Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays

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 hamper...

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Bibliographic Details
Published in:Viruses 2019-10, Vol.11 (10), p.953
Main Authors: Gruber, Cesare E. M., Bartolini, Barbara, Castilletti, Concetta, Mirazimi, Ali, Hewson, Roger, Christova, Iva, Avšič, Tatjana, Grunow, Roland, Papa, Anna, Sánchez-Seco, María P., Koopmans, Marion, Ippolito, Giuseppe, Capobianchi, Maria R., Reusken, Chantal B. E. M., Di Caro, Antonino
Format: Article
Language:English
Subjects:
Arachnids
arthropod-borne virus
Binding sites
Bioinformatics
cchfv
Crimean hemorrhagic fever
crimean–congo hemorrhagic fever virus
Data collection
DNA probes
emerging diseases
Epidemics
Genetic variability
Genomes
Genomics
Geographical distribution
Geography
Hemorrhage
Infections
Infectious diseases
laboratory preparedness
Medicin och hälsovetenskap
molecular detection
Phylogenetics
Software
Strains (organisms)
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Summary: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.
ISSN:1999-4915
1999-4915
DOI:10.3390/v11100953