Preview

Инфекция и иммунитет

Расширенный поиск

ПЕРЕДОВЫЕ ТЕХНОЛОГИИ В ДИАГНОСТИКЕ ВИРУСНЫХ ЗАБОЛЕВАНИЙ НЕЯСНОЙ ЭТИОЛОГИИ

Полный текст:

Аннотация

Расшифровка инфекционных заболеваний неясной этиологии является одной из  актуальных проблем современной медицины, потому как получение лабораторно подтвержденного диагноза, к сожалению, удается осуществить лишь в весьма небольшой доле случаев таких заболеваний. Так как большая часть часто встречающихся в средних широтах инфекционных заболеваний имеет характерную выраженную клиническую картину, до недавнего времени этой проблеме не уделялось должного внимания. Возрастание числа случаев инфекционных заболеваний, не характеризующихся идентифицируемым набором клинических признаков, наблюдаемое в последнее время, заставляет рассматривать проблему более пристально. Считается, что такая тенденция обусловлена рядом обстоятельств, включая ослабление санитарного контроля территорий, усиление миграционных потоков, как внутренних, так и внешних, отказ от вакцинации на фоне длительного периода эпидемического благополучия, возникновение атипичных штаммов бактерий, как следствие нерациональной антибиотикотерапии и другие. Вирусы являются наиболее распространенными организмами на нашей планете, что обуславливает  ведущую роль инфекционных агентов вирусной природы в структуре инфекционных заболеваний неясной этиологии. По некоторым оценкам, полученным методами математического моделирования, существует не менее 320,000 видов вирусов, способных к инфицированию млекопитающих, большая часть которых еще не описана. Поэтому мониторинг циркуляции известных вирусных патогенов, отслеживание путей их распространения, эволюции и изменений нуклеотидной последовательности их геномов, а также выявление новых видов вирусов становятся жизненно важными аспектами эпидемиологического надзора, необходимыми для своевременного реагирования на возникающие угрозы, прогнозирования и раннего выявления вспышек вирусных заболеваний человека и животных. В представленном обзоре рассматриваются, как традиционные молекулярно-генетические методы выявления вирусных патогенов, такие как методы ПЦР, ПЦР в режиме реального времени, секвенирование по Сенгеру с предварительным клонированием, так и методы, основанные на применении секвенирования второго и третьего поколений. В связи с тем, что исследование вирусных инфекционных агентов с помощью технологий высокопроизводительного секвенирования NGS (от англ. Next Generation Sequencing) на сегодняшний день приобретает все большее практическое значение для диагностики, борьбы с болезнями, молекулярной эпидемиологии и инфекционного контроля, более подробное рассмотрение получили различные методы, основанные на применении этих технологий. Особое место было также отведено подходам, применяющимся для обогащения вирусного генетического материала в образцах с низкой представленностью нуклеиновых кислот патогена.

Об авторах

К. Ф. Хафизов
ФБУН Центральный научно-исследовательский институт эпидемиологии Роспотребнадзора
Россия
Руководитель научной группы


А. С. Сперанская
ФБУН Центральный научно-исследовательский институт эпидемиологии Роспотребнадзора Московский Государственный Университет имени М.В. Ломоносова
Россия
Научный сотрудник


А. Д. Мацвай
ФБУН Центральный научно-исследовательский институт эпидемиологии Роспотребнадзора Московский физико-технический институт
Россия
Младший научный сотрудник


Г. А. Шипулин
ФГБУ “ЦСП” Минздрава России
Россия
Заместитель директора по научно-производственной работе


В. Г. Дедков
ФБУН НИИЭМ им. Пастера, Санкт-Петербург НИИ медицинской паразитологии и тропической медицины им. Е.И. Марциновского Первого МГМУ им. И.М. Сеченова
Россия
Заместитель директора по научной работе


Список литературы

1. Aanensen D.M., Feil E.J., Holden M.T.G., Dordel J., Yeats C.A., Fedosejev A., Goater R., Castillo-Ramírez S., Corander J., Colijn C., Chlebowicz M.A., Schouls L., Heck M., Pluister G., Ruimy R., Kahlmeter G., Åhman 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. - http://mbio.asm.org/lookup/doi/10.1128/mBio.00444-16 [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., Hébert 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. - http://doi.wiley.com/10.1111/petr.12610 [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. - http://linkinghub.elsevier.com/retrieve/pii/S0022283605803602 [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. - http://doi.wiley.com/10.1002/rmv.515 [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. - http://mbio.asm.org/cgi/doi/10.1128/mBio.00598-13 [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. Nucleic Acids Res., 2012, vol. 40, no. W1, pp. W597–W603. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gks400 [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. - https://www.hindawi.com/journals/av/2018/3248285/ [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., López-Galíndez C., Casado C., Rauch A., Günthard 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., Müller 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. - https://elifesciences.org/articles/01123 [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. - http://doi.wiley.com/10.1002/ece3.3123 [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. - http://bmcinfectdis.biomedcentral.com/articles/10.1186/1471-2334-14-275 [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. - https://f1000research.com/articles/4-1062/v1 [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. - http://mbio.asm.org/lookup/doi/10.1128/mBio.01491-15 [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. / ed. Tang Y.-W., 2016, vol. 54, no. 10, pp. 2530–2537. - http://jcm.asm.org/lookup/doi/10.1128/JCM.01052-16 [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 Mendonça 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. - https://linkinghub.elsevier.com/retrieve/pii/S1473309916000955 [10.1016/S1473-3099(16)00095-5.]

15. Castrignano S.B., Nagasse-Sugahara T.K., Kisielius J.J., Ueda-Ito M., Brandão 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. - https://linkinghub.elsevier.com/retrieve/pii/S0168170213003109 [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. - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts665 [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. - https://linkinghub.elsevier.com/retrieve/pii/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. - https://www.ncbi.nlm.nih.gov/pubmed/3760253 [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. - http://jvi.asm.org/cgi/doi/10.1128/JVI.01333-14 [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 / ed. Poon L.L.M., 2011, vol. 6, no. 1, p. e16118. - https://dx.plos.org/10.1371/journal.pone.0016118 [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. - https://linkinghub.elsevier.com/retrieve/pii/S1386653216300403 [10.1016/j.jcv.2016.03.012.]

22. Denesvre C., Dumarest M., Rémy 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. - http://link.springer.com/10.1007/s11262-015-1231-8 [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, p. 181. - http://virologyj.biomedcentral.com/articles/10.1186/1743-422X-10-181 [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. - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mst210 [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 / ed. Jhaveri R., 2011, vol. 6, no. 11, p. e27805. - http://dx.plos.org/10.1371/journal.pone.0027805 [10.1371/journal.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, p. 5. - http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-5 [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. Genome Announc., 2013, vol. 1, no. 5. - http://genomea.asm.org/cgi/doi/10.1128/genomeA.00830-13 [10.1128/genomeA.00830-13.]

28. Drosten C., Günther S., Preiser W., van der Werf S., Brodt H.-R., Becker S., Rabenau H., Panning M., Kolesnikova L., Fouchier R.A.M., Berger A., Burguière A.-M., Cinatl J., Eickmann M., Escriou N., Grywna K., Kramme S., Manuguerra J.-C., Müller S., Rickerts V., Stürmer 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. - http://www.nejm.org/doi/abs/10.1056/NEJMoa030747 [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. - http://jvi.asm.org/cgi/doi/10.1128/JVI.01654-13 [10.1128/JVI.01654-13.]

30. Eckert S.E., Chan J.Z.-M., Houniet D., Breuer J., Speight G. Enrichment of long DNA fragments from mixed samples for Nanopore sequencing, 2016. - http://biorxiv.org/lookup/doi/10.1101/048850 [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 / ed. Jeang K.T., 2011, vol. 6, no. 8, p. e23484. - https://dx.plos.org/10.1371/journal.pone.0023484 [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. - http://www.sciencemag.org/cgi/doi/10.1126/science.aaf5036 [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. - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts605 [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. - https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jiv271 [10.1093/infdis/jiv271.]

35. Geoghegan J.L., Holmes E.C. Predicting virus emergence amid evolutionary noise. Open Biol., 2017, vol. 7, no. 10. - https://royalsocietypublishing.org/doi/10.1098/rsob.170189 [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, no. Database, pp. D367–D370. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl874 [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 / ed. Imperiale M.J., 2018, vol. 3, no. 2. - http://msphere.asm.org/lookup/doi/10.1128/mSphereDirect.00069-18 [10.1128/mSphereDirect.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. - http://www.nature.com/articles/nbt.1883 [10.1038/nbt.1883.]

39. Günther S., Lenz O. Lassa virus. Crit. Rev. Clin. Lab. Sci., 2004, vol. 41, no. 4, pp. 339–390. - [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. - http://www.frontiersin.org/Virology/10.3389/fmicb.2015.00224/abstract [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, p. 517. - http://genomebiology.com/2014/15/11/517 [10.1186/PREACCEPT-6768001251451949.]

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. - http://www.nature.com/articles/nrmicro.2016.182 [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. - http://journal.frontiersin.org/Article/10.3389/fmicb.2015.00188/abstract [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, p. 111. - http://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-7-111 [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, no. suppl_1, pp. D576–D582. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq901 [10.1093/nar/gkq901.]

46. Jaenicke S., Ander C., Bekel T., Bisdorf R., Dröge M., Gartemann K.-H., Jünemann S., Kaiser O., Krause L., Tille F., Zakrzewski M., Pühler A., Schlüter A., Goesmann A. Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE / ed. Aziz R.K., 2011, vol. 6, no. 1, p. e14519. - https://dx.plos.org/10.1371/journal.pone.0014519 [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 / ed. He J., 2015, vol. 10, no. 4, p. e0122636. - https://dx.plos.org/10.1371/journal.pone.0122636 [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. - http://mbio.asm.org/lookup/doi/10.1128/mBio.02214-15 [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. - http://www.pnas.org/cgi/doi/10.1073/pnas.1208059110 [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. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv773 [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. Off. Publ. Eur. Soc. Clin. Microbiol., 2018, vol. 37, no. 11, pp. 2035–2043. - https://www.sciencedirect.com/science/article/pii/S1876034116300636 [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. - http://www.genome.org/cgi/doi/10.1101/gr.229202 [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. - https://www.ncbi.nlm.nih.gov/pubmed/9182098 []

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. - https://linkinghub.elsevier.com/retrieve/pii/S0166093418300144 [10.1016/j.jviromet.2018.08.001.]

55. Kohl C., Brinkmann A., Dabrowski P.W., Radonić A., Nitsche A., Kurth A. Protocol for metagenomic virus detection in clinical specimens. Emerg. Infect. Dis., 2015, vol. 21, no. 1, pp. 48–57. - https://dx.doi.org/10.3201/eid2101.140766 [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. - https://linkinghub.elsevier.com/retrieve/pii/S1567134818305690 [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. - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bth485 [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. - https://academic.oup.com/cid/article-lookup/doi/10.1093/cid/cit287 [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. - http://dx.doi.org/10.1038/nmeth.1923 [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, p. R25. - http://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25 [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. - http://journal.frontiersin.org/article/10.3389/fcimb.2014.00025/abstract [10.3389/fcimb.2014.00025.]

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 / ed. Hsiao C.K., 2014, vol. 9, no. 3, p. e90581. - https://dx.plos.org/10.1371/journal.pone.0090581 [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. - https://elifesciences.org/articles/05378 [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. - https://academic.oup.com/gigascience/article-lookup/doi/10.1186/s13742-016-0140-7 [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, no. suppl 1, pp. S26–S30. - https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jiu649 [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. - http://jvi.asm.org/cgi/doi/10.1128/JVI.00823-11 [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 of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol., 2014, vol. 15, no. 11. - http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0519-7 [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. - http://link.springer.com/10.1007/s12686-018-1016-1 [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. - https://academic.oup.com/cid/article-lookup/doi/10.1093/cid/civ393 [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. - http://link.springer.com/10.1007/s00705-015-2424-0 [10.1007/s00705-015-2424-0.]

71. Mlakar J., Korva M., Tul N., Popović M., Poljšak-Prijatelj M., Mraz J., Kolenc M., Resman Rus K., Vesnaver Vipotnik T., Fabjan Vodušek V., Vizjak A., Pižem J., Petrovec M., Avšič Županc T. Zika Virus Associated with Microcephaly. N. Engl. J. Med., 2016, vol. 374, no. 10, pp. 951–958. - http://www.nejm.org/doi/10.1056/NEJMoa1600651 [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. - http://www.nejm.org/doi/10.1056/NEJMc1509458 [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. - http://journal.frontiersin.org/Article/10.3389/fimmu.2016.00029/abstract [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. - https://www.futuremedicine.com/doi/10.2217/fvl.16.5 [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. - http://jvi.asm.org/cgi/doi/10.1128/JVI.02323-13 [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. - https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jis679 [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. - https://academic.oup.com/nar/article/40/20/10345/2414624 [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 / ed. Thiel V., 2013, vol. 8, no. 11, p. e78454. - https://dx.plos.org/10.1371/journal.pone.0078454 [10.1371/journal.pone.0078454.]

79. Palser A.L., Grayson N.E., White R.E., Corton C., Correia S., Ba abdullah 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. / ed. Longnecker R.M., 2015, vol. 89, no. 10, pp. 5222–5237. - http://jvi.asm.org/lookup/doi/10.1128/JVI.03614-14 [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. - http://jvi.asm.org/lookup/doi/10.1128/JVI.00736-12 [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. - http://www.ajtmh.org/cgi/pmidlookup?view=long&pmid=9430533 []

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. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkr859 [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 / ed. Menéndez-Arias L., 2016, vol. 11, no. 9, p. e0163746. - https://dx.plos.org/10.1371/journal.pone.0163746 [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., Ouédraogo N., Afrough B., Bah A., Baum J.H.J., Becker-Ziaja B., Boettcher J.P., Cabeza-Cabrerizo M., Camino-Sánchez Á., 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., Wölfel R., Stoecker K., Fleischmann E., Gabriel M., Weller S.A., Koivogui L., Diallo B., Keïta S., Rambaut A., Formenty P., Günther S., Carroll M.W. Real-time, portable genome sequencing for Ebola surveillance. Nature, 2016, vol. 530, no. 7589, pp. 228–232. - http://www.nature.com/articles/nature16996 [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. / ed. Sugden B., 2011, vol. 7, no. 5, p. e1001344. - http://dx.plos.org/10.1371/journal.ppat.1001344 [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. - http://linkinghub.elsevier.com/retrieve/pii/S0890850805800209 [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. - http://linkinghub.elsevier.com/retrieve/pii/S0166354210007345 [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. - http://doi.wiley.com/10.1111/tbed.12251 [10.1111/tbed.12251.]

89. Sabina J., Leamon J.H. Bias in Whole Genome Amplification: Causes and Considerations. Whole Genome Amplification / ed. Kroneis T., New York, NY: Springer New York, 2015, vol. 1347, pp. 15–41. - http://link.springer.com/10.1007/978-1-4939-2990-0_2 [10.1007/978-1-4939-2990-0_2.]

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. - https://linkinghub.elsevier.com/retrieve/pii/S1877959X18303455 [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. - http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-014-0087-z [10.1186/s12915-014-0087-z.]

92. Sauvage V., Eloit M. Viral metagenomics and blood safety. Transfus. Clin. Biol. J. Soc. Francaise Transfus. Sang., 2016, vol. 23, no. 1, pp. 28–38. - https://linkinghub.elsevier.com/retrieve/pii/S1246-7820(15)00429-2 [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. - https://academic.oup.com/jac/article-lookup/doi/10.1093/jac/dkw397 [10.1093/jac/dkw397.]

94. Shafer R.W. Rationale and Uses of a Public HIV Drug‐Resistance Database. J. Infect. Dis., 2006, vol. 194, no. s1, pp. S51–S58. - https://academic.oup.com/jid/article-lookup/doi/10.1086/505356 [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 of vertebrate RNA viruses. Nature, 2018, vol. 556, no. 7700, pp. 197–202. - http://www.nature.com/articles/s41586-018-0012-7 [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. - http://www.nature.com/articles/nature20167 [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. - https://linkinghub.elsevier.com/retrieve/pii/S0956713518302032 [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. BGRSSB-2018, 2018. - http://conf.bionet.nsc.ru/bgrssb2018/wp-content/uploads/sites/15/2018/10/Elektra_BGRS-SB-2018BOOK.pdf [10.18699/BGRSSB-2018-059.]

99. Stano M., Beke G., Klucar L. viruSITE—integrated database for viral genomics. Database, 2016, vol. 2016, p. baw162. - https://academic.oup.com/database/article-lookup/doi/10.1093/database/baw162 [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. / ed. Loeffelholz M.J., 2016, vol. 54, no. 10, pp. 2470–2484. - http://jcm.asm.org/lookup/doi/10.1128/JCM.00330-16 [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. - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq543 [10.1093/nar/gkq543.]

102. Tsangaras K., Wales N., Sicheritz-Pontén 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 / ed. El-Maarri O., 2014, vol. 9, no. 10, p. e109101. - https://dx.plos.org/10.1371/journal.pone.0109101 [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. - http://genomea.asm.org/lookup/doi/10.1128/genomeA.01498-14 [10.1128/genomeA.01498-14.]

104. UFO Sequencing Consortium within the I-BFM Study Group, Forster M., Szymczak S., Ellinghaus D., Hemmrich G., Rühlemann 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. - http://www.nature.com/articles/srep11534 [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. - http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=8784566 []

106. Venter J.C. Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science, 2004, vol. 304, no. 5667, pp. 66–74. - http://www.sciencemag.org/cgi/doi/10.1126/science.1093857 [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 / ed. Zhu D., 2013, vol. 8, no. 5, p. e64465. - http://dx.plos.org/10.1371/journal.pone.0064465 [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., Dürrwald R., Schlegel M., Huovilainen A., Davidson I., Dán Á., 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. / ed. García-Sastre A., 2015, vol. 89, no. 19, pp. 9920–9931. - http://jvi.asm.org/lookup/doi/10.1128/JVI.00840-15 [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. - http://wwwnc.cdc.gov/eid/article/18/1/11-1026_article.htm [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 exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. Off. J. Am. Coll. Med. Genet., 2011, vol. 13, no. 3, pp. 255–262. - http://dx.doi.org/10.1097/GIM.0b013e3182088158 [10.1097/GIM.0b013e3182088158.]

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. - http://genome.cshlp.org/lookup/doi/10.1101/gr.191049.115 [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. - https://linkinghub.elsevier.com/retrieve/pii/S0092867418302204 [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 / ed. Dutilh B.E., 2013, vol. 8, no. 10, p. e78470. - https://dx.plos.org/10.1371/journal.pone.0078470 [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 South-east Australia. J. Virol. Methods, 2015, vol. 214, pp. 1–9. - https://linkinghub.elsevier.com/retrieve/pii/S0166093414004601 [10.1016/j.jviromet.2014.11.022.]


Дополнительные файлы

1. Метаданные
Тема
Тип Метаданные
Скачать (18KB)    
Метаданные
2. Резюме
Тема
Тип Резюме
Скачать (17KB)    
Метаданные
3. Титульный лист
Тема
Тип Титульный лист
Скачать (18KB)    
Метаданные
4. Литература
Тема
Тип Прочее
Скачать (39KB)    
Метаданные

Для цитирования:


Хафизов К.Ф., Сперанская А.С., Мацвай А.Д., Шипулин Г.А., Дедков В.Г. ПЕРЕДОВЫЕ ТЕХНОЛОГИИ В ДИАГНОСТИКЕ ВИРУСНЫХ ЗАБОЛЕВАНИЙ НЕЯСНОЙ ЭТИОЛОГИИ. Инфекция и иммунитет. 2019;.

For citation:


Khafizov K.F., Speranskaya A.S., Matsvay A.D., Shipulin G.A., Dedkov V.G. ADVANCED TECHNOLOGIES IN DIAGNOSTICS OF VIRAL DISEASES OF UNKNOWN ETIOLOGY. Russian Journal of Infection and Immunity. 2019;. (In Russ.) (In Russ.)

Просмотров: 57


Creative Commons License
Контент доступен под лицензией Creative Commons Attribution 4.0 License.


ISSN 2220-7619 (Print)
ISSN 2313-7398 (Online)