Viral metagenomics, genetic and evolutionary characteristics of Crimean-Congo hemorrhagic fever orthonairovirus in humans, Kosovo.

Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) is a tick-borne virus which causes severe disease in humans with fatality cases up to 30%. We investigated the genetic and evolutionary characteristics of CCHFV in Kosovo, in particular in humans and found that different virus variants of genotype V circulate, with Turkey as a possible origin for the progenitor of southern European CCHF outbreaks. Phylogenetic analyses also revealed a single introduction event and in situ evolution of CCHFV in this country. The viral metagenomics revealed a more abundant virome in the fatal CCHF cases and the presence of a novel tick-borne segmented RNA virus belonging to the recently discovered Jingmenvirus group which raises questions about the potential pathogenic effect of this novel virus on human and animal health.