Geographical variability affects CCHFV detection by RT-PCR : a tool for in-silico evaluation of molecular assays

Gruber, Cesare E. M. (author), Bartolini, Barbara (author), Castilletti, Concetta (author), Mirazimi, Ali (author), Hewson, Roger (author), Christova, Iva (author), Avšič-Županc, Tatjana (author), Grunow, Roland (author), Papa, Anna (author), Sánchez-Seco, María P. (author), Koopmans, Marion (author), Ippolito, Giuseppe (author), Capobianchi, Maria Rosaria (author), Reusken, Chantal B. E. M. (author), Di Caro, Antonino (author)

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
• UDC: 616.9
• ISSN on article: 1999-4915
• DOI: 10.3390/v11100953
• COBISS.SI-ID: 34533081
• Publication date in RUL: 12.11.2021

Record is a part of a journal

• Title: Viruses
• Shortened title: Viruses
• Publisher: MDPI
• ISSN: 1999-4915
• COBISS.SI-ID: 517597977

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