Dynamics of Evolution of Poliovirus Neutralizing Antigenic Sites and Other Capsid Functional Domains during a Large and Prolonged Outbreak

Abstract

We followed the dynamics of capsid amino acid replacement among 403 Nigerian outbreak isolates of type 2 circulating vaccine-derived poliovirus (cVDPV2) from 2005 through 2011. Four different functional domains were analyzed: 1) neutralizing antigenic (NAg) sites, 2) residues binding the poliovirus receptor (PVR), 3) VP1 residues 1-32, and 4) the capsid structural core. Amino acid replacements mapped to 37 of 43 positions across all 4 NAg sites; the most variable and polymorphic residues were in NAg sites 2 and 3b. The most divergent of the 120 NAg variants had no more than 5 replacements in all NAg sites, and were still neutralized at titers similar to those of Sabin 2. PVR-binding residues were less variable (25 different variants; 0-2 replacements/isolate; 30/44 invariant positions), with the most variable residues also forming parts of NAg sites 2 and 3a. Residues 1-32 of VP1 were highly variable (133 different variants; 0-6 replacements/isolate; 5/32 invariant positions), with residues 1-18 predicted to form a well-conserved amphipathic helix. Replacement events were dated by mapping them onto the branches of time-scaled phylogenies. Rates of amino acid replacement varied widely across positions and followed no simple substitution model. Replacements into the structural core were the most conservative and were fixed at an overall rate ∼20-fold lower than rates for the NAg sites and VP1 1-32, and ∼5-fold lower than the rate for the PVR-binding sites. Only VP1-143-Ile, a non-NAg site surface residue and known attenuation site, appeared to be under strong negative selection. The high rate of poliovirus evolution is offset by strong selection against amino acid replacement at most positions of the capsid. Consequently, poliovirus vaccines developed from strains isolated decades ago have been used worldwide to bring wild polioviruses almost to extinction. The apparent antigenic stability of poliovirus obscures a dynamic of continuous change within the neutralizing antigenic (NAg) sites. During seven years of a large outbreak in Nigeria, the circulating type 2 vaccine-derived polioviruses generated 120 different NAg site variants via multiple independent pathways. Nonetheless, overall antigenic evolution was constrained, as no isolate had fixed more than 5 amino acid differences from the Sabin 2 NAg sites, and the most divergent isolates were efficiently neutralized by human immune sera. Evolution elsewhere in the capsid was also constrained. Amino acids binding the poliovirus receptor were strongly conserved, and extensive variation in the VP1 amino terminus still conserved a predicted amphipathic helix.

The early evolution of oral poliovirus vaccine is shaped by strong positive selection and tight transmission bottlenecks

“…Not all capsid antigenic sites may be involved in this process. There can be frequent amino acid substitution at many antigenic sites in the OPV2 capsid, often reverting back to previous replacements, suggesting that some sites are more tolerant to mutation and evolve more by genetic drift than selection (11). However, our results indicate that a subset of these capsid sites experience positive selection and likely have functional effects related to improved replication and transmission within the human host.…”

“…Similarly, phylogenetic studies have yielded important insights into the evolution and epidemiology of cVDPV, but may not be able to infer selective advantage of mutations with weaker effects due to limitations in sampling or statistical power. Whereas, previous phylogenetic work on cVDPV2 found only limited evidence for positive selection at VP3-77 and VP1-222, they appear to be strongly selected within hosts (9,11). Finally, it is important to recognize that phylogenetic studies may differ in the fitness effects they reveal due to differences in time and scale.…”

“…Mutations in the capsid enable adaptation to replication at physiologic temperatures, and could provide increased structural stability or modulate receptor binding and viral entry (15,47). Although some of the capsid sites identified here are recognized by neutralizing antibodies (11,48), there is little evidence that these mutations lead to antigenic escape, as they do in influenza virus or HIV (49). Even highly diverged cVDPV strains with significant antigenic site evolution are still neutralized by serum from vaccinated individuals (11), and vaccination with OPV is used to control outbreaks of cVDPV (6).…”

“…Although some of the capsid sites identified here are recognized by neutralizing antibodies (11,48), there is little evidence that these mutations lead to antigenic escape, as they do in influenza virus or HIV (49). Even highly diverged cVDPV strains with significant antigenic site evolution are still neutralized by serum from vaccinated individuals (11), and vaccination with OPV is used to control outbreaks of cVDPV (6). Rather than antigenic escape, we suggest that these mutations lead to improved within-host replication, and therefore greater shedding and transmission.…”

“…The emergence of cVDPV is a recurrent evolutionary process that exhibits a high degree of parallel, or convergent, evolution. Most data on cVDPV come from poliovirus isolates in cases of acute flaccid paralysis or environmental surveillance (9)(10)(11)(12). A recent study of type 2 cVDPV sequences from multiple outbreaks in five countries identified a limited number of sites under positive selection across independent lineages (9).…”