Identification of cellular inhibitors against Chikungunya virus replication by a cDNA expression cloning combined with MinION sequencing

• Published in: Biochemical and biophysical research communications 2020-10, Vol.530 (4), p.617-623
• Main Authors: Sakaguchi, Shoichi, Suzuki, Youichi, Emi, Akino, Wu, Hong, Nakano, Takashi
• Format: Article
• Language: English
• Subjects: cDNA expression cloning; Cell Line; Chikungunya Fever - genetics; Chikungunya Fever - virology; Chikungunya virus; Chikungunya virus - physiology; Dodecenoyl-CoA Isomerase - genetics; ECI1; Gene Library; High-Throughput Nucleotide Sequencing; Host-Pathogen Interactions; Humans; Membrane Proteins - genetics; MinION sequence; Mitochondrial Proteins - genetics; Mutation; S100 Proteins - genetics; S100A16; TOM7; Up-Regulation; Virus Replication
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2020.07.036

cDNA expression cloning has been shown to be a powerful approach in the search for cellular factors that control virus replication. In this study, cDNA library screening using a pool of cDNA derived from interferon-treated human cells was combined with the MinION sequencer to identify cellular genes inhibiting Chikungunya virus (CHIKV) replication. Challenge infection of CHIKV to Vero cells transduced with the cDNA library produced virus-resistant cells. Then, the MinION sequence of cDNAs extracted from the surviving cells revealed that the open reading frames of TOM7, S100A16, N-terminally truncated form of ECI1 (ECI1ΔN59), and RPL29 were inserted in many of the cells. Importantly, the transient expression of TOM7, S100A16, and ECI1ΔN59 was found to inhibit the replication of CHIKV in Huh7 cells, indicating that these cellular factors were potentially anti-CHIKV molecules. Thus, our study demonstrated that cDNA expression cloning combined with the MinION sequencer allowed a rapid and comprehensive detection of cellular inhibitors against CHIKV. •cDNA expression cloning was combined with a next-generation MinION sequencer.•This strategy successfully identified human genes inhibiting CHIKV replication.•Over-expression of TOM7, S100A16, and an ECI1 mutant suppressed CHIIV infection.•This combined approach was useful for the identification of antiviral factors.