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Abstract
To screen diagnostic specimens for the presence of hantavirus genomes or to identify new hantaviruses in nature, the pan-hanta L-PCR assay, a broadly reactive nested reverse transcription polymerase chain reaction (RT-PCR) assay targeting the L segment, is highly preferred over other assays because of its universality and high sensitivity. In contrast, the geographic allocation of Puumala virus strains to defined outbreak regions in Germany was previously done based on S segment sequences. We show that the routinely generated partial L segment sequences resulting from the pan-hanta L-PCR assay provide sufficient phylogenetic signal to inform the molecular epidemiology of the Puumala virus. Consequently, an additional S segment analysis seems no longer necessary for the identification of the spatial origin of a virus strain.
Highlights
Hantaviruses are tri-segmented negative stranded RNA viruses that are carried by small mammals
Most human hantavirus disease cases in Germany are caused by Puumala virus (PUUV) which usually manifests as a mild form of hemorrhagic fever with renal syndrome (HFRS), sometimes named as nephropathia epidemica [1,2,3]
When analysing PUUV S segment sequences obtained from patients during 2017 and 2018 together with sequences available in Genbank, 194/206 (94.2%) human-derived sequences fall into well-supported phylogeographic clusters (Figure 1A)
Summary
Hantaviruses (family Hantaviridae) are tri-segmented negative stranded RNA viruses that are carried by small mammals (rodents, insectivores, and bats). Human infections are thought to occur through the inhalation of rodent excretions. In Germany, two pathogenic hantaviruses have been circulating, the Dobrava-Belgrade virus (DOBV), restricted to northern and eastern Germany, and Puumala virus (PUUV), endemic in the southern and western parts of the country. Most human hantavirus disease cases in Germany are caused by PUUV which usually manifests as a mild form of hemorrhagic fever with renal syndrome (HFRS), sometimes named as nephropathia epidemica [1,2,3]. Since hantavirus disease became notifiable in Germany in 2001, several outbreaks have occurred over the years with up to 2825 cases being recorded, the latest one in 2017 with 1731 notified cases [5]
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