Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Opinion
  • Published:

Clinical and biological insights from viral genome sequencing

Nature Reviews Microbiology volume 15, pages 183–192 (2017)Cite this article

Subjects

Abstract

Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

39,95 €

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Methods for sequencing viral genomes from clinical specimens.
The alternative text for this image may have been generated using AI.

Similar content being viewed by others

References

  1. Gardner, R. C. et al. The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing. Nucleic Acids Res. 9, 2871–2888 (1981).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  PubMed  Google Scholar 

  3. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).

    Article  CAS  PubMed  Google Scholar 

  4. Fraser, C. M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403 (1995).

    Article  CAS  PubMed  Google Scholar 

  5. Hayden, E. C. Technology: the $1,000 genome. Nature 507, 294–295 (2014).

    Article  CAS  PubMed  Google Scholar 

  6. Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Grigoriev, I. V. et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42, D699–D704 (2014).

    Article  CAS  PubMed  Google Scholar 

  8. Worthey, E. A. et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13, 255–262 (2011).

    Article  PubMed  Google Scholar 

  9. Bryant, J. M. et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 381, 1551–1560 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Lamelas, A. et al. Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion. mBio 5, e01974-14 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Zaraket, H. et al. Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. J. Clin. Microbiol. 48, 1085–1092 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Houldcroft, C. J. et al. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front. Microbiol. 7, 1317 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Witney, A. A. et al. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J. Clin. Microbiol. 53, 1473–1483 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Simen, B. B. et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis. 199, 693–701 (2009).

    Article  PubMed  Google Scholar 

  15. Smith, G. J. et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459, 1122–1125 (2009).

    Article  CAS  PubMed  Google Scholar 

  16. Gire, S. K. et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369–1372 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Koser, C. U. et al. Routine use of microbial whole-genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 8, e1002824 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cartwright, E. J., Koser, C. U. & Peacock, S. J. Microbial sequences benefit health now. Nature 471, 578 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Paredes, R. & Clotet, B. Clinical management of HIV-1 resistance. Antiviral Res. 85, 245–265 (2010).

    Article  CAS  PubMed  Google Scholar 

  20. Van Laethem, K., Theys, K. & Vandamme, A. M. HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr. Opin. Virol. 14, 16–23 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Durant, J. et al. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet 353, 2195–2199 (1999).

    Article  CAS  PubMed  Google Scholar 

  22. Clevenbergh, P. et al. Persisting long-term benefit of genotype-guided treatment for HIV-infected patients failing HAART. The Viradapt Study: week 48 follow-up. Antivir. Ther. 5, 65–70 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Khudyakov, Y. Molecular surveillance of hepatitis C. Antivir. Ther. 17, 1465–1470 (2012).

    Article  CAS  PubMed  Google Scholar 

  24. Kim, J. H., Park, Y. K., Park, E. S. & Kim, K. H. Molecular diagnosis and treatment of drug-resistant hepatitis B virus. World J. Gastroenterol. 20, 5708–5720 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. McGinnis, J., Laplante, J., Shudt, M. & George, K. S. Next generation sequencing for whole genome analysis and surveillance of influenza A viruses. J. Clin. Virol. 79, 44–50 (2016).

    Article  CAS  PubMed  Google Scholar 

  26. Pawlotsky, J. M. Hepatitis C virus resistance to direct-acting antiviral drugs in interferon-free regimens. Gastroenterology 151, 70–86 (2016).

    Article  CAS  PubMed  Google Scholar 

  27. Thomson, E. et al. Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes. J. Clin. Microbiol. 54, 2470–2484 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Brunnemann, A. K. et al. Drug resistance of clinical varicella-zoster virus strains confirmed by recombinant thymidine kinase expression and by targeted resistance mutagenesis of a cloned wild-type isolate. Antimicrob. Agents Chemother. 59, 2726–2734 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Karamitros, T. et al. De novo assembly of human herpes virus type 1 (HHV-1) genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies. PLoS ONE 11, e0157600 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Piret, J. & Boivin, G. Antiviral drug resistance in herpesviruses other than cytomegalovirus. Rev. Med. Virol. 24, 186–218 (2014).

    Article  CAS  PubMed  Google Scholar 

  31. Melendez, D. P. & Razonable, R. R. Letermovir and inhibitors of the terminase complex: a promising new class of investigational antiviral drugs against human cytomegalovirus. Infect. Drug Resist. 8, 269–277 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Lassalle, F. et al. Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evol. 2, vew017 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Lanier, E. R. et al. Analysis of mutations in the gene encoding cytomegalovirus DNA polymerase in a phase 2 clinical trial of brincidofovir prophylaxis. J. Infect. Dis. 214, 32–35 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kaverin, N. V. et al. Epitope mapping of the hemagglutinin molecule of a highly pathogenic H5N1 influenza virus by using monoclonal antibodies. J. Virol. 81, 12911–12917 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Franco, S. et al. Detection of a sexually transmitted hepatitis C virus protease inhibitor-resistance variant in a human immunodeficiency virus-infected homosexual man. Gastroenterology 147, 599–601.e1 (2014).

    Article  PubMed  Google Scholar 

  36. Fujisaki, S. et al. Outbreak of infections by hepatitis B virus genotype A and transmission of genetic drug resistance in patients coinfected with HIV-1 in Japan. J. Clin. Microbiol. 49, 1017–1024 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Pierucci, P. et al. Novel autologous T-cell therapy for drug-resistant cytomegalovirus disease after lung transplantation. J. Heart Lung Transplant. 35, 685–687 (2016).

    Article  PubMed  Google Scholar 

  38. Agoti, C. N. et al. Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. J. Virol. 89, 3444–3454 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Aanensen, D. M. et al. Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe. mBio 7, e00444-16 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Faria, N. R. et al. Zika virus in the Americas: early epidemiological and genetic findings. Science 352, 345–349 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Mbisa, J. L. et al. Evidence of self-sustaining drug resistant HIV-1 lineages among untreated patients in the United Kingdom. Clin. Infect. Dis. 61, 829–836 (2015).

    Article  PubMed  Google Scholar 

  43. Bartha, I. et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife 2, e01123 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Power, R. A. et al. Genome-wide association study of HIV whole genome sequences validated using drug resistance. PLoS ONE 11, e0163746 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Cuevas, J. M., Geller, R., Garijo, R., Lopez-Aldeguer, J. & Sanjuan, R. Extremely high mutation rate of HIV-1 in vivo. PLoS Biol. 13, e1002251 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Vandenhende, M. A. et al. Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure. PLoS ONE 9, e86771 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Zhou, B. et al. Composition and interactions of hepatitis B virus quasispecies defined the virological response during telbivudine therapy. Sci. Rep. 5, 17123 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Itakura, J. et al. Resistance-associated NS5A variants of hepatitis C virus are susceptible to interferon-based therapy. PLoS ONE 10, e0138060 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Rogers, M. B. et al. Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection. mBio 6, e02464-14 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Swenson, L. C., Daumer, M. & Paredes, R. Next-generation sequencing to assess HIV tropism. Curr. Opin. HIV AIDS 7, 478–485 (2012).

    Article  CAS  PubMed  Google Scholar 

  51. Hutter, G. et al. Long-term control of HIV by CCR5 delta32/delta32 stem-cell transplantation. N. Engl. J. Med. 360, 692–698 (2009).

    Article  PubMed  Google Scholar 

  52. Kordelas, L. et al. Shift of HIV tropism in stem-cell transplantation with CCR5 delta32 mutation. N. Engl. J. Med. 371, 880–882 (2014).

    Article  PubMed  Google Scholar 

  53. Coaquette, A. et al. Mixed cytomegalovirus glycoprotein B genotypes in immunocompromised patients. Clin. Infect. Dis. 39, 155–161 (2004).

    Article  PubMed  Google Scholar 

  54. Solmone, M. et al. Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen. J. Virol. 83, 1718–1726 (2009).

    Article  CAS  PubMed  Google Scholar 

  55. Chou, S. et al. Improved detection of emerging drug-resistant mutant cytomegalovirus subpopulations by deep sequencing. Antimicrob. Agents Chemother. 58, 4697–4702 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Fonager, J. et al. Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing. J. Clin. Virol. 73, 95–100 (2015).

    Article  CAS  PubMed  Google Scholar 

  57. Kyeyune, F. et al. Low-frequency drug resistance in HIV-infected Ugandans on antiretroviral treatment is associated with regimen failure. Antimicrob. Agents Chemother. 60, 3380–3397 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Liu, P. et al. Direct sequencing and characterization of a clinical isolate of Epstein–Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J. Virol. 85, 11291–11299 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Loman, N. J. & Pallen, M. J. Twenty years of bacterial genome sequencing. Nat. Rev. Microbiol. 13, 787–794 (2015).

    Article  CAS  PubMed  Google Scholar 

  60. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

    Article  CAS  PubMed  Google Scholar 

  61. Mulcahy-O'Grady, H. & Workentine, M. L. The challenge and potential of metagenomics in the clinic. Front. Immunol. 7, 29 (2016).

    PubMed  PubMed Central  Google Scholar 

  62. Hoffmann, B. et al. A variegated squirrel bornavirus associated with fatal human encephalitis. N. Engl. J. Med. 373, 154–162 (2015).

    Article  CAS  PubMed  Google Scholar 

  63. Perlejewski, K. et al. Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: unexpected detection of human herpesvirus 1 while searching for RNA pathogens. J. Virol. Methods 226, 1–6 (2015).

    Article  CAS  PubMed  Google Scholar 

  64. Duncan, C. J. et al. Human IFNAR2 deficiency: lessons for antiviral immunity. Sci. Transl Med. 7, 307ra154 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  65. Morfopoulou, S. et al. Human coronavirus OC43 associated with fatal encephalitis. N. Engl. J. Med. 375, 497–498 (2016).

    Article  PubMed  Google Scholar 

  66. Naccache, S. N. et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin. Infect. Dis. 60, 919–923 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Huang, W. et al. Whole-genome sequence analysis reveals the enterovirus D68 isolates during the United States 2014 outbreak mainly belong to a novel clade. Sci. Rep. 5, 15223 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Wilson, M. R. et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370, 2408–2417 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  69. Depledge, D. P. et al. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS ONE 6, e27805 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Allen, U. D. et al. The genetic diversity of Epstein–Barr virus in the setting of transplantation relative to non-transplant settings: a feasibility study. Pediatr. Transplant. 20, 124–129 (2016).

    Article  CAS  PubMed  Google Scholar 

  71. Matranga, C. B. et al. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol. 15, 519 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Calvet, G. et al. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect. Dis. 16, 653–660 (2016).

    Article  PubMed  Google Scholar 

  73. Lei, H. et al. Epstein–Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations. Sci. Rep. 5, 16706 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Kohl, C. et al. Protocol for metagenomic virus detection in clinical specimens. Emerg. Infect. Dis. 21, 48–57 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Sauvage, V. & Eloit, M. Viral metagenomics and blood safety. Transfus. Clin. Biol. 23, 28–38 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Lecuit, M. & Eloit, M. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front. Cell. Infect. Microbiol. 4, 25 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Oude Munnink, B. B. et al. Autologous antibody capture to enrich immunogenic viruses for viral discovery. PLoS ONE 8, e78454 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Sabina, J. & Leamon, J. H. Bias in whole genome amplification: causes and considerations. Methods Mol. Biol. 1347, 15–41 (2015).

    Article  CAS  PubMed  Google Scholar 

  79. Jensen, R. H. et al. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS ONE 10, e0122636 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  80. 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 51, 209–216 (2015).

    Article  CAS  PubMed  Google Scholar 

  81. Mlakar, J. et al. Zika virus associated with microcephaly. N. Engl. J. Med. 374, 951–958 (2016).

    Article  CAS  PubMed  Google Scholar 

  82. Hall, R. J., Draper, J. L., Nielsen, F. G. & Dutilh, B. E. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Front. Microbiol. 6, 224 (2015).

    PubMed  PubMed Central  Google Scholar 

  83. Greninger, A. L. et al. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–2014): a retrospective cohort study. Lancet Infect. Dis. 15, 671–682 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  84. Breitwieser, F. P., Pardo, C. A. & Salzberg, S. L. Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection. F1000Res. 4, 180 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  85. Gardy, J. L. et al. 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. 212, 1574–1578 (2015).

    Article  PubMed  Google Scholar 

  86. Cotten, M. et al. Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. J. Virol. 88, 11056–11069 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Kundu, S. et al. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin. Infect. Dis. 57, 407–414 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Watson, S. J. et al. Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013. J. Virol. 89, 9920–9931 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Parameswaran, P. et al. Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. J. Virol. 86, 8546–8558 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Newman, R. M. et al. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J. Infect. Dis. 208, 17–31 (2013).

    Article  CAS  PubMed  Google Scholar 

  91. Jakava-Viljanen, M. et al. Evolutionary trends of European bat lyssavirus type 2 including genetic characterization of Finnish strains of human and bat origin 24 years apart. Arch. Virol. 160, 1489–1498 (2015).

    Article  CAS  PubMed  Google Scholar 

  92. Brown, J. R. et al. Norovirus whole genome sequencing by SureSelect target enrichment: a robust and sensitive method. J. Clin. Microbiol. 54, 2530–2537 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. 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. 7, e1001344 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Bialasiewicz, S. et al. Detection of a divergent parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing. BMC Infect. Dis. 14, 275 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Johnson, T. A. et al. Clusters of antibiotic resistance genes enriched together stay together in swine agriculture. mBio 7, e02214-15 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Ocwieja, K. E. et al. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Res. 40, 10345–10355 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Bonsall, D. et al. ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Res. 4, 1062 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  98. Wylie, T. N., Wylie, K. M., Herter, B. N. & Storch, G. A. Enhanced virome sequencing using targeted sequence capture. Genome Res. 25, 1910–1920 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Tsangaras, K. et al. Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank). PLoS ONE 9, e109101 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  100. Depledge, D. P. et al. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol. Biol. Evol. 31, 397–409 (2014).

    Article  CAS  PubMed  Google Scholar 

  101. 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. 87, 10389–10393 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Palser, A. L. et al. Genome diversity of Epstein–Barr virus from multiple tumor types and normal infection. J. Virol. 89, 5222–5237 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Tweedy, J. et al. Complete genome sequence of the human herpesvirus 6A strain AJ from Africa resembles strain GS from North America. Genome Announc. 3, e01498-14 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  104. 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. 1, e00830-13 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  105. Kamperschroer, C., Gosink, M. M., Kumpf, S. W., O'Donnell, L. M. & Tartaro, K. R. The genomic sequence of lymphocryptovirus from cynomolgus macaque. Virology 488, 28–36 (2016).

    Article  CAS  PubMed  Google Scholar 

  106. Briese, T. et al. Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio 6, e01491-15 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  107. Naccache, S. N. et al. Distinct Zika virus lineage in Salvador, Bahia, Brazil. Emerg. Infect. Dis. 22, 1788–1792 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  108. Hofmann, B. Incidental findings of uncertain significance: to know or not to know — that is not the question. BMC Med. Ethics 17, 13 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  109. Public Health England. Good laboratory practice when performing molecular amplification assays. Public Health England https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/344076/Q_4i4.4.pdf (2013).

  110. Viana, R. V. & Wallis, C. L. in Wide Spectra of Quality Control Ch. 3 (ed Akyar, I.) (InTech, 2011).

    Google Scholar 

  111. Blomquist, T., Crawford, E. L., Yeo, J., Zhang, X. & Willey, J. C. Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing. Biomol. Detect. Quantif. 5, 30–37 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Houldcroft, C. J. & Breuer, J. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front. Microbiol. 6, 188 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  113. Munro, A. C. & Houldcroft, C. Human cancers and mammalian retroviruses: should we worry about bovine leukemia virus? Future Virol. 11, 163–166 (2016).

    Article  CAS  Google Scholar 

  114. Hue, S. et al. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7, 111 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Erlwein, O. et al. DNA extraction columns contaminated with murine sequences. PLoS ONE 6, e23484 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. 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. 61, 293–299 (2014).

    Article  CAS  PubMed  Google Scholar 

  117. Naccache, S. N. et al. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J. Virol. 87, 11966–11977 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  119. Lipkin, W. I. A. Vision for investigating the microbiology of health and disease. J. Infect. Dis. 212 (Suppl. 1), S26–S30 (2015).

    Article  PubMed  Google Scholar 

  120. Shafer, R. W. Rationale and uses of a public HIV drug-resistance database. J. Infect. Dis. 194 (Suppl. 1), S51–S58 (2006).

    Article  PubMed  Google Scholar 

  121. Gnaneshan, S., Ijaz, S., Moran, J., Ramsay, M. & Green, J. HepSEQ: international public health repository for hepatitis B. Nucleic Acids Res. 35, D367–D370 (2007).

    Article  CAS  PubMed  Google Scholar 

  122. Rhee, S. Y. et al. Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Antiviral Res. 88, 269–275 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Kuiken, C., Yusim, K., Boykin, L. & Richardson, R. The Los Alamos hepatitis C sequence database. Bioinformatics 21, 379–384 (2005).

    Article  CAS  PubMed  Google Scholar 

  124. Hong, L. Z. et al. BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biol. 15, 517 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  125. Schmidt, K. et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J. Antimicrob. Chemother. 72, 104–114 (2017).

    Article  CAS  PubMed  Google Scholar 

  126. Kilianski, A. et al. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 4, 12 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  127. Eckert, S. E., Chan, J. Z.-M., Houniet, D., Breuer, J. & Speight, G. Enrichment of long DNA fragments from mixed samples for Nanopore sequencing. Preprint at bioRxiv http://dx.doi.org/10.1101/048850 (2016).

    Google Scholar 

  128. Greninger, A. L. et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7, 99 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  129. Mathijs, E., Vandenbussche, F., Verpoest, S., De Regge, N. & Van Borm, S. Complete genome sequence of pseudorabies virus reference strain NIA3 using single-molecule real-time sequencing. Genome Announc. 4, e00440-16 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  130. Bull, R. A. et al. A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics 17, 247 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  131. Kimberlin, D. W. & Whitley, R. J. Antiviral resistance: mechanisms, clinical significance, and future implications. J. Antimicrob. Chemother. 37, 403–421 (1996).

    Article  CAS  PubMed  Google Scholar 

  132. Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351 (2016).

    Article  CAS  PubMed  Google Scholar 

  133. Li, C. et al. INC-Seq: accurate single molecule reads using nanopore sequencing. Gigascience 5, 34 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. 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. 38, e159 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  135. 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. 43, e152 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  136. Guan, H. et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing. J. Neurovirol. 22, 240–245 (2016).

    Article  CAS  PubMed  Google Scholar 

  137. Morfopoulou, S. et al. Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis. Acta Neuropathol. http://dx.doi.org/10.1007/s00401-016-1629-y (2016).

  138. Brown, J. R. et al. Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients. Clin. Infect. Dis. 60, 881–888 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Fremond, M. L. et al. Next-generation sequencing for diagnosis and tailored therapy: a case report of astrovirus-associated progressive encephalitis. J. Pediatric Infect. Dis. Soc. 4, e53–e57 (2015).

    Article  PubMed  Google Scholar 

  140. Barjas-Castro, M. L. et al. Probable transfusion-transmitted Zika virus in Brazil. Transfusion 56, 1684–1688 (2016).

    Article  PubMed  Google Scholar 

  141. Musso, D. et al. Potential for Zika virus transmission through blood transfusion demonstrated during an outbreak in French Polynesia, November 2013 to February 2014. Euro Surveill. 19, 20761 (2014).

    Article  PubMed  Google Scholar 

  142. Ellison, D. W. et al. Complete genome sequences of Zika virus strains isolated from the blood of patients in Thailand in 2014 and the Philippines in 2012. Genome Announc. 4, e00359-16 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  143. Faria, N. R. et al. Mobile real-time surveillance of Zika virus in Brazil. Genome Med. 8, 97 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  144. Chitsaz, H. et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol. 29, 915–921 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Feehery, G. R. et al. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS ONE 8, e76096 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank J. Brown and K. Gilmour (Great Ormond Street Hospital (GOSH), London, UK) and R. Doyle (University College London (UCL), UK) for their helpful discussions, and J. Quick (University of Birmingham, UK) for sharing unpublished MinION statistics. C.J.H. was funded by Action Medical Research (grant GN2424). M.A.B. was funded through the European Union's Seventh Programme for research, technological development and demonstration under grant agreement number 304875 held by J.B. This work was supported by the UK National Institute for Health Research Biomedical Research Centre at GOSH National Health Service (NHS) Foundation Trust and UCL. J.B. receives funding from the University College London Hospitals (UCLH)/UCL National Institute for Health Research Biomedical Research Centre. The authors acknowledge infrastructure support for the UCL Pathogen Genomics Unit, from the UCL UK Medical Research Council (MRC) Centre for Molecular Medical Virology and the UCLH/UCL National Institute for Health Research Biomedical Research Centre. The funders had no role in study design, data collection and interpretation, or the decision to submit work for publication.

Author information

Authors and Affiliations

  1. Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,

    Charlotte J. Houldcroft

  2. and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,

    Charlotte J. Houldcroft

  3. Division of Infection and Immunity, University College London, London, WC1E 6BT, UK

    Mathew A. Beale

  4. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridge, UK

    Mathew A. Beale

  5. Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,

    Judith Breuer

  6. and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,

    Judith Breuer

Authors
  1. Charlotte J. Houldcroft
    View author publications

    Search author on:PubMed Google Scholar

  2. Mathew A. Beale
    View author publications

    Search author on:PubMed Google Scholar

  3. Judith Breuer
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Judith Breuer.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

FURTHER INFORMATION

Omicsomics blogspot article

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Houldcroft, C., Beale, M. & Breuer, J. Clinical and biological insights from viral genome sequencing. Nat Rev Microbiol 15, 183–192 (2017). https://doi.org/10.1038/nrmicro.2016.182

Download citation

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/nrmicro.2016.182

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology