Engineering attenuated virus vaccines by controlling replication fidelity

Abstract

Long-lasting protection against viral infection is best achieved by vaccination with attenuated viruses. Obtaining stably attenuated vaccine strains has traditionally been an empirical process, which greatly restricts the number of effective vaccines for viral diseases. Here we describe a rational approach for engineering stably attenuated viruses that can serve as safe and effective vaccines. Our approach exploits the observation that restricting viral population diversity by increasing replication fidelity greatly reduces viral tissue tropism and pathogenicity. We show that poliovirus variants with reduced genetic diversity elicit a protective immune response in an animal model of infection. Indeed, these novel vaccine candidates are comparable in efficacy to the currently available Sabin type 1 vaccine strain, but have the added advantage of being more stable, as their increased replication fidelity prevents reversion to the pathogenic wild-type phenotype. We propose that restricting viral quasispecies diversity provides a general approach for the rational design of stable, attenuated vaccines for a wide variety of viruses.

Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA

“…Eight mutations were detected in 45,000 bases of sequence data from wild-type virion RNA, corresponding to an average of 1.33 mutations per genome. Only two mutations were detected in 45,000 bases of sequence data from G64S virion RNA, corresponding to 0.33 mutation per genome, consistent with the previously reported impact of the G64S mutation on the fidelity of RNA replication (31). The R128A and L420A 3D pol mutations had no significant impact on the fidelity of RNA replication compared to that in wild-type 3D pol (Table 4).…”

“…The fidelity of RNA replication is reported to influence the quasispecies diversity and the pathogenesis of poliovirus infections (27). A G64S mutation in 3D pol renders poliovirus resistant to ribavirin (25), increases the fidelity of RNA replication (26), and attenuates poliovirus replication in mice (26,27,31). Similar fidelity effects are also seen for a K359R mutation that subtly alters a key charged residue that contacts and helps to position the gamma phosphate of the incoming NTP (47).…”

“…It is important to note, however, that HeLa cells are extremely permissive host cells that do not reveal every important, biologically relevant phenotype. For instance, a G64S 3D pol mutation has little impact on the specific infectivity of poliovirus RNA or the replication of poliovirus in HeLa cells (Table 1); however, this mutation has a dramatic impact on the replication and pathogenesis of poliovirus in animal models (26,27,31). Thus, the biological significance of slightly longer or shorter poly(A) tails in poliovirus RNA is yet to be determined.…”

Amino acid residues Ala283 and His421 in the RNA-dependent RNA polymerase of porcine reproductive and respiratory syndrome virus play important roles in viral ribavirin sensitivity and quasispecies diversity

“…One crucial mechanism of the high mutation rate for RNA viruses is the low fidelity of RNA-dependent RNA polymerase (RdRp) due to its lack of proofreading ability during RNA replication (Domingo & Holland, 1997;Smith et al, 2013). Studies of poliovirus and other RNA viruses revealed that certain amino acid residues in RdRp are fidelity checkpoints which affect the fidelity of RdRp, and that the fidelity of RdRp can be modulated by change of these checkpoint residues (Gnädig et al, 2012;Rozen-Gagnon et al, 2014;Sadeghipour et al, 2013;Vignuzzi et al, 2008;Zeng et al, 2014). Mutants carrying a high fidelity RdRp showed a decreased population quasispecies diversity and attenuated pathogenicity to hosts (Van Slyke et al, 2015).…”

“…Mutants carrying a high fidelity RdRp showed a decreased population quasispecies diversity and attenuated pathogenicity to hosts (Van Slyke et al, 2015). Therefore, high fidelity virus mutants could serve as potential safer modified live-attenuated vaccines (MLVs) for RNA viruses (Vignuzzi et al, 2008).…”