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Nippert S, Rubbenstroth D, Geers JA, Ebinger A, Hoffmann D, Breithaupt A, Wylezich C, Wang X, Haring VC, Starcky P, Fruci P, Langner C, Trapp C, Schulz H, Stubbe W, Imholt C, Heckel G, Beer M, Pfaff F, Ulrich RG. Continuous presence of genetically diverse rustrela virus lineages in yellow-necked field mouse reservoir populations in northeastern Germany. Virus Evol 2023; 9:vead048. [PMID: 37744713 PMCID: PMC10516363 DOI: 10.1093/ve/vead048] [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: 01/24/2023] [Revised: 06/14/2023] [Accepted: 07/26/2023] [Indexed: 09/26/2023] Open
Abstract
Rustrela virus (RusV; species Rubivirus strelense, family Matonaviridae) was discovered in different zoo animal species affected by fatal encephalitis. Simultaneous RusV RNA detection in multiple yellow-necked field mice (Apodemus flavicollis) suggested this rodent as a reservoir of RusV. Here, we investigated 1,264 yellow-necked field mice and sympatric other small mammals from different regions in Germany for RusV RNA using an optimized reverse transcription-quantitative polymerase chain reaction (RT-qPCR) protocol and high-throughput sequencing. The investigation resulted in the detection of RusV RNA exclusively in 50 of 396 (12.6 per cent) yellow-necked field mice but absence in other sympatric species. RT-qPCR-determined tissue distribution of RusV RNA revealed the highest viral loads in the central nervous system, with other tissues being only very rarely affected. The histopathological evaluation did not reveal any hints of encephalitis in the brains of infected animals despite the detection of viral RNA in neurons by in situ hybridization (ISH). The positive association between the body mass of yellow-necked field mice and RusV RNA detection suggests a persistent infection. Phylogenetic analysis of partial E1 and full-genome sequences showed a high diversification with at least four RusV lineages (1A-1D) in northeastern Germany. Moreover, phylogenetic and isolation-by-distance analyses indicated evolutionary processes of RusV mostly in local reservoir populations. A comparison of complete genome sequences from all detected RusV lineages demonstrated a high level of amino acid and nucleotide sequence variability within a part of the p150 peptide of the non-structural polyprotein and its coding sequence, respectively. The location of this region within the RusV genome and its genetic properties were comparable to the hypervariable region of the rubella virus. The broad range of detected RusV spillover hosts in combination with its geographical distribution in northeastern Germany requires the assessment of its zoonotic potential and further analysis of encephalitis cases in mammals. Future studies have to prove a putative co-evolution scenario for RusV in the yellow-necked field mouse reservoir.
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Affiliation(s)
- Sina Nippert
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Dennis Rubbenstroth
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Jessica Anna Geers
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstraße 6, Bern CH-3012, Switzerland
| | - Viola C Haring
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Philip Starcky
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Paola Fruci
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, Via Renato Balzarini 1, Teramo 64100, Italy
| | - Christoph Langner
- Stralsund Zoological Garden, Grünhufer Bogen 2, Stralsund 18437, Germany
| | - Christin Trapp
- Tierpark Grimmen, Friedrichstraße 20, Grimmen 18507, Germany
| | - Heiko Schulz
- Betriebsteil Forstplanung/Versuchswesen/Informationssysteme, Landesforst Mecklenburg-Vorpommern—Anstalt des öffentlichen Rechts, Zeppelinstraße 3, Schwerin 19061, Germany
| | - Wilko Stubbe
- Institut für Allgemeine und Systematische Zoologie, Universität Greifswald, Loitzer Straße 26, Greifswald 17489, Germany
| | - Christian Imholt
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Toppheideweg 88, Münster 48161, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstraße 6, Bern CH-3012, Switzerland
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Rainer G Ulrich
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research (DZIF), Germany
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Martin Cerezo ML, Kucka M, Zub K, Chan YF, Bryk J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq. BMC Genomics 2020; 21:241. [PMID: 32183700 PMCID: PMC7079423 DOI: 10.1186/s12864-020-6603-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Results Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Conclusion Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Karol Zub
- The Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | | | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Winter temperature correlates with mtDNA genetic structure of yellow-necked mouse population in NE Poland. PLoS One 2019; 14:e0216361. [PMID: 31067251 PMCID: PMC6505929 DOI: 10.1371/journal.pone.0216361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/18/2019] [Indexed: 11/19/2022] Open
Abstract
We analysed a fragment (247 bp) of cytochrome b of mitochondrial DNA sequenced using 353 samples of yellow-necked mice Apodemus flavicollis trapped in seven forests and along three woodlot transects in north-eastern Poland. Our aims were to identify the phylogeographic pattern and mtDNA structure of the population and to evaluate the role of environmental conditions in shaping the spatial pattern of mtDNA diversity. We found out that three European haplogroups occurred sympatrically in north-eastern Poland. Inferences based on mtDNA haplotype distribution and frequency defined five subpopulations. The mtDNA-based structure of mice significantly correlated with winter temperature: frequency of Haplogroup 1 was positively, and that of Haplogroup 3 negatively correlated to mean temperature of January in the year of trapping. Synthesis of the published pan-European data on the species phylogeography also showed that the possibly 'thermophilous' Haplogroup 1 has the westernmost occurrence, whereas the more 'cold-resistant' Haplogroup 3 occurs much further to north-east than the other haplogroups. The observed patter may be a byproduct of the tight coevolution with nuclear genes, as we have earlier found that - in mice population in NE Poland - the spatial pattern of nuclear DNA was best explained by January temperature. Alternatively, the observed association of mitochondrial genetic variation with temperature is possible to be adaptive as cytochrome b is involved in the process of ATP production via oxidative phosphorylation.
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Affiliation(s)
| | | | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Regional and local patterns of genetic variation and structure in yellow-necked mice - the roles of geographic distance, population abundance, and winter severity. Ecol Evol 2018; 8:8171-8186. [PMID: 30250693 PMCID: PMC6145024 DOI: 10.1002/ece3.4291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/01/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023] Open
Abstract
The goal of this study, conducted in seven large woodlands and three areas with small woodlots in northeastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harbored two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.
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Affiliation(s)
- Sylwia D. Czarnomska
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences (IBB PAS)WarszawaPoland
| | | | - Tomasz Borowik
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
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