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

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.

Epidemiological Aspects of Crimean-Congo Hemorrhagic Fever in Western Europe: What about the Future?

“…When 613 ticks from hunter harvested wild ungulates in South-western Spain in September-December 2017 were screened for CCHFV, different sequences within the genotype Europe V (commonly designated Europe-1) were detected in H. lusitanicum from deer and wild boar and in D. marginatus from wild boar (sequences similar to human isolates from Russia and Iran), probably introduced from eastern Europe. In addition, genotype Africa IV (designated genotype IIIb, Africa-4, according to Gruber et al [ 24 ]) was found in one H. lusitanicum from a deer (similar to an isolate from Nigeria), probably coming from Africa through migratory birds, as previously suggested [ 31 , 41 ]. Curiously, in more than one case, co-feeding CCHFV-infected ticks collected from the same ungulate host exhibited different genotypes [ 37 ].…”

“…Based on these data, the reassortant S segment was similar to genotype IV and related to a Nigeria strain that differed from the Asia strains of this genotype. Other authors [ 24 ] had already included this same S sequence from Spain within a new genotype designated IIIb (Africa-4). To reach a consensus about designation of genotypes, genetic linages and groups is a pending challenge.…”

“…Since increasing complete genomic sequences of CCHFV are becoming available, new viral classifications are appearing in the last years. Previously classified into six main geographical clades [ 6 ], up to nine genetically different clades are currently proposed for CCHFV, according to the phylogenetic analysis of the complete genetic sequence of the S RNA segment of the genome, and based on the geographical origin [ 24 ]. Four of them are predominantly distributed in Africa, two in Asia and three in Europe, as follows: Africa-1 (genotype I), Africa-2 (genotype II), Africa-3, (genotype IIIa) and Africa 4 (genotype IIIb); Asia-1 (genotype IVa) and Asia-2 (genotype IVb); Europe-1 (genotype V), Europe-2 (genotype VI) and Europe-3 (genotype VII) [ 24 ].…”

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir

“…ticks in India and China [ 7 , 8 ] has highlighted the need for a more complete genomic dataset in order to better understand the epidemiology of the virus, including viral transmission routes and the extent of re-assortment among genotypes. The potential for such re-assortment is particularly important, as many molecular tests for CCHFV are only capable of detecting a restricted number of closely related genotypes [ 9 ]. It also remains to be seen whether recently reported vaccine candidates, including one based on the S and M segments of the Hoti strain (genotype V) [ 10 ] and another based on the M segment of the IbAr102000 strain (genotype III) [ 11 ], can elicit a protective immune response against viruses belonging to other more distantly related genotypes.…”

Development of a novel recombinant ELISA for the detection of Crimean-Congo hemorrhagic fever virus IgG antibodies

“…The virus is transmitted to humans through a bite from an infected tick or direct contact with infected body fluids of patients. The ixodid tick Hyalomma m. marginatum , plays a major role for the transmission of the disease and it is the natural reservoir of CCHFV 1 – 4 . CCHF is a neglected disease and re-emerging due to the climate change effecting tick distribution worldwide 5 .…”