Genetic diversity of Crimean Congo hemorrhagic fever virus strains from Iran

Sadegh Chinikar, Saeid Bouzari, Mohammad Ali Shokrgozar, Ehsan Mostafavi, Tahmineh Jalali, Sahar Khakifirouz, Norbert Nowotny, Anthony R. Fooks, Nariman Shah-Hossein

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18 Citations (Scopus)


Background: Crimean Congo hemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family and Nairovirus genus. It has a negative-sense, single stranded RNA genome approximately 19.2 kb, containing the Small, Medium, and Large segments. CCHFVs are relatively divergent in their genome sequence and grouped in seven distinct clades based on S-segment sequence analysis and six clades based on M-segment sequences. Our aim was to obtain new insights into the molecular epidemiology of CCHFV in Iran. Methods: We analyzed partial and complete nucleotide sequences of the S and M segments derived from 50 Iranian patients. The extracted RNA was amplified using one-step RT-PCR and then sequenced. The sequences were analyzed using Mega5 software. Results: Phylogenetic analysis of partial S segment sequences demonstrated that clade IV-(Asia 1), clade IV-(Asia 2) and clade V-(Europe) accounted for 80 %, 4 % and 14 % of the circulating genomic variants of CCHFV in Iran respectively. However, one of the Iranian strains (Iran-Kerman/22) was associated with none of other sequences and formed a new clade (VII). The phylogenetic analysis of complete S-segment nucleotide sequences from selected Iranian CCHFV strains complemented with representative strains from GenBank revealed similar topology as partial sequences with eight major clusters. A partial M segment phylogeny positioned the Iranian strains in either association with clade III (Asia-Africa) or clade V (Europe). Conclusion: The phylogenetic analysis revealed subtle links between distant geographic locations, which we propose might originate either from international livestock trade or from long-distance carriage of CCHFV by infected ticks via bird migration.

Original languageEnglish
Pages (from-to)127-140
Number of pages14
JournalJournal of Arthropod-Borne Diseases
Issue number2
Publication statusPublished - 2016


  • Iran
  • Molecular epidemiology
  • Phylogeny
  • Reassortant virus
  • RT-PCR

ASJC Scopus subject areas

  • Parasitology
  • Infectious Diseases

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    Chinikar, S., Bouzari, S., Shokrgozar, M. A., Mostafavi, E., Jalali, T., Khakifirouz, S., Nowotny, N., Fooks, A. R., & Shah-Hossein, N. (2016). Genetic diversity of Crimean Congo hemorrhagic fever virus strains from Iran. Journal of Arthropod-Borne Diseases, 10(2), 127-140.