gms | German Medical Science

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing.

In collaboration with NimbleGen Systems, we have developed a DNA array containing 383,102 in situ synthesized oligonucleotide features that together interrogate the entire SARS-CoV genome. The genomic sequence and all genetic variations of 14 SARS isolates are represented on the array. Every base of sequence is represented in both the positive and negative strands at the 15^th position of a perfect-match 29-mer oligonucleotide which is synthesized together with the three possible mismatch oligos that vary at the 15^th position.

We have found that full genome sequence can be obtained using as little as 100ng cDNA derived from SARS-CoV RNA isolated from Vero E culture medium or patient samples. The sequence obtained from the array is both reproducible and accurate (>99.99% accuracy). Here, we report on the strategy and sequencing results using cDNA amplified directly from RNA extracted from patient tissue samples, and demonstrate the ability of the array to accurately classify genetic variants. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale. Whereas we have used this technology for resequencing the SARS-CoV genome, the iterative design flexibility and high density of probes makes this a highly attractive platform for gene expression analysis, comparative genomic hybridization, SNP discovery and other genomic applications.