ELM: Enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Ueno, Keisuke ^a   Ishii, Akihiro ^a   Ito, Kimihito ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Diagnostic virology; Next generation sequencing; Taxonomic identification; Virome; Virus discovery

Indexed keywords

DATABASE SYSTEMS; DIAGNOSIS; HEALTH RISKS; SEARCH ENGINES;

DIAGNOSTIC VIROLOGY; HUMAN POSE; LARGE SEQUENCES; LOWEST COMMON ANCESTORS; NEXT-GENERATION SEQUENCING; PATHOGENIC VIRUS; TAXONOMIC IDENTIFICATIONS; VIRAL DISEASE; VIROME; VIRUS DISCOVERY;

VIRUSES;

ANIMALIA;

PRIMER DNA;

ALGORITHM; ARTICLE; BIOLOGY; CLASSIFICATION; FACTUAL DATABASE; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; METHODOLOGY; PROBABILITY; VIRUS; VIRUS GENOME; VIRUS INFECTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DATABASES, GENETIC; DNA PRIMERS; FALSE POSITIVE REACTIONS; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROBABILITY; VIRUS DISEASES; VIRUSES;

EID: 84904772427     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-254     Document Type: Article

References (22)

1. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, Lopez-Gatell H, Olivera H, Lopez I, Myers CA, Faix D, Blair PJ, Yu C, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009, 325(5937):197-201. 10.1126/science.1176225, 3250984, 19465683.
2. Gao R, Cao B, Hu Y, Feng Z, Wang D, Hu W, Chen J, Jie Z, Qiu H, Xu K, Xu X, Lu H, Zhu W, Gao Z, Xiang N, Shen Y, He Z, Gu Y, Zhang Z, Yang Y, Zhao X, Zhou L, Li X, Zou S, Zhang Y, Yang L, Guo J, Dong J, Li Q, Dong L, et al. Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 2013, 368(20):1888-1897. 10.1056/NEJMoa1304459, 23577628.
3. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005, 310(5748):676-679. 10.1126/science.1118391, 16195424.
4. Feldmann H, Wahl-Jensen V, Jones SM, Stroher U. Ebola virus ecology: a continuing mystery. Trends Microbiol 2004, 12(10):433-437. 10.1016/j.tim.2004.08.009, 15381189.
5. Nash D, Mostashari F, Fine A, Miller J, O'Leary D, Murray K, Huang A, Rosenberg A, Greenberg A, Sherman M, Wong S, Layton M. The outbreak of West Nile virus infection in the New York City area in 1999. N Engl J Med 2001, 344(24):1807-1814. 10.1056/NEJM200106143442401, 11407341.
6. Yu XJ, Liang MF, Zhang SY, Liu Y, Li JD, Sun YL, Zhang L, Zhang QF, Popov VL, Li C, Qu J, Li Q, Zhang YP, Hai R, Wu W, Wang Q, Zhan FX, Wang XJ, Kan B, Wang SW, Wan KL, Jing HQ, Lu JX, Yin WW, Zhou H, Guan XH, Liu JF, Bi ZQ, Liu GH, Ren J. Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med 2011, 364(16):1523-1532. 10.1056/NEJMoa1010095, 3113718, 21410387.
7. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 2011, 12(11):7861-7884. 3233444, 22174638.
8. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17(3):377-386. 10.1101/gr.5969107, 1800929, 17255551.
9. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444(7122):1027-1031. 10.1038/nature05414, 17183312.
10. Handley SA, Thackray LB, Zhao G, Presti R, Miller AD, Droit L, Abbink P, Maxfield LF, Kambal A, Duan E, Stanley K, Kramer J, Macri SC, Permar SR, Schmitz JE, Mansfield K, Brenchley JM, Veazey RS, Stappenbeck TS, Wang D, Barouch DH, Virgin HW. Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome. Cell 2012, 151(2):253-266. 10.1016/j.cell.2012.09.024, 3490196, 23063120.
11. Tong S, Li Y, Rivailler P, Conrardy C, Castillo DA, Chen LM, Recuenco S, Ellison JA, Davis CT, York IA, Turmelle AS, Moran D, Rogers S, Shi M, Tao Y, Weil MR, Tang K, Rowe LA, Sammons S, Xu X, Frace M, Lindblade KA, Cox NJ, Anderson LJ, Rupprecht CE, Donis RO. A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci U S A 2012, 109(11):4269-4274. 10.1073/pnas.1116200109, 3306675, 22371588.
12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
13. Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS. SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 2009, 25(14):1722-1730. 10.1093/bioinformatics/btp317, 19439565.
14. Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 2011, 39(14):e91. 10.1093/nar/gkr225, 3152360, 21586583.
15. Ishii A, Thomas Y, Moonga L, Nakamura I, Ohnuma A, Hang'ombe B, Takada A, Mweene A, Sawa H. Novel arenavirus, Zambia. Emerg Infect Dis 2011, 17(10):1921-1924. 10.3201/eid1710.10452, 3310648, 22000372.
16. Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL. Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. MBio 2012, 3(4):e00180-00112. 3419519, 22893382.
17. Chen EC, Yagi S, Kelly KR, Mendoza SP, Tarara RP, Canfield DR, Maninger N, Rosenthal A, Spinner A, Bales KL, Schnurr DP, Lerche NW, Chiu CY. Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony. PLoS Pathog 2011, 7(7):e1002155. 10.1371/journal.ppat.1002155, 3136464, 21779173.
18. Sachsenroder J, Twardziok SO, Scheuch M, Johne R. The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium. PLoS One 2014, 9(2):e88888. 10.1371/journal.pone.0088888, 3929612, 24586429.
19. Warren RL, Sutton GG, Jones SJ, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 2007, 23(4):500-501. 10.1093/bioinformatics/btl629, 17158514.
20. Cheung AK, Ng TF, Lager KM, Bayles DO, Alt DP, Delwart EL, Pogranichniy RM, Kehrli ME. A divergent clade of circular single-stranded DNA viruses from pig feces. Arch Virol 2013, 158(10):2157-2162. 10.1007/s00705-013-1701-z, 23612924.
21. Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS. Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma. Science 1994, 266(5192):1865-1869. 10.1126/science.7997879, 7997879.
22. Simons JN, Pilot-Matias TJ, Leary TP, Dawson GJ, Desai SM, Schlauder GG, Muerhoff AS, Erker JC, Buijk SL, Chalmers ML, van Sant CL, Mushahwar IK. Identification of two flavivirus-like genomes in the GB hepatitis agent. Proc Natl Acad Sci U S A 1995, 92(8):3401-3405. 10.1073/pnas.92.8.3401, 42174, 7724574.