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PMID: 23602435 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Review

Viral surveillance and discovery.

Current opinion in virology ·Vol. 3 ·No. 2 ·2013-04-00 ·Pages 199-204

Lipkin WI, Firth C

Abstract

The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health.

MeSH Terms
Animals Communicable Diseases, Emerging/epidemiology,prevention & control,veterinary,virology Epidemiological Monitoring High-Throughput Nucleotide Sequencing/methods Humans Virology/methods Virus Diseases/epidemiology,prevention & control,veterinary,virology Viruses/classification,genetics,isolation & purification
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lipkin Walter Ian
Center for Infection and Immunity, Mailman School of Public Health of Columbia University, 722 West 168th Street, New York, NY 10025, USA. wil2001@columbia.edu
Firth Cadhla
References (76)
76 references, click to expand
  1. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC).
    Arch Microbiol. 2011 Dec;193(12):883-91 PMID: 21713444
  2. Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.
    PLoS One. 2012;7(10):e46953 PMID: 23071673
  3. Identification of a Kunjin/West Nile-like flavivirus in brains of patients with New York encephalitis.
    Lancet. 1999 Oct 9;354(9186):1261-2 PMID: 10520637
  4. High-throughput DNA sequencing--concepts and limitations.
    Bioessays. 2010 Jun;32(6):524-36 PMID: 20486139
  5. Detection of enteroviral RNA and specific DNA of herpesviruses by multiplex genome amplification.
    J Virol Methods. 1997 Jun;66(1):39-50 PMID: 9220389
  6. Localization of pandemic 2009 H1N1 influenza A virus RNA in lung and lymph nodes of fatal influenza cases by in situ hybridization: new insights on virus replication and pathogenesis.
    J Clin Virol. 2013 Mar;56(3):232-7 PMID: 23246358
  7. Cross-species virus transmission and the emergence of new epidemic diseases.
    Microbiol Mol Biol Rev. 2008 Sep;72(3):457-70 PMID: 18772285
  8. LIPS arrays for simultaneous detection of antibodies against partial and whole proteomes of HCV, HIV and EBV.
    Mol Biosyst. 2011 May;7(5):1453-62 PMID: 21336381
  9. Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade.
    J Clin Virol. 2008 Oct;43(2):219-22 PMID: 18674964
  10. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae.
    Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17486-91 PMID: 21987820
  11. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2.
    Diagn Mol Pathol. 2006 Sep;15(3):169-73 PMID: 16932073
  12. Outbreak of West Nile-like viral encephalitis--New York, 1999.
    MMWR Morb Mortal Wkly Rep. 1999 Oct 1;48(38):845-9 PMID: 10563521
  13. Metagenomics and future perspectives in virus discovery.
    Curr Opin Virol. 2012 Feb;2(1):63-77 PMID: 22440968
  14. The role of pathology in an investigation of an outbreak of West Nile encephalitis in New York, 1999.
    Emerg Infect Dis. 2000 Jul-Aug;6(4):370-2 PMID: 10905969
  15. Transmission of lymphocytic choriomeningitis virus by organ transplantation.
    N Engl J Med. 2006 May 25;354(21):2235-49 PMID: 16723615
  16. Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence.
    Philos Trans R Soc Lond B Biol Sci. 2001 Jul 29;356(1411):991-9 PMID: 11516377
  17. Using a resequencing microarray as a multiple respiratory pathogen detection assay.
    J Clin Microbiol. 2007 Feb;45(2):443-52 PMID: 17135438
  18. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
    Nucleic Acids Res. 2008 Sep;36(16):e105 PMID: 18660515
  19. Optimization of protocol for sequencing of difficult templates.
    J Biomol Tech. 2010 Jul;21(2):97-102 PMID: 20592873
  20. Metagenome plasticity of the bovine abomasal microbiota in immune animals in response to Ostertagia ostertagi infection.
    PLoS One. 2011;6(9):e24417 PMID: 21931709
  21. Sequencing technologies - the next generation.
    Nat Rev Genet. 2010 Jan;11(1):31-46 PMID: 19997069
  22. Viruses and Koch's Postulates.
    J Bacteriol. 1937 Jan;33(1):1-12 PMID: 16559982
  23. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections.
    J Clin Microbiol. 2007 Jul;45(7):2105-9 PMID: 17507510
  24. Effective replication of human influenza viruses in mice lacking a major alpha2,6 sialyltransferase.
    Virus Res. 2007 Jun;126(1-2):9-18 PMID: 17313986
  25. Human papillomavirus and cervical cancer.
    Lancet. 2007 Sep 8;370(9590):890-907 PMID: 17826171
  26. Novel picornavirus in Turkey poults with hepatitis, California, USA.
    Emerg Infect Dis. 2011 Mar;17(3):480-7 PMID: 21392440
  27. Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness.
    Science. 1993 Nov 5;262(5135):914-7 PMID: 8235615
  28. Transgenic mice expressing a human poliovirus receptor: a new model for poliomyelitis.
    Cell. 1990 Oct 19;63(2):353-62 PMID: 2170026
  29. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.
    Clin Infect Dis. 2006 Oct 15;43(8):e71-6 PMID: 16983602
  30. Eilat virus, a unique alphavirus with host range restricted to insects by RNA replication.
    Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14622-7 PMID: 22908261
  31. Autoantigen microarrays for multiplex characterization of autoantibody responses.
    Nat Med. 2002 Mar;8(3):295-301 PMID: 11875502
  32. Integrated capillary electrophoresis microsystem for multiplex analysis of human respiratory viruses.
    Anal Chem. 2010 Dec 15;82(24):10102-9 PMID: 21114282
  33. Genome sequencing in clinical microbiology.
    Nat Biotechnol. 2012 Nov;30(11):1068-71 PMID: 23138305
  34. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology.
    J Clin Microbiol. 2006 Nov;44(11):4157-62 PMID: 17005760
  35. The Global Public Health Intelligence Network and early warning outbreak detection: a Canadian contribution to global public health.
    Can J Public Health. 2006 Jan-Feb;97(1):42-4 PMID: 16512327
  36. MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses.
    J Clin Microbiol. 2007 Sep;45(9):2779-86 PMID: 17596361
  37. Chinese highly pathogenic porcine reproductive and respiratory syndrome virus exhibits more extensive tissue tropism for pigs.
    Virol J. 2012 Sep 17;9:203 PMID: 22978380
  38. Metagenomics for the discovery of novel human viruses.
    Future Microbiol. 2010 Feb;5(2):177-89 PMID: 20143943
  39. Mice transgenic for a human porcine endogenous retrovirus receptor are susceptible to productive viral infection.
    J Virol. 2006 Apr;80(7):3135-46 PMID: 16537582
  40. Emerging pathogens: the epidemiology and evolution of species jumps.
    Trends Ecol Evol. 2005 May;20(5):238-44 PMID: 16701375
  41. Burkitt's lymphoma.
    Lancet. 2012 Mar 31;379(9822):1234-44 PMID: 22333947
  42. The changing face of pathogen discovery and surveillance.
    Nat Rev Microbiol. 2013 Feb;11(2):133-41 PMID: 23268232
  43. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.
    Genome Res. 2004 Mar;14(3):398-405 PMID: 14993206
  44. Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates.
    Clin Microbiol Rev. 1996 Jan;9(1):18-33 PMID: 8665474
  45. Viral haemorrhagic fever in southern Sudan and northern Zaire. Preliminary studies on the aetiological agent.
    Lancet. 1977 Mar 12;1(8011):571-3 PMID: 65662
  46. Serology-enabled discovery of genetically diverse hepaciviruses in a new host.
    J Virol. 2012 Jun;86(11):6171-8 PMID: 22491452
  47. The fecal virome of pigs on a high-density farm.
    J Virol. 2011 Nov;85(22):11697-708 PMID: 21900163
  48. Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification.
    Arch Virol. 2012 May;157(5):907-15 PMID: 22327393
  49. Performance comparison of benchtop high-throughput sequencing platforms.
    Nat Biotechnol. 2012 May;30(5):434-9 PMID: 22522955
  50. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay.
    J Clin Microbiol. 2007 Sep;45(9):2965-70 PMID: 17596360
  51. Detection of enterovirus in the thyroid tissue of patients with graves' disease.
    J Med Virol. 2013 Mar;85(3):512-8 PMID: 23280563
  52. Emergence of fatal avian influenza in New England harbor seals.
    mBio. 2012 Jul 31;3(4):e00166-12 PMID: 22851656
  53. Integrated nanopore sensing platform with sub-microsecond temporal resolution.
    Nat Methods. 2012 Mar 18;9(5):487-92 PMID: 22426489
  54. Immunity to dengue virus: a tale of original antigenic sin and tropical cytokine storms.
    Nat Rev Immunol. 2011 Jul 15;11(8):532-43 PMID: 21760609
  55. Emerging viruses in transplantation.
    Curr Opin Infect Dis. 2010 Aug;23(4):374-8 PMID: 20592533
  56. Induction of sterilizing immunity against West Nile Virus (WNV), by immunization with WNV-like particles produced in insect cells.
    J Infect Dis. 2004 Dec 15;190(12):2104-8 PMID: 15551208
  57. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
    N Engl J Med. 2011 Aug 25;365(8):718-24 PMID: 21793736
  58. Advances in the diagnosis of respiratory tract infections: role of the Luminex xTAG respiratory viral panel.
    Ann N Y Acad Sci. 2011 Mar;1222:6-13 PMID: 21434937
  59. Emerging nanotechnology-based strategies for the identification of microbial pathogenesis.
    Adv Drug Deliv Rev. 2010 Mar 18;62(4-5):408-23 PMID: 19914316
  60. Cancer and viral infections in immunocompromised individuals.
    Int J Cancer. 2009 Oct 15;125(8):1755-63 PMID: 19588503
  61. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.
    Nat Methods. 2009 Apr;6(4):291-5 PMID: 19287394
  62. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.
    Genome Biol. 2011;12(2):R18 PMID: 21338519
  63. Comparative fecal metagenomics unveils unique functional capacity of the swine gut.
    BMC Microbiol. 2011 May 15;11:103 PMID: 21575148
  64. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections.
    J Clin Microbiol. 2008 Jan;46(1):97-102 PMID: 17977985
  65. HealthMap: global infectious disease monitoring through automated classification and visualization of Internet media reports.
    J Am Med Inform Assoc. 2008 Mar-Apr;15(2):150-7 PMID: 18096908
  66. Merkel cell carcinoma: recent insights and new treatment options.
    Curr Opin Oncol. 2012 Mar;24(2):141-9 PMID: 22234254
  67. Microbe hunting.
    Microbiol Mol Biol Rev. 2010 Sep;74(3):363-77 PMID: 20805403
  68. A new arenavirus in a cluster of fatal transplant-associated diseases.
    N Engl J Med. 2008 Mar 6;358(10):991-8 PMID: 18256387
  69. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision.
    Nat Biotechnol. 2012 Feb 14;30(4):344-8 PMID: 22334048
  70. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray.
    J Clin Microbiol. 2007 Jul;45(7):2340-3 PMID: 17494722
  71. Diagnosis of human respiratory syncytial virus infection using reverse transcription loop-mediated isothermal amplification.
    J Virol Methods. 2007 Jan;139(1):78-84 PMID: 17052763
  72. Microarrays for pathogen detection and analysis.
    Brief Funct Genomics. 2011 Nov;10(6):342-53 PMID: 21930658
  73. Characterization of the reconstructed 1918 Spanish influenza pandemic virus.
    Science. 2005 Oct 7;310(5745):77-80 PMID: 16210530
  74. Rapid pneumococcal evolution in response to clinical interventions.
    Science. 2011 Jan 28;331(6016):430-4 PMID: 21273480
  75. Recent advances in peptide-based microarray technologies.
    Comb Chem High Throughput Screen. 2004 Sep;7(6):547-56 PMID: 15379626
  76. ProMED-mail: an early warning system for emerging diseases.
    Clin Infect Dis. 2004 Jul 15;39(2):227-32 PMID: 15307032
Article Info
Journal
Current opinion in virology
Abbr.
Curr Opin Virol
ISSN
1879-6265
DOI
10.1016/j.coviro.2013.03.010
Email
wil2001@columbia.edu
Published
2013-04-00
Epub
2013-00-17
Pages
199-204
Language
English
Region
Netherlands
NLM ID
101560941
PMCID
PMC4310698
Subset
IM
Grants
NIAID NIH HHS · R01 AI079231 · United States
NIAID NIH HHS · U54 AI057158 · United States
NIAID NIH HHS · AI057158 · United States
External Links
PubMed source DOI: 10.1016/j.coviro.2013.03.010 PMC Full Text View journal details
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