MChip, a low density microarray, differentiates among seasonal human H1N1, North American swine H1N1, and the 2009 pandemic H1N1.
BACKGROUND
The MChip uses data from the hybridization of amplified viral RNA to 15 distinct oligonucleotides that target the influenza A matrix (M) gene segment. An artificial neural network (ANN) automates the interpretation of subtle differences in fluorescence intensity patterns from the microarray. The complete process from clinical specimen to identification including amplification of viral RNA can be completed in <8 hours for under US$10.


OBJECTIVE
The work presented here represents an effort to expand and test the capabilities of the MChip to differentiate influenza A/H1N1 of various species origin.


METHODS
The MChip ANN was trained to recognize fluorescence image patterns of a variety of known influenza A viruses, including examples of human H1N1, human H3N2, swine H1N1, 2009 pandemic influenza A H1N1, and a wide variety of avian, equine, canine, and swine influenza viruses. Robustness of the MChip ANN was evaluated using 296 blinded isolates.


RESULTS
Training of the ANN was expanded by the addition of 71 well-characterized influenza A isolates and yielded relatively high accuracy (little misclassification) in distinguishing unique H1N1 strains: nine human A/H1N1 (88·9% correct), 35 human A/H3N2 (97·1% correct), 31 North American swine A/H1N1 (80·6% correct), 14 2009 pandemic A/H1N1 (87·7% correct), and 23 negative samples (91·3% correct). Genetic diversity among the swine H1N1 isolates may have contributed to the lower success rate for these viruses.


CONCLUSIONS
The current study demonstrates the MChip has the capability to differentiate the genetic variations among influenza viruses with appropriate ANN training. Further selective enrichment of the ANN will improve its ability to rapidly and reliably characterize influenza viruses of unknown origin.
Heil
Gary L
GL
Emerging Pathogens Institute and College of Public Health and Health Professions, The University of Florida, Gainesville, FL 32611, USA. glheil@phhp.ufl.edu
McCarthy
Troy
T
Yoon
Kyoung-Jin
KJ
Liu
Siyuan
S
Saad
Magdi D
MD
Smith
Catherine B
CB
Houck
Julie A
JA
Dawson
Erica D
ED
Rowlen
Kathy L
KL
Gray
Gregory C
GC
D000818:Animals; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000235:genetics*; D046228:Microarray Analysis / Q000191:economics / Q000379:methods*; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D012680:Sensitivity and Specificity; D013997:Time Factors; D014481:United States; D014763:Viral Matrix Proteins / Q000235:genetics*; D014773:Virology / Q000191:economics / Q000379:methods*
C031540:M-protein, influenza virus; D014763:Viral Matrix Proteins