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Open AccessArticle

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

1
National Institute for Infectious Diseases (INMI) “L. Spallanzani” IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy
2
Public Health agency of Sweden, 17182 Solna, Sweden
3
National veterinary Institute, 75189 Uppsala, Sweden
4
Department of laboratory Medicine, Clinical Microbiology, Karolinska Institute and Karolinska, 17177 Stockholm, Sweden
5
Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens) Porton Down, Salisbury SP40JG, UK
6
National Reference Laboratory on Vector-Borne Pathogens, Leptospira and Listeria, Microbiology Department, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria
7
Faculty of Medicine, Institute of Microbiology and Immunology, 1000 Ljubljana, Slovenia
8
Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany
9
Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
10
National Centre of Microbiology, Institute of Health “Carlos III”, Majadahonda, 28220 Madrid, Spain
11
Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands
12
Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(10), 953; https://doi.org/10.3390/v11100953
Received: 8 October 2019 / Accepted: 15 October 2019 / Published: 16 October 2019
(This article belongs to the Special Issue Emerging Arboviruses)
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. View Full-Text
Keywords: CCHFV; molecular detection; Crimean–Congo hemorrhagic fever virus; arthropod-borne virus; laboratory preparedness; emerging diseases CCHFV; molecular detection; Crimean–Congo hemorrhagic fever virus; arthropod-borne virus; laboratory preparedness; emerging diseases
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Gruber, C.E.M.; Bartolini, B.; Castilletti, C.; Mirazimi, A.; Hewson, R.; Christova, I.; Avšič, T.; Grunow, R.; Papa, A.; Sánchez-Seco, M.P.; Koopmans, M.; Ippolito, G.; Capobianchi, M.R.; Reusken, C.B.E.M.; Di Caro, A. Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays. Viruses 2019, 11, 953.

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