Computational protocol: First Molecular Evidence for Puumala Hantavirus in Poland

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Protocol publication

[…] An initial comparison of the novel PUUV sequences with existing data was done using the BLAST search module [].For phylogenetic analyses of PUUV and cytochrome b sequences, published sequences were included in the analyses in order to cover the known genetic diversity and geographical distribution of PUUV and bank voles widely, which is analogous to previous investigations [,,]. For the PUUV S segment, the 465 nt alignment contained 165 sequences including four sequences from Latvia (Madona Mg99, Jelgava Mg136, Jelgava Mg140, Jelgava Mg149 []), and sequences of TULV strains Lodz AF063892 and Moravia Z69991 as outgroup. For the M segment, the analyses covered 177 nt with a similar geographical spread of sequences and the same outgroup strains. For the identification of the genetic lineage of the bank voles, cytochrome b sequences of the lineages Eastern, Carpathian, Balkan and Western, which have been found previously in the larger region [], were retrieved from GenBank. Phylogenetic analyses involved the estimation of the optimal nucleotide substitution model based on the Bayesian information criterion in Mega version 5.2 [] before tree reconstruction with Neighbor-Joining (NJ) algorithms incorporated in Mega and Bayesian algorithms incorporated in MrBayes 3.1.2. []. For analyses of the PUUV S segment, the GTR model with gamma shape parameter and invariable sites was used with the estimated values, and for the cytochrome b sequences (843 nt) the T3P model with gamma parameter and a fraction of invariable sites was applied. For the NJ analyses, 5,000 bootstrap replicates were performed for each data set. Bayesian analyses were run two times for each dataset with one cold and three hot chains for 5 million generations with every 10th generation sampled. The first 25% of the samples were discarded as burn-in and convergence of chains was confirmed according to standard procedures (see [] for details). […]

Pipeline specifications

Software tools MEGA, MrBayes
Application Phylogenetics
Organisms , Homo sapiens, Saccharomyces cerevisiae
Diseases Hemorrhagic Fever with Renal Syndrome