Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus

Abstract

DNA microarrays have proven to be powerful tools for gene expression analyses and are becoming increasingly attractive for diagnostic applications, e.g., for virus identification and subtyping. The selection of appropriate sequences for use on a microarray poses a challenge, particularly for highly mutable organisms such as influenza viruses, human immunodeficiency viruses, and hepatitis C viruses. The goal of this work was to develop an efficient method for mining large databases in order to identify regions of conservation in the influenza virus genome. From these regions of conservation, capture and label sequences capable of discriminating between different viral types and subtypes were selected. The salient features of the method were the use of phylogenetic trees for data reduction and the selection of a relatively small number of capture and label sequences capable of identifying a broad spectrum of influenza viruses. A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at http://www.colorado.edu/chemistry/RGHP/software/.

Infectious diseases detection by microarray: An overview of clinical relevant infections

“…They tested 72 samples comprising of controls and isolates from human, avian, equine, and swine species. The results provided the correct types and subtypes for an average of 72% of the isolates, the correct type and partially correct subtype information for 13% of the isolates, the correct type only for 10% of the isolates, false-negative signals for 4% of the isolates, and false-positive signals for 1% of the isolates [22,23].…”

Impact of Microarray Technology in Influenza Virus Research and Diagnostics

“…They developed microarrays containing 476 probes based on HA (Hemagglutinin) and NA (Neuraminidase) surface proteins and could identify viruses of H1N1 subtypes and recommended use of smaller oligonucleotides for influenza virus detection [12]. At present, various software and algorithms are used for designing specific probes against influenza viruses and different combinations of oligonucleotides are used for virus detection [14,17,18]. Recently probes based on amino acid sequences of influenza surface proteins were used to design universal microchip that could determine all sub-types of HA and NA of influenza A virus.…”

“…For this low-density oligonucleotide microarrays containing limited number of highly multiplexed unique conserved genome "signatures" sequences as probes are used [9][10][11][12][13]. These microarrays are used to detect both influenza A and B viruses as well as various subtypes of influenza A viruses on the basis of three gene targets the HA, NA and M (Matrix) gene segments [6,10,14,15]. Numerous short DNA capture sequences were designed and used to both identify and subtype influenza A viruses on the basis of sequence similarity and differences.…”

Evaluation of MChip with Historic Subtype H1N1 Influenza A Viruses, Including the 1918 “Spanish Flu” Strain

“…The MChip utilizes only 15 short oligonucleotide capture and label pairs, which effectively discriminate influenza A viruses of the H1N1 (A/H1N1), H3N2, and H5N1 subtypes (1,2). In designing the MChip, publicly available sequence information was used to locate conserved regions in the M gene segment for viruses that circulated between the years 1998 and 2005 (7). Several sequences were chosen to provide discrimination between the different subtypes of influenza virus, while others were selected to broadly react with a wide range of influenza A virus subtypes.…”

“…Low-density microarrays were prepared as previously described (1,7). The viruses were obtained by reconstitution of lyophilized egg-passaged virus stored at the Centers for Disease Control and Prevention (CDC) Influenza Division in Atlanta, GA. A/Brevig Mission/1/1918 viral RNA was generously provided by Terrence Tumpey of the CDC.…”