Detection of minority variants within bovine respiratory syncytial virus populations using oligonucleotide-based microarrays

Microarray technology, originally developed for highly parallel examination of gene expression is regarded as a potential tool in prognosis and diagnosis. With respect to a discrimination analysis, difference as small as one nucleotide base can be distinguished using oligonucleotide-based microarrays. However, this degree of specificity is dependent on several parameters, including the size of the oligoprobes and the sequence context of the probes (e.g. local melting temperature), hybridization conditions and to some extent the chemistry of the glass slides onto which the probes are deposited. Using bovine respiratory syncytial virus (BRSV) as a model study, an oligonucleotide-based microarray approach was developed to measure the relative abundance of a particular single nucleotide variant within mixed BRSV populations. Using this technology, we show that it is possible to discriminate at a rate of 1%, minority variants in a BRSV population.