Metagenomics study of viral pathogens in undiagnosed respiratory specimens and identification of human enteroviruses at a Thailand hospital

American Journal of Tropical Medicine and Hygiene

Volumn 95, Issue 3, 2016, Pages 663-669

  Zhou, Yanfei ^a   Fernandez, Stefan ^b   Yoon, In Kyu ^b,c   Simasathien, Sriluck ^d   Watanaveeradej, Veerachai ^d   Yang, Yu ^a   Marte Salcedo, Omely A ^a   Shuck Lee, Deidra J ^a   Thomas, Stephen J ^a   Hang, Jun ^a   Jarman, Richard G ^a  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^b ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^c International Vaccine Institute   (South Korea)

^d PHRAMONGKUTKLAO HOSPITAL   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN;

ADENOVIRIDAE; AMINO ACID SEQUENCE; ARBOVIRUS; ARTICLE; BHUTAN; CYTOPATHOGENIC EFFECT; DENGUE VIRUS 1; ENTEROVIRUS; ENTEROVIRUS 71; ENTEROVIRUS A TYPE 12; ENTEROVIRUS B; ENTEROVIRUS INFECTION; FEMALE; GENE SEQUENCE; GENETIC RECOMBINATION; GENOTYPE; HAND FOOT AND MOUTH DISEASE; HERPANGINA; HUMAN; HUMAN PARAINFLUENZA VIRUS 4; HUMAN RESPIRATORY SYNCYTIAL VIRUS; IMMUNOFLUORESCENCE TEST; INFLUENZA C VIRUS; MAJOR CLINICAL STUDY; MALE; METAGENOME; METAGENOMICS; NEPAL; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHILIPPINES; PHYLOGENETIC TREE; PHYLOGENY; PICORNAVIRIDAE; PYROSEQUENCING; RESPIRATORY SYNCYTIAL VIRUS B; RESPIRATORY TRACT INFECTION; RHINOVIRUS; TERMINAL SEQUENCE; THAILAND; THROAT CULTURE; VIRUS CULTURE; VIRUS IDENTIFICATION; ADOLESCENT; ADULT; CHILD; ENTEROVIRUS INFECTIONS; EPIDEMIOLOGY; GENETICS; HOSPITAL; INFANT; MIDDLE AGED; NEWBORN; PRESCHOOL CHILD; PROCEDURES; RESPIRATORY TRACT INFECTIONS; STATISTICS AND NUMERICAL DATA; VIROLOGY; YOUNG ADULT;

ADENOVIRIDAE; ADOLESCENT; ADULT; CHILD; CHILD, PRESCHOOL; ENTEROVIRUS; ENTEROVIRUS INFECTIONS; FEMALE; HOSPITALS; HUMANS; INFANT; INFANT, NEWBORN; MALE; METAGENOMICS; MIDDLE AGED; PARAINFLUENZA VIRUS 4, HUMAN; PHYLOGENY; RESPIRATORY SYNCYTIAL VIRUSES; RESPIRATORY TRACT INFECTIONS; RHINOVIRUS; THAILAND; YOUNG ADULT;

EID: 84984797957     PISSN: 00029637     EISSN: None     Source Type: Journal    
DOI: 10.4269/ajtmh.16-0062     Document Type: Article

References (34)

1. Burke RL, Vest KG, Eick AA, Sanchez JL, Johns MC, Pavlin JA, Jarman RG, Mothershead JL, Quintana M, Palys T, Cooper MJ, Guan J, Schnabel D, Waitumbi J, Wilma A, Daniels C, Brown ML, Tobias S, Kasper MR, Williams M, Tjaden JA, Oyofo B, Styles T, Blair PJ, Hawksworth A, Montgomery JM, Razuri H, Laguna-Torres A, Schoepp RJ, Norwood DA, Macintosh VH, Gibbons T, Gray GC, Blazes DL, Russell KL; AFHSC-GEIS Influenza SurveillanceWriting Group, Rubenstein J, Hathaway K, Gibbons R, Yoon IK, Saunders D, Gaywee J, Stoner M, Timmermans A, Shrestha SK, Velasco JM, Alera MT, Tannitisupawong D, Myint KS, Pichyangkul S, Woods B, Jerke KH, Koenig MG, Byarugaba DK, Mangen FW, Assefa B, Williams M, Brice G, Mansour M, Pimentel G, Sebeny P, Talaat M, Saeed T, Espinosa B, Faix D, Maves R, Kochel T, Smith J, Guerrero A, Maupin G, Sjoberg P, Duffy M, Garner J, Canas L, Macias E, Kuschner RA, Shanks D, Lewis S, Nowak G, Ndip LM, Wolfe N, Saylors K, 2011. Department of Defense influenza and other respiratory disease surveillance during the 2009 pandemic. BMC Public Health 11 (Suppl 2): S6.
2. Nguyen-Van-Tam JS, Sellwood C, 2013. Intervention strategies for emerging respiratory virus infections: policy and public health considerations. Curr Opin Virol 3: 192-198.
3. Lipkin WI, 2013. The changing face of pathogen discovery and surveillance. Nat Rev Microbiol 11: 133-141.
4. Jartti T, Jartti L, Ruuskanen O, Soderlund-Venermo M, 2012. New respiratory viral infections. Curr Opin Pulm Med 18: 271-278.
5. Lipkin WI, 2010. Microbe hunting. Microbiology and molecular biology reviews. Microbiol Mol Biol Rev 74: 363-377.
6. Fischer N, Indenbirken D, Meyer T, Lutgehetmann M, Lellek H, Spohn M, Aepfelbacher M, Alawi M, Grundhoff A, 2015. Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples. J Clin Microbiol 53: 2238-2250.
7. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F, 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4: e7370.
8. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N, 2012. Application of next-generation sequencing technologies in virology. J Gen Virol 93: 1853-1868.
9. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G, 2011. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12: 7861-7884.
10. Thorburn F, Bennett S, Modha S, Murdoch D, Gunson R, Murcia PR, 2015. The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol 69: 96-100.
11. Muehlenbachs A, Bhatnagar J, Zaki SR, 2014. Tissue tropism, pathology and pathogenesis of enterovirus infection. J Pathol 235: 217-228.
12. Stephenson J, 2014. CDC tracking enterovirus D-68 outbreak causing severe respiratory illness in children in the Midwest. JAMA 312: 1290.
13. Jubelt B, Lipton HL, 2014. Enterovirus/picornavirus infections. Handb Clin Neurol 123: 379-416.
14. Hang J, Forshey BM, Kochel TJ, Li T, Solorzano VF, Halsey ES, Kuschner RA, 2012. Random amplification and pyrosequencing for identification of novel viral genome sequences. J Biomol Tech 23: 4-10.
15. Kroneman A, Vennema H, Deforche K, van der Avoort H, Penaranda S, Oberste MS, Vinje J, Koopmans M, 2011. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol 51: 121-125.
16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S, 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729.
17. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P, 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
18. Tavakoli NP, Tobin EH, Wong SJ, Dupuis AP 2nd, Glasheen B, Kramer LD, Bernard KA, 2007. Identification of dengue virus in respiratory specimens from a patient who had recently traveled from a region where dengue virus infection is endemic. J Clin Microbiol 45: 1523-1527.
19. Linsuwanon P, Puenpa J, Huang SW, Wang YF, Mauleekoonphairoj J, Wang JR, Poovorawan Y, 2014. Epidemiology and seroepidemiology of human enterovirus 71 among Thai populations. J Biomed Sci 21: 16.
20. Solomon T, Lewthwaite P, Perera D, Cardosa MJ, McMinn P, Ooi MH, 2010. Virology, epidemiology, pathogenesis, and control of enterovirus 71. Lancet Infect Dis 10: 778-790.
21. Zhang Y, Tan X, Cui A, Mao N, Xu S, Zhu Z, Zhou J, Shi J, Zhao Y, Wang X, Huang X, Zhu S, Zhang Y, Tang W, Ling H, Xu W, 2013. Complete genome analysis of the C4 subgenotype strains of enterovirus 71: predominant recombination C4 viruses persistently circulating in China for 14 years. PLoS One 8: e56341.
22. Wang Y, Zhu Q, Zeng M, Altmeyer R, Zou G, 2014. Complete genome sequence of a human enterovirus 71 strain isolated from a fatal case in Shanghai, China, in 2012. Genome Announc 2: e00457-14.
23. Oberste MS, Maher K, Pallansch MA, 2004. Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven (sero)types. J Virol 78: 855-867.
24. McVean G, Auton A, 2007. LDhat 2.1: A Package for the Population Genetic Analysis of Recombination. Oxford, United Kingdom: Department of Statistics. Accessed at: http://www.stats.ox.ac.uk/ ~mcvean/LDhat/manual.pdf.
25. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL, 2012. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6: e1485.
26. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY, 2014. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 370: 2408-2417.
27. Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palu G, 2013. Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58: 346-350.
28. Huaman JL, Carrion G, Ampuero JS, Gomez J, Ocana V, Paz I, Gomez E, Chavez E, Sarmiento F, Pozo E, Laguna-Torres VA, Halsey ES, 2014. Non-rhinovirus enteroviruses associated with respiratory infections in Peru (2005-2010). Virol J 11: 169.
29. Zwaans WA, Mallia P, van Winden ME, Rohde GG, 2014. The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease: a systematic review. J Clin Virol 61: 181-188.
30. Chan YF, Sam IC, AbuBakar S, 2010. Phylogenetic designation of enterovirus 71 genotypes and subgenotypes using complete genome sequences. Infect Genet Evol 10: 404-412.
31. Garcia J, Espejo V, Nelson M, Sovero M, Villaran MV, Gomez J, Barrantes M, Sanchez F, Comach G, Arango AE, Aguayo N, de Rivera IL, Chicaiza W, Jimenez M, Aleman W, Rodriguez F, Gonzales MS, Kochel TJ, Halsey ES, 2013. Human rhinoviruses and enteroviruses in influenza-like illness in Latin America. Virol J 10: 305.
32. Richter J, Tryfonos C, Panagiotou C, Nikolaou E, Koliou M, Christodoulou C, 2013. Newly emerging C group enteroviruses may elude diagnosis due to a divergent 5'-UTR. Int J Infect Dis 17: e1245-e1248.
33. Nix WA, Oberste MS, Pallansch MA, 2006. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus (sero)types from original clinical specimens. J Clin Microbiol 44: 2698-2704.
34. Bessaud M, Razafindratsimandresy R, Nougairede A, Joffret ML, Deshpande JM, Dubot-Peres A, Heraud JM, de Lamballerie X, Delpeyroux F, Bailly JL, 2014. Molecular comparison and evolutionary analyses of VP1 nucleotide sequences of new African human enterovirus 71 isolates reveal a wide genetic diversity. PLoS One 9: e90624.