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Geographical variability affects CCHFV detection by RT-PCR : a tool for in-silico evaluation of molecular assays
ID Gruber, Cesare E. M. (Author), ID Bartolini, Barbara (Author), ID Castilletti, Concetta (Author), ID Mirazimi, Ali (Author), ID Hewson, Roger (Author), ID Christova, Iva (Author), ID Avšič-Županc, Tatjana (Author), ID Grunow, Roland (Author), ID Papa, Anna (Author), ID Sánchez-Seco, María P. (Author), ID Koopmans, Marion (Author), ID Ippolito, Giuseppe (Author), ID Capobianchi, Maria Rosaria (Author), ID Reusken, Chantal B. E. M. (Author), ID Di Caro, Antonino (Author)

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Abstract
The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.

Language:English
Keywords:Crimean-Congo hemorrhagic fever, molecular detection, CCHFV, Crimean–Congo hemorrhagic fever virus, arthropod-borne virus, laboratory preparedness, emerging diseases
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:MF - Faculty of Medicine
Publication status:Published
Publication version:Version of Record
Year:2019
Number of pages:14 str.
Numbering:Vol. 11, iss. 10, art. 953
PID:20.500.12556/RUL-133136 This link opens in a new window
UDC:616.9
ISSN on article:1999-4915
DOI:10.3390/v11100953 This link opens in a new window
COBISS.SI-ID:34533081 This link opens in a new window
Publication date in RUL:12.11.2021
Views:663
Downloads:130
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Record is a part of a journal

Title:Viruses
Shortened title:Viruses
Publisher:MDPI
ISSN:1999-4915
COBISS.SI-ID:517597977 This link opens in a new window

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:16.10.2019

Secondary language

Language:Slovenian
Keywords:krimsko-kongoška hemoragična mrzlica, molekularno odkrivanje, arbovirus

Projects

Funder:Other - Other funder or multiple funders
Funding programme:Italian Ministry of Health, Ricerca Corrente–Linea 1

Funder:EC - European Commission
Project number:677066
Name:Efficient response to highly dangerous and emerging pathogens at EU level
Acronym:EMERGE

Funder:EC - European Commission
Funding programme:EVD-LabNet
Project number:ECDC/2016/00

Funder:EC - European Commission
Funding programme:H2020
Project number:653316
Name:European Virus Archive goes global
Acronym:EVAg

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