Design of a set of probes with high potential for influenza virus epidemiological surveillance

Abstract

An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences with Tm values between 34.5 and 36.5oC were applied for selecting probes with high sequential entropy. Virtual Hybridization was used to predict Genomic Fingerprints to assess the capability of the IPS to discriminate between influenza and related strains. Distance scores between pairs of Influenza Genomic Fingerprints were calculated, and used for estimating Taxonomic Trees. Visual examination of both Genomic Fingerprints and Taxonomic Trees suggest that the IPS is able to discriminate between distant and closely related Influenza strains. It is proposed that the IPS can be used to investigate, by virtual or experimental hybridization, any new, and potentially virulent, strain.

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

“…This makes it more difficult to find, by chance, a similar 21-nucleotide long probe. Each of the sites thus identified confirm that the duplex formation and potential sites are not random [ 14 ].…”

“…Other studies designed Influenza Probe Set (IPS, consisting in 1249 probes with a length 9-mer, extracted from sequence alignment zones with maximum entropy within the full viral genome of over 5000 viruses reported, considering almost all viral subtypes of Influenza A [ 14 ].…”