De novo identification of viral pathogens from cell culture hologenomes

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Patowary, Ashok ^a   Chauhan, Rajendra Kumar ^a   Singh, Meghna ^a   Kv, Shamsudheen ^a   Periwal, Vinita ^a   Kp, Kushwaha ^b   Sapkal, Gajanand N ^c   Bondre, Vijay P ^c   Gore, Milind M ^d   Sivasubbu, Sridhar ^a   Scaria, Vinod ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b BRD MEDICAL COLLEGE   (India)

^c NATIONAL INSTITUTE OF VIROLOGY   (India)

^d National Institute of Virology (ICMR)   (India)

Author keywords

De novo assembly; Epidemics; Hologenome; Japanese encephalitis; Mixed Population Genomes; Next generation sequencing

Indexed keywords

JAPANESE ENCEPHALITIS VIRUS;

EID: 84857580322     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-11     Document Type: Article

References (29)

1. SARS: epidemiology. Chan-Yeung M, Xu RH, Respirology 2003 8 Suppl 9 14 15018127
2. Fatal encephalitis due to Nipah virus among pig-farmers in Malaysia. Chua KB, Goh KJ, Wong KT, Kamarulzaman A, Tan PS, Ksiazek TG, et al. Lancet 1999 354 1257 1259 10.1016/S0140-6736(99)04299-3 10520635 (Pubitemid 29469355)
3. Chikungunya. Fact sheet N°327. World Health Organization, 2008 http://www.who.int/mediacentre/factsheets/fs327/en/
4. Role of the laboratory in diagnosis of influenza during seasonal epidemics and potential pandemics. Petric M, Comanor L, Petti CA, J Infect Dis 2006 194 Suppl 2 98 110 17163396
5. The limitations of point of care testing for pandemic influenza: what clinicians and public health professionals need to know. Hatchette TF, Bastien N, Berry J, Booth TF, Chernesky M, Couillard M, et al. Can J Public Health 2009 100 204 207 19507723
6. Truly emerging-a new disease caused by a novel virus. Feldmann H, N Engl J Med 2011 364 1561 1563 10.1056/NEJMe1102671 21410394
7. Global climate change and emerging infectious diseases. Patz JA, Epstein PR, Burke TA, Balbus JM, JAMA 1996 275 217 223 10.1001/jama.1996.03530270057032 8604175 (Pubitemid 26028563)
8. The evolution of viruses, the emergence of viral diseases: a synthesis that Martinus Beijerinck might enjoy. Murphy FA, Arch Virol Suppl 1999 15 73 85 10470271
9. The evolutionary genetics of viral emergence. Holmes EC, Drummond AJ, Curr Top Microbiol Immunol 2007 315 51 66 10.1007/978-3-540-70962-6-3 17848060
10. Pandemic response lessons from influenza H1N1 2009 in Asia. Fisher D, Hui D, Gao Z, Lee C, Oh MD, Bin C, et al. Respirology 2011 16 876 882 10.1111/j.1440-1843.2011.02003.x 21627715
11. Pandemic potential of a strain of influenza A (H1N1): early findings. Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van K, Hollingsworth TD, et al. Sci 2009 19 324 1557 1561
12. Hot spots in a wired world: WHO surveillance of emerging and re-emerging infectious diseases. Heymann DL, Rodier GR, Lancet Infect Dis 2001 1 345 353 10.1016/S1473-3099(01)00148-7 11871807 (Pubitemid 33586615)
13. Challenges and opportunities for pathogen detection using DNA microarrays. Call DR, Crit Rev Microbiol 2005 31 91 99 10.1080/10408410590921736 15988839 (Pubitemid 40762632)
14. Hybridization of genomic DNA to microarrays: a challenge for the analysis of environmental samples. Avarre JC, de LP, Bena G, J Microbiol Methods 2007 69 242 248 10.1016/j.mimet.2006.11.007 17188770 (Pubitemid 46551287)
15. Improved strategies for sequence-independent amplification and sequencing of viral double-stranded RNA genomes. Potgieter AC, Page NA, Liebenberg J, Wright IM, Landt O, van Dijk AA, J Gen Virol 2009 90 1423 1432 10.1099/vir.0.009381-0 19264638
16. A comprehensive deep sequencing strategy for full-length genomes of influenza A. Hoper D, Hoffmann B, Beer M, PLoS One 2011 6 19075 10.1371/journal.pone.0019075 21559493
17. Next-generation DNA sequencing. Shendure J, Ji H, Nat Biotechnol 2008 26 1135 1145 10.1038/nbt1486 18846087
18. The impact of next-generation sequencing technology on genetics. Mardis ER, Trends Genet 2008 24 133 141 10.1016/j.tig.2007.12.007 18262675
19. The new science of metagenomics: revealing the secrets of our microbial planet. National Research Council (US) Committee, National Academies Press (US) 2007
20. Metagenomics: concept, methodology, ecological inference and recent advances. Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, et al. Biotechnol J 2009 4 480 494 10.1002/biot.200800201 19288513
21. Metagenomics for the discovery of novel human viruses. Tang P, Chiu C, Future Microbiol 2010 5 177 189 10.2217/fmb.09.120 20143943
22. Pathogen Detection Using Short-RNA Deep Sequencing Subtraction and Assembly. Isakov O, Modai S, Shomron N, Bioinformatics 2011 27 2027 2030 10.1093/bioinformatics/btr349 21666269
23. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. Zilber-Rosenberg I, Rosenberg E, FEMS Microbiol Rev 2008 32 723 735 10.1111/j.1574-6976.2008.00123.x 18549407
24. Metagenomics: application of genomics to uncultured microorganisms. Handelsman J, Microbiol Mol Biol Rev 2004 68 669 685 10.1128/MMBR.68.4.669-685. 2004 15590779 (Pubitemid 39628532)
25. Enteroviruses in patients with acute encephalitis, uttar pradesh, India. Sapkal GN, Bondre VP, Fulmali PV, Patil P, Gopalkrishna V, Dadhania V, et al. Emerg Infect Dis 2009 15 295 298 10.3201/eid1502.080865 19193277
26. Introduction of Japanese encephalitis virus genotype I, India. Fulmali PV, Sapkal GN, Athawale S, Gore MM, Mishra AC, Bondre VP, Emerg Infect Dis 2011 17 319 321 21291622
27. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Li H, Ruan J, Durbin R, Genome Res 2008 18 1851 1858 10.1101/gr.078212.108 18714091
28. Database resources of the National Center for Biotechnology Information. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, et al. Nucleic Acids Res 2000 28 10 14 10.1093/nar/28.1.10 10592169 (Pubitemid 30047702)
29. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 821 829 10.1101/gr.074492.107 18349386 (Pubitemid 351645072)