Evolutionary and genetic analysis of human bocavirus genotype-1 strains reveals an evidence of intragenomic recombination

Purpose. Human bocavirus (HBoV) exsits in four genotypes: 1 to 4, with HBoV-1 being the most prevalent genotype. The aim of the current study was to genetically analyze the full-length genome of the HBoV-1 of recently detected Egyptian strains. Methodology. Seven overlapping sets of primers were developed to amplify an almost complete HBoV-1 genome from the clinical samples. The primer sets were tested on three recently identified Egyptian HBoV-1 strains with viral loads >= 10(5) ml(-1). Sequencing was conducted using the same sets of primers. HBoV-1 virus strains were genetically analyzed based on the sequences of their complete genomes and the individual ORFs. Results. The new sets of primers successfully amplified the three tested strains. Sequence analysis of the full-length genome of the HBoV-1 revealed a considerable level of genetic heterogenicity between different strains. Based on the full genome and VP1 ORF, HBoV-1 viruses were clustered into three main lineages, A to C, and lineage A was further subdivided into three sublineages, A1-A3. The Egyptian strains were clustered within two sublineages, A1 and A2. New amino acid substitutions were detected in NS1 and VP1/VP2 proteins. Both inter- and intragenomic recombination events were detected among the Egyptian strains. Conclusion. The existence of both intragenomic recombination event and multiple amino acid substitutions in the examined Egyptian HBoV-1 strains elucidates considerable level of genetic alterations among bocaviruses. Their possible effects on the virus virulence and multiplication efficiency need to be investigated.