J Vector Borne Dis 53, December 2016, pp. 384–386
Genetic evidence for circulation of Kunjin-related West Nile virus strain in Iran
Nariman Shahhosseini
1& Sadegh Chinikar
21Department of Virology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany; 2Pasteur Institute of Tehran, Iran
Key words Iran; Kunjin strain; Phylogenetic; West Nile virus
West Nile virus (WNV) is a mosquito-borne flavivirus of the Japanese encephalitis virus antigenic group. The WNV genome encodes three structural and seven nonstructural proteins1. WNV strains are grouped in 9 lineages. Lineage 1 is subdivided into two clades, clade 1A is formed by widespread strains and clade 1B by Aus- tralian WNV Kunjin strains. Lineage 2 is mainly distrib- uted in Sub-Sahara Africa, but since the beginning of the 21st century, it has also been observed in Europe. Lin- eage 3 “Rabensburg” contains a strain circulating in Culex pipiens mosquitoes in the Czech Republic. Lineage 4 (strain LEIVKrnd88–190) is represented by a strain iso- lated from Dermacentor marginatus ticks from the Caucasus in 1998. Lineage 5 contains a WNV isolate from India (strain 804994). Lineage 6 contains a Malaysian Kunjin virus, which is genetically different from other Kunjin viruses2. The African Koutango virus is closely related to WNV and considered as lineage 7. Lineage 8 consists of WNV strains, which were detected in Cx.
pipiens mosquitoes collected in Spain in 20063. WNV lineage 9 has been detected in Uranotaenia unguiculata mosquitoes from Austria in 20134.
In order to get a deeper understanding of WNV cir- culation in Iran, several studies have investigated the pres- ence of WNV in mosquito reservoirs5–6. Bagheri et al6 reported the detection of WNV in mosquitoes collected from wetlands in the northwest of Iran during the year 2015. A total of 2143 specimens were collected. Six mos- quito species were identified including Anopheles maculipennis, Cx. hortensis, Cx. pipiens, Cx. theileri, Culiseta longiareolata, and Ochlerotatus caspius. Mos- quitoes were pooled in 45 groups, and then screened for WNV by RT-PCR. West Nile virus-RNA was found in two mosquito pools of Oc. caspius. These positive WNV samples were partially sequenced (252-bp corresponds to nt 10465–10717 in 3'-untranslated region) and then deposited to GenBank under accession numbers KP168714 and KP1687157. A genomic analysis was,
however, not conducted. The main objective of this com- mentary article was to carry out phylogenetic analysis of these two WNV sequences, to provide an insight into their molecular epidemiology.
The data set used for the analyses comprised of a to- tal of 62 WNV sequences; which included two WNV se- quences previously obtained from mosquito samples in northwestern Iran, and 60 globally representative isolates, covering all lineages of WNV, retrieved from public da- tabase, GenBank. Alignment was performed using the MAFFT algorithm, and initial phylogenetic tree was de- veloped by Geneious v 7.1.8. Similar sequences with the same isolation year and country were omitted from the original set of 62 sequences, resulting in a dataset consisting of 22 sequences with known time (year), isolation source and geographical origin (country) of detection, combined with one Japanese encephalitis virus (JEV) as an out-group. Final alignment was per- formed and a phylogenetic tree was subsequently con- structed by using the neighbour-joining algorithm in Geneious v 7.1.8.
The blast result of two Iranian WNV sequences de- rived from mosquitoes in GenBank indicated 94% se- quence identity value (100% query cover) with Kunjin virus from Australia. The developed phylogenetic tree indicated the grouping of these two WNV sequences in the clade 1B of lineage 1, demonstrating a close relation- ship (97% bootstrap value supporting branching) with WNV Kunjin strains from Australia (Fig. 1).
Understanding the molecular epidemiology of WNV is essential for the development and implementation of surveillance strategies for its control. In this regard, an earlier phylogenetic study on a WNV sequence (acces- sion number: KJ486150) derived from a encephalitic pa- tient in central Iran indicated a grouping of the Iranian WNV sample into lineage 2 with 99% identity within the 358-bp region, which corresponds to nt 259–616 in the late region of the capsid gene and the early region of the
Shahhosseiniet al: Kunjin virus emergence in Iran 385
membrane gene, of WNV strain ArB3573/82 from the central African Republic8.
Unlike the previous report by Shah-Hosseini et al8, this study reports the detection of the WNV Kunjin strain in mosquito samples previously collected from the north- western Iran for the first time, far beyond their supposed restricted geographic distribution9–10. Although, Kunjin strain from Sarawak, Malaysia has been previously observed outside Australia, it is genetically distinguish- able from Australian WNV Kunjin and named as the 6th lineage9.
The tree topology presented in this study is supported by other phylogenetic studies reporting the same overall topology for WNV phylogenetic tree based on full ge- nome compared with partial sequences of C, NS5, and 3'-untranslated region2, 11. In addition, a considerable num- ber of WNV sequences available at GenBank are classi- fied as Australian Kunjin strains based on partial se-
Fig. 1: Phylogenetic tree of WNV strains was developed on a 252-bp by using the neighbour-joining algorithm in Geneious v 7.1.8. The two sequences discussed in this study are in bold. The numbers above the branches indicate the bootstrap values in percentages of 1000 replicates. Japanese encephalitis virus (JEV) was used as an out-group. CAR is the abbreviation for Central African Republic.
quences of 3'-untranslated region. Additional mosquito collections and WNV screening in Iran is necessary in order to provide a clear picture of the molecular epidemi- ology of WNV in Iran.
ACKNOWLEDGEMENTS
The authors thank Dr Renke Lühken and Dr Mayke Leggewie for their suggestions and comments that im- proved the manuscript.
Conflict of interest
No conflicts of interest exist.
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Correspondence to: Mr Nariman Shahhosseini, Bernhard Nocht Strasse 74, 20359, Hamburg, Germany.
E-mail: [email protected]
Received: 12 April 2016 Accepted in revised form: 14 September 2016
