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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 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
Externally publishedYes


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

ASJC Scopus subject areas

  • Parasitology
  • Infectious Diseases


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