Computational protocol: Presence of Vaccine-Derived Newcastle Disease Viruses in Wild Birds

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Protocol publication

[…] All available complete fusion-gene (F-gene) sequences of class II NDV were downloaded from GenBank as of July 2015 [] and aligned using ClustalW [], resulting in 1452 complete fusion protein gene sequences. Initial phylogenetic analyses were performed utilizing the complete F-gene sequences using the Neighbor Joining method based upon 100 bootstrap replicates [], as implemented in the MEGA version 6 software [] (data not shown). To ensure that all viruses used in further analyses were isolated only from wild birds, we subjected the dataset to rigorous selection criteria. Specifically, viruses isolated from domestic non-poultry species such as waterfowl from live bird markets [], and sporting, racing, or pet birds where conspecifics may have been vaccinated [] were excluded from the dataset. Viral sequences of wild bird isolates (n = 54, including the 24 sequenced in this study) () that were evolutionarily closely related to reference vaccine strains (n = 5) from genotypes I and II were parsed from the initial compilation. An additional 15 representative sequences from the remaining genotypes (III-XIV and XVI-XVIII) were also included, resulting in a final dataset of 74 sequences.Analysis of the best-fit substitution model was performed and the goodness-of-fit for each model was measured by the corrected Akaike Information Criterion (AICc) and the Bayesian Information Criterion (BIC) []. Tamura 3-parameter model with 500 bootstrap replicates was used for constructing the phylogenetic tree []. Finally, estimates of the means and pairwise genetic distances were computed using the Maximum Composite Likelihood method as implemented in MEGA6 []. The pairwise distances per decade were also calculated as the nucleotide distance per site divided by the number of years separating the isolation of each virus and the respective vaccine strain, multiplied by ten. The rate variation among sites was modeled with a gamma distribution (shape parameter = 4). For each statistical inference, codon positions consisting of 1st+2nd+3rd+Noncoding were retained, while gaps and/or missing data were trimmed.In the past, both topology and nucleotide distance have been used to demonstrate that the sources (direct or indirect) of isolated viruses were live vaccines used in poultry [, , ]. It has been previously reported that a nucleotide distance of approximately 1% per decade is the natural rate of NDV evolution [, ]. In the present study, more stringent selection criterion to identify vaccine-derived viruses was used. NDV isolates with nucleotide distances lower than 0.1% per decade, when compared to the most closely related vaccine strains, were termed “vaccine-derived” viruses. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Viruses, Human poliovirus 1 Mahoney, Homo sapiens
Diseases Newcastle Disease