M., da Silva, R.R., Kaianoa, J.H.L., Silvestre, R.V.D., Oliveiraa, D., Linharesa, A.C., Gabbaya, Y.B. We recommend the use of the proposed primers in molecular surveillance studies for efficient detection of avian rotavirus.īezerra, D. Thus, a successful surveillance of rotaviruses requires that primer pairs be updated regularly in order to detect the emergence of novel or “unusual types”, which have occurred by genetic drift causing nucleotide changes at the primer binding sites that result in typing failures.
The designed primers had specific bands and were efficient in detecting rotavirus in faecal samples than previously published primers. The derived primer sequences were submitted for a BLAST search to ensure alignment was exclusive to the desired target genes.
Bioedit journal software#
The consensus sequences were aligned using the BioEdit program and then treated with the Fast PCR software to derive the primers. Degenerate nucleotides were included due to the reassortant nature of rotavirus. The alignments were generated using clustal analysis from the BioEdit program. Gene-specific primer pairs were designed by analysing different rotavirus strains isolated during the last decade by downloading them from the GenBank. This study was aimed at designing and evaluating new oligonucleotide degenerate primer pairs that provide increased sensitivity and specificity for detecting avian rotavirus. Reagents and methods for genotyping the virus need constant modification because of the reassortant nature of the virus. The use of molecular methods for rotavirus characterisation provides increased sensitivity for typing and allows the identification of putative reassortant strains.