Phenotypic and genetic changes of Crimean-Congo hemorrhagic fever virus during serial passage in susceptible cell lines

Background Single-stranded RNA viruses such as the Crimean-Congo hemorrhagic fever virus (CCHFV) exhibit a high degree of genetic diversity that can result in the emergence of new viral quasispecies. The aim of this study was to examine the kinetics of CCHFV replication and to identify genetic variations resulting from serial passage in susceptible cell lines that could potentially affect the infectivity and fitness of laboratory virus strains. As efficacy studies of candidate therapeutics and vaccines rely on well-characterized virus stocks, mutations emerging due to virus propagation might result in inaccurate test results. Methods Viral growth kinetics were examined in four cell lines (Vero E6, Vero, SW13, and BHK-21), using different multiplicity-of-infection values. After 10 rounds of serial passaging and cross-passaging, whole-genome sequencing and bioinformatic analysis were performed to map growth-adaptive signature mutations. Results All four cell lines were found to be susceptible to CCHFV infection, and permissivity increased during serial passaging in Vero and BHK-21 cells. Mutations emerged in a cell-line-specific manner, and the particular cell line used for virus propagation had a significant effect on the mutation frequency, especially in the L segment. Conclusions By mapping mutations that occurred during serial passage, we were able to observe viral evolution in a controlled laboratory setting, as well as the accompanying phenotypic changes. Our results provide information about how CCHFV adapts to commonly used cell lines that might be applied for the development of diagnostic tests, antiviral drugs, and vaccines.