Comparative analysis of the taxonomic classification criteria for a number of groups of pathogenic DNA and RNA viruses based on genomic data
- 作者: Sizikova T.1, Lebedev V.1, Borisevich S.1
-
隶属关系:
- 48th Central Scientific Research Institute of the Ministry of Defense of the Russian Federation
- 期: 卷 69, 编号 3 (2024)
- 页面: 203-218
- 栏目: REVIEWS
- URL: https://journals.rcsi.science/0507-4088/article/view/259213
- DOI: https://doi.org/10.36233/0507-4088-238
- EDN: https://elibrary.ru/njrkwu
- ID: 259213
如何引用文章
全文:
详细
The basis for criteria of the taxonomic classification of DNA and RNA viruses based on data of the genomic sequencing are viewed in this review. The genomic sequences of viruses, which have genome represented by double-stranded DNA (orthopoxviruses as example), positive-sense single-stranded RNA (alphaviruses and flaviviruses as example), non-segmented negative-sense single-stranded RNA (filoviruses as example), segmented negative-sense single-stranded RNA (arenaviruses and phleboviruses as example) are analyzed. The levels of genetic variability that determine the assignment of compared viruses to taxa of various orders are established for each group of viruses.
作者简介
Tatiana Sizikova
48th Central Scientific Research Institute of the Ministry of Defense of the Russian Federation
Email: 48cnii@mil.ru
ORCID iD: 0000-0002-1817-0126
PhD in Biology
俄罗斯联邦, Sergiev PosadVitaliy Lebedev
48th Central Scientific Research Institute of the Ministry of Defense of the Russian Federation
Email: 48cnii@mil.ru
ORCID iD: 0000-0002-6552-4599
D. Sc. in Biology, Professor, Leading Researcher
俄罗斯联邦, Sergiev PosadSergey Borisevich
48th Central Scientific Research Institute of the Ministry of Defense of the Russian Federation
编辑信件的主要联系方式.
Email: 48cnii@mil.ru
ORCID iD: 0000-0002-6742-3919
D. Sc. in Biology, Professor, Academician of the Russian Academy of Sciences, Head of the Institute
俄罗斯联邦, Sergiev Posad参考
- Lwoff A., Tournier P. The classification of viruses. Annu. Rev. Microbiol. 1966; 20: 45–74. DOI: https://doi.org/10.1146/annurev.mi.20.100166.000401
- Gintsburg A.L. Genodiagnosis of infectious diseases. Zhurnal mikrobiologii, epidemiologii i immunologii. 1998; 75(3): 86–95. EDN: https://elibrary.ru/mozshn (in Russian)
- Glick B.R., Pasternak J.J. Molecular Biotechnology. Principles and Applications of Recombinant DNA. Washington: American Society for Microbiology; 1994.
- Alekseeva A.E., Brusnigina N.F. Possibility and perspectives of massive parallel sequencing methods application in the diagnostics and epidemiological surveillance of infection diseases. Zhurnal MediAl’. 2014; (2): 6–28. EDN: https://elibrary.ru/sgxcgt (in Russian)
- Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat. Biotechnol. 2012; 30(4): 295–6. DOI: https://doi.org/10.1038/nbt0412-295
- Kuznetsova I.V., Efremenko D.V., Kulichenko A.N. Applying principles of multi-factor genetic analysis of infectious disease agents in the work of the Rospotrebnadzor SAET during mass events. Problemy osobo opasnykh infektsii. 2018; (2): 68–72. DOI: https://doi.org/10.21055/0370-1069-2018-2-68-72 EDN: https://elibrary.ru/xrvhfz (in Russian)
- Behbehani A.M. The smallpox story: life and death of old disease. Microbiol. Rev. 1983; 47(4): 455–505. DOI: https://doi.org/10.1128/mr.47.4.455-509.1983
- Onishchenko G.G., Maksimov V.A., Vorob’ev A.A., Podkuiko V.N., Mel’nikov S.A. The topicality of return to smallpox vaccination: problems and prospects. Vestnik Rossiiskoi akademii meditsinskikh nauk. 2006; (7): 32–8. EDN: https://elibrary.ru/htvfyn (in Russian)
- Lofquist J.M., Weimert N.A., Hayney M.S. Smallpox: A review of clinical disease and vaccination. Am. J. Heath Syst. Pharm. 2003; 60(8): 749–56. DOI: https://doi.org/10.1093/ajhp/60.8.749
- Booss J., Davis L.E. Smallpox and smallpox vaccination. Neurological implications. Neurology. 2003; 60(8): 1241–5. DOI: https://doi.org/10.1212/01.wnl.0000063319.64515.6b
- Fenner F. Smallpox and Its Eradication. Geneva: WHO; 1988.
- Mikheev M.V., Feshchenko V.M., Shchelkunov S.N. Phylogenetic analysis of a chemokine-binding protein gene of orthopoxviruses. Molekulyarnaya genetika, mikrobiologiya i virusologiya. 2004; (1): 29–36. EDN: https://elibrary.ru/okkpev (in Russian)
- Safronov P.F., Ryazankina O.I., Petrov N.A., Totmenin A.V., Kolosova I.V., Shchelkunov S.N. Structural and functional organization of the genome of the cowpox virus, strain GRI-90. Report 2. Comparative analysis of the structure of the left species-specific region of the orthopoxvirus genome. Molekulyarnaya biologiya. 1999; 33(2): 291–302. (in Russian)
- Marennikova S.S., Shchelkunov S.N. Orthopoxviruses Pathogenic to Humans [Patogennye dlya cheloveka ortopoksvirusy]. Moscow; 1998. (in Russian)
- Safronov P.F., Totmenin A.V., Ryazankina O.I., Shchelkunov S.N. Structural and functional organization of the genome of the cowpox virus, strain GRI-90. Report 3. Functional characteristics of the left species-specific region of the orthopoxvirus genome. Molekulyarnaya biologiya. 1999; 33(2): 303–13. (in Russian)
- Emerson G.L., Li Y., Frace M.A., Olsen-Rasmussen M.A., Khristova M.L., Govil D., et al. The phylogenetics and ecology of the orthopoxviruses endemic to North America. PLoS One. 2009; 4(10): e7666. DOI: https://doi.org/10.1371/journal.pone.0007666
- Mauldin M.R., Antwerpen M., Emerson G.L., Li Y., Zoeller G., Carroll D.S., et al. Cowpox virus: what’s in a name? Viruses. 2017; 9(5): 101. DOI: https://doi.org/10.3390/v9050101
- Springer Y.P., Hsu C.H., Werle Z.R., Olson L.E., Cooper M.P., Castrodale L.J., et al. Novel orthopoxvirus infection in an Alaska resident. Clin. Infect. Dis. 2017; 64(12): 1737–41. DOI: https://doi.org/10.1093/cid/cix219
- Vora N.M., Li Y., Geleishvili M., Emerson G.L., Khmaladze E., Maghlakelidze G., et al. Human infection with a zoonotic orthopoxvirus in the country of Georgia. N. Engl. J. Med. 2015; 372(13): 1223–30. DOI: https://doi.org/10.1056/NEJMoa1407647
- Cardeti G., Gruber C.E.M., Eleni C., Carletti F., Castilletti C., Manna G., et al. Fatal outbreak in Tonkean macaques caused by possibly novel orthopoxvirus, Italy, January 2015. Emerg. Infect. Dis. 2017; 23(12): 1941–9. DOI: https://doi.org/10.3201/ eid2312.162098
- Gao J., Gigante C., Khmaladze E., Liu P., Tang S., Wilkins K., et al. Genome sequences of Akhmeta virus, an early divergent old world orthopoxvirus. Viruses. 2018; 10(5): 252. DOI: https://doi.org/10.3390/v10050252
- Lanave G., Dowgier G., Decaro N., Albanese F., Brogi E., Parisi A., et al. Novel orthopoxvirus and lethal disease in Cat, Italy. Emerg. Infect. Dis. 2018; 24(9): 1665–73. DOI: https://doi.org/10.3201/eid2409.171283
- Volchkov V.E., Volchkova V.A., Netesov S.V. Complete nucleotide sequence of the Eastern equine encephalomyelitis virus genome. Molekulyarnaya genetika, mikrobiologiya i virusologiya. 1991; (5): 8–15. (in Russian)
- Agular P., Adams A.P., Suarez V., Beingolea L., Vargas J., Manock S., et al. Genetic characterization of VEE virus from Bolivia, Ecuador and Peru: identification of a new subtype ID lineage. PLoS Negl. Trop. Dis. 2009; 3(9): e514. DOI: https://doi.org/10.1371/journal.pntd.0000514
- Chang G.J., Trent D.W. Nucleotide sequence of the genomic region encoding the 26S mRNA of EEE virus and the deduced aminoacid sequence of the viral structural proteins. J. Gen. Virol. 1987; 62(Pt. 8): 2129–42. DOI: https://doi.org/10.1099/0022-1317-68-8-2129.
- Weaver S.C., Pfeffer M., Marriott K., Kang W., Kinney R.M. Genetic evidence for the origins of Venezuelan equine encephalitis virus subtype IAB outbreaks. Am. J. Trop. Med. Hyg. 1999; 60(3): 441–8. DOI: https://doi.org/10.4269/ajtmh.1999.60.441
- Arrigo N.C., Adams A.P., Weaver S.C. Evolutionary patterns of eastern equine encephalitis virus in North versus South America suggest ecological differences and taxonomic revision. J. Virol. 2010; 84(2): 1014–25. DOI: https://doi.org/10.1128/JVI.01586-09
- Forrester N.L., Weitheim J.O., Dugan V.G., Auguste A.J., Lin D., Adams A.P., et al. Evolution and spread of VEE complex alphavirus in the Americas. PLoS Negl. Trop. Dis. 2017; 11(8): e0005693. DOI: https://doi.org/10.1371/journal.pntd.0005693
- Weaver S.C., Winegar R., Manger I.D., Forrester N.L. Alpaviruses: Population genetics and determinants emergence. Antiviral. Res. 2012; 94(3): 242–57. DOI: https://doi.org/10.1016/j.antiviral.2012.04.002
- Powers A.M., Huang H.V., Roehrig J.T., Strauss E.G., Weaver S.C. Togaviridae. In: King A.M.G., Adams M.J., Carstens E.B., Lefcovitz E.J., eds. Virus Taxonomy, Ninth Report of International Committee on taxonomy of Viruses. Oxford: Elsevier; 2011: 1103–10.
- Kinney R.M., Pfeffer M., Tsuchiya K.R., Chang G.J., Roehrig J.T. Nucleotide sequences of 26S mRNAs of the viruses, defining the VEE antigenic complex. Am. J. Trop. Med. Hyg. 1998; 59(6): 952–64. DOI: https://doi.org/10.4269/ajtmh.1998.59.952
- Quiroz E., Aguilar P.V., Cisneros J., Tesh R.B., Weaver S.C. Venezuelan equine encephalitis in Panama: fatal endemic disease and genetic diversity of etiologic viral strains. PLoS Negl. Trop. Dis. 2009; 3(6): e472. DOI: https://doi.org/10.1371/journal.pntd.0000472
- Brault A.C., Powers A.M., Weaver S.C. Vector infection determinants of Venezuelan equine encephalitis virus reside within the E2 envelope glycoprotein. J. Virol. 2002; 76(12): 6387–92. DOI: https://doi.org/10.1128/jvi.76.12.6387-6392.2002
- Brault A.C., Powers A.M., Holmes E.C., Woelk C.H., Weaver S.C. Positively-charged amino acid substitutions in the E2 envelope glycoprotein are associated with the emergence of VEE virus. J. Virol. 2002; 76(4): 1718–30. DOI: https://doi.org/10.1128/jvi.76.4.1718-1730.2002
- Greene I.P., Paessler S., Austgen L., Anischenko M., Brault A.C., Bowen R.A., et al. Envelope glycoprotein mutations mediate equine amplification and virulence of epizootic VEE virus. J. Virol. 2005; 79(14): 9128–33. DOI: https://doi.org/10.1128/JVI.79.14.9128-9133.2005
- Anischenko M., Bowen R.A. Paessler S., Austgen L., Greene I.P., Weaver S.C. Venezuelan encephalitis emergence mediated by a phylogenetically predicted virus mutation. Proc. Natl Acad. Sci. USA. 2006; 103(13): 4994–9. DOI: https://doi.org/10.1073/pnas.0509961103
- Agular P.V., Estrada-Franco J.C., Navarro-Lopes R., Ferro C., Haddow A.D., Weaver S.C. Endemic VEE in the Americas: Hidden under dengue umbrella. Future Virol. 2011; 6(6): 721–40. DOI: https://doi.org/10.2217/FVL.11.5
- Sharma A., Knollmann-Ritchel B. Current understanding of molecular basis of VEE virus pathogenesis and vaccine development. Viruses. 2019; 11(2): 164. DOI: https://doi.org/10.3390/v11020164
- Lednicky J.A., White S.K., Mavian C.N., Badry M.A., Telisma T., Salemi M., et al. Emergence of Madariaga virus as cause of acute febrile illness of children, Haiti 2015. PLoS Negl. Trop. Dis. 2019; 13(1): e006972. DOI: https://doi.org/10.1371/journal.pntd.0006972
- Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5): 1792–7. DOI: https://doi.org/10.1093/nar/gkh340
- Barrows N.J., Campos R.K., Liao K., Prasanth K.R., Soto-Acosta R., Yeh S., et al. Biochemistry and molecular biology of flaviviruses. Chem. Rev. 2018; 118(8): 4448–82. DOI: https://doi.org/10.1021/acs.chemrev.7b00719
- Pierson T.C., Diamond M.S. Flaviviruses. In: Knipe D.M., Howley P.M., eds. Field virology. Philadelphia; 2013: 714–94.
- Karabatsos N. International Catalogue of Arboviruses: Including Certain other Viruses of Vertebrates. San Antonio: Published for the Subcommittee on Information Exchange of the American Committee on Arthropod-borne Viruses by the American Society of Tropical Medicine and Hygiene; 1985.
- Kuno G., Chang G.J., Tsuchiya K.R., Karabatsos N., Cropp C.B. Phylogeny of the genus Flavivirus. J. Virol. 1998; 72(1): 73–83. DOI: https://doi.org/10.1128/JVI.72.1.73-83.1998
- de Souza Lopes O., de Abreu Sacchetta L., Coimbra T.L., Pinto G.H., Glasser C.M. Emergence of a new arbovirus disease in Brazil. II. Epidemiologic studies on 1975 epidemic. Am. J. Epidemiol. 1978; 108(5): 394–401. DOI: https://doi.org/10.1093/oxfordjournals.aje.a112637
- Saivish M.V., da Costa V.G., da Silva R.A., Dutra da Silva G.C., Menezes G., Moreli M.L. Rocio Virus: An updated view on an elusive flavivirus. Viruses. 2021; 13(11): 2293. DOI: https://doi.org/10.3390/v13112293
- Mitchell C.J., Monath T.P., Cropp C.B. Experimental transmission of Rocio virus by mosquitoes. Am. J. Trop. Med. Hyg. 1981; 30(2): 465–72. DOI: https://doi.org/10.4269/ajtmh.1981.30.465
- Tiriba A.C., Miziara A.M., Lorenço R., da Costa R.B., Costa C.S., Pinto G.H. Primary human epidemic encephalitis induced by Arbovirus found at the sea shore south of the State of São Paulo. Clinical study in an emergency hospital. AMB Rev. Assoc. Med. Bras. 1976; 22(11): 415–20. (in Portuguese)
- Medeiros D.B., Nunes M.R., Vasconcelos P.F., Chang G.J., Kuno G. Complete genome characterization of Rocio virus (Flavivirus: Flaviviridae), a Brazilian flavivirus isolated from a fatal case of encephalitis during an epidemic in Sao Paulo state. J. Gen. Virol. 2007; 88(8): 2237-46. DOI: https://doi.org/10.1099/vir.0.82883-0
- Faye O., Freire C.C., Imarino A., Faye O., Oliveira J.V.C., Diallo M., et al. Molecular evolution of Zika virus during its emerging in the 20th century. PLoS Negl. Trop. Dis. 2014; 8(1): е2636. DOI: https://doi.org/10.1371/journal.pntd.0002636
- Kiley M.P., Bowen E.T., Eddy G.A., Isaacson M., Johnson K.M., McCormick J.B., et al. Filoviridae: A taxonomic home for Marburg and Ebola viruses? Intervirology. 1982; 18(1-2): 24–32. DOI: https://doi.org/10.1159/000149300
- Kuhn J.H., Becker S., Ebihara H., Geisbert T.W., Johnson K.M., Kawaoka Y., et al. Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch. Virol. 2010; 155(12): 2083–103. DOI: https://doi.org/10.1007/s00705-010-0814-x
- Biedenkopf N., Bukreyev A., Chandran K., Di Paola N., Formenty P.B.H., Griffiths A., et al. Renaming of genera Ebolavirus and Marburgvirus to Orthoebolavirus and Orthomarburgvirus, respectively, and introduction of binomial species names within family Filoviridae. Arch. Virol. 2023; 168(8): 220. DOI: https://doi.org/10.1007/s00705-023-05834-2
- Kuhn J.H., Adachi T., Adhikari N.K.J., Arribas J.R., Bah I.E., Bausch D.G., et al. New filovirus disease classification and nomenclature. Nat. Rev. Microbiol. 2019; 17(5): 261–3. DOI: https://doi.org/10.1038/s41579-019-0187-4
- Le Guenno B., Formenty P., Wyers M., Gounon P., Walker F., Boesch C. Isolation and partial characterisation of a new strain of Ebola virus. Lancet. 1995; 345(8960): 1271–4. DOI: https://doi.org/10.1016/s0140-6736(95)90925-7
- Towner J.S., Sealy T.K., Khristova M.L., Albarino C.G., Conlan S., Reeder S.A., et al. Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog. 2008; 4(11): e1000212. DOI: https://doi.org/10.1371/journal.ppat.1000212
- Miranda M.E.G., Miranda N.L.J. Reston ebolavirus in humans and animals in the Philippines: A review. J. Infect. Dis. 2011; 204(3): 757–60. DOI: https://doi.org/10.1093/infdis/jir296
- Goldstein T., Anthony S.J., Gbakima A., Bird B.H., Bangura J., Tremeau-Bravard A. The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses. Nat. Microbiol. 2018; 3(10): 1084–9. DOI: https://doi.org/10.1038/s41564-018-0227-2
- de La Vega M.A., Stein D., Kobinger G.P. Ebolavirus evolution: past and present. PLoS Pathog. 2015; 11(11): e1005221. DOI: https://doi.org/10.1371/journal.ppat.1005221
- Towner J.S., Khristova M.L., Sealy T.K., Vincent M.J., Erickson B.R., Bawies D.A., et al. Marburg virus genomics and association with a large hemorrhagic fever outbreak in Angola. J. Virol. 2006; 80(13): 6497–516. DOI: https://doi.org/10.1128/JVI.00069-06
- Carroll S.A., Towner J.S., Sealy T.K., McMullan L.K., Khristova M.L., Burt F.J., et al. Molecular evolution of viruses of the family Filoviridae based on 97 whole-genome sequences. J. Virol. 2013; 87(5): 2608–16. DOI: https://doi.org/10.1128/jvi.03118-12
- He B., Feng Y., Zhang H., Xu L., Yang W., Zhang Y., et al. Filovirus RNA in fruit bats, China. Emerg. Infect. Dis. 2015; 21(9): 1675–7. DOI: https://doi.org/10.3201/eid2109.150260
- Negredo A., Palacios G., Vazquez-Moron S., Gonzales F., Dopazo H., Molero F., et al. Discovery of an Ebola-like filovirus in Europe. PLoS Pathog. 2011; 7(10): e1002304. DOI: https://doi.org/10.1371/journal.ppat.1002304
- Di Paola N., Sanchez-Lockhart M., Zeng X., Kuhn J.H., Palacios G. Viral genomics in Ebola virus research. Nat. Rev. Microbiol. 2020; 18(7): 365–78. DOI: https://doi.org/10.1038/s41579-020-0354-7
- Southern P.J. Arenaviridae: The viruses and their replication. In: Fields B.N., Knipe D.M., Howley P.M. Field’s Virology. Volume 1. Philadelphia: Lippincott-Raven Publishers; 1996: 1505–19.
- Hallam S.J., Koma T., Maruyama J., Paessler S. Review of Mammarenavirus Biology and Replication. Front. Microbiol. 2018; 9: 1751. DOI: https://doi.org/10.3389/fmicb.2018.01751
- Munning J.T., Forester N., Paesler S.J.T. Lassa virus isolates from Mali and Ivory Coast represent an emerging fifth lineage. Front. Microbiol. 2015; 6: 1037. DOI: https://doi.org/10.3389/fmicb.2015.01037
- Whitmer S.L.M., Strecker T. Cadar D., Dienes H.P., Faber K., Patel K., et al. New lineage of Lassa virus Togo 2016. Emerg. Infect. Dis. 2018; 24(3): 596–602. DOI: https://doi.org/10.3201/eid2403.171905
- Charrel R.N., Feldmann H., Fulhorst C.F., Khelifa R., de Chesse R., de Lambalerie X. Phylogeny of New World arenaviruses based on the complete coding sequences of the small genomic segment identified an evolutionary lineage produced by intrasegmental recombination. Biochem. Biophys. Res. Commun. 2002; 296(5): 1118–24. DOI: https://doi.org/10.1016/s0006-291x(02)02053-3
- Li A., Liu L., Wu W., Liu Y., Huang X., Li C., et al. Molecular evolution and genetic diversity analysis of SFTS virus based on next-generation sequencing. Biosaf. Health. 2021; 3(02): 105–15. DOI: https://doi.org/10.1016/j.bsheal.2021.02.002
- Ning Y.J., Feng K., Min Y.Q., Cao W.C., Wang M., Deng F., et al. Disruption of type I interferon signaling by the nonstructural protein of severe fever with thrombocytopenia syndrome virus via the hijacking of STAT2 and STAT1 into inclusion bodies. J. Virol. 2015; 89(8): 4227–36. DOI: https://doi.org/10.1128/JVI.00154-15
- Qu B., Qi X., Wu X., Liang M., Li C., Cardona C.J., et al. Supression of the interferon and NF-kB responses by severe fever with thrombocytopenia syndrome virus. J. Virol. 2012; 86(16): 8388–401. DOI: https://doi.org/10.1128/JVI.00612-12
- Huang X., Liu L., Du Y., Wu W., Wang H., Su J., et al. The evolutionary history and spatiotemporal dynamics of the fever, thrombocytopenia and leukocytopenia syndrome virus (FTLSV) in China. PLoS Negl. Trop. Dis. 2014; 8(10): e3237. DOI: https://doi.org/10.1371/journal.pntd.0003237
- Lam T.T., Liu W., Bowden T.A., Cui N., Zhuang L., Liu K., et al. Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus. Epidemics. 2013; 5(1): 1–10. DOI: https://doi.org/10.1016/j.epidem.2012.09.002
- Zhang Y.Z., Zhou D.J., Qin X.C., Tian J.H., Xiong Y., Wang J.B., et al. The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China. J. Virol. 2012; 86(5): 2864-8. DOI: https://doi.org/10.1128/JVI.06192-11
- Xu B., Liu L., Huang X., Ma H., Zhang Y., Du Y., et al. Metagenomic analysis of fever, thrombocytopenia and leucopenia syndrome (FTLS) in Henen province, China: Discovery of a new Bunyavirus. PLoS Patog. 2011; 7(11): e1002369. DOI: https://doi.org/10.1371/journal.ppat.1002369
- Liu L., Chen W., Yang Y., Jiang Y. Molecular evolution of fever, thrombocytopenia and leukocytopenia virus (FTLSV) based on whole-genome sequences. Infect. Genet. Evol. 2016; 39: 55-63. DOI: https://doi.org/10.1016/j.meegid.2015.12.022
- Lefkowitz E.J., Dempsey D.M., Hendrickson R.C., Orton R.J., Siddell S.G., Smith D.B. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 2018; 46(D1): D708–17. DOI: https://doi.org/10.1093/nar/gkx932