Puumala orthohantavirus genome sequence variations in the Republic of Tatarstan, Russia

Abstract

Background: Hemorrhagic fever with renal syndrome (HFRS) is endemic in Republic of Tatarstan (RT), where Puumala orthohatavirus (PUUV) is identified as the main cause of infection. Eight genetic lineages of PUUV were shown to circulate in Eurasia; however, the diversity of PUUV variants in RT remains largely unknown. Methods & Materials: Total RNA extracted from lung tissues of bank voles captured in multiple location in RT was used for RT-PCR analysis. More than hundred PCR products containing partial S, M and L segments coding regions (566/1057, 1014 and 665 bp, respectively) were sequenced and used to determine genome variations. Results: Most of PUUV sequences revealed low divergence as compared to previously identified in Udmurtia, Bashkortostan and Samara. All these samples belong to the Russian lineage. Interestingly, in addition to the Russian lineage, three RT PUUV strains were part of the Finnish lineage, suggesting co-circulation of two PUUV lineages in some RT locations. Phylogenetic analysis revealed that RT PUUV partial S, M and L segments of RUS lineage formed six subclades, corresponding to their geographic locations in RT districts. Subclades I–IV contained strains from Pre-Kama area, subclade V strains are distributed in Trans-Kama area, while strains from subclade VI are found in Pre-Volga area. Subclades IV and V clustered together on the S and M segment trees, while subclade IV located as a separate group of the L segment. Also, subclade III clustered with subclade II for the S segment, with subclades IV–V for the M segment and with subclades I–II for the L segment. These differences in tree topologies suggest the reassortment or/and recombination origin of some PUUV strains circulating in the RT. Conclusion: Collected data improves our understanding of PUUV diversity and distribution in different regions of RT, which help better control the epidemiological situation in the region. The Russian Government Program of Competitive Growth of Kazan Federal University supported this study. Also, Albert Rizvanov was supported by state assignment 20.5175.2017/6.7 of the Ministry of Education and Science of the Russian Federation. Part of this work was conducted with the support of RFFI perspective grant 19-34-60012 given to Emmanuel Kabwe.