Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis?
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Sample Selection and Its Effect on the Ancestry Inference Estimates
3.2. Suitability of TBEV Genomic Data for Molecular Clock Analysis
3.3. Phylogenetic Analysis
3.4. Population Dynamics
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Strain | Nearest Neighbor in Terms of Genetic Distance (Nearly Identical Sequences from the Same Place Were Omitted) | Nt Sequence Identity between Strain of Interest and Its Nearest Neighbor, % | Approximate Direct Air Distance, km | tMRCA (95% HPD) |
---|---|---|---|---|
EUR | ||||
Eu3 MH663428 Russia Moscow 2017 | Eu3 JQ654701 Slovenia 1992 | 98.1 | 2000 | 1681 (1228–1799) |
Eu3 MK801803 Finland 2005 | Eu3 JF501414 Czech Republic 1986 | 99,3 | 1300 | 1876 (1541–1937) |
Eu3 AF091007 France Alsace 1975 | Eu3 JF501408 Czech Republic 1978 | 99,4 | 500 | 1898 (1745–1950) |
Eu3 AJ319583 Latvia 1997 | Eu3 MH704574 Germany Battaune 2017 | 99,91 | 950 | 1967 (1882–1996) |
Eu3 KY069126 Russia Altai 1986 | Eu3 AF091005 Russia Saint Petersburg 1951 | 99.91 | 3200 | 1934 (1851–1951) |
Eu3 MH021184 Netherlands 2016 | Eu3 AF091005 Russia Saint Petersburg 1951 | 98.39 | 1750 | 1624 (814–1793) |
Eu3 KJ994330 Italy 2013 | Eu3 AF091005 Russia Saint Petersburg 1951 | 99.43 | 1900 | 1724 (1468–1836) |
SIB | ||||
Sib3 KF826916 Russia Sakhalin 2011 | Sib3 KC422663 Russia Chita 2000 | 100.00 | 2200 | 1993 (1973–2000) |
Sib1 FJ214123 Russia Ekaterinburg 2006 | Sib1 FJ214145 Russia Yaroslavl 2001 | 98.54 | 1200 | 1855 (1699–1940) |
Sib1 GQ845418 Russia Ekaterinburg 2009 | Sib1 Baltic GQ845439 Russia Yaroslavl 2008 | 98.73 | 1200 | 1883 (1764–1057) |
Sib1 FJ214131 Russia Kurgan 2007 | Sib1 FJ214153 Russia Vologda 2007 | 99.90 | 1600 | 1995 (1956–2007) |
Sib1 KY319395 Russia Kurgan 2010 | Sib1 GQ845440 Russia Yaroslavl 2008 | 100.00 | 1600 | 2003 (1986–2008) |
Sib2 GQ845427 Russia Ekaterinburg 2009 | Sib2 MG598843 Russia Novosibirsk 2013 | 98.86 | 1400 | 1873 (1751–1944) |
Sib2 FJ214150 Russia Kurgan 2007 | Sib2 FJ214137 Russia Vologda 1975 | 98.10 | 1600 | 1882 (1766–1956) |
Sib2 AF527415 Russia Tomsk Zausaev 1985 | Sib2 KR633032 Russia Kirov 2012 | 98.54 | 2100 | 1757 (1560–1875) |
Sib2 JF274481 Mongolia Bulgan 2010 | Sib2 MG598825 Russia Novosibirsk 2011 | 98.01 | 1700 | 1756 (1543–1879) |
Sib2 KC417475 Russia Irkutsk 2010 | Sib2 KR633015 Russia Kemerovo 2014 | 98.39 | 1200 | 1872 (1741–1952) |
Sib2 MF161158 Russia Irkutsk 2015 | Sib2 GQ845421 Russia Ekaterinburg 2009 | 99.05 | 2800 | 1863 (1741–1933) |
Sib3 KF826916 Russia Sakhalin 2011 | Sib3 KC422663 Russia Chita 2000 | 100.00 | 2200 | 1993 (1972–2000) |
FE | ||||
Fe2 LC440460 Japan-Nanporo 2018 | Fe2 GU121642 Russia Vladivostok 2008 | 98.96 | 800 | 1946 (1884–1989) |
Fe3 JX987281 Russia Khabarovsk 1973 | Fe3 KJ739731 Russia Tomsk Sorex araneus 2006 | 100.00 | 3400 | 1949 (1916–1969) |
Fe3 FJ214120 Russia Ekaterinburg 1959 | Fe3 KJ739731 Russia Tomsk Sorex araneus 2006 | 99.43 | 1500 | 1898 (1831–1944) |
Fe3 AF091008 Ukraine 1987 | Fe3 AY169390 Russia Prymorye Prymorye-332 human blood 1991 | 99.53 | 7300 | 1905 (1850–1951) |
Fe4 LC440459 Japan- Sapporo Ixodes ovatus 2017 | Fe4 KP869172 Russia-Khabarovsk 1985 | 97.91 | 780 | 1810 (1639–1927) |
Fe4 DQ393779 Estonia Laanemaa 1996 | Fe4 AB049345 Russia-Vladivostok 1999 | 98.48 | 6900 | 1835 (1725–1919) |
Fe4 FJ214119 Russia Ekaterinburg 1943 | Fe4 FJ214119 Russia- SaintPetersburg 1943 | 99.81 | 1800 | 1924 (1901–1940) |
Fe4 FJ214147 Russia Yaroslavl 1989 | Fe4 AF091013 Russia Vladivostok 1979 | 99.72 | 6200 | 1954 (1917–1977) |
Fe4 AF091016 Latvia 1977 | Fe4 FJ214133 Russia Kemerovo 1967 | 99.72 | 3700 | 1961 (1948–1967) |
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Deviatkin, A.A.; Kholodilov, I.S.; Vakulenko, Y.A.; Karganova, G.G.; Lukashev, A.N. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses 2020, 12, 247. https://doi.org/10.3390/v12020247
Deviatkin AA, Kholodilov IS, Vakulenko YA, Karganova GG, Lukashev AN. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses. 2020; 12(2):247. https://doi.org/10.3390/v12020247
Chicago/Turabian StyleDeviatkin, Andrei A., Ivan S. Kholodilov, Yulia A. Vakulenko, Galina G. Karganova, and Alexander N. Lukashev. 2020. "Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis?" Viruses 12, no. 2: 247. https://doi.org/10.3390/v12020247