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Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
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Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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Beermann S, Dobler G, Faber M, Frank C, Habedank B, Hagedorn P, Kampen H, Kuhn C, Nygren T, Schmidt-Chanasit J, Schmolz E, Stark K, Ulrich RG, Weiss S, Wilking H. Impact of climate change on vector- and rodent-borne infectious diseases. JOURNAL OF HEALTH MONITORING 2023; 8:33-61. [PMID: 37342429 PMCID: PMC10278376 DOI: 10.25646/11401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/10/2023] [Indexed: 06/22/2023]
Abstract
Background Endemic and imported vector- and rodent-borne infectious agents can be linked to high morbidity and mortality. Therefore, vector- and rodent-borne human diseases and the effects of climate change are important public health issues. Methods For this review, the relevant literature was identified and evaluated according to the thematic aspects and supplemented with an analysis of surveillance data for Germany. Results Factors such as increasing temperatures, changing precipitation patterns, and human behaviour may influence the epidemiology of vector- and rodent-borne infectious diseases in Germany. Conclusions The effects of climatic changes on the spread of vector- and rodent-borne infectious diseases need to be further studied in detail and considered in the context of climate adaptation measures.
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Affiliation(s)
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology, Munich, Germany, National Consulting Laboratory for Tick-Borne Encephalitis
| | - Mirko Faber
- Robert Koch Institute, Berlin, Germany Department of Infectious Disease Epidemiology
| | - Christina Frank
- Robert Koch Institute, Berlin, Germany Department of Infectious Disease Epidemiology
| | - Birgit Habedank
- German Environment Agency, Berlin, Germany, Section IV 1.4 Health Pests and their Control
| | - Peter Hagedorn
- Robert Koch Institute, Berlin, Germany Centre for Biological Threats and Special Pathogens
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany, Institute of Infectology
| | - Carola Kuhn
- German Environment Agency, Berlin, Germany, Section IV 1.4 Health Pests and their Control
| | - Teresa Nygren
- Robert Koch Institute, Berlin, Germany Department of Infectious Disease Epidemiology
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Arbovirus and Entomology Department
| | - Erik Schmolz
- German Environment Agency, Berlin, Germany, Section IV 1.4 Health Pests and their Control
| | - Klaus Stark
- Robert Koch Institute, Berlin, Germany Department of Infectious Disease Epidemiology
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany, Institute of Novel and Emerging Infectious Diseases
- German Center for Infection Research Greifswald - Insel Riems, Germany
| | - Sabrina Weiss
- Robert Koch Institute, Berlin, Germany Centre for International Health Protection
| | - Hendrik Wilking
- Robert Koch Institute, Berlin, Germany Department of Infectious Disease Epidemiology
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Cirkovic V, Dellicour S, Stamenkovic G, Siljic M, Gligic A, Stanojevic M. Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe. Virus Evol 2022; 8:veac112. [PMID: 37954511 PMCID: PMC10634634 DOI: 10.1093/ve/veac112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/07/2022] [Accepted: 12/21/2022] [Indexed: 11/14/2023] Open
Abstract
Orthohantaviruses are zoonotic pathogens of humans, unique among the bunyaviruses in not being transmitted by an arthropod vector. Tula orthohantavirus (TULV) is an old-world hantavirus, of yet unclear human pathogenicity, with few reported cases of clinically relevant human infection. So far, phylogeographic studies exploring the global pathways of hantaviral migration are scarce and generally do not focus on a specific hantavirus species. The aim of the present study was to reconstruct the dispersal history of TULV lineages across Eurasia based on S segment sequences sampled from different geographic areas. Maximum-likelihood and Bayesian inference methods were used to perform the phylogenetic analysis and phylogeographic reconstructions. Sampling time and trapping localities were obtained for a total of 735 TULV S segment sequences available in public databases at the time of the study. The estimated substitution rate of the analyzed partial S segment alignment was 2.26 × 10-3 substitutions/site/year (95 per cent highest posterior density interval: 1.79 × 10-3 to 2.75 × 10-3). Continuous phylogeography of TULV S segment sequences placed the potential root and origin of TULV spread in the Black Sea region. In our study, we detect a single-lineage introduction of TULV to Europe, followed by local viral circulation further on.
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Affiliation(s)
- Valentina Cirkovic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université
Libre de Bruxelles, CP160/13, 50, av. FD Roosevelt, Bruxelles 1050,
Belgium
- Department of Microbiology, Immunology and
Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000,
Belgium
| | - Gorana Stamenkovic
- University of Belgrade, Institute for Biological Research ‘Siniša
Stanković’, Bulevar despota Stefana 142, Belgrade 11108, Serbia
| | - Marina Siljic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
| | - Ana Gligic
- Institute of Virology, Vaccines and Sera Torlak, Vojvode
Stepe 458, Belgrade 11000, Serbia
| | - Maja Stanojevic
- Faculty of Medicine, University of
Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
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Molecular Characterisation and Phylogeny of Tula Virus in Kazakhstan. Viruses 2022; 14:v14061258. [PMID: 35746729 PMCID: PMC9230364 DOI: 10.3390/v14061258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 01/18/2023] Open
Abstract
Orthohantaviruses are zoonotic pathogens that play a significant role in public health. These viruses can cause haemorrhagic fever with renal syndrome in Eurasia. In the Republic of Kazakhstan, the first human cases were registered in the year 2000 in the West Kazakhstan region. Small mammals can be reservoirs of orthohantaviruses. Previous studies showed orthohantavirus antigens in wild-living small mammals in four districts of West Kazakhstan. Clinical studies suggested that there might be further regions with human orthohantavirus infections in Kazakhstan, but genetic data of orthohantaviruses in natural foci are limited. The aim of this study was to investigate small mammals for the presence of orthohantaviruses by molecular biological methods and to provide a phylogenetic characterization of the circulating strains in Kazakhstan. Small mammals were trapped at 19 sites in West Kazakhstan, four in Almaty region and at seven sites around Almaty city during all seasons of 2018 and 2019. Lung tissues of small mammals were homogenized and RNA was extracted. Orthohantavirus RT-PCR assays were applied for detection of partial S and L segment sequences. Results were compared to published fragments. In total, 621 small mammals from 11 species were analysed. Among the collected small mammals, 2.4% tested positive for orthohantavirus RNA, one sample from West Kazakhstan and 14 samples from Almaty region. None of the rodents caught in Almaty city were infected. Sequencing parts of the small (S) and large (L) segments specified Tula virus (TULV) in these two regions. Our data show that geographical distribution of TULV is more extended as previously thought. The detected sequences were found to be split in two distinct genetic clusters of TULV in West Kazakhstan and Almaty region. TULV was detected in the common vole (Microtus arvalis) and for the first time in two individuals of the forest dormouse (Dryomys nitedula), interpreted as a spill-over infection in Kazakhstan.
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Saxenhofer M, Labutin A, White TA, Heckel G. Host genetic factors associated with the range limit of a European hantavirus. Mol Ecol 2021; 31:252-265. [PMID: 34614264 PMCID: PMC9298007 DOI: 10.1111/mec.16211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022]
Abstract
The natural host ranges of many viruses are restricted to very specific taxa. Little is known about the molecular barriers between species that lead to the establishment of this restriction or generally prevent virus emergence in new hosts. Here, we identify genomic polymorphisms in a natural rodent host associated with a strong genetic barrier to the transmission of European Tula orthohantavirus (TULV). We analysed the very abrupt spatial transition between two major phylogenetic clades in TULV across the comparatively much wider natural hybrid zone between evolutionary lineages of their reservoir host, the common vole (Microtus arvalis). Genomic scans of 79,225 single nucleotide polymorphisms (SNPs) in 323 TULV‐infected host individuals detected 30 SNPs that were consistently associated with the TULV clades CEN.S or EST.S in two replicate sampling transects. Focusing the analysis on 199 voles with evidence of genomic admixture at the individual level (0.1–0.9) supported statistical significance for all 30 loci. Host genomic variation at these SNPs explained up to 37.6% of clade‐specific TULV infections. Genes in the vicinity of associated SNPs include SAHH, ITCH and two members of the Syngr gene family, which are involved in functions related to immune response or membrane transport. This study demonstrates the relevance of natural hybrid zones as systems not only for studying processes of evolutionary divergence and speciation, but also for the detection of evolving genetic barriers for specialized parasites.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas A White
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
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