Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan
Tick-borne encephalitis virus (TBEV) is the most prevalent tick-borne viral disease in Europe and Asia. There are three main subtypes of the virus: European, Siberian, and Far Eastern, each of which having distinctive ecology, clinical presentation, and geographic distribution. In recent years, othe...
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Elsevier
2025-01-01
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| Series: | Virus Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0168170224002107 |
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| author | Jake D'Addiego Mollie Curran-French Jack Smith Asankadyr T Junushov Irena Breininger Barry Atkinson John Hay Roger Hewson |
| author_facet | Jake D'Addiego Mollie Curran-French Jack Smith Asankadyr T Junushov Irena Breininger Barry Atkinson John Hay Roger Hewson |
| author_sort | Jake D'Addiego |
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| description | Tick-borne encephalitis virus (TBEV) is the most prevalent tick-borne viral disease in Europe and Asia. There are three main subtypes of the virus: European, Siberian, and Far Eastern, each of which having distinctive ecology, clinical presentation, and geographic distribution. In recent years, other TBEV subtypes have been described, namely the Himalayan and Baikalian subtypes. Differences in virulence between TBEV subtypes have been described, with the Far Eastern subtype causing the most severe disease in humans. Considering the emergence of new TBEV foci, the genetic characterisation of the virus in endemic regions is crucial to not only better understand its epidemiology, but also to identify possible genetic determinants of virulence, as well as develop accurate diagnostics and therapeutics.In our previous study, we identified TBEV in six localities of the Kyrgyz Republic (Kyrgyzstan), and Ala-Archa National Nature Park as a focus of TBEV transmission. Whilst we were able to retrieve the first partial TBEV sequence from Kyrgyzstan from Ixodes persulcatus ticks, we were unable to retrieve a complete genome sequence at that time.In this study, we have utilised a sequence-independent single-primer amplification (SISPA) protocol and retrieved the complete genome sequence of our previous 2009 TBEV tick sample (strain KY09) producing the third complete TBEV genome from Kyrgyzstan, and the first genome from the region clustering within the Vasilchenko lineage, suggesting a wider distribution for the lineage than was previously thought.We have also developed a tiling amplicon scheme for Siberian TBEV (TBEV-Sib) which produced > 90 % reference coverage at 100x sequencing depths for samples with as little as 1.13×104 RNA copies/ml. Since high viral loads are rare in TBEV clinical samples, the developed protocol adds value to TBEV-Sib endemic regions by offering a novel set of primers to further amplify the viral genome prior to sequencing. |
| format | Article |
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| institution | Kabale University |
| issn | 1872-7492 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
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| series | Virus Research |
| spelling | doaj-art-c922573648ed4e73a0914e63805670fb2025-01-09T06:12:15ZengElsevierVirus Research1872-74922025-01-01351199517Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in KyrgyzstanJake D'Addiego0Mollie Curran-French1Jack Smith2Asankadyr T Junushov3Irena Breininger4Barry Atkinson5John Hay6Roger Hewson7UK Health Security Agency, Science Group, Porton Down, Salisbury, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Corresponding author at: UK Health Security Agency, Science Group, Porton Down, Salisbury, UK.UK Health Security Agency, Science Group, Porton Down, Salisbury, UK; Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections, Institute of Infection and Veterinary and Ecological Science, University of Liverpool, Liverpool, UKUK Health Security Agency, Science Group, Porton Down, Salisbury, UKNational Academy of Sciences of the Kyrgyz Republic, Bishkek, Kyrgyz RepublicMinistry of Healthcare of the Kyrgyz Republic, Bishkek, Kyrgyz RepublicUK Health Security Agency, Science Group, Porton Down, Salisbury, UKState University of New York, Buffalo, NY, USAUK Health Security Agency, Science Group, Porton Down, Salisbury, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections, Institute of Infection and Veterinary and Ecological Science, University of Liverpool, Liverpool, UKTick-borne encephalitis virus (TBEV) is the most prevalent tick-borne viral disease in Europe and Asia. There are three main subtypes of the virus: European, Siberian, and Far Eastern, each of which having distinctive ecology, clinical presentation, and geographic distribution. In recent years, other TBEV subtypes have been described, namely the Himalayan and Baikalian subtypes. Differences in virulence between TBEV subtypes have been described, with the Far Eastern subtype causing the most severe disease in humans. Considering the emergence of new TBEV foci, the genetic characterisation of the virus in endemic regions is crucial to not only better understand its epidemiology, but also to identify possible genetic determinants of virulence, as well as develop accurate diagnostics and therapeutics.In our previous study, we identified TBEV in six localities of the Kyrgyz Republic (Kyrgyzstan), and Ala-Archa National Nature Park as a focus of TBEV transmission. Whilst we were able to retrieve the first partial TBEV sequence from Kyrgyzstan from Ixodes persulcatus ticks, we were unable to retrieve a complete genome sequence at that time.In this study, we have utilised a sequence-independent single-primer amplification (SISPA) protocol and retrieved the complete genome sequence of our previous 2009 TBEV tick sample (strain KY09) producing the third complete TBEV genome from Kyrgyzstan, and the first genome from the region clustering within the Vasilchenko lineage, suggesting a wider distribution for the lineage than was previously thought.We have also developed a tiling amplicon scheme for Siberian TBEV (TBEV-Sib) which produced > 90 % reference coverage at 100x sequencing depths for samples with as little as 1.13×104 RNA copies/ml. Since high viral loads are rare in TBEV clinical samples, the developed protocol adds value to TBEV-Sib endemic regions by offering a novel set of primers to further amplify the viral genome prior to sequencing.http://www.sciencedirect.com/science/article/pii/S0168170224002107TBEVWhole-genome sequencingMolecular surveillanceTargeted enrichmentTick-borne viruses |
| spellingShingle | Jake D'Addiego Mollie Curran-French Jack Smith Asankadyr T Junushov Irena Breininger Barry Atkinson John Hay Roger Hewson Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan Virus Research TBEV Whole-genome sequencing Molecular surveillance Targeted enrichment Tick-borne viruses |
| title | Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan |
| title_full | Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan |
| title_fullStr | Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan |
| title_full_unstemmed | Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan |
| title_short | Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan |
| title_sort | whole genome sequencing surveillance of siberian tick borne encephalitis virus tbev identifies an additional lineage in kyrgyzstan |
| topic | TBEV Whole-genome sequencing Molecular surveillance Targeted enrichment Tick-borne viruses |
| url | http://www.sciencedirect.com/science/article/pii/S0168170224002107 |
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