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Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses Cover

Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

Open Access
|Nov 2019

References

  1. Biek R., Real L.A.: The landscape genetics of infectious disease emergence and spread. Mol Ecol 2010, 19, 3515–3531.
  2. Bolger A.M., Lohse M., Usadel B.: Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, 2014, 30, 2114–2120.
  3. Boukadida C., Torres-Flores J.M., Yocupicio-Monroy M., Piten-Isidro E., Rivero-Arrieta A.Y., Luna-Villalobos Y.A., Martínez-Vargas L., Alcaraz-Estrada S.L., Torres K.J., Lira R., Reyes-Terán G., Sevilla-Reyes E.E.: Complete genome sequences, before and after mammalian cell culture, of Zika virus isolated from the serum of a symptomatic male patient from Oaxaca, Mexico. Genome Announc 2017, 5, e00072-17, doi: 10.1128/ genomeA.00072-17.
  4. Bourhy H., Kissi B., Audry L., Smreczak M., Sadkowska-Todys M., Kulonen K., Tordo N., Żmudziński J.F., Holmes E.: Ecology and evolution of rabies virus in Europe. J Gen Virol 1999, 80, 2545–2557.
  5. Brunker K., Marston D., Horton D.L., Cleaveland S., Fooks A.R., Kazwala R., Ngeleja C., Lembo T., Sambo M., Mtema Z.J., Sikana L., Wilkie G., Biek R., Hampson K.: Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus Evol 2015, 1, 1–11.
  6. Cheval J., Sauvage V., Frangeul L., Dacheux L., Guigon G., Dumey N., Pariente K., Rousseaux C., Dorange F., Berthet N., Brisse S., Moszer I., Bourhy H., Manuguerra C.J., Lecuit M., Burguiere A., Caro V., Eloit M.: Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 2011, 49, 3268–3275, doi: 10.1128/JCM.00850-11.
  7. Cliquet F., Picard-Meyer E., Mojzis M., Dirbakova Z., Muizniece Z., Jaceviciene I., Mutinelli F., Matulova M., Frolichova J., Rychlik I., Celer V.: In-depth characterization of live vaccines used in Europe for oral rabies vaccination of wildlife. PLoS One, 2015, 10, e0141537, doi: 10.1371/journal.pone.0141537.
  8. Dedkov V.G., Lukashev A.N., Deviatkin A.A., Kuleshov K.V., Safonova M.V., Poleshchuk E.M., Drexler J.F., Shipulin G.A.: Retrospective diagnosis of two rabies cases in humans by high throughput sequencing. J Clin Virol 2016, 78, 74–81, doi: 10.1016/j.jcv.2016.03.012.
  9. Drummond A.J., Pybus O.G., Rambaut A., Forsberg A., Rodrigo A.G.: Measurable evolving populations. Trends Ecol Evol 2003, 18, 481–488.
  10. Elson R., Awofisayo-Okuyelu A., Greener T., Swift C., Painset A., Amar C.F.L., Newton A., Aird H., Swindlehurst M., Elviss N., Foster K., Dallman T.J., Ruggles R., Grant K.: Utility of whole genome sequencing to describe the persistence and evolution of listeria monocytogenes strains within crabmeat processing environments linked to two outbreaks of listeriosis. J Food Prot 2019, 82, 30–38, doi: 10.4315/0362-028X.JFP-18-206.
  11. Hoffmann B., Freuling C.M., Wakeley P.R., Rasmussen T.B., Leech S., Fooks A.R., Beer M., Müller T.: Improved safety for molecular diagnosis of classical rabies viruses by use of a TaqMan real-time reverse transcription-PCR “double check” strategy. J Clin Microbiol 2010, 48, 3970–3978, doi: 10.1128/JCM.00612-10.
  12. https://www.illumina.com/science/education/sequencing-coverage.html
  13. Johnson N., McElhinney L.M., Smith J., Lowings P., Fooks A.R.: Phylogenetic comparison of the genus Lyssavirus using distal coding sequences of the glycoprotein and nucleoprotein genes. Arch Virol 2002, 147, 2111–2123.
  14. Kim D., Song L., Breitwieser F.P., Salzberg S.L.: Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 2016, 26, 1721–1729.
  15. Lewandowska D.W., Zagordi O., Geissberger F., Kufner V., Schmutz S., Böni J., Metzner K.J., Trkola A., Huber M.: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. Microbiome 2017, 5, 1–13, https://doi.org/10.1186/s40168-017-0317-z
  16. Marston D.A., McElhinney L.M., Ellis R.J., Horton D.L., Wise E.L., Leech S.L., David D., de Lambellerie X., Fooks A.R.: Next generation sequencing of viral RNA genomes. BMC Genomics 2013, 14, 444.
  17. McElhinney L.M., Marston D.A, Brookes S.M., Fooks A.R.: Effects of carcass decomposition on rabies virus infectivity and detection. J Virol Methods 2014, 207, 110–113.
  18. Nadin-Davis S.A., Colville A., Trewby H., Biek R., Real L.: Application of high-throughput sequencing to whole rabies viral genome characterization and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario. Virus Res 2017, 232, 123–133.
  19. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelsky A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Clingenpeel S.R., Woyke T., Tesler G., Alekseyev M.A., Pevzner P.A.: Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. In: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, edited by M. Deng, R. Jiang, F. Sun, X. Zhang, Springer, Heidelberg, 2013, pp 158–170.
  20. Orłowska A., Żmudziński J.F.: Molecular epidemiology of rabies virus in Poland. Arch Virol 2014, 159, 2043–2050.
  21. Picard-Meyer E., Robarded E., Moroz D., Trotsenko Z., Drozhzhe Z., Biarnais M., Solodchuk V., Smreczak M., Cliquet F.: Molecular epidemiology of rabies in Ukraine. Arch Virol 2012, 157, 1689–1698.
  22. Reis-Cunha J.L., Baptista R.P., Rodrigues-Luiz G.F., Coqueiro-Dos-Santos A., Valdivia H.O., de Almeida L.V., Cardoso M.S., D’Ávila D.A., Dias F.H.C., Fujiwara R.T., Galvão L.M.C., Chiari E., Cerqueira G.C., Bartholomeu D.C.: Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU. BMC Genomics 2018, 19, 816, doi: 10.1186/s12864-018-5198-4.
  23. Siira L., Naseer U., Alfsnes K., Hermansen N.O., Lange H., Brandal L.T.: Whole genome sequencing of Salmonella chester reveals geographically distinct clusters, Norway, 2000 to 2016. Euro Surveill 2019, 24, doi: 10.2807/1560-7917.ES.2019.24.4. 1800186.
  24. Simon B., Pichon M., Valette M., Burfin G., Richard M., Lina B., Josset L.: Whole genome sequencing of A(H3N2) influenza viruses reveals variants associated with severity during the 2016–2017 season. Viruses 2019, 11, 108, doi: 10.3390/v11020108.
  25. Steinhauer D.A., Holland J.J.: Rapid evolution of RNA viruses. Ann rev microbiol 1987, 41, 409–433.
  26. Tordo N., Poch O., Ermine A., Keith G., Rougeon F.: Walking along the rabies genome: is the large G-L intergenic region a remnant gene? Proc Natl Acad Sci USA 1986, 83, 3914–3918.
  27. Tordo N., Poch O., Ermine A., Keith G., Rougeon F.: Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses. Virology 1988, 165, 565–576.
  28. Tricou V., Berthet N., Nakoune E., Kazanji M.: Complete genome sequence of a rabies virus isolated from a human in Central African Republic. Genome Announc 2014, 2, e00598–e005914.
  29. Wakeley P.R., Johnson N., McElhinney L.M., Marston D., Sawyer J., Fooks A.R.: Development of a real-time, TaqMan reverse transcription-PCR assay for detection and differentiation of lyssavirus genotypes 1, 5, and 6. J Clin Microbiol 2005, 43, 2786–2792.
  30. Wood D.E., Salzberg S.L.: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014, 15, R46.
  31. Wylezich C., Papa A., Beer M., Hӧper D.: A versatile sample processing workflow for metagenomic pathogen detection. Sci Rep 2018, 30, 13108, doi: 10.1038/s41598-018-31496-1.
Language: English
Page range: 471 - 479
Submitted on: Mar 6, 2019
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Accepted on: Nov 4, 2019
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Published on: Nov 16, 2019
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2019 Anna Orłowska, Ewelina Iwan, Marcin Smreczak, Jerzy Rola, published by National Veterinary Research Institute in Pulawy
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.