Genetic features of Orthonairovirus haemorrhagiae variants detected in ixodid ticks in Armenia

Abstract

INTRODUCTION: Crimean-Congo hemorrhagic fever (CCHF) is a viral transmissible febrile disease, featuring hemorrhagic manifestations and a high mortality rate, caused by Orthonairovirus haemorrhagiae (CCHFV). CCHF is endemic in the Republic of Armenia (RA) and neighboring countries. Currently, there is no genetic information on CCHFV circulating in the RA. This work presents the results of genetic identification of CCHF viral variants detected in ixodid ticks collected in 2022-2023. METHODOLOGY: Ixodid ticks were collected from cattle, horses, and vegetation in seven Armenian regions (Vayots Dzor, Gegharkunik, Kotayk, Lori, Syunik, Tavush, Shirak). Tick pools were tested for the presence of CCHFV RNA by RT-PCR. Genetic identification of CCHFV isolates was performed based on partial and complete genomic segment sequencing (S, M, L). RESULTS: Of 860 total tick pools, 77 were positive for CCHFV RNA. Such RNA was detected in Hyalomma marginatum (n = 71), Haemaphysalis punctate (n = 2), Ixodes ricinus (n = 2), Rhipicephalus bursa (n = 2). CCHFV circulation was confirmed in the Syunik and Tavush regions. Phylogenetic analysis based on partial and full-length genomic segments showed that CCHFV strains of the Europe 1 and Europe 3 lineages circulated in the RA. Within the Europe 1 lineage, Armenian viral isolates belonged to different genetic subgroups: Vb, strains of which are widespread in the south of the European region of Russia; and new subgroups (Armenia-1, Armenia-2). Genomic segment reassortment events were revealed in the analyzed CCHFV sequences. CONCLUSION: This study provides new data on CCHFV genetic diversity in the RA. Further genetic studies of CCHFV circulating in countries of the Transcaucasian region are necessary to reconstruct the temporal and spatial viral distribution.