Development and evaluation of a one-step real-time RT-PCR assay for universal detection of influenza A viruses from avian and mammal species
Jazyk angličtina Země Rakousko Médium print-electronic
Typ dokumentu časopisecké články
PubMed
20229116
PubMed Central
PMC7086820
DOI
10.1007/s00705-010-0636-x
Knihovny.cz E-zdroje
- MeSH
- koně virologie MeSH
- lidé MeSH
- polymerázová řetězová reakce s reverzní transkripcí metody MeSH
- prasata virologie MeSH
- ptáci virologie MeSH
- virus chřipky A genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The objective of our study was to develop and evaluate a TaqMan real-time RT-PCR (RRT-PCR) assay for universal detection of influenza A (IA) viruses. The primers and LNA-modified octanucleotide probe were selected to correspond to extremely conserved regions of the membrane protein (MP) segment identified by a comprehensive bioinformatics analysis including 10,405 IA viruses MP sequences, i.e., all of the sequences of the Influenza Virus Sequence database collected as of August 20, 2009. The RRT-PCR has a detection limit of approximately five copies of target RNA/reaction and excellent reaction parameters tested in four IA viruses reference laboratories. The inclusivity of the assay was estimated at both the bioinformatic and the experimental level. Our results predicted that this RRT-PCR assay was able to detect 99.5% of known human IA virus strains, 99.84% of pandemic influenza A (H1N1) strains, 99.75% of avian strains, 98.89% of swine strains, 98.15% of equine strains, and 100% of influenza A viruses of other origin.
Zobrazit více v PubMed
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D (2008) The Influenza Virus Resource at the National Center for Biotechnology Information. J Virol 82:596–601. http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html PubMed PMC
Capua I, Alexander DJ. Avian influenza: recent developments. Avian Pathol. 2004;33:393–404. doi: 10.1080/03079450410001724085. PubMed DOI
Di Trani L, Bedini B, Donatelli I, Campitelli L, Chiappini B, De Marco MA, Delogu M, Buonavoglia C, Vaccari G. A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal control. BMC Infect Dis. 2006;6:1–8. doi: 10.1186/1471-2334-6-87. PubMed DOI PMC
Diagnostic manual for avian influenza (2006) Official Journal of the European Union. Document number C(2006) 3477. http://forums.flu-lab-net.eu/files/ with methods http://www.defra.gov.uk/corporate/vla/science/science-viral-ai-reflab-prot.htm
Fouchier RAM, Bestebroer TM, Herfst S, Van Der Kemp L, Rimmelzwaan GF, Osterhaus DME. Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. J Clin Microbiol. 2000;38:4096–4101. PubMed PMC
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98. http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html
Hoffmann E, Stech J, Guan Y, Webster RG, Perez DR. Universal primer set for the full-length amplification of all influenza A viruses. Arch Virol. 2001;146:2275–2289. doi: 10.1007/s007050170002. PubMed DOI
Ito T, Gorman OT, Kawaoka Y, Bean WJ, Webster RG. Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins. J Virol. 1991;65:5491–5498. PubMed PMC
Karlsson M, Wallensen A, Lundkvist A, Olsen B, Brytting M. A real-time PCR assay for the monitoring of influenza A virus in wild birds. J Virol Methods. 2007;144:27–31. doi: 10.1016/j.jviromet.2007.03.013. PubMed DOI
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res 30:3059–3066. http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ PubMed PMC
Munster VJ, Baas Ch, Lexmond P, Waldenström J, Wallensten A, Fransson T, Rimmelzwaan GF, Beyer WEP, Schutten M, Olsen B, Osterhaus ADME, Fouchier RAM. Spatial, temporal and species variation in prevalence of influenza A viruses in wild migratory birds. PLOS Pathog. 2007;3:630–638. doi: 10.1371/journal.ppat.0030061. PubMed DOI PMC
Muska A, Peck E, Palmer S. Standards and controls: concepts for preparation and use in real-time PCR applications. Test strategies. In: Mackay J, editor. Real-time PCR in microbiology. Norfolk, UK: Caister Academic Press; 2007. pp. 117–122.
Nitsche A. Oligonucleotide design for in-house real-time PCR applications in microbiology. In: Mackay J, editor. Real-time PCR in microbiology. Norfolk, UK: Caister Academic Press; 2007. p. 48.
Olsen B, Munster VJ, Wallensten A, Waldenström J, Osterhaus ADME, Fouchier RAM. Global patterns of influenza A virus in wild birds. Science. 2006;312:384–388. doi: 10.1126/science.1122438. PubMed DOI
Palese P. Influenza: old and new threats. Nat Med. 2004;10:S82–S87. doi: 10.1038/nm1141. PubMed DOI
Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue MI, Lohman K, Daum LT, Suarez DL. Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J Clin Microbiol. 2002;40:3256–3260. doi: 10.1128/JCM.40.9.3256-3260.2002. PubMed DOI PMC
Spackman E, Stallknecht DE, Slemons RD, Winker K, Suarez DL, Scott M, Swayne DE. Phylogenetic analyses of type A influenza genes in natural reservoir species in North America reveals genetic variation. Virus Res. 2005;114:89–100. doi: 10.1016/j.virusres.2005.05.013. PubMed DOI
Ward CL, Dempsey MH, Ring CJA, Kempston RE, Yhang L, Gor D, Snowden BW, Tisdale M. Design and performance testing of quantitative real time PCR assays for influenza A and B viral load measurement. J Clin Virol. 2004;29:179–188. doi: 10.1016/S1386-6532(03)00122-7. PubMed DOI PMC
Webby RJ, Webster RG. Emergence of influenza A viruses. Phil Trans R Soc Lond B. 2001;356:1817–1828. doi: 10.1098/rstb.2001.0997. PubMed DOI PMC
Widjaja L, Krauss SL, Webby RJ, Xie T, Webster RG. Matrix gene of influenza A viruses from wild aquatic birds: ecology and emergence of influenza A viruses. J Virol. 2004;78:8771–8779. doi: 10.1128/JVI.78.16.8771-8779.2004. PubMed DOI PMC
Wu Ch, Cheng X, He J, Lv X, Wang J, Deng R, Long Q, Wang X. A multiplex real-time RT-PCR for detection and identification of influenza virus types A and B and subtypes H5 and N1. J Virol Methods. 2008;148:81–88. doi: 10.1016/j.jviromet.2007.10.023. PubMed DOI
