Development of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)

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dc.authoridD'Addiego, Jake/0000-0003-2249-2942
dc.contributor.authorD'Addiego, Jake
dc.contributor.authorShah, Sonal
dc.contributor.authorPektas, Ayse Nur
dc.contributor.authorBagci, Binnur Koksal
dc.contributor.authorOz, Murtaza
dc.contributor.authorSebastianelli, Sasha
dc.contributor.authorElaldi, Nazif
dc.date.accessioned2024-10-26T18:11:05Z
dc.date.available2024-10-26T18:11:05Z
dc.date.issued2024
dc.departmentSivas Cumhuriyet Üniversitesi
dc.description.abstractCrimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis. Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage. We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages. CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.
dc.description.sponsorshipUK Health Security Agency (UKHSA) [119N515]; Medical Research Council [MR/T029196/1]; Defence Threat Reduction Agency (DTRA) [HDTRA12110024]; UK Aid from the Department of Health and Social Care and is jointly run by the UK Health Security Agency; London School of Hygiene and Tropical Medicine; UK Health Security Agency [113371]
dc.description.sponsorshipThe study was part of a joint project (Newton-TUBITAK Katip Celebi) between the UK Health Security Agency (UKHSA) and Tuerkiye (project no: 119N515) . This work was also supported by the Medical Research Council (grant number MR/T029196/1) , Grant-in-Aid UK Health Security Agency (grant number 113371) and the Defence Threat Reduction Agency (DTRA, grant number BAA #HDTRA12110024) . The UK Public Health Rapid Support Team is funded by UK Aid from the Department of Health and Social Care and is jointly run by the UK Health Security Agency and the London School of Hygiene and Tropical Medicine. The views expressed are those of the authors and not necessarily those of the funding bodies or the Department of Health and Social Care.
dc.identifier.doi10.1016/j.virusres.2024.199464
dc.identifier.issn0168-1702
dc.identifier.issn1872-7492
dc.identifier.pmid39270938
dc.identifier.scopus2-s2.0-85204468577
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1016/j.virusres.2024.199464
dc.identifier.urihttps://hdl.handle.net/20.500.12418/30504
dc.identifier.volume350
dc.identifier.wosWOS:001321566800001
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherElsevier
dc.relation.ispartofVirus Research
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectCCHFV
dc.subjectProbe hybridisation capture
dc.subjectNext-generation sequencing
dc.subjectTargeted
dc.subjectenrichment
dc.titleDevelopment of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)
dc.typeArticle

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