Next generation sequencing of DNA-launched Chikungunya vaccine virus

• Published in: Virology (New York, N.Y.) Vol. 490; pp. 83 - 90
• Main Authors: Hidajat, Rachmat, Nickols, Brian, Forrester, Naomi, Tretyakova, Irina, Weaver, Scott, Pushko, Peter
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2016
• Subjects: 60 APPLIED LIFE SCIENCES; Alphavirus; Base Sequence; Chikungunya fever; Chikungunya Fever - virology; Chikungunya virus; Chikungunya virus - genetics; Chikungunya virus - isolation & purification; CHIKV; DNA; DNA vaccine; High-Throughput Nucleotide Sequencing - methods; Humans; IN VITRO; IN VIVO; Infectious Disease; Live attenuated vaccine; Molecular Sequence Data; MUTATIONS; NUCLEOTIDES; PLASMIDS; Polymorphism, Single Nucleotide; RNA; VACCINES; Vaccines, DNA - genetics; Vaccines, DNA - immunology; Viral Vaccines - genetics; VIRUSES; DNA vaccine; Alphavirus; Chikungunya fever; Live attenuated vaccine; CHIKV; Chikungunya virus
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1016/j.virol.2016.01.009

Abstract Chikungunya virus (CHIKV) represents a pandemic threat with no approved vaccine available. Recently, we described a novel vaccination strategy based on iDNA® infectious clone designed to launch a live-attenuated CHIKV vaccine from plasmid DNA in vitro or in vivo . As a proof of concept, we prepared iDNA plasmid pCHIKV-7 encoding the full-length cDNA of the 181/25 vaccine. The DNA-launched CHIKV-7 virus was prepared and compared to the 181/25 virus. Illumina HiSeq2000 sequencing revealed that with the exception of the 3′ untranslated region, CHIKV-7 viral RNA consistently showed a lower frequency of single-nucleotide polymorphisms than the 181/25 RNA including at the E2-12 and E2-82 residues previously identified as attenuating mutations. In the CHIKV-7, frequencies of reversions at E2-12 and E2-82 were 0.064% and 0.086%, while in the 181/25, frequencies were 0.179% and 0.133%, respectively. We conclude that the DNA-launched virus has a reduced probability of reversion mutations, thereby enhancing vaccine safety.