Dates and Rates of Tick-Borne Encephalitis Virus-The Slowest Changing Tick-Borne Flavivirus. 2023

Artem N Bondaryuk, and Nina V Kulakova, and Olga I Belykh, and Yurij S Bukin
Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, 664047 Irkutsk, Russia.

We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.87 × 10-5 substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3-2.4 × 10-5 s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0-1.8 × 10-5 s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6-4.5 × 10-5 s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373-13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291-697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596-1112 years), LIV (2424 years; 95% HPD, 1572-3400 years), TBEV-FE (1936 years, 95% HPD, 1344-2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700-3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages.

UI MeSH Term Description Entries
D009711 Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed) Nucleotide
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D004669 Encephalitis Viruses, Tick-Borne A subgroup of the genus FLAVIVIRUS that causes encephalitis and hemorrhagic fevers and is found in eastern and western Europe and the former Soviet Union. It is transmitted by TICKS and there is an associated milk-borne transmission from viremic cattle, goats, and sheep. Hemorrhagic Fever Virus, Omsk,Kyasanur Forest disease virus,Langat virus,Louping ill virus,Omsk hemorrhagic fever virus,Powassan virus,Al-Khurma Hemorrhagic Fever Virus,Al-Khurma virus,Al-Khurma virus (ALKV),Alkhurma Hemorrhagic Fever Virus,Alkhurma virus,Alkhurma virus (ALKV),Encephalitis Virus, Tick-Borne,Tick-Borne Encephalitis Virus,Tick-Borne Encephalitis Viruses,Viruses, Tick-Borne Encephalitis,Al Khurma Hemorrhagic Fever Virus,Al Khurma virus,Al Khurma virus (ALKV),Encephalitis Virus, Tick Borne,Encephalitis Viruses, Tick Borne,Louping ill viruses,Tick Borne Encephalitis Virus,Tick Borne Encephalitis Viruses
D004675 Encephalitis, Tick-Borne Encephalitis caused by neurotropic viruses that are transmitted via the bite of TICKS. In Europe, the diseases are caused by ENCEPHALITIS VIRUSES, TICK-BORNE, which give rise to Russian spring-summer encephalitis, central European encephalitis, louping ill encephalitis, and related disorders. Powassan encephalitis occurs in North America and Russia and is caused by the Powassan virus. ASEPTIC MENINGITIS and rarely encephalitis may complicate COLORADO TICK FEVER which is endemic to mountainous regions of the western United States. (From Joynt, Clinical Neurology, 1996, Ch26, pp14-5) Far Eastern Russian Encephalitis,Powassan Encephalitis,Central European Encephalitis,Encephalitis, Central European,Encephalitis, European Tick-Borne,Encephalitis, Far Eastern Russian,Encephalitis, Louping Ill,Encephalitis, Russian Spring-Summer,European Tick-Borne Encephalitis,Louping Ill Encephalitis,Powassan Virus Disease,Russian Spring-Summer Encephalitis,Tick-Borne Encephalitis,Disease, Powassan Virus,Encephalitis, European Tick Borne,Encephalitis, Powassan,Encephalitis, Russian Spring Summer,Encephalitis, Tick Borne,European Tick Borne Encephalitis,Powassan Encephalitides,Powassan Virus Diseases,Russian Spring Summer Encephalitis,Spring-Summer Encephalitis, Russian,Tick Borne Encephalitis,Tick-Borne Encephalitis, European,Virus Disease, Powassan,Virus Diseases, Powassan
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D013987 Ticks Blood-sucking acarid parasites of the order Ixodida comprising two families: the softbacked ticks (ARGASIDAE) and hardbacked ticks (IXODIDAE). Ticks are larger than their relatives, the MITES. They penetrate the skin of their host by means of highly specialized, hooked mouth parts and feed on its blood. Ticks attack all groups of terrestrial vertebrates. In humans they are responsible for many TICK-BORNE DISEASES, including the transmission of ROCKY MOUNTAIN SPOTTED FEVER; TULAREMIA; BABESIOSIS; AFRICAN SWINE FEVER; and RELAPSING FEVER. (From Barnes, Invertebrate Zoology, 5th ed, pp543-44) Ixodida,Ixodidas,Tick

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