Computational protocol: Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats

Similar protocols

Protocol publication

[…] Genbank accession numbers are described in . Phylogenetic analyses were performed separately on two sets of data: one comprising 25 whole genome sequences including those of 18 representative historical Marburg isolates, plus the 2 isolates obtained from miners and 5 isolates obtained from bats during the present investigations, and the second data set was comprised of 64 concatenated partial NP and VP35 gene sequences including 48 derived from historical Marburg isolates plus 2 derived from the isolates obtained from miners and 14 determined for PCR products obtained from bats during the present study. A representative sample of Ebola Zaire (Genbank accession NC 002549) was used as an outgroup.Modeltest 3.730 was used to examine 56 models of nucleotide substitution to determine the model most appropriate for the data. For whole genome analysis, the General Time Reversible model incorporating invariant sites and a gamma distribution (GTR+I+G) was selected using the Akaike Information Criterion (AIC). Nucleotide frequencies were A = 0.326, C = 0.195, G = 0.185, T = 0.294, the proportion of invariant sites = 0.451, and the gamma shape parameter = 7.244. The Kimura 3-parameter model with unequal base frequencies and a proportion of invariant sites (K81uf+I) was selected for the concatenated NP-VP35 dataset. Nucleotide frequencies were A = 0.310, C = 0.233, G = 0.202, T = 0.255, and the proportion of invariant sites = 0.659. Maximum likelihood analyses were subsequently performed in PAUP*4.0b10 using the GTR+I+G or K81uf+I model parameters.In addition, Bayesian phylogenetic analyses were conducted for each of the datasets in MrBayes 3.2 using the GTR+I+G model of nucleotide substitution. For each dataset, two simultaneous analyses, each with four Markov chains, were run for 10,000,000–40,000,000 generations, sampling every 100 generations. Prior to termination of the run, the AWTY program was used to assess convergence to ensure that the length of the analysis was sufficient . Trees generated before the stabilization of the likelihood scores were discarded as burn-in, and the remaining trees were used to construct a consensus tree. Nodal support was assessed by posterior probability values (≥95 = statistical support). […]

Pipeline specifications

Software tools ModelTest-NG, MrBayes, AWTY
Application Phylogenetics
Organisms Rousettus aegyptiacus, Homo sapiens
Diseases Marburg Virus Disease