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.
Highlights
Influenza viruses are part of Orthomixoviridae Family and possess segmented genomes consisting of seven or eight separate RNA molecules, each coding for one or more viral proteins
The Virtual Hybridization (VH) programs conducts a rigorous and reliable analysis to find and track all the sites in each viral genome where the probe sequences can hybridize taking into account the degree of complementarity between the probe and the recognized site in the target and the thermodynamic stability between them
The generated information constitutes an in silico genomic fingerprint listing details of the specific sites in each target DNA where hybridization occurred, the number and sequence of the probe that hybridized as well as the free energy value of the hybridizations and it provides the sequence of the target site recognized by each probe
Summary
Influenza viruses are part of Orthomixoviridae Family and possess segmented genomes consisting of seven or eight separate RNA molecules, each coding for one or more viral proteins. It provides them with the ability to rapidly adapt to the pressure of the host immune system and leads to the continuous emergence of new virus variants that cause seasonal and pandemic outbreaks of influenza. Because of this ability, segmented viruses can exist in numerous genotypes and serotypes, presenting a challenge to the creation of protective vaccines and detection methods [1, 2]. Because of these reasons, the early detection and diagnostic confirmation of influenza virus infections is fundamental for an appropriate control of the disease. Other techniques such as sequencing are able to perform a precise
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