TBEV Analyzer: a Platform for Evolutionary Analysis of Tick-borne Encephalitis Virus

Forghani, Majid; Kovalev, Sergey Y.; Vasev, Pavel; Bolkov, Mikhail A.

doi:10.1109/sibircon48586.2019.8958021

Cited by 4 publications

(3 citation statements)

References 19 publications

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“…Evolutionary rates were determined based on a previously described molecular clock rate of 5.96 × 10 −5 substitutions per site per year with a standard deviation of 6.6 × 10 −6 [ 32 ]. Furthermore, TBEV Analyzer was utilized for the subtype classification of the genome [ 33 ].…”

Section: Methodsmentioning

confidence: 99%

Molecular Detection and Phylogenetic Analysis of Tick-Borne Encephalitis Virus from Ticks Collected from Cattle in Kyrgyzstan, 2023

Jung,

Choi,

Lee

et al. 2024

Viruses

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Ticks are important vectors of the tick-borne encephalitis virus (TBEV). In Kyrgyzstan, the livestock farming trade and nomadic lifestyle enable tick-borne diseases to be imported from neighboring countries, but there are few relevant studies. In this study, we collected 40 ticks from cattle in Kyrgyzstan. Molecular marker analysis identified the ticks as Ixodes persulcatus (97.5%; n = 39) and Haemaphysalis punctata (2.5%; n = 1). Real-time PCR screening revealed two ticks to be positive for TBEV, but only one tick was amplified using nested PCR targeting the TBEV envelope (E) and non-structure 5 (NS5) gene. The obtained sequences belonged to the TBEV Siberian subtype and phylogenetic tree analysis results confirmed that the virus was related to the Bosnia strain. We also performed next-generation sequencing, which confirmed the TBEV Siberian subtype. Continuous research and surveillance of TBEV in Kyrgyzstan are required to provide further information on tick-borne diseases.

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Section: Methodsmentioning

confidence: 99%

Molecular Detection and Phylogenetic Analysis of Tick-Borne Encephalitis Virus from Ticks Collected from Cattle in Kyrgyzstan, 2023

Jung,

Choi,

Lee

et al. 2024

Viruses

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“…According to our computational pipeline, assigning a clusteron to a query requires verification at the nucleotide and amino acid levels. The overall schema of our pipeline was described previously [ 19 , 23 ], and is illustrated (with adjustment) in Figure 1 .…”

Section: Methodsmentioning

confidence: 99%

“…The lack of a dedicated platform for studying TBEV evolution motivated us to develop the first version of the TBEV analyzer in 2019 [ 19 ]. The primary goal of the project was to create a standard, integrated, and interactive platform for TBEV population analysis based on the Clusteron Approach (CA) [ 6 , 20 ], yet with the ability to monitor external genetic resources, e.g., GenBank [ 21 ], for emerging novel phylogenetic strain groups and TBEV natural foci population dynamics.…”

Section: Introductionmentioning

confidence: 99%

Identifying New Clusterons: Application of TBEV Analyzer 3.0

et al. 2023

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Early knowledge about novel emerging viruses and rapid determination of their characteristics are crucial for public health. In this context, development of theoretical approaches to model viral evolution are important. The clusteron approach is a recent bioinformatics tool which analyzes genetic patterns of a specific E protein fragment and provides a hierarchical network structure of the viral population at three levels: subtype, lineage, and clusteron. A clusteron is a group of strains with identical amino acid (E protein fragment) signatures; members are phylogenetically closely related and feature a particular territorial distribution. This paper announces TBEV Analyzer 3.0, an analytical platform for rapidly characterizing tick-borne encephalitis virus (TBEV) strains based on the clusteron approach, workflow optimizations, and simplified parameter settings. Compared with earlier versions of TBEV Analyzer, we provide theoretical and practical enhancements to the platform. Regarding the theoretical aspect, the model of the clusteron structure, which is the core of platform analysis, has been updated by analyzing all suitable TBEV strains available in GenBank, while the practical enhancements aim at improving the platform’s functionality. Here, in addition to expanding the strain sets of prior clusterons, we introduce eleven novel clusterons through our experimental results, predominantly of the European subtype. The obtained results suggest effective application of the proposed platform as an analytical and exploratory tool in TBEV surveillance.

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TBEV analyzer platform for evolutionary analysis and monitoring tick-borne encephalitis virus: 2020 update

Forghani

Kovalev

Bolkov

et al. 2021

Biostatistics & Epidemiology

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TBEV Analyzer: a Platform for Evolutionary Analysis of Tick-borne Encephalitis Virus

Cited by 4 publications

References 19 publications

Molecular Detection and Phylogenetic Analysis of Tick-Borne Encephalitis Virus from Ticks Collected from Cattle in Kyrgyzstan, 2023

Molecular Detection and Phylogenetic Analysis of Tick-Borne Encephalitis Virus from Ticks Collected from Cattle in Kyrgyzstan, 2023

Identifying New Clusterons: Application of TBEV Analyzer 3.0

TBEV analyzer platform for evolutionary analysis and monitoring tick-borne encephalitis virus: 2020 update

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