Computational protocol: Molecular characterization of hepatitis A virus isolates from environmental and clinical samples in Greece

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Protocol publication

[…] All positive samples (environmental and clinical) were confirmed by sequencing of the PCR product. The purified PCR products of the clinical HAV strains were sequenced by Lark Technologies (Essex, UK), and the environmental strains by VBC-Biotech (Austria). The nucleotide sequences obtained were analyzed by BLAST N program at the NIH website (NCBI, National Centre for Technology Control, NIH, USA), and were compared with each other and with other published sequences deposited in the GenBank database. Multiple alignments were performed using Clustal W2 software The neighbour-joining method was applied for the phylogenetic tree analysis, the reliability of which was assessed by bootstrap resampling (1,000 pseudoreplicates), using MEGA 4.0.2 software. The HAV genotype was determined by comparing the different sequences of the Greek strains included in the phylogenetic analysis with the reference sequences of different HAV genotypes. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Hepatovirus A
Diseases Hepatitis B