Genetic Variations in Crimean‐Congo Hemorrhagic Fever Virus: Challenges for Molecular Diagnostic Assays—A Case Report

<b>Background:</b> Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne viral disease with a high mortality rate which is endemic in Iran. Laboratory diagnosis of CCHF is routinely conducted using PCR and IgM ELISA tests. However, nucleotide variations within CCHF virus (CCHFV) may lead to false-negative PCR results. <b>Case Presentation:</b> A 51-year-old patient suspected to have CCHF was tested for CCHFV infection using two different molecular assays. The results were discrepant, as our homemade SYBR green-based real-time PCR yielded a strong positive result, while the RealStar CCHFV RT-PCR Kit returned a negative result. Due to the discrepancies in the real-time PCR tests, a homemade conventional RT-PCR method was performed, resulting in a positive result similar to the SYBR green-based real-time PCR assay. Partial sequencing of S segment of viral genome and phylogenetic analysis revealed that the strain clustered with a strain from Africa-3 genotype, which was isolated in Namibia in 1987. CCHF antigen and IgM ELISA also confirmed the CCHFV infection in this case. <b>Conclusions:</b> This report underlines the requirement of CCHFV genomic surveillance to update the molecular diagnostic assays. Moreover, the circulation of an African CCHFV strain in Iran supports previous data suggesting that Iran harbors the greatest CCHFV genetic diversity among endemic countries. Discrepancies in PCR results, likely due to this diversity, may hinder timely diagnosis and subsequently affect patient management and treatment measures.