Genetic Diversity of Crimean Congo Hemorrhagic Fever Virus Strains from Iran.
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).


CONCLUSIONS
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.
Arboviruses and Viral Hemorrhagic Fevers Laboratory (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran.
Sadegh
S
Chinikar
Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran.
Saeid
S
Bouzari
National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran.
Mohammad Ali
MA
Shokrgozar
Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.
Ehsan
E
Mostafavi
Arboviruses and Viral Hemorrhagic Fevers Laboratory (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran.
Tahmineh
T
Jalali
Arboviruses and Viral Hemorrhagic Fevers Laboratory (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran.
Sahar
S
Khakifirouz
Institute of Virology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria.
Norbert
N
Nowotny
Animal Health and Veterinary Laboratories Agency, Wildlife Zoonoses and Vector-Borne Diseases Research Group, Weybridge, New Haw, Addlestone, Surrey, United Kingdom.
Anthony R
AR
Fooks
Arboviruses and Viral Hemorrhagic Fevers Laboratory (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran.
Nariman
N
Shah-Hosseini
CCHFV; Iran; Molecular epidemiology; Phylogeny; RT-PCR; Reassortant virus