Complete genome of a Puumala virus strain from Central Europe

Sheikh Ali, Hanan; Drewes, Stephan; Weber de Melo, Vanessa; Schlegel, Mathias; Freise, Jona; Groschup, Martin H.; Heckel, Gerald; Ulrich, Rainer G. (2015). Complete genome of a Puumala virus strain from Central Europe. Virus genes, 50(2), pp. 292-298. Nijhoff 10.1007/s11262-014-1157-6

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Population Genetics
08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)

UniBE Contributor:

Weber de Melo, Vanessa and Heckel, Gerald

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

0920-8569

Publisher:

Nijhoff

Language:

English

Submitter:

Isabelle Duperret

Date Deposited:

04 May 2016 10:22

Last Modified:

04 May 2016 10:22

Publisher DOI:

10.1007/s11262-014-1157-6

PubMed ID:

25543297

BORIS DOI:

10.7892/boris.79903

URI:

https://boris.unibe.ch/id/eprint/79903

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