Molecular Characterization of Leishmania RNA virus 2 in Leishmaniamajor from Uzbekistan
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
31640177
PubMed Central
PMC6826456
DOI
10.3390/genes10100830
PII: genes10100830
Knihovny.cz E-zdroje
- Klíčová slova
- LRV2, Leishmania RNA virus, next-generation sequencing,
- MeSH
- fylogeneze MeSH
- genom virový * MeSH
- jednonukleotidový polymorfismus MeSH
- Leishmania major virologie MeSH
- Leishmaniavirus klasifikace genetika patogenita MeSH
- mutace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Uzbekistán MeSH
Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.
CEITEC Central European Institute of Technology Masaryk University 62500 Brno Czech Republic
Department of Molecular Biology Faculty of Biology Moscow State University 119991 Moscow Russia
Life Sciences Research Centre Faculty of Science University of Ostrava 71000 Ostrava Czech Republic
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Ghabrial S.A., Castón J.R., Jiang D., Nibert M.L., Suzuki N. 50-plus years of fungal viruses. Virology. 2015;479–480:356–368. doi: 10.1016/j.virol.2015.02.034. PubMed DOI
Janssen M.E., Takagi Y., Parent K.N., Cardone G., Nibert M.L., Baker T.S. Three-dimensional structure of a protozoal double-stranded RNA virus that infects the enteric pathogen Giardia lamblia. J. Virol. 2015;89:1182–1194. doi: 10.1128/JVI.02745-14. PubMed DOI PMC
Parent K.N., Takagi Y., Cardone G., Olson N.H., Ericsson M., Yang M., Lee Y., Asara J.M., Fichorova R.N., Baker T.S., et al. Structure of a protozoan virus from the human genitourinary parasite Trichomonas vaginalis. MBio. 2013 doi: 10.1128/mBio.00056-13. PubMed DOI PMC
Dunn S.E., Li H., Cardone G., Nibert M.L., Ghabrial S.A., Baker T.S. Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core. PLoS Pathog. 2013;9:e1003225. doi: 10.1371/journal.ppat.1003225. PubMed DOI PMC
Stuart K.D., Weeks R.L., Guilbride P.J. Myler molecular organization of Leishmania RNA virus 1. Proc. Natl. Acad. Sci. USA. 1992;89:8596–8600. doi: 10.1073/pnas.89.18.8596. PubMed DOI PMC
Scheffter S., Widmer G., Patterson J.L. Complete sequence of Leishmania RNA virus 1–4 and identification of conserved sequences. Virology. 1994;199:479–483. doi: 10.1006/viro.1994.1149. PubMed DOI
Lee S.E., Suh J.M., Scheffter S., Patterson J.L., Chung I.K. Identification of a ribosomal frameshift in Leishmania RNA virus 1–4. J. Biochem. 1996;120:22–25. doi: 10.1093/oxfordjournals.jbchem.a021387. PubMed DOI
Zangger H., Hailu A., Desponds C., Lye L.F., Akopyants N.S., Dobson D.E., Ronet C., Ghalib H., Beverley S.M., Fasel N. Leishmania aethiopica field isolates bearing an endosymbiontic dsRNA virus induce pro-inflammatory cytokine response. PLoS Negl. Trop. Dis. 2014;8:e2836. doi: 10.1371/journal.pntd.0002836. PubMed DOI PMC
Scheffter S.M., Ro Y.T., Chung I.K., Patterson J.L. The complete sequence of Leishmania RNA virus LRV2-1, a virus of an Old World parasite strain. Virology. 1995;212:84–90. doi: 10.1006/viro.1995.1456. PubMed DOI
Widmer G., Dooley S. Phylogenetic analysis of Leishmania RNA virus and Leishmania suggests ancient virus-parasite association. Nucleic Acids Res. 1995;23:2300–2304. doi: 10.1093/nar/23.12.2300. PubMed DOI PMC
Okamoto K., Miyazaki N., Larsson D.S., Kobayashi D., Svenda M., Muhlig K., Maia F.R., Gunn L.H., Isawa H., Kobayashi M., et al. The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes. Sci. Rep. 2016;6:33170. doi: 10.1038/srep33170. PubMed DOI PMC
Grybchuk D., Kostygov A.Y., Macedo D.H., Votypka J., Lukes J., Yurchenko V. RNA viruses in Blechomonas (Trypanosomatidae) and evolution of Leishmaniavirus. MBio. 2018 doi: 10.1128/mBio.01932-18. PubMed DOI PMC
Atayde V.D., da Silva A., Filho L., Chaparro V., Zimmermann A., Martel C., Jaramillo M., Olivier M. Exploitation of the Leishmania exosomal pathway by Leishmania RNA virus 1. Nat. Microbiol. 2019;4:714–723. doi: 10.1038/s41564-018-0352-y. PubMed DOI
Ives A., Ronet C., Prevel F., Ruzzante G., Fuertes-Marraco S., Schutz F., Zangger H., Revaz-Breton M., Lye L.F., Hickerson S.M., et al. Leishmania RNA virus controls the severity of mucocutaneous leishmaniasis. Science. 2011;331:775–778. doi: 10.1126/science.1199326. PubMed DOI PMC
Hartley M.A., Drexler S., Ronet C., Beverley S.M., Fasel N. The immunological, environmental, and phylogenetic perpetrators of metastatic leishmaniasis. Trends Parasitol. 2014;30:412–422. doi: 10.1016/j.pt.2014.05.006. PubMed DOI PMC
Hartley M.A., Ronet C., Zangger H., Beverley S.M., Fasel N. Leishmania RNA virus: When the host pays the toll. Front. Cell Infect Microbiol. 2012;2:99. PubMed PMC
Tirera S., Ginouves M., Donato D., Caballero I.S., Bouchier C., Lavergne A., Bourreau E., Mosnier E., Vantilcke V., Couppie P., et al. Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana. PLoS Negl. Trop. Dis. 2017;11:e0005764. doi: 10.1371/journal.pntd.0005764. PubMed DOI PMC
Grybchuk D., Kostygov A.Y., Macedo D.H., d’Avila-Levy C.M., Yurchenko V. RNA viruses in trypanosomatid parasites: A historical overview. Mem. Inst. Oswaldo Cruz. 2018;113:e170487. doi: 10.1590/0074-02760170487. PubMed DOI PMC
Grybchuk D., Akopyants N.S., Kostygov A.Y., Konovalovas A., Lye L.F., Dobson D.E., Zangger H., Fasel N., Butenko A., Frolov A.O., et al. Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania. Proc. Natl. Acad. Sci. USA. 2018;115:E506–E515. doi: 10.1073/pnas.1717806115. PubMed DOI PMC
Adaui V., Lye L.F., Akopyants N.S., Zimic M., Llanos-Cuentas A., Garcia L., Maes I., De Doncker S., Dobson D.E., Arevalo J., et al. Association of the endobiont double-stranded RNA virus LRV1 with treatment failure for human leishmaniasis caused by Leishmania braziliensis in Peru and Bolivia. J. Infect. Dis. 2016;213:112–121. doi: 10.1093/infdis/jiv354. PubMed DOI PMC
Ginouvès M., Simon S., Bourreau E., Lacoste V., Ronet C., Couppie P., Nacher M., Demar M., Prevot G. Prevalence and distribution of Leishmania RNA Virus 1 in Leishmania parasites from French Guiana. Am. J. Trop. Med. Hyg. 2016;94:102–106. doi: 10.4269/ajtmh.15-0419. PubMed DOI PMC
Rossi M., Castiglioni P., Hartley M.A., Eren R.O., Prevel F., Desponds C., Utzschneider D.T., Zehn D., Cusi M.G., Kuhlmann F.M., et al. Type I interferons induced by endogenous or exogenous viral infections promote metastasis and relapse of leishmaniasis. Proc. Natl. Acad. Sci. USA. 2017;114:4987–4992. doi: 10.1073/pnas.1621447114. PubMed DOI PMC
Paranaiba L.F., Pinheiro L.J., Macedo D.H., Menezes-Neto A., Torrecilhas A.C., Tafuri W.L., Soares R.P. An overview on Leishmania (Mundinia) enriettii: Biology, immunopathology, LRV and extracellular vesicles during the host-parasite interaction. Parasitology. 2018;145:1265–1273. doi: 10.1017/S0031182017001810. PubMed DOI
Bruschi F., Gradoni L. The Leishmaniases: Old Neglected Tropical Diseases. Springer; Cham, Switzerland: 2018.
Sukla S., Roy S., Sundar S., Biswas S. Leptomonas seymouri narna-like virus 1 and not leishmaniaviruses detected in kala-azar samples from India. Arch. Virol. 2017;162:3827–3835. doi: 10.1007/s00705-017-3559-y. PubMed DOI
Kraeva N., Butenko A., Hlaváčová J., Kostygov A., Myškova J., Grybchuk D., Leštinová T., Votýpka J., Volf P., Opperdoes F., et al. Leptomonas seymouri: Adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Pathog. 2015;11:e1005127. doi: 10.1371/journal.ppat.1005127. PubMed DOI PMC
Lye L.F., Akopyants N.S., Dobson D.E., Beverley S.M. A Narnavirus-like element from the trypanosomatid protozoan parasite Leptomonas seymouri. Genome Announc. 2016 doi: 10.1128/genomeA.00713-16. PubMed DOI PMC
Hajjaran H., Mahdi M., Mohebali M., Samimi-Rad K., Ataei-Pirkooh A., Kazemi-Rad E., Naddaf S.R., Raoofian R. Detection and molecular identification of Leishmania RNA virus (LRV) in Iranian Leishmania species. Arch. Virol. 2016;161:3385–3390. doi: 10.1007/s00705-016-3044-z. PubMed DOI
Kurt O., Mansur N., Cavus I., Ozcan O., Batir M.B., Gunduz C., Sezerman O.U., Ozbilgin A. First report and in silico analysis of Leishmania virus (LRV2) identified in an autochthonous Leishmania major isolate in Turkey. New Microbiol. 2019;42:64–67. PubMed
Faulde M.K., Werner A., Heyl G. Untreated zoonotic cutaneous leishmaniasis characterizing a highly aggressive strain type of Leishmania major in Uzbekistan. J. Eur. Acad. Dermatol. Venereol. 2007;21:1432–1433. doi: 10.1111/j.1468-3083.2007.02240.x. PubMed DOI
Zhirenkina E.N., Ponirovskii E.N., Strelkova M.V., Morozov E.N., Flegontov P.N., Kolesnikov A.A., Ponomareva V.I., Nasyrova R.M., Kovalenko D.A., Fatullaeva A.A., et al. The epidemiological features of visceral leishmaniasis, revealed on examination of children by Polymerase Chain Reaction, in the Papsky District, Namangan Region, Uzbekistan. Med. Parazitol. Parazit. Bolezn. 2011:37–41. (in Russian) PubMed
Strelkova M.V., Ponirovsky E.N., Morozov E.N., Zhirenkina E.N., Razakov S.A., Kovalenko D.A., Schnur L.F., Schonian G. A narrative review of visceral leishmaniasis in Armenia, Azerbaijan, Georgia, Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, Uzbekistan, the Crimean Peninsula and Southern Russia. Parasit. Vectors. 2015;8:330. doi: 10.1186/s13071-015-0925-z. PubMed DOI PMC
Chajbullinova A., Votýpka J., Sádlová J., Kvapilová K., Seblová V., Kreisinger J., Jirků M., Sanjoba C., Gantuya S., Matsumoto Y., et al. The development of Leishmania turanica in sand flies and competition with L. major. Parasit. Vectors. 2012;5:219. doi: 10.1186/1756-3305-5-219. PubMed DOI PMC
Akhoundi M., Kuhls K., Cannet A., Votýpka J., Marty P., Delaunay P., Sereno D. A historical overview of the classification, evolution, and dispersion of Leishmania parasites and sandflies. PLoS Negl. Trop. Dis. 2016;10:e0004349. doi: 10.1371/journal.pntd.0004349. PubMed DOI PMC
Bolger A.M., Lohse M., Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC
Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R.S. Genome Project Data Processing The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011;29:644–652. doi: 10.1038/nbt.1883. PubMed DOI PMC
Quinlan A.R. BEDTools: The swiss-army tool for genome feature analysis. Curr. Protoc. Bioinform. 2014 doi: 10.1002/0471250953.bi1112s47. PubMed DOI PMC
Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., Dicuccio M., Edgar R., Federhen S., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2008;36:D13–D21. doi: 10.1093/nar/gkm1000. PubMed DOI PMC
Karagiannis K., Simonyan V., Chumakov K., Mazumder R. Separation and assembly of deep sequencing data into discrete sub-population genomes. Nucleic Acids Res. 2017;45:10989–11003. doi: 10.1093/nar/gkx755. PubMed DOI PMC
Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC
Capella-Gutiérrez S., Silla-Martinez J.M., Gabaldon T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC
Villesen P. FaBox: An online toolbox for fasta sequences. Mol. Ecol. Notes. 2007;7:965–968. doi: 10.1111/j.1471-8286.2007.01821.x. DOI
Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A., Jermiin L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC
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;32:268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC
Lukeš J., Butenko A., Hashimi H., Maslov D.A., Votýpka J., Yurchenko V. Trypanosomatids are much more than just trypanosomes: Clues from the expanded family tree. Trends Parasitol. 2018;34:466–480. doi: 10.1016/j.pt.2018.03.002. PubMed DOI
Lukeš J., Skalický T., Týč J., Votýpka J., Yurchenko V. Evolution of parasitism in kinetoplastid flagellates. Mol. Biochem. Parasitol. 2014;195:115–122. doi: 10.1016/j.molbiopara.2014.05.007. PubMed DOI
Zangger H., Ronet C., Desponds C., Kuhlmann F.M., Robinson J., Hartley M.A., Prevel F., Castiglioni P., Pratlong F., Bastien P., et al. Detection of Leishmania RNA virus in Leishmania parasites. PLoS Negl. Trop. Dis. 2013;7:e2006. doi: 10.1371/journal.pntd.0002006. PubMed DOI PMC
Lye L.F., Owens K., Shi H., Murta S.M., Vieira A.C., Turco S.J., Tschudi C., Ullu E., Beverley S.M. Retention and loss of RNA interference pathways in trypanosomatid protozoans. PLoS Pathog. 2010;6:e1001161. doi: 10.1371/journal.ppat.1001161. PubMed DOI PMC
Matveyev A.V., Alves J.M., Serrano M.G., Lee V., Lara A.M., Barton W.A., Costa-Martins A.G., Beverley S.M., Camargo E.P., Teixeira M.M., et al. The evolutionary loss of RNAi key determinants in kinetoplastids as a multiple sporadic phenomenon. J. Mol. Evol. 2017;84:104–115. doi: 10.1007/s00239-017-9780-1. PubMed DOI PMC
Brettmann E.A., Shaik J.S., Zangger H., Lye L.F., Kuhlmann F.M., Akopyants N.S., Oschwald D.M., Owens K.L., Hickerson S.M., Ronet C., et al. Tilting the balance between RNA interference and replication eradicates Leishmania RNA virus 1 and mitigates the inflammatory response. Proc. Natl. Acad. Sci. USA. 2016;113:11998–12005. doi: 10.1073/pnas.1615085113. PubMed DOI PMC
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