A family-wide rt-pcr assay for detection of paramyxoviruses and application to a large-scale surveillance study

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  van Boheemen, Sander ^a   Bestebroer, Theo M ^a   Verhagen, Josanne H ^a   Osterhaus, Albert D M E ^a   Pas, Suzan D ^a   Herfst, Sander ^a   Fouchier, Ron A M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; PROTEIN PMX 1; PROTEIN PMX 2; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DISEASE SURVEILLANCE; ENTROPY; EPIDEMIC; FLUORESCENCE ANALYSIS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC DISTANCE; GENOMIC FRAGMENT; HENDRA VIRUS; HENIPAVIRUS; MOLECULAR DIAGNOSIS; NIPAH VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAMYXOVIRUS; PARAMYXOVIRUS INFECTION; PHYLOGENETIC TREE; PNEUMOVIRINAE; PROTEIN DOMAIN; PROTEIN MOTIF; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; VIRUS DETECTION; ANIMAL; ANIMAL DISEASE; CLASSIFICATION; GENETICS; HIGH THROUGHPUT SCREENING; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; PHYLOGENY; VALIDATION STUDY;

ANIMALIA; ANSER; ANSER ALBIFRONS; AVES; AVIAN METAPNEUMOVIRUS TYPE C; BRANTA LEUCOPSIS; PARAMYXOVIRIDAE; PARAMYXOVIRINAE; PNEUMOVIRINAE; THORACICA;

ANIMALS; DISEASE OUTBREAKS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; PARAMYXOVIRIDAE; PARAMYXOVIRIDAE INFECTIONS; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84859344092     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034961     Document Type: Article

References (21)

1. Lamb RA, Parks GD, (2007) Paramyxoviridae. In: Fields BN, Knipe DM, Howley PM, editors. Fields virology. 5th ed Philadelphia Wolters Kluwer/Lippincott Williams & Wilkins pp. 1449-1496.
2. Tregoning JS, Schwarze J, (2010) Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology. Clin Microbiol Rev 23: 74-98.
3. Murray K, Selleck P, Hooper P, Hyatt A, Gould A, et al. (1995) A morbillivirus that caused fatal disease in horses and humans. Science 268: 94-97.
4. Chua KB, Goh KJ, Wong KT, Kamarulzaman A, Tan PS, et al. (1999) Fatal encephalitis due to Nipah virus among pig-farmers in Malaysia. Lancet 354: 1257-1259.
5. Chua KB, Bellini WJ, Rota PA, Harcourt BH, Tamin A, et al. (2000) Nipah virus: a recently emergent deadly paramyxovirus. Science 288: 1432-1435.
6. Kitchen A, Shackelton LA, Holmes EC, (2011) Family level phylogenies reveal modes of macroevolution in RNA viruses. Proc Natl Acad Sci U S A 108: 238-243.
7. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA, (2005) Virus Taxonomy: VIIIth Report of the International Committee on Taxonomy of Viruses.
8. Scaramozzino N, Crance JM, Jouan A, DeBriel DA, Stoll F, et al. (2001) Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences. J Clin Microbiol 39: 1922-1927.
9. Drosten C, Gunther S, Preiser W, van der Werf S, Brodt HR, et al. (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348: 1967-1976.
10. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, et al. (2003) A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348: 1953-1966.
11. Kidd AH, Jonsson M, Garwicz D, Kajon AE, Wermenbol AG, et al. (1996) Rapid subgenus identification of human adenovirus isolates by a general PCR. J Clin Microbiol 34: 622-627.
12. Tong S, Chern SW, Li Y, Pallansch MA, Anderson LJ, (2008) Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses. J Clin Microbiol 46: 2652-2658.
13. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
14. Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
15. Malur AG, Gupta NK, De Bishnu P, Banerjee AK, (2002) Analysis of the mutations in the active site of the RNA-dependent RNA polymerase of human parainfluenza virus type 3 (HPIV3). Gene Expr 10: 93-100.
16. Munster VJ, Baas C, Lexmond P, Waldenstrom J, Wallensten A, et al. (2007) Spatial, temporal, and species variation in prevalence of influenza A viruses in wild migratory birds. PLoS Pathog 3: e61.
17. Poch O, Blumberg BM, Bougueleret L, Tordo N, (1990) Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains. J Gen Virol 71 (Pt 5): 1153-1162.
18. Svenda M, Berg M, Moreno-Lopez J, Linne T, (1997) Analysis of the large (L) protein gene of the porcine rubulavirus LPMV: identification of possible functional domains. Virus Res 48: 57-70.
19. Swofford DL, (2002) PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta (Sinauer Associates, Inc., Sunderland, MA).
20. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
21. Pierce JR, (1980) An introduction to information theory: symbols, signals and noise, 2nd ed Dover Publications, Inc., New York, N.Y.