A novel bacterium-free approach for rapid assembly of flavivirus infectious cDNAs using circular polymerase extension reaction was applied to generate infectious cDNA for the virulent New South Wales isolate of the Kunjin strain of West Nile virus (KUNV) that recently emerged in Australia. Recovered virus recapitulated the genetic heterogeneity present in the original isolate. The approach was utilized to generate viral mutants with designed phenotypic properties and to identify E protein glycosylation as one of the virulence determinants.
Generation of flavivirus infectious clones has been traditionally hindered by the toxicity of their full-length cDNAs in bacteria. Various approaches have been employed to overcome this problem, including the use of very-low-copy-number plasmids (1, 2), bacterial artificial chromosomes (3), cosmid vectors (4), specific Escherichia coli strains (5, 6), mutation of cryptic bacterial promoter sites in the flavivirus genome (7), separation of the genome into two plasmids followed by in vitro ligation and RNA transcription (8)(9)(10)(11)(12), and use of a yeast recombination system to assemble full-length clones (13,14). All of these approaches require substantial efforts, are time-consuming, and are prone to introducing undesired mutations during amplification of plasmid DNA in bacteria and during in vitro RNA transcription by bacteriophage DNA-dependent RNA polymerases (T7 or SP6). A bacterium-free approach involving either in vitro ligation of two large overlapping cDNA fragments generated by reverse transcription and PCR (RT-PCR) or linking these two large cDNA fragments by fusion PCR was developed for tick-borne encephalitis virus (TBEV) (15). The resulting product containing the SP6 RNA polymerase promoter upstream of TBEV sequence was then used to produce RNA by in vitro transcription and virus was recovered by injecting in vitro-transcribed RNA into the brain of suckling mice. This approach allows rapid generation of infectious cDNA without a need for plasmid DNA amplification in bacteria; however, it still requires an in vitro RNA transcription step as well as the highly sensitive suckling mouse model to recover infectious virus. The former is prone to introduction of undesired mutations, and the latter is not applicable for flaviviruses that do not replicate well in mice (e.g., dengue viruses). We and others have previously developed infectious cDNA clones for West Nile virus (WNV) and Japanese encephalitis virus (JEV) in which the in vitro RNA transcription step is eliminated by replacing SP6 or T7 polymerase promoters with the cytomegalovirus (CMV) promoter, thus allowing transcription of viral RNA in cells directly from plasmid DNAs by the cellular RNA polymerase II (16-18). Although an infectious cDNA clone for the Kunjin strain of West Nile virus (KUNV) has been demonstrated to be relatively stable, further manipulations, including mutagenesis could render it less stable (A. Khromykh, unpublished results). To solve the problem of stability for CMV-based JEV and WNV i...