a tool for in-silico evaluation of molecular assays
Cesare E. M. Gruber (Author), Barbara Bartolini (Author), Concetta Castilletti (Author), Ali Mirazimi (Author), Roger Hewson (Author), Iva Christova (Author), Tatjana Avšič-Županc (Author), Roland Grunow (Author), Anna Papa (Author)

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.

Keywords

Crimean-Congo hemorrhagic fever;molecular detection;arthropodborne virus;

Data

Language: English
Year of publishing:
Typology: 1.01 - Original Scientific Article
Organization: UL MF - Faculty of Medicine
UDC: 616.9
COBISS: 34533081 Link will open in a new window
ISSN: 1999-4915
Views: 185
Downloads: 64
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Other data

Secondary language: Slovenian
Secondary keywords: krimsko-kongoška hemoragična mrzlica;molekularno odkrivanje;arbovirus;
Type (COBISS): Article
Pages: str. 1-13
Volume: ǂVol. ǂ11
Issue: ǂiss. ǂ10
Chronology: 2019
DOI: 10.3390/v11100953
ID: 13925515