for the analysis of genomics data. Sistemnyi analiz i upravlenie v biomeditsinskikh sistemakh (System analysis and control in biomedical systems). 2022;21(4):129–139 (in Russ.). doi: 10.36622/VSTU.2022.21.4.018
  2. GISAID. https://gisaid.org (accessed 14.06.2023).
  3. GenBank. https://www.ncbi.nlm.nih.gov/genbank (accessed 14.06.2023).
  4. ENA. https://www.ebi.ac.uk/ena/browser/home (accessed 14.06.2023).
  5. CNGBdb. https://db.cngb.org (accessed 14.06.2023).
  6. Liu B., Liu K., Zhang H., Zhang L., Bian Y., Huang L. CoV-Seq, a new tool for SARS-CoV-2 genome analysis and visualization: development and usability study. J. Med. Internet Res. 2020;22(10). Article No. e22299. doi: 10.2196/22299
  7. Cleemput S., Dumon W., Fonseca V., Abdool Karim W., Giovanetti M., Alcantara L.C., Deforche K., de Oliveira T. Genome detective coronavirus typing tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. 2020;36(11):3552–3555. doi: 10.1093/bioinformatics/btaa145
  8. Seong D.Y., Park J., Yi K., Hong D. Systematic guidelines for effective utilization of COVID-19 databases in genomic, epidemiologic, and clinical research. Viruses. 2023;15(3). Article No. 692. doi: 10.3390/v15030692
  9. Edgar R.C. Taylor J., Lin V., Altman T., Barbera P., Meleshko D., Lohr D., Novakovsky G., Buchfink B., Al-Shayeb B. et al. Petabase-scale sequence alignment catalyses viral discovery. Nature. 2022;602:142–147. doi: 10.1038/s41586-021-04332-2
  10. Gorbalenya A.E., Siddell S.G. Recognizing species as a new focus of virus research. PLoS Pathog. 2021;17:(3). Article No. e1009318. doi: 10.1371/journal.ppat.1009318
  11. Höper D., Wylezich C., Beer M. Loeffler 4.0: diagnostic metagenomics. Adv. Virus Res. 2017;99:17–37. doi: 10.1016/bs.aivir.2017.08.001
  12. Greninger A.L. A decade of RNA virus metagenomics is (not) enough. Virus Res. 2018;244:218–229. doi: 10.1016/j.virusres.2017.10.014
  13. Zhang Y.Z., Shi M., Holmes E.C. Using metagenomics to characterize an expanding virosphere. Cell. 2018;172(6):1168–1172. doi: 10.1016/j.cell.2018.02.043
  14. Adams M.J., Lefkowitz E.J., King A.M.Q., Harrach B., Harrison R.L., Knowles N.J., Kropinski A.M., Krupovic M., Kuhn J.H., Mushegian A.R. et al. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch. Virol. 2017;162:1441–1446. doi: 10.1007/s00705-016-3215-y
  15. Siddell S.G., Walker P.J., Lefkowitz E.J., Mushegian A.R., Adams M.J., Dutilh B.E., Gorbalenya A.E., Harrach B., Harrison R.L., Junglen S. et al. Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018). Arch. Virol. 2019;164:943–946. doi: 10.1007/s00705-018-04136-2
  16. Spaan W.J.M., Brian D., Cavanagh D., de Groot R.J., Enjuanes L., Gorbalenya A.E., Holmes K.V., Masters P., Rottier P., Taguchi F. et al. Coronaviridae. In: Virus taxonomy. Eighth report of the International Committee on Taxonomy of Viruses. Eds. Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., Ball L.A. Elsevier, Academic Press., 2005:947–964. doi: 10.1016/B978-0-12-249951-7.50015-8
  17. Gorbalenya A.E., Krupovic M., Mushegian A., Kropinski A.M., Siddell S.G., Varsani A., Adams M.J., Davison A.J., Dutilh B.E., Harrach B. et al. The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat. Microbiol. 2020;5(5):668–674. doi: 10.1038/s41564-020-0709-x
  18. Walker P.J., Siddell S.G., Lefkowitz E.J., Mushegian A.R., Adriaenssens E.M., Alfenas-Zerbini P., Davison A.J., Dempsey D.M., Dutilh B.E., García M.L., et al. Changes to virus taxonomy and to the international code of virus classification and nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch. Virol. 2021;166(9):2633–2648. doi: 10.1007/s00705-021-05156-1
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981;17:368–376. doi: 10.1007/BF01734359
  20. Felsenstein J. Inferring Phylogenies. Sunderland, MA: Sinauer Associates, 2003. 664 p.
  21. Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 2015;32(1):268–274. doi: 10.1093/molbev/msu300
  22. Katoh K., Rozewicki J., Yamada K.D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 2019;20(4):1160–1166. doi: 10.1093/bib/bbx108
  23. Mavrodiev E.V., Tursky M.L., Mavrodiev N.E., Schroder L., Laktionov A.P., Ebach M.C., Williams D.M. On classification and taxonomy of coronaviruses (Riboviria, Nidovirales, Coronaviridae) with special focus on severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Math. Biol. Bioinf. 2022;17(2):289–311. doi: 10.17537/2022.17.289
  24. Kitching I.J., Forey P., Forey P.L., Humphries C., Williams D.M. Cladistics, the Theory and Practice of Parsimony Analysis. Oxford and New York: Oxford University Press, 1998. 228 p.
  25. Nelson G., Platnick N. Three-taxon statements, a more precise use of parsimony? Cladistics. 1991;7(4):351–366. doi: 10.1111/j.1096-0031.1991.tb00044.x
  26. Creevey C.J., McInerney J.O. Trees from trees: construction of phylogenetic supertrees using Clann. In: Bioinformatics for DNA Sequence Analysis. Ed. Posada D. New York: Springer Humana Press, 2009. P. 139–161. doi: 10.1007/978-1-59745-251-9_7
  27. Chaley M.B., Kutyrkin V.A. Coronavirus genus recognition based on prototype virus variants. Mathematical Biology and Bioinformatics. 2022;17(1):10–27. doi: 10.17537/2022.17.10
  28. Shchelkanov M.Y., Popova A.Y., Dedkov V.G., Akimkin V.G., Maleyev V.V. History of investigation and current classification of coronaviruses (Nidovirales: Coronaviridae). Russian Journal of Infection and Immunity. 2020;10(2):221–246. doi: 10.15789/2220-7619-HOI-1412
  29. Borisova N.I., Kotov I.A., Kolesnikov A.A., Kaptelova V.V., Speranskaya A.S., Kondrasheva L.Y., Tivanova E.V., Khafizov K.F., Akimkin V.G. Monitoring the spread of the SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) variants in the Moscow region using targeted high-throughput sequencing. Problems of Virology. 2021;66(4):269–278. doi: 10.36233/0507-4088-72
  30. Vlasova A.N., Saif L.J. Bovine coronavirus and the associated diseases. Front. Vet. Sci. 2021;8. Article No. 643220. doi: 10.3389/fvets.2021.643220
  31. Glotov A.G., Nefedchenko A.V., Yuzhakov A.G., Koteneva S.V., Glotova T.I., Komina A.K., Krasnikov N.Y. Genetic diversity of Siberian bovine coronavirus isolates (Coronaviridae: Coronavirinae: Betacoronavirus-1: Bovine-Like coronaviruses). Problems of Virology. 2022;67(6):465–474. doi: 10.36233/0507-4088-141
  32. Sayers E.W., Cavanaugh M., Clark K., Ostell J., Pruitt K.D., Karsch-Mizrachi I. GenBank. Nucleic Acids Res. 2019;47(D1):D94–D99. doi: 10.1093/nar/gky989
  33. Sayers E.W., Beck J., Bolton E.E., Bourexis D., Brister J.R., Canese K., Comeau D.C., Funk K., Kim S., Klimke W., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2021;49(D1):D10-D17. doi: 10.1093/nar/gkaa892
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2023;18(2):267-281
doi: 10.17537/2023.18.267
опубликована на рус. яз.

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