Advanced technologies in diagnostics of viral diseases of unknown etiology

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Abstract

Unveiling origin of infectious diseases with unknown etiology is one of the major issues in contemporary medicine, since a laboratory-confirmed diagnosis may, unfortunately, be obtained solely in very few cases. Because the majority of the most common mid-latitude infections display a typical overt clinical picture, this problem has not been paid a proper attention until recently. Recent rise in incidence rate of infectious diseases lacking typical clinical signs observed lately makes it extremely important to consider the problem more closely. It is believed that such trend is due to a whole body of reasons, including impaired sanitary control, increased both internal and external migration flows, refusal of vaccination in case of long-lasting epidemic wellbeing, emergence of atypical bacterial strains of bacteria resulting from irrational antibiotic therapy etc. Viruses constitute the largest group of organisms on our planet accounting for them as the most common causative agent of infectious diseases of unknown etiology. Some estimates obtained by mathematical modeling propose that at least 320,000 types of viruses capable of infecting mammals may exist, most of which have not been described yet. Hence, monitoring circulation of the known viral pathogens, tracing down their spreading and changes in genome nucleotide sequence as well as revealing new types of viruses become important aspects of epidemiological surveillance necessary for timely response to emerging threats, prediction and early detection of outbreaks both in humans and animals. This review summarizes traditional molecular genetics methods for detection of viral pathogens, such as PCR, real-time PCR, Sanger sequencing with pre-cloning, and methods based on the second and third generation sequencing. Therefore, a more detailed overview was provided to diverse methods based on using such technologies because viral infectious agents investigated with high-throughput sequencing (or NGS — Next Generation Sequencing) has been increasingly appreciated as feasible for diagnostics, disease control, molecular epidemiology and infection control. Finally, a special attention was also paid to the approaches used to enrich the viral genetic material in samples containing low amount of pathogen nucleic acids.

About the authors

K. F. Khafizov

Central Research Institute of Epidemiology; Center of Strategical Planning of the Ministry of Health

Author for correspondence.
Email: kkhafizov@gmail.com
ORCID iD: 0000-0001-5524-0296

Kamil F. Khafizov - PhD (Biology), Scientific Group Leader, CRIE; Head of the Laboratory for the Development of New Genomics Methods, CSP.

111123, Moscow, Novogireevskaya str. 3a,Phone: +7 917 597-20-85 (mobile)


Russian Federation

A. S. Speranskaya

Central Research Institute of Epidemiology; Lomonosov Moscow State University

Email: hanna.s.939@gmail.com
ORCID iD: 0000-0001-6326-1249

Speranskaya A.S., PhD, Researcher, Department of Molecular Diagnostics and Epidemiology, CRIE; Researcher, Department of Higher Plants, Lomonosov MSU

Moscow

Russian Federation

A. D. Matsvay

Central Research Institute of Epidemiology; Moscow Institute of Physics and Technology

Email: arity767@gmail.com
ORCID iD: 0000-0002-6301-9169

Matsvay A.D., Junior Researcher, Department of Molecular Diagnostics, Group for the Development of New Diagnostic Methods Based on Next-Generation Sequencing, CRIE; Laboratory Assistant, Laboratory of Historical Genetics, Radiocarbon Analysis and Applied Physics, MIPT.

Dolgoprudny, Moscow Region Russian Federation

G. A. Shipulin

Center of Strategical Planning of the Ministry of Health

Email: shipgerman@gmail.com
ORCID iD: 0000-0002-3668-6601

Shipulin G.A., PhD (Medicine), Deputy Director on Science and Production, CSP.

Moscow

Russian Federation

V. G. Dedkov

St. Petersburg Pasteur Institute; Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases

Email: vgdedkov@yandex.ru
ORCID iD: 0000-0002-5500-0169

Dedkov V.G., PhD (Medicine), Deputy Director on Science, St.PPI; Leading Researcher, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases.

St. Petersburg, Moscow Russian Federation

References

  1. Aanensen D.M., Feil E.J., Holden M.T.G., Dordel J., Yeats C.A., Fedosejev A., Goater R., Castillo-Ramfrez S., Corander J., Colijn C., Chlebowicz M.A., Schouls L., Heck M., Pluister G., Ruimy R., Kahlmeter G., Ahman J., Matuschek E., Friedrich A.W., Parkhill J., Bentley S.D., Spratt B.G., Grundmann H. Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe. mBio, 2016, vol. 7, no. 3. doi: 10.1128/mBio.00444-16
  2. Allen U.D., Hu P., Pereira S.L., Robinson J.L., Paton T.A., Beyene J., Khodai-Booran N., Dipchand A., Hebert D., Ng V., Nalpathamkalam T., Read S. The genetic diversity of Epstein—Barr virus in the setting of transplantation relative to non-transplant settings: a feasibility study. Pediatr. Transplant., 2016, vol. 20, no. 1, pp. 124—129. doi: 10.1111/petr.12610
  3. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403-410. doi: 10.1016/S0022-2836(05)80360-2
  4. Ambrose H.E., Clewley J.P. Virus discovery by sequence-independent genome amplification. Rev. Med. Virol., 2006, vol. 16, no. 6, pp. 365-383. doi: 10.1002/rmv.515
  5. Anthony S.J., Epstein J.H., Murray K.A., Navarrete-Macias I., Zambrana-Torrelio C.M., Solovyov A., Ojeda-Flores R., Arrigo N.C., Islam A., Ali Khan S., Hosseini P., Bogich T.L., Olival K.J., Sanchez-Leon M.D., Karesh W.B., Goldstein T., Luby S.P., Morse S.S., Mazet J.A.K., Daszak P., Lipkin W.I. A Strategy to estimate unknown viral diversity in mammals. mBio, 2013, vol. 4, no. 5. doi: 10.1128/mBio.00598-13
  6. Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E., Grosdidier A., Hernandez C., Ioannidis V., Kuznetsov D., Liechti R., Moretti S., Mostaguir K., Redaschi N., Rossier G., Xenarios I., Stockinger H. ExPASy: SIB bioinformatics resource portal. Nucl. Acids Res., 2012, vol. 40, no. W1, pp. W597-W603. doi: 10.1093/nar/gks400
  7. Ayginin A.A., Pimkina E.V., Matsvay A.D., Speranskaya A.S., Safonova M.V., Blinova E.A., Artyushin I.V., Dedkov V.G., Shipulin G.A., Khafizov K. The Study of viral RNA diversity in bird samples using de novo designed multiplex genus-specific primer panels. Adv. Virol, 2018, vol. 2018, pp. 1-10. doi: 10.1155/2018/3248285
  8. Bartha I., Carlson J.M., Brumme C.J., McLaren P.J., Brumme Z.L., John M., Haas D.W., Martinez-Picado J., Dalmau J., Lopez-Gallndez C., Casado C., Rauch A., Gunthard H.F., Bernasconi E., Vernazza P., Klimkait T., Yerly S., O’Brien S. J., Listgarten J., Pfeifer N., Lippert C., Fusi N., Kutalik Z., Allen T.M., Muller V., Harrigan P.R., Heckerman D., Telenti A., Fellay J., for the HIV Genome-to-Genome Study and the Swiss HIV Cohort Study. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife, 2013, vol. 2. doi: 10.7554/eLife.01123
  9. Berry T.E., Osterrieder S.K., Murray D.C., Coghlan M.L., Richardson A.J., Grealy A.K., Stat M., Bejder L., Bunce M. DNA metabarcoding for diet analysis and biodiversity: a case study using the endangered Australian sea lion (Neophoca cinerea). Ecol. Evol, 2017, vol. 7, no. 14, pp. 5435-5453. doi: 10.1002/ece3.3123
  10. Bialasiewicz S., McVernon J., Nolan T., Lambert S.B., Zhao G., Wang D., Nissen M.D., Sloots T.P. Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing. BMC Infect. Dis, 2014, vol. 14, no. 1. doi: 10.1186/1471-2334-14-275
  11. Bonsall D., Ansari M.A., Ip C., Trebes A., Brown A., Klenerman P, Buck D., STOP-HCV Consortium, Piazza P., Barnes E., Bowden R. ve-SEQ: robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Research, 2015, vol. 4, p. 1062. doi: 10.12688/f1000research.7111.1
  12. Briese T., Kapoor A., Mishra N., Jain K., Kumar A., Jabado O.J., Lipkin W.I. Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio, 2015, vol. 6, no. 5. doi: 10.1128/mBio.01491-15
  13. Brown J.R., Roy S., Ruis C., Yara Romero E., Shah D., Williams R., Breuer J. Norovirus whole-genome sequencing by sureselect target enrichment: a robust and sensitive method. J. Clin. Microbiol., 2016, vol. 54, no. 10,pp. 2530—2537. doi: 10.1128/JCM.01052-16
  14. Calvet G., Aguiar R.S., Melo A.S.O., Sampaio S.A., de Filippis I., Fabri A., Araujo E.S.M., de Sequeira P.C., de Mendon^a M.C.L., de Oliveira L., Tschoeke D.A., Schrago C.G., Thompson F.L., Brasil P., dos Santos F.B., Nogueira R.M.R., Tanuri A., de Filippis A.M.B. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect. Dis., 2016, vol. 16, no. 6, pp. 653—660. doi: 10.1016/S1473-3099(16)00095-5
  15. Castrignano S.B., Nagasse-Sugahara T.K., Kisielius J.J., Ueda-Ito M., Brandao P.E., Curti S.P. Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis. Virus Res., 2013, vol. 178, no. 2, pp. 364— 373. doi: 10.1016/j.virusres.2013.09.018
  16. Chen Y., Yao H., Thompson E.J., Tannir N.M., Weinstein J.N., Su X. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics, 2013, vol. 29, no. 2, pp. 266—267. doi: 10.1093/bioinformatics/bts665
  17. Choi S.K., Choi J.K., Park W.M., Ryu K.H. RT-PCR detection and identification of three species of cucumoviruses with a genus-specific single pair of primers. J. Virol. Methods, 1999, vol. 83, no. 1-2, pp. 67—73. doi: 10.1016/s0166-0934(99)00106-8
  18. Clarke S., Innocenti G.M. Organization of immature intrahemispheric connections. J. Comp. Neurol., 1986, vol. 251, no. 1, pp. 1—22. doi: 10.1002/cne.902510102
  19. Cotten M., Petrova V., Phan M.V.T., Rabaa M.A., Watson S.J., Ong S.H., Kellam P, Baker S. Deep sequencing of Norovirus genomes defines evolutionary patterns in an urban tropical setting. J. Virol., 2014, vol. 88, no. 19, pp. 11056—11069. doi: 10.1128/JVI. 01333-14
  20. De Vries M., Deijs M., Canuti M., van Schaik B.D.C., Faria N.R., van de Garde M.D.B., Jachimowski L.C.M., Jebbink M.F., Jakobs M., Luyf A.C.M., Coenjaerts F.E.J., Claas E.C.J., Molenkamp R., Koekkoek S.M., Lammens C., Leus F., Goossens H., Ieven M., Baas F., van der Hoek L. A sensitive assay for virus discovery in respiratory clinical samples. PLoS One, 2011, vol. 6, no. 1: e16118. doi: 10.1371/journal.pone.0016118
  21. 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, vol. 78, pp. 74—81. doi: 10.1016/j.jcv.2016.03.012
  22. Denesvre C., Dumarest M., Remy S., Gourichon D., Eloit M. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin. Virus Genes, 2015, vol. 51, no. 2, pp. 209—216. doi: 10.1007/s11262-015-1231-8
  23. DePew J., Zhou B., McCorrison J.M., Wentworth D.E., Purushe J., Koroleva G., Fouts D.E. Sequencing viral genomes from a single isolated plaque. Virol. J., 2013, vol. 10, no. 1:181. doi: 10.1186/1743-422X-10-181
  24. Depledge D.P., Kundu S., Jensen N.J., Gray E.R., Jones M., Steinberg S., Gershon A., Kinchington P.R., Schmid D.S., Balloux F., Nichols R.A., Breuer J. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of Varicella Zoster virus and its vaccine in humans. Mol. Biol. Evol., 2014, vol. 31, no. 2, pp. 397—409. doi: 10.1093/molbev/mst210
  25. Depledge D.P., Palser A.L., Watson S.J., Lai I.Y.-C., Gray E.R., Grant P., Kanda R.K., Leproust E., Kellam P., Breuer J. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One, 2011, vol. 6, no. 11: e27805. doi: 10.1371/jour-nal.pone.0027805
  26. Djikeng A., Halpin R., Kuzmickas R., DePasse J., Feldblyum J., Sengamalay N., Afonso C., Zhang X., Anderson N.G., Ghedin E., Spiro D.J. Viral genome sequencing by random priming methods. BMC Genomics, 2008, vol. 9, no. 1:5. doi: 10.1186/1471-2164-9-5
  27. Donaldson C.D., Clark D.A., Kidd I.M., Breuer J., Depledge D.D. Genome sequence of Human Herpesvirus 7 strain UCL-1. GenomeAnnounc., 2013, vol. 1, no. 5. doi: 10.1128/genomeA.00830-13
  28. Drosten C., Gunther S., Preiser W., van der Werf S., Brodt H.-R., Becker S., Rabenau H., Panning M., Kolesnikova L., Fouchier R.A.M., Berger A., Burguiere A.-M., Cinatl J., Eickmann M., Escriou N., Grywna K., Kramme S., Manuguerra J.-C., Muller S., Rickerts V., Sturmer M., Vieth S., Klenk H.-D., Osterhaus A.D.M.E., Schmitz H., Doerr H.W. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N. Engl. J. Med., 2003, vol. 348, no. 20, pp. 1967—1976. doi: 10.1056/NEJMoa030747
  29. Ebert K., Depledge D.P., Breuer J., Harman L., Elliott G. Mode of virus rescue determines the acquisition of VHS mutations in VP22-negative Herpes Simplex Virus 1. J. Virol., 2013, vol. 87, no. 18, pp. 10389—10393. doi: 10.1128/JVI.01654-13
  30. Eckert S.E., Chan J.Z.-M., Houniet D., Breuer J., Speight G. Enrichment oflong DNA fragments from mixed samples for Nanopore sequencing. bioRxiv: The preprint server for biology, 2016. doi: 10.1101/048850
  31. Erlwein O., Robinson M.J., Dustan S., Weber J., Kaye S., McClure M.O. DNA extraction columns contaminated with murine sequences. PLoS One, 2011, vol. 6, no. 8: e23484. doi: 10.1371/journal.pone.0023484
  32. Faria N.R., Azevedo R.D.S.D.S., Kraemer M.U.G., Souza R., Cunha M.S., Hill S.C., Theze J., Bonsall M.B., Bowden T.A., Rissanen I., Rocco I.M., Nogueira J.S., Maeda A.Y., Vasami F.G.D.S., Macedo F.L.D.L., Suzuki A., Rodrigues S.G., Cruz A.C.R., Nunes B.T., Medeiros D.B.D.A., Rodrigues D.S.G., Nunes Queiroz A.L., Silva E.V.P.D., Henriques D.F., Travassos da Rosa E.S., de Oliveira C.S., Martins L.C., Vasconcelos H.B., Casseb L.M.N., Simith D.D.B., Messina J.P., Abade L., Lourenco J., Alcantara L.C.J., Lima M.M.D., Giovanetti M., Hay S.I., de Oliveira R.S., Lemos P.D.S., Oliveira L.F.D., de Lima C.P.S., da Silva S.P., Vasconcelos J.M.D., Franco L., Cardoso J.F., Vianez-Junior J.L.D.S.G., Mir D., Bello G., Delatorre E., Khan K., Creatore M., Coelho G.E., de Oliveira W.K., Tesh R., Pybus O.G., Nunes M.R.T., Vasconcelos P.F.C. Zika virus in the Americas: Early epidemiological and genetic findings. Science, 2016, vol. 352, no. 6283, pp. 345—349. doi: 10.1126/science.aaf5036
  33. Fonseca N.A., Rung J., Brazma A., Marioni J.C. Tools for mapping high-throughput sequencing data. Bioinformatics, 2012, vol. 28, no. 24, pp. 3169—3177. doi: 10.1093/bioinformatics/bts605
  34. Gardy J.L., Naus M., Amlani A., Chung W., Kim H., Tan M., Severini A., Krajden M., Puddicombe D., Sahni V., Hayden A.S., Gustafson R., Henry B., Tang P. Whole-genome sequencing of measles virus genotypes H1 and D8 during outbreaks of infection following the 2010 Olympic Winter Games reveals viral transmission routes. J. Infect. Dis, 2015, vol. 212, no. 10, pp. 1574—1578. doi: 10.1093/infdis/jiv271
  35. Geoghegan J.L., Holmes E.C. Predicting virus emergence amid evolutionary noise. Open Biol., 2017, vol. 7, no. 10. doi: 10.1098/ rsob.170189
  36. Gnaneshan S., Ijaz S., Moran J., Ramsay M., Green J. HepSEQ: international public health repository for hepatitis B. Nucleic Acids Res., 2007, vol. 35, pp. D367—D370. doi: 10.1093/nar/gkl874
  37. Goodacre N., Aljanahi A., Nandakumar S., Mikailov M., Khan A.S. A Reference Viral Database (RVDB) to enhance bioinformatics analysis of high-throughput sequencing for novel virus detection. mSphere, 2018, vol. 3, no. 2. doi: 10.1128/mSphereDi-rect.00069-18
  38. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 2011, vol. 29, no. 7, pp. 644-652. doi: 10.1038/nbt.1883
  39. Gunther S., Lenz O. Lassa virus. Crit. Rev. Clin. Lab. Sci., 2004, vol. 41, no. 4, pp. 339-390. doi: 10.1080/10408360490497456
  40. Hall R.J., Draper J.L., Nielsen F.G.G., Dutilh B.E. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Front. Microbiol., 2015, vol. 6. doi: 10.3389/fmicb.2015.00224
  41. Hong L.Z., Hong S., Wong H., Aw P., Yan C., Wilm A., de Sessions P.F., Lim S., Nagarajan N., Hibberd M.L., Quake S.R., Burkholder W.F. BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biol., 2014, vol. 15, no. 11:517. doi: 1fJ.1186/PREACCEPT-6768fJfJ1251451949
  42. Houldcroft C.J., Beale M.A., Breuer J. Clinical and biological insights from viral genome sequencing. Nat. Rev. Microbiol., 2017, vol. 15, no. 3, pp. 183-192. doi: 10.1038/nrmicro.2016.182
  43. Houldcroft C.J., Breuer J. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front. Microbiol., 2015, vol. 6. doi: 10.3389/fmicb.2015.00188
  44. Hue S., Gray E.R., Gall A., Katzourakis A., Tan C.P., Houldcroft C.J., McLaren S., Pillay D., Futreal A., Garson J.A., Pybus O.G., Kellam P., Towers G.J. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology, 2010, vol. 7, no. 1:111. doi: 10.1186/1742-4690-7-111
  45. Hulo C., de Castro E., Masson P., Bougueleret L., Bairoch A., Xenarios I., Le Mercier P. ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res., 2011, vol. 39, suppl. 1, pp. D576-D582. doi: 10.1093/nar/gkq901
  46. Jaenicke S., Ander C., Bekel T., Bisdorf R., Droge M., Gartemann K.-H., Junemann S., Kaiser O., Krause L., Tille F., Zakrzewski M., Puhler A., Schluter A., Goesmann A. Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One, 2011, vol. 6, no. 1: e14519. doi: 10.1371/journal.pone.0014519
  47. Jensen R.H., Mollerup S., Mourier T., Hansen T.A., Fridholm H., Nielsen L.P., Willerslev E., Hansen A.J., Vinner L. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS One, 2015, vol. 10, no. 4: e0122636. doi: 10.1371/journal.pone.0122636
  48. Johnson T.A., Stedtfeld R.D., Wang Q., Cole J.R., Hashsham S.A., Looft T., Zhu Y.-G., Tiedje J.M. Clusters of antibiotic resistance genes enriched together stay together in swine agriculture. mBio, 2016, vol. 7, no. 2. doi: 10.1128/mBio.02214-15
  49. Jones B.A., Grace D., Kock R., Alonso S., Rushton J., Said M.Y., McKeever D., Mutua F., Young J., McDermott J., Pfeiffer D.U. Zoonosis emergence linked to agricultural intensification and environmental change. Proc. Natl. Acad. Sci., 2013, vol. 110, no. 21, pp. 8399-8404. doi: 10.1073/pnas.1208059110
  50. Karamitros T., Magiorkinis G. A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits. Nucleic Acids Res., 2015, vol. 43, no. 22, pp. e152-e152. doi: 10.1093/nar/gkv773
  51. Karkhah A., Nouri H.R., Javanian M., Koppolu V., Masrour-Roudsari J., Kazemi S., Ebrahimpour S. Zika virus: epidemiology, clinical aspects, diagnosis, and control of infection. Eur. J. Clin. Microbiol. Infect. Dis., 2018, vol. 37, no. 11, pp. 2035-2043. doi: 10.1007/s10096-018-3354-z
  52. Kent W.J. BLAT — the BLAST-like alignment tool. Genome Res., 2002, vol. 12, no. 4, pp. 656- 664. doi: 10.1101/gr.229202
  53. Kimberlin D.W., Whitley R.J. Antiviral resistance: mechanisms, clinical significance, and future implications. J. Antimicrob. Chemother., 1996, vol. 37, no. 3, pp. 403-421.
  54. Kireev D.E., Lopatukhin A.E., Murzakova A.V., Pimkina E.V., Speranskaya A.S., Neverov A.D., Fedonin G.G., Fantin Y.S., Shipulin G.A. Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing. J. Virol. Methods, 2018, vol. 261, pp. 40-45. doi: 10.1016/j.jviromet.2018.08.001
  55. Kohl C., Brinkmann A., Dabrowski P.W., Radonic A., Nitsche A., Kurth A. Protocol for metagenomic virus detection in clinical specimens. Emerg. Infect. Dis., 2015, vol. 21, no. 1, pp. 48-57. doi: 10.3201/eid2101.140766
  56. Kruppa J., Jo W.K., van der Vries E., Ludlow M., Osterhaus A., Baumgaertner W., Jung K. Virus detection in high-throughput sequencing data without a reference genome of the host. Infect. Genet. Evol., 2018, vol. 66, pp. 180-187. doi: 10.1016/j.meegid.2018.09.026
  57. Kuiken C., Yusim K., Boykin L., Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics, 2005, vol. 21, no. 3, pp. 379-384. doi: 10.1093/bioinformatics/bth485
  58. Kundu S., Lockwood J., Depledge D.P., Chaudhry Y., Aston A., Rao K., Hartley J.C., Goodfellow I., Breuer J. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin. Infect. Dis., 2013, vol. 57, no. 3, pp. 407-414. doi: 10.1093/cid/cit287
  59. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods, 2012, vol. 9, no. 4,pp. 357-359. doi: 10.1038/nmeth.1923
  60. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 2009, vol. 10, no. 3: R25. doi: 10.1186/gb-2009-10-3-r25
  61. Lecuit M., Eloit M. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front. Cell. Infect. Microbiol., 2014, vol. 4. doi: 10.3389/fcimb.2()14.()()()25
  62. Lee W.-P., Stromberg M.P., Ward A., Stewart C., Garrison E.P., Marth G.T. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One, 2014, vol. 9, no. 3: e90581. doi: 10.1371/journal.pone.0090581
  63. Li C.-X., Shi M., Tian J.-H., Lin X.-D., Kang Y.-J., Chen L.-J., Qin X.-C., Xu J., Holmes E.C., Zhang Y.-Z. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 2015, vol. 4. doi: 10.7554/eLife.05378
  64. Li C., Chng K.R., Boey E.J.H., Ng A.H.Q., Wilm A., Nagarajan N. INC-Seq: accurate single molecule reads using nanopore sequencing. GigaScience, 2016, vol. 5, no. 1. doi: 10.1186/s13742-016-0140-7
  65. Lipkin W.I. A Vision for investigating the microbiology of health and disease. J. Infect. Dis., 2015, vol. 212, suppl. 1, pp. S26—S30. doi: 10.1093/infdis/jiu649
  66. Liu P., Fang X., Feng Z., Guo Y.-M., Peng R.-J., Liu T., Huang Z., Feng Y., Sun X., Xiong Z., Guo X., Pang S.-S., Wang B., Lv X., Feng F.-T., Li D.-J., Chen L.-Z., Feng Q.-S., Huang W.-L., Zeng M.-S., Bei J.-X., Zhang Y., Zeng Y.-X. Direct sequencing and characterization of a clinical isolate of Epstein—Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J. Virol., 2011, vol. 85, no. 21, pp. 11291—11299. doi: 10.1128/JVI.00823-11
  67. Matranga C.B., Andersen K.G., Winnicki S., Busby M., Gladden A.D., Tewhey R., Stremlau M., Berlin A., Gire S.K., England E., Moses L.M., Mikkelsen T.S., Odia I., Ehiane P.E., Folarin O., Goba A., Kahn S.H., Grant D.S., Honko A., Hensley L., Happi C., Garry R.F., Malboeuf C.M., Birren B.W., Gnirke A., Levin J.Z., Sabeti P.C. Enhanced methods for unbiased deep sequencing ofLassa and Ebola RNA viruses from clinical and biological samples. Genome Biol, 2014, vol. 15, no. 11. doi: 10.1186/s13059-014-0519-7
  68. Matsvay A.D., Alborova I.E., Pimkina E.V., Markelov M.L., Khafizov K., Mustafin K.K. Experimental approaches for ancient DNA extraction and sample preparation for next generation sequencing in ultra-clean conditions. Conserv. Genet. Resour., 2018. doi: 10.1007/s12686-018-1016-1
  69. Mbisa J.L., Fearnhill E., Dunn D.T., Pillay D., Asboe D., Cane P.A. Evidence of self-sustaining drug resistant HIV-1 lineages among untreated patients in the United Kingdom. Clin. Infect. Dis., 2015, vol. 61, no. 5, pp. 829—836. doi: 10.1093/cid/civ393
  70. Miia J.-V., Tiina N., Tarja S., Olli V., Liisa S., Anita H. Evolutionary trends of European bat lyssavirus type 2 including genetic characterization of Finnish strains of human and bat origin 24 years apart. Arch. Virol., 2015, vol. 160, no. 6, pp. 1489—1498. doi: 10.1007/s00705-015-2424-0
  71. Mlakar J., Korva M., Tul N., Popovic M., Poljsak-Prijatelj M., Mraz J., Kolenc M., Resman Rus K., Vesnaver Vipotnik T., Fabjan Vodusek V., Vizjak A., Pizem J., Petrovec M., Avsic Zupanc T. Zika virus associated with microcephaly. N. Engl. J. Med., 2016, vol. 374, no. 10, pp. 951-958. doi: 10.1056/NEJMoa1600651
  72. Morfopoulou S., Brown J.R., Davies E.G., Anderson G., Virasami A., Qasim W., Chong W.K., Hubank M., Plagnol V., Desforges M., Jacques T.S., Talbot P.J., Breuer J. Human Coronavirus OC43 associated with fatal encephalitis. N. Engl. J. Med., 2016, vol. 375, no. 5, pp. 497-498. doi: 10.1056/NEJMc1509458
  73. Mulcahy-O’Grady H., Workentine M.L. The challenge and potential of metagenomics in the clinic. Front. Immunol., 2016, vol. 7. doi: 10.3389/fimmu.2016.00029
  74. Munro A.C., Houldcroft C. Human cancers and mammalian retroviruses: should we worry about bovine leukemia virus? Future Virol, 2016, vol. 11, no. 3, pp. 163-166. doi: 10.2217/fvl.16.5
  75. Naccache S.N., Greninger A.L., Lee D., Coffey L.L., Phan T., Rein-Weston A., Aronsohn A., Hackett J., Delwart E.L., Chiu C.Y. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J. Virol, 2013, vol. 87, no. 22,pp. 11966-11977. doi: 10.1128/JVI.02323-13
  76. Newman R.M., Kuntzen T., Weiner B., Berical A., Charlebois P., Kuiken C., Murphy D.G., Simmonds P., Bennett P., Lennon N.J., Birren B.W., Zody M.C., Allen T.M., Henn M.R. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J. Infect. Dis., 2013, vol. 208, no. 1, pp. 17-31. doi: 10.1093/infdis/jis679
  77. Ocwieja K.E., Sherrill-Mix S., Mukherjee R., Custers-Allen R., David P., Brown M., Wang S., Link D.R., Olson J., Travers K., Schadt E., Bushman F.D. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Res., 2012, vol. 40, no. 20, pp. 10345-10355. doi: 10.1093/nar/gks753
  78. Oude Munnink B.B., Jazaeri Farsani S.M., Deijs M., Jonkers J., Verhoeven J.T.P., Ieven M., Goossens H., de Jong M.D., Berkhout B., Loens K., Kellam P., Bakker M., Canuti M., Cotten M., van der Hoek L. Autologous antibody capture to enrich immunogenic viruses for viral discovery. PLoS One, 2013, vol. 8, no. 11: e78454. doi: 10.1371/journal.pone.0078454
  79. Palser A.L., Grayson N.E., White R.E., Corton C., Correia S., Baabdullah M.M., Watson S.J., Cotten M., Arrand J.R., Murray P.G., Allday M.J., Rickinson A.B., Young L.S., Farrell P.J., Kellam P. Genome diversity of Epstein—Barr Virus from multiple tumor types and normal infection. J. Virol., 2015, vol. 89, no. 10, pp. 5222-5237. doi: 10.1128/JVI.03614-14
  80. Parameswaran P., Charlebois P., Tellez Y., Nunez A., Ryan E.M., Malboeuf C.M., Levin J.Z., Lennon N.J., Balmaseda A., Harris E., Henn M.R. Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. J. Virol., 2012, vol. 86, no. 16, pp. 8546-8558. doi: 10.1128/JVI.00736-12
  81. Pfeffer M., Proebster B., Kinney R.M., Kaaden O.R. Genus-specific detection of alphaviruses by a semi-nested reverse transcription-polymerase chain reaction. Am. J. Trop. Med. Hyg, 1997, vol. 57, no. 6, pp. 709-718.
  82. Pickett B.E., Sadat E.L., Zhang Y., Noronha J.M., Squires R.B., Hunt V., Liu M., Kumar S., Zaremba S., Gu Z., Zhou L., Larson C.N., Dietrich J., Klem E.B., Scheuermann R.H. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res, 2012, vol. 40, no. D1, pp. D593-D598. doi: 10.1093/nar/gkr859
  83. Power R.A., Davaniah S., Derache A., Wilkinson E., Tanser F., Gupta R.K., Pillay D., de Oliveira T. Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance. PLoS One, 2016, vol. 11, no. 9: e0163746. doi: 10.1371/journal.pone.0163746
  84. Quick J., Loman N.J., Duraffour S., Simpson J.T., Severi E., Cowley L., Bore J.A., Koundouno R., Dudas G., Mikhail A., Ouedraogo N., Afrough B., Bah A., Baum J.H.J., Becker-Ziaja B., Boettcher J.P., Cabeza-Cabrerizo M., Camino-Sanchez A., Carter L.L., Doerrbecker J., Enkirch T., Dorival I.G., Hetzelt N., Hinzmann J., Holm T., Kafetzopoulou L.E., Koropogui M., Kosgey A., Kuisma E., Logue C.H., Mazzarelli A., Meisel S., Mertens M., Michel J., Ngabo D., Nitzsche K., Pallasch E., Patrono L.V., Portmann J., Repits J.G., Rickett N.Y., Sachse A., Singethan K., Vitoriano I., Yemanaberhan R.L., Zekeng E.G., Racine T., Bello A., Sall A.A., Faye O., Faye O., Magassouba N., Williams C.V., Amburgey V., Winona L., Davis E., Gerlach J., Washington F., Monteil V., Jourdain M., Bererd M., Camara A., Somlare H., Camara A., Gerard M., Bado G., Baillet B., Delaune D., Nebie K.Y., Diarra A., Savane Y., Pallawo R.B., Gutierrez G.J., Milhano N., Roger I., Williams C.J., Yattara F., Lewandowski K., Taylor J., Rachwal P., J. Turner D., Pollakis G., Hiscox J.A., Matthews D.A., Shea M.K.O., Johnston A.M., Wilson D., Hutley E., Smit E., Di Caro A., Wolfel R., Stoecker K., Fleischmann E., Gabriel M., Weller S.A., Koivogui L., Diallo B., Ke'ita S., Rambaut A., Formenty P., Gunther S., Carroll M.W. Real-time, portable genome sequencing for Ebola surveillance. Nature, 2016, vol. 530, no. 7589, pp. 228—232. doi: 10.1038/nature16996
  85. Renzette N., Bhattacharjee B., Jensen J.D., Gibson L., Kowalik T.F. Extensive genome-wide variability of Human cytomegalovirus in congenitally infected infants. PLoS Pathog., 2011, vol. 7, no. 5: e1001344. doi: 10.1371/journal.ppat.1001344
  86. Reyes G.R., Kim J.P. Sequence-independent, single-primer amplification (SISPA) of complex DNA populations. Mol. Cell. Probes, 1991, vol. 5, no. 6, pp. 473-481. doi: 10.1016/S0890-8508(05)80020-9
  87. Rhee S.-Y., Margeridon-Thermet S., Nguyen M.H., Liu T.F., Kagan R.M., Beggel B., Verheyen J., Kaiser R., Shafer R.W. Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Antiviral Res., 2010, vol. 88, no. 3, pp. 269-275. doi: 10.1016/j.antiviral.2010.09.012
  88. Rosseel T., Pardon B., De Clercq K., Ozhelvaci O., Van Borm S. False-positive results in metagenomic virus discovery: a strong case for follow-up diagnosis. Transbound. Emerg. Dis., 2014, vol. 61, no. 4, pp. 293-299. doi: 10.1111/tbed.12251
  89. Sabina J., Leamon J.H. Bias in whole genome amplification: causes and considerations. In: Whole genome amplification; ed. Kroneis T. New York, NY: Springer New York, 2015, vol. 1347, pp. 15-41. doi: 10.1007/978-1-4939-2990-02
  90. Safonova M.V., Shchelkanov M.Y., Khafizov K., Matsvay A.D., Ayginin A.A., Dolgova A.S., Shchelkanov E.M., Pimkina E.V., Speranskaya A.S., Galkina I.V., Dedkov V.G. Sequencing and genetic characterization of two strains Paramushir virus obtained from the Tyuleniy Island in the Okhotsk Sea (2015). Ticks Tick-Borne Dis., 2018. doi: 10.1016/j.ttbdis.2018.11.004
  91. Salter S.J., Cox M.J., Turek E.M., Calus S.T., Cookson W.O., Moffatt M.F., Turner P., Parkhill J., Loman N.J., Walker A.W. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol., 2014, vol. 12, no. 1. doi: 10.1186/s12915-014-0087-z
  92. Sauvage V., Eloit M. Viral metagenomics and blood safety. Transfus. Clin. Biol., 2016, vol. 23, no. 1, pp. 28-38. doi: 10.1016/j. tracli.2015.12.002
  93. Schmidt K., Mwaigwisya S., Crossman L.C., Doumith M., Munroe D., Pires C., Khan A.M., Woodford N., Saunders N.J., Wain J., O’Grady J., Livermore D.M. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J. Antimicrob. Chemother., 2017, vol. 72, no. 1, pp. 104-114. doi: 10.1093/jac/dkw397
  94. Shafer R.W. Rationale and uses of a public HIV drug-resistance database. J. Infect. Dis., 2006, vol. 194, suppl. 1, pp. S51-S58. doi: 10.1086/505356
  95. Shi M., Lin X.-D., Chen X., Tian J.-H., Chen L.-J., Li K., Wang W., Eden J.-S., Shen J.-J., Liu L., Holmes E.C., Zhang Y.-Z. The evolutionary history ofvertebrate RNA viruses. Nature, 2018, vol. 556, no. 7700,pp. 197-202. doi: 10.1038/s41586-018-0012-7
  96. Shi M., Lin X.-D., Tian J.-H., Chen L.-J., Chen X., Li C.-X., Qin X.-C., Li J., Cao J.-P., Eden J.-S., Buchmann J., Wang W., Xu J., Holmes E.C., Zhang Y.-Z. Redefining the invertebrate RNA virosphere. Nature, 2016, vol. 540, no. 7634, pp. 539-543. doi: 10.1038/nature20167
  97. Speranskaya A.S., Khafizov K., Ayginin A.A., Krinitsina A.A., Omelchenko D.O., Nilova M.V., Severova E.E., Samokhina E.N., Shipulin G.A., Logacheva M.D. Comparative analysis of Illumina and Ion Torrent high-throughput sequencing platforms for identification of plant components in herbal teas. Food Control, 2018, vol. 93, pp. 315-324. doi: 10.1016/j.foodcont.2018.04.040
  98. Speranskaya A.S., Lopatukhin A.E., Khafizov K., Ayginin A.A., Korneenko E.V., Kireev D.E., Shipulin G.A. Evaluation of MinION nanopore platform for HIV whole coding regions sequencing. Bioinformatics of genome regulation and structure/systems biology: The Eleventh International Conference, 2018. doi: 10.18699/BGRSSB-2018-059
  99. Stano M., Beke G., Klucar L. viruSITE — integrated database for viral genomics. Database, 2016, vol. 2016,p. baw162. doi: 10.1093/database/baw162
  100. Thomson E., Ip C.L.C., Badhan A., Christiansen M.T., Adamson W., Ansari M.A., Bibby D., Breuer J., Brown A., Bowden R., Bryant J., Bonsall D., Da Silva Filipe A., Hinds C., Hudson E., Klenerman P., Lythgow K., Mbisa J.L., McLauchlan J., Myers R., Piazza P., Roy S., Trebes A., Sreenu V.B., Witteveldt J., STOP-HCV Consortium, Barnes E., Simmonds P. Comparison of next-generation sequencing technologies for comprehensive assessment of full-length hepatitis C viral genomes. J. Clin. Microbiol., 2016, vol. 54, no. 10, pp. 2470-2484. doi: 10.1128/JCM.00330-16
  101. Travers K.J., Chin C.-S., Rank D.R., Eid J.S., Turner S.W. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res., 2010, vol. 38, no. 15, pp. e159-e159. doi: 10.1093/nar/gkq543
  102. Tsangaras K., Wales N., Sicheritz-Ponten T., Rasmussen S., Michaux J., Ishida Y., Morand S., Kampmann M.-L., Gilbert M.T.P., Greenwood A.D. Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank). PLoS One, 2014, vol. 9, no. 10: e109101. doi: 10.1371/journal.pone.0109101
  103. Tweedy J., Spyrou M.A., Donaldson C.D., Depledge D., Breuer J., Gompels U.A. Complete genome sequence of the Human Herpesvirus 6A strain AJ from Africa resembles strain GS from North America. Genome Announc., 2015, vol. 3, no. 1. doi: 10.1128/genomeA.01498-14
  104. UFO Sequencing Consortium within the I-BFM Study Group, Forster M., Szymczak S., Ellinghaus D., Hemmrich G., Ruhlemann M., Kraemer L., Mucha S., Wienbrandt L., Stanulla M., Franke A. Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data. Sci. Rep., 2015, vol. 5, no. 1. doi: 10.1038/srep11534
  105. VanDevanter D.R., Warrener P., Bennett L., Schultz E.R., Coulter S., Garber R.L., Rose T.M. Detection and analysis of diverse herpesviral species by consensus primer PCR. J. Clin. Microbiol., 1996, vol. 34, no. 7, pp. 1666-1671.
  106. Venter J.C. Environmental genome shotgun sequencing of the sargasso sea. Science, 2004, vol. 304, no. 5667, pp. 66-74. doi: 10.1126/science.1093857
  107. Wang Q., Jia P., Zhao Z. VirusFinder: Software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One, 2013, vol. 8, no. 5: e64465. doi: 10.1371/journal.pone.0064465
  108. Watson S.J., Langat P., Reid S.M., Lam T.T.-Y., Cotten M., Kelly M., Van Reeth K., Qiu Y., Simon G., Bonin E., Foni E., Chiapponi C., Larsen L., Hjulsager C., Markowska-Daniel I., Urbaniak K., Durrwald R., Schlegel M., Huovilainen A., Davidson I., Dan A., Loeffen W., Edwards S., Bublot M., Vila T., Maldonado J., Valls L., ESNIP3 Consortium, Brown I.H., Pybus O.G., Kellam P. Molecular epidemiology and evolution of influenza viruses circulating within european swine between 2009 and 2013. J. Virol, 2015, vol. 89, no. 19, pp. 9920-9931. doi: 10.1128/JVI.00840-15
  109. Weiss S., Witkowski P.T., Auste B., Nowak K., Weber N., Fahr J., Mombouli J.-V., Wolfe N.D., Drexler J.F., Drosten C., Klempa B., Leendertz F.H., Kruger D.H. Hantavirus in bat, Sierra Leone. Emerg. Infect. Dis., 2012, vol. 18, no. 1, pp. 159-161. doi: 10.3201/eid1801.111026
  110. Worthey E.A., Mayer A.N., Syverson G.D., Helbling D., Bonacci B.B., Decker B., Serpe J.M., Dasu T., Tschannen M.R., Veith R.L., Basehore M.J., Broeckel U., Tomita-Mitchell A., Arca M.J., Casper J.T., Margolis D.A., Bick D.P., Hessner M.J., Routes J.M., Verbsky J.W., Jacob H.J., Dimmock D.P. Making a definitive diagnosis: successful clinical application of whole ex-ome sequencing in a child with intractable inflammatory bowel disease. Genet. Med., 2011, vol. 13, no. 3, pp. 255-262. doi: 10.1097/GIM.0b 013e3182088158
  111. Wylie T.N., Wylie K.M., Herter B.N., Storch G.A. Enhanced virome sequencing using targeted sequence capture. Genome Res., 2015, vol. 25, no. 12, pp. 1910-1920. doi: 10.1101/gr.191049.115
  112. Zhang Y.-Z., Shi M., Holmes E.C. Using metagenomics to characterize an expanding virosphere. Cell, 2018, vol. 172, no. 6, pp. 1168-1172. doi: 10.1016/j.cell.2018.02.043
  113. Zhao G., Krishnamurthy S., Cai Z., Popov V.L., Travassos da Rosa A.P., Guzman H., Cao S., Virgin H.W., Tesh R.B., Wang D. Identification of novel viruses using virushunter — an automated data analysis pipeline. PLoS One, 2013, vol. 8, no. 10: e78470. doi: 10.1371/journal.pone.0078470
  114. Zheng L., Tang J., Clover G.R.G., Spackman M.E., Freeman A.J., Rodoni B.C. Novel genus-specific broad range primers for the detection of furoviruses, hordeiviruses and rymoviruses and their application in field surveys in Southeast Australia. J. Virol. Methods, 2015, vol. 214, pp. 1-9. doi: 10.1016/j.jviromet.2014.11.022

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