Summary auto-generated
This study provides evidence for recombination in Crimean-Congo hemorrhagic fever (CCHF) virus, a tick-borne pathogen with 15-80% human fatality rate found across Africa, Asia, and Europe. The researcher analyzed available full-length sequences of the virus's three RNA segments (S, M, and L) using multiple phylogenetic methods including similarity plots, bootscan analysis, hidden Markov models, and probabilistic divergence measures. Strong evidence of recombination was found in the S segment, with multiple recombination events detected between geographically distant CCHF strains from southern Europe, Asia, and Africa. However, no unambiguous recombination signals were detected in the M and L segments, though the analysis did not exclude the possibility. The findings suggest these recombination events occurred in the distant past, likely facilitated by co-infection in tick vectors or other hosts. The author emphasizes that previous phylogenetic studies based on short S segment sequences (200-250 nucleotides) may be unreliable for assessing CCHF virus evolution, particularly given concurrent evidence of genome reassortment. The results indicate a global CCHF virus reservoir with local sub-reservoirs, likely maintained through migrant birds translocating infected ticks across regions.
Key findings
- Strong evidence of recombination was detected in the CCHF virus S segment involving multiple geographically distant strains, though M and L segments showed inconclusive results.
- Phylogenetic trees of different S segment regions showed conflicting topologies, with different strains acting as outgroups in various regions, consistent with recombination events.
- Recombination events appear to be phylogenetically ancient, occurring between the most distant CCHF virus strains from distant geographic locations.
- Previous phylogenetic studies using short S segment sequences (200-250 nt) may be unreliable; comprehensive molecular studies should utilize all three segments and full S segment sequences.
- The evidence of both recombination and reassortment in CCHF virus suggests the existence of a global viral reservoir with frequent co-infections, implying potential emergence of genetically and serologically novel variants.
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Abstract
Crimean-Congo hemorrhagic fever (CCHF) virus has attracted considerable attention recently and a number of phylogenetic studies have been published, based mostly on partial sequences of S and M RNA segments. In this study, available full-length S, M and L segment sequences of CCHF virus were checked for recombination. Similarity plots and bootscan analysis of the S segment suggested multiple recombination events between southern European, Asian and African CCHF virus strains, with additional evidence provided by phylogenetic trees, the hidden Markov model and probabilistic divergence measures methods. No unambiguous signs of recombination were observed for M and L segments; however, the results did not exclude the possibility of this. These findings, coupled with a recent report on reassortment in CCHF virus, suggest caution when assessing CCHF virus phylogeny based on short sequence fragments.