Genetic Background of Adaptation of Crimean-Congo Haemorrhagic Fever Virus to the Different Tick Hosts

B.Sc. Seyma Celina, BSc

Diplomová práce

Abstract:

Crimean-Congo haemorrhagic fever (CCHF) has become one of the most geographically widely distributed tick-borne viral diseases in the world. Its causative agent, Crimean-Congo haemorrhagic fever virus (CCHFV), is among the deadliest human pathogens in Africa and Eurasia. CCHFV is transmitted mainly by tick species in Hyalomma genus, particularly by H. marginatum in Europe, but other tick species such as representatives of genera Dermacentor and Rhipicephalus are also involved in virus transmission. The framework of this thesis consists of three main parts. Firstly, it was focused to understand the evolutionary adaptation of CCHFV to Hyalomma and Rhipicephalus tick species. Study of tick collection from livestock in Kosovo and from birds in Czechia and investigate possible presence of CCHFV was the second focus of the thesis. The Balkan region is considered to be highly endemic region for CCHF. On the other hand, risk areas for tick presence occur in all regions of Czechia. Moreover, migratory birds play an important role in the distribution of CCHFV vectors into Czechia. Tick collection, thus, was carried out in these countries to collect Hyalomma species and screen for CCHFV presence. Apart from migratory birds, other factors such as climate change and international animal trade might influence the expansion of H. marginatum, the principal vector of CCHFV, in Europe. Up to the present, there are sporadic occurrences of this tick species in all countries of Central Europe except Czechia. In this regard, the final part of this thesis was focused on ecological niche modeling analysis to map the environmental suitability of H. marginatum in Europe, with a focus on Central Europe. In order to better understand the evolutionary characteristics of the virus and general codon usage pattern in CCHFV strains isolated from different tick hosts, effective number of codons (ENC) and the GC-content at the 3rd codon position (GC3) of synonymous codons were calculated. Analysis of ENC and GC3 shows that Hyalomma- and Rhipicephalus-isolated CCHFV strains use different codons. The same result is apparent from correspondence analysis (COA) and supports the results of ENC and GC3 analysis. Furthermore, codon adaptation index (CAI) analysis was performed which is a widely used technique for analyzing codon usage bias in order to measure the adaptation of the virus. CAI analysis showed that Rhipicephalus-isolated strains are more adapted for using codons which are being preferred by Hyalomma species and the same for Hyalomma-isolated strains. Results of the study indicate that the CCHFV adaptation to the different tick hosts supports the effect of evolutionary processes on codon usage patterns of the virus. In relation to tick collection, in total 171 ticks were collected from livestock in Kosovo in August 2020 and from birds in Czechia in September-October 2020. H. marginatum dominated in Kosovo, while Ixodes ricinus was the majority of collection in Czechia. No viral RNA was detected in collected ticks, suggesting seasonality of the CCHF might be related with tick abundance and activity. Ecological niche modeling analysis and the predictions of H. marginatum in our model depicts medium suitability for the occurrence of H. marginatum in many regions of southern and northern parts of Czechia. The results of this work gave us new information regarding the adaptation of CCHFV to different tick vector species and gain insight into transmission dynamics of the virus. Besides, collecting tick species in Kosovo and Czechia was highly important to screen the possible presence of the virus. Moreover, the results of this work were highly valuable for possible establishment of Hyalomma species in Czechia and making inferences regarding the virus transmission for the future.

Keywords

Crimean-Congo haemorrhagic fever virus, molecular evolution, codon usage bias, ecological niche modeling, Hyalomma, Rhipicephalus

Jazyk práce: angličtina

Datum vytvoření / odevzdání či podání práce: 23. 4. 2021

Obhajoba závěrečné práce

• Vedoucí: RNDr. Jiří Černý, Ph.D.

Česká zemědělská univerzita v Praze

Fakulta tropického zemědělství

Magisterský studijní program / specializace:
Wildlife and Livestock Production, Management and Conservation / Wildlife Management and Conservation