Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden

Abstract Shrews are primary hosts for mammalian hantaviruses and are thus considered to be important reservoirs for viruses, similar to rodents and bats. To explore the diversity of hantaviruses in Swedish common shrews (Sorex araneus), we investigated lung tissue from shrews collected between 2015 and 2017. The collection took place at three separate locations in south-central Sweden. Screening for hantaviruses was performed using two different approaches. (i) A total of 113 common shrews were investigated for hantaviruses by a pan-hantavirus L-gene reverse transcriptase PCR, and Sanger sequencing was performed on the 13 positive samples. (ii) In addition, 88 RNA samples were pooled into eight libraries subjected to RNA sequencing. The RNA sequencing data analysis, which focused specifically on identifying hantaviruses, revealed two divergent hantaviruses: the complete genome of an Altai virus (ALTV) and the partial genome of the Seewis virus. Evolutionary analysis revealed that Swedish ALTVs are closely related to Russian ALTVs but distinct from Finnish strains. On the contrary, the Swedish Seewis virus shares closer ancestry with Finnish Seewis virus strains. Given that these viruses were identified in several pools, Seewis virus and ALTV are likely circulating in Swedish common shrews. Supported by earlier studies, common shrews are probably a natural host for at least these two distinct hantaviruses.