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Complete genome of a Puumala virus strain from Central Europe

Abstract

Puumala virus (PUUV) is one of the predominant hantavirus species in Europe causing mild to moderate cases of haemorrhagic fever with renal syndrome. Parts of Lower Saxony in north-western Germany are endemic for PUUV infections. In this study, the complete PUUV genome sequence of a bank vole-derived tissue sample from the 2007 outbreak was determined by a combined primer-walking and RNA ligation strategy. The S, M and L genome segments were 1,828, 3,680 and 6,550 nucleotides in length, respectively. Sliding-window analyses of the nucleotide sequences of all available complete PUUV genomes indicated a non-homogenous distribution of variability with hypervariable regions located at the 3′-ends of the S and M segments. The overall similarity of the coding genome regions to the other PUUV strains ranged between 80.1 and 84.7 % at the level of the nucleotide sequence and between 89.5 and 98.1 % for the deduced amino acid sequences. In comparison to the phylogenetic trees of the complete coding sequences, trees based on partial segments revealed a general drop in phylogenetic support and a lower resolution. The Astrup strain S and M segment sequences showed the highest similarity to sequences of strains from geographically close sites in the Osnabrück Hills region. In conclusion, a primer-walking-mediated strategy resulted in the determination of the first complete nucleotide sequence of a PUUV strain from Central Europe. Different levels of variability along the genome provide the opportunity to choose regions for analyses according to the particular research question, e.g., large-scale phylogenetics or within-host evolution.

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Acknowledgments

We thank Dörte Kaufmann, Thomas Büchner, Kati Sevke and Brita Oltmann for their help in trapping and necropsy of the rodents and their excellent technical assistance. The critical reading and helpful comments of Sandra Essbauer, Jonas Schmidt-Chanasit and Christoph Gertler are kindly acknowledged. The work was supported by the Robert Koch-Institut with funds of the German Ministry of Public Health (Grant No. 1362/1-924, 1362/1-980) and the EU Grant FP7-261504 EDENext and is catalogued by the EDENext Steering Committee as EDENext245 (http://www.edenext.eu). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. G.H. is supported by Swiss National Science Foundation grant 31003A-149585. H.S.A. acknowledges support by scholarship from German Academic Exchange Service (DAAD) desk number 413, Eastern and Southern Africa; Code Number A/09/90015.

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Correspondence to Rainer G. Ulrich.

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Ali, H.S., Drewes, S., Weber de Melo, V. et al. Complete genome of a Puumala virus strain from Central Europe. Virus Genes 50, 292–298 (2015). https://doi.org/10.1007/s11262-014-1157-6

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Keywords

  • Hantavirus
  • Puumala virus
  • Complete genome
  • Nucleocapsid protein
  • Glycoprotein
  • RNA polymerase