Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays
Cesare E. M. Gruber,
Barbara Bartolini,
Concetta Castilletti,
Ali Mirazimi,
Roger Hewson,
Iva Christova,
Tatjana Avšič,
Roland Grunow,
Anna Papa,
María P. Sánchez-Seco,
Marion Koopmans,
Giuseppe Ippolito,
Maria R. Capobianchi,
Chantal B. E. M. Reusken,
Antonino Di Caro
Affiliations
Cesare E. M. Gruber
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
Barbara Bartolini
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
Concetta Castilletti
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
Ali Mirazimi
Public Health agency of Sweden, 17182 Solna, Sweden
Roger Hewson
Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens) Porton Down, Salisbury SP40JG, UK
Iva Christova
National Reference Laboratory on Vector-Borne Pathogens, Leptospira and Listeria, Microbiology Department, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria
Tatjana Avšič
Faculty of Medicine, Institute of Microbiology and Immunology, 1000 Ljubljana, Slovenia
Roland Grunow
Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany
Anna Papa
Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
María P. Sánchez-Seco
National Centre of Microbiology, Institute of Health “Carlos III”, Majadahonda, 28220 Madrid, Spain
Marion Koopmans
Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands
Giuseppe Ippolito
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
Maria R. Capobianchi
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
Chantal B. E. M. Reusken
Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands
Antonino Di Caro
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
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.
