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The differentiation of virus strains by restriction enzyme analysis and determination of strain similarities

The differentiation of 35 field isolates of the infectious bursal disease virus (IBDV) was carried out by the restriction enzyme (RE) analysis of the products obtained by reverse transcription (RT)/polymerase chain reaction (PCR). The 422 bp hypervariable region of the VP2 gene (nucleotides 732-1153), amplified by RT/PCR, was digested using the restriction endonucleases CfoI, SacI, SspI, StuI and TaqI. The knowledge of the nucleotide sequence recognized by the endonuclease, the literature and the GenBank nucleotide data for the analyzed VP2 gene region, as well as the size of the fragments obtained by the endonuclease digestion, enabled the determination of the nucleotide position corresponding to a restriction site. The differentiation of the analysed IBDV species was obtained by comparing the position of the restriction sites in analysed IBDV species with the data reported elsewhere. The experimentally obtained results were analysed by partition around medoids (PAM) and monothetetic clustering (MONA) algorithms for unsupervised learning. Five groups of viral strains were extracted by both methods and the viral strains classification based the restriction site similarities is presented by the banner plot of PAM method.

classification; infectious bursal disease virus; monothetic clustering; partition around medoids; restriction enzyme analysis; RT/PCR; viral strains

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