Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir

Abstract

Crimean-Congo hemorrhagic fever virus (CCHFV) is the most geographically widespread of the tick-borne viruses. However, African strains of CCHFV are poorly represented in sequence databases. In addition, almost all sequence data collected to date have been obtained from cases of human disease, while information regarding the circulation of the virus in tick and animal reservoirs is severely lacking. Here, we characterize the complete coding region of a novel CCHFV strain, detected in African blue ticks (Rhipicephalus (Boophilus) decoloratus) feeding on cattle in an abattoir in Kampala, Uganda. These cattle originated from a farm in Mbarara, a major cattle-trading hub for much of Uganda. Phylogenetic analysis indicates that the newly sequenced strain belongs to the African genotype II clade, which predominantly contains the sequences of strains isolated from West Africa in the 1950s, and South Africa in the 1980s. Whilst the viral S (nucleoprotein) and L (RNA polymerase) genome segments shared >90% nucleotide similarity with previously reported genotype II strains, the glycoprotein-coding M segment shared only 80% nucleotide similarity with the next most closely related strains, which were derived from ticks in Western India and Northern China. This genome segment also displayed a large number of non-synonymous mutations previously unreported in the genotype II strains. Characterization of this novel strain adds to our limited understanding of the natural diversity of CCHFV circulating in both ticks and in Africa. Such data can be used to inform the design of vaccines and diagnostics, as well as studies exploring the epidemiology and evolution of the virus for the establishment of future CCHFV control strategies.

Mutational analysis of catalytic site domain of CCHFV L RNA segment

“…: YP_325663.1) was generated and clustered into genotypes. Reference sequence belongs to genotype III [ 35 ] and it was observed that sequences belonging to genotype III showed less divergence from reference sequence (Fig. 1 ), whereas genotype V sequences have shown large evolutionary distance.…”

“…CCHFV genome has three RNA segments (L, M and S segment) with fatality rate of 10–40% and has been classified into six genotypes based on their geographical predominance [ 35 , 40 ]. Phylogenetic tree developed with 107 sequences represented less divergence among the sequences belonging to same CCHFV genotypes and results were in concordance with studies reported in the literature [ 8 , 9 , 35 , 41 ]. NCBI reference sequence (Accession No.…”

Prevalence of Crimean-Congo haemorrhagic fever in livestock following a confirmed human case in Lyantonde district, Uganda

“…In Uganda, previous reports have indicated that over 65% of human cases in the country occur among animal handlers [ 25 ]. Evidence of CCHFV prevalence in humans and ticks has been documented in this and other studies [ 26 – 28 ]; however, serosurvey of CCHF in livestock either as part of a viral haemorrhagic fever surveillance program or during outbreaks has not been well described. We report a very high CCHFV seroprevalence in both cattle and goats during an ongoing outbreak, with no interspecies statistical differences, in an area associated with a fatal human infection.…”

Advances and perspectives in the development of vaccines against highly pathogenic bunyaviruses

“…For instance, 15 deaths from 480 cases (3%) in Turkey during 2020, and 19 deaths from 37 cases (51%) in India during 2019 ( Kuehnert et al., 2021 ), but the general case fatality rate is usually considered to be around 30% ( Sanchez et al., 2002 ; Papa et al., 2017 ; Tipih et al., 2021 ; Hawman and Feldmann, 2023 ). The envelope glycoproteins Gn and Gc of CCHFV are known to be the main immunogen and possess neutralizing epitopes, but some of these neutralizing epitopes not always conserved due to the genetic diversity of CCHFV ( Ahmed et al., 2005 ; Wampande et al., 2021 ). Meanwhile, as a more conserved domain, NP could also be used as a target antigen against CCHFV ( Karaaslan et al., 2021 ).…”