Computational protocol: Molecular analysis of partial VP-2 gene amplified from rectal swab samples of diarrheic dogs in Pakistan confirms the circulation of canine parvovirus genetic variant CPV-2a and detects sequences of feline panleukopenia virus (FPV)

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Protocol publication

[…] PCR amplified fragments were cloned in pTZ57R/T vector (Fermentas) and completely sequenced by chain termination method of sequencing on automated sequencer Applied Biosystem 3100. Sequences were analyzed and assembled by the Lasergene DNA analysis package (v8; DNA-STAR Inc., Madison, WI, USA). Phylogenetic trees were generated, first by aligning the molecules using CLUSTAL-W, followed by Maximum likelihood method of phylogenetic tree construction with 1000 bootstrap replications in MEGA7 program []. MegAlign program in DNA STAR was used to produce pairwise comparisons for amino acid sequence similarities. The accession numbers for CPV and FPV isolated in this study are provided in Tables and . The other viral sequences used for amino acid sequence comparisons and phylogenetic analyses were downloaded from GenBank. The branch lengths were measured in terms of the number of substitutions per site. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Canis lupus familiaris, Canine parvovirus, Human poliovirus 1 Mahoney, Fowlpox virus, Viruses
Diseases Feline Panleukopenia, Parvoviridae Infections, Virus Diseases, Coinfection
Chemicals Amino Acids