Computational protocol: Identification and Characterization of a New Bocavirus Species in Gorillas

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Protocol publication

[…] Complete genome of the GBoV1 was acquired using primer walking approach as previously described . In brief, each extension step of PCR used one primer specific for the novel virus sequence and other degenerated to hybridize all known bocavirus sequences. After the complete genome was assembled, each base is sequenced in triplicate to confirm the sequence. The near complete genome of GBoV1 is submitted to Genbank under accession number HM145750.To determine the sequence relationship between GBoV1 and other known bocavirus species, at least one representative virus member, including the reference genome from each species and their translated protein sequences, were used for generating sequence alignments. Sequences used for the comparison comprised the following: HBoV1 (GenBank accession no. 196168955, 161137732, 149389636, 125616893, 161137737, 149389621, 149389676, 223670836, 196168950, 149389626, 284799140, 256692975, 149389721, 149389656, 241995009, 223951374, 196169010, 149389641, 92087153, 226434473, 223670876, 223670861, 196169000, 196168975, 196168960, 149389651, 149389611, 66356133, 66356128, 219879196, 196168985, 196168970, 196168945, 149389711, 149389706, 149389696, 149389661, 149389646, 149389606, 125616883, 196168995, 149389701, 149389691, 149389681, 149389671, 149389666, 149389631, 130918044, 84873482, 260779772, 256692980, 226434468, 223670851, 223670846, 223670841, 223670831, 125719360, 226434443), HBoV2 (GenBank accession no. 241994927, 213012741, 237690160, 237690166, 158714105, 238476986, 158713998, 290565732, 213012746, 290565722, 213012751, 284080644, 237690154, 284080639, 290565727), HBoV3 (GenBank accession no. 238476991,206572554,290565737,237690178,237690184), HBoV4 (GenBank accession no. 289163341), canine minute virus (GenBank accession no. NC_004442) and bovine parvovirus-1 (GenBank accession no. 9627190). Phylogenetic analyses of CLUSTAL W aligned regions were carried out by neighbour joining of nucleotide or amino acid p-distances, implemented in the program MEGA4. Bootstrap resampling was carried out to demonstrate robustness of groupings. Recombination analysis was performed by Symplot, using reference genomes of all four HBoV species and GBoV1. To assess similarity across the genomes, sequence scans were performed using a fragment length of 300 bases and an increment of bases between fragments. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Gorilla gorilla, Homo sapiens, Canine minute virus, Bovine parvovirus
Diseases Enteritis, Encephalomyelitis, Western Equine