Genetic diversity analysis and in silico prediction of potential siRNAs against human bocavirus (HBoV)

The human bocavirus (HBoV) is a serious emerging virus globally with high rates of infection in children (0.6-5 years) as well as in adults, and has been detected in respiratory samples, stools, urine, saliva, sewage, and river water. In Saudi Arabia, the infection rate is increasing at an alarming rate, and few reports have been published related to prevalence and superficial molecular characterization, but there is no published report on the use of RNAi against HBoV. This paper discussed genetic diversity, phylogenetic relationship analysis, secondary structure prediction, recombination analysis and silico prediction of potential siRNAs against HBoV. The sequence alignment showed significant homology, and the phylogenetic tree showed 3 distinct cluster. The secondary structure, mountain plot and centroid secondary structure were designed, and dot-bracket code detected a minimum free energy of -1332.70 kcal/mol for whole genome and -88.90 kcal/mol for VP1 gene. The recombination analysis showed the Ethiopian isolate as a recombinant and Russian and Nigerian were identified as the primary and secondary parent. Total 442 siRNAs were predicted and 19 candidates passed the multi-tool scoring thresholds, and only 6 siRNAs were finally selected based on stringent filtration criteria and used in this work. The designed and predicted siRNAs may be further utilized as antiviral molecules in Saudi Arabia only after experimental evaluation in multiple cell lines.