Universal Oligonucleotide Microarray for Sub-Typing of Influenza A Virus

被引：24

作者：

Ryabinin, Vladimir A. ^{[1
]}

Kostina, Elena V. ^{[1
]}

Maksakova, Galiya A. ^{[1
]}

Neverov, Alexander A. ^{[2
]}

Chumakov, Konstantin M. ^{[2
]}

Sinyakov, Alexander N. ^{[1
]}

机构：

[1] Russian Acad Sci, Inst Chem Biol & Fundamental Med, Siberian Branch, Novosibirsk, Russia

[2] US FDA, Ctr Biol Evaluat & Res, Rockville, MD 20857 USA

来源：

PLOS ONE | 2011年 / 6卷 / 04期

关键词：

FLUCHIP DIAGNOSTIC MICROARRAY; SUBTYPE IDENTIFICATION; DNA MICROARRAYS; RT-PCR; HYBRIDIZATION; SELECTION; SET;

D O I：

10.1371/journal.pone.0017529

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.

引用

页数：11

共 34 条

[1] AMINO-ACID SUBSTITUTION MATRICES FROM AN INFORMATION THEORETIC PERSPECTIVE [J].

ALTSCHUL, SF .

JOURNAL OF MOLECULAR BIOLOGY, 1991, 219 (03) :555-565

[2]

[Anonymous], 2009, Pandemic influenza preparedness and response

[3] MChip: A tool for influenza surveillance [J].

Dawson, Erica D. ;

Moore, Chad L. ;

Smagala, James A. ;

Dankbar, Daniela M. ;

Mehlmann, Martin ;

Townsend, Michael B. ;

Smith, Catherine B. ;

Cox, Nancy J. ;

Kuchta, Robert D. ;

Rowlen, Kathy L. .

ANALYTICAL CHEMISTRY, 2006, 78 (22) :7610-7615

[4]

Fauquet C.M., 2005, 8 INT COMM TAX VIR, DOI DOI 10.1006/RWVI.1999.0277

[5] Oligonucleotide microchip for subtyping of influenza A virus [J].

Fesenko, Eugeny E. ;

Kireyev, Dmitry E. ;

Gryadunov, Dmitry A. ;

Mikhailovich, Vladimir M. ;

Grebennikova, Tatyana V. ;

L'vov, Dmitry K. ;

Zasedatelev, Alexander S. .

INFLUENZA AND OTHER RESPIRATORY VIRUSES, 2007, 1 (03) :121-129

[6] Characterization of a novel influenza a virus hemagglutinin subtype (H16) obtained from black-headed gulls [J].

Fouchier, RAM ;

Munster, V ;

Wallensten, A ;

Bestebroer, TM ;

Herfst, S ;

Smith, D ;

Rimmelzwaan, GF ;

Olsen, B ;

Osterhaus, ADME .

JOURNAL OF VIROLOGY, 2005, 79 (05) :2814-2822

[7] Rapid haemagglutinin subtyping and pathotyping of avian influenza viruses by a DNA microarray [J].

Gall, Astrid ;

Hoffmann, Bernd ;

Harder, Timm ;

Grund, Christian ;

Ehricht, Ralf ;

Beer, Martin .

JOURNAL OF VIROLOGICAL METHODS, 2009, 160 (1-2) :200-205

[8] Design and Validation of a Microarray for Detection, Hemagglutinin Subtyping, and Pathotyping of Avian Influenza Viruses [J].

Gall, Astrid ;

Hoffmann, Bernd ;

Harder, Timm ;

Grund, Christian ;

Hoeper, Dirk ;

Beer, Martin .

JOURNAL OF CLINICAL MICROBIOLOGY, 2009, 47 (02) :327-334

[9] Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution [J].

Ghedin, E ;

Sengamalay, NA ;

Shumway, M ;

Zaborsky, J ;

Feldblyum, T ;

Subbu, V ;

Spiro, DJ ;

Sitz, J ;

Koo, H ;

Bolotov, P ;

Dernovoy, D ;

Tatusova, T ;

Bao, YM ;

St George, K ;

Taylor, J ;

Lipman, DJ ;

Fraser, CM ;

Taubenberger, JK ;

Salzberg, SL .

NATURE, 2005, 437 (7062) :1162-1166

[10] DIRECT FLUORESCENCE ANALYSIS OF GENETIC POLYMORPHISMS BY HYBRIDIZATION WITH OLIGONUCLEOTIDE ARRAYS ON GLASS SUPPORTS [J].

GUO, Z ;

GUILFOYLE, RA ;

THIEL, AJ ;

WANG, RF ;

SMITH, LM .

NUCLEIC ACIDS RESEARCH, 1994, 22 (24) :5456-5465

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