Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns

Abstract

There is an increasing burden of circulating vaccine-derived polioviruses (cVDPVs) due to the continued use of oral poliovirus vaccine (OPV). However, the informativeness of routine OPV VP1 sequencing for the early identification of viruses carrying virulence-associated reversion mutations has not been directly evaluated in a controlled setting. We prospectively collected 15,331 stool samples to track OPV shedding from children receiving OPV and their contacts for ten weeks following an immunization campaign in Veracruz State, Mexico and sequenced VP1 genes from 358 samples. We found that OPV was genetically unstable and evolves at an approximately clocklike rate that varies across serotypes and by vaccination status. Overall, 61% (11/18) of OPV-1, 71% (34/48) OPV-2, and 96% (54/56) OPV-3 samples with available data had evidence of a reversion at the key 5' UTR attenuating position and 28% (13/47) of OPV-1, 12% (14/117) OPV-2, and 91% (157/173) OPV-3 of Sabin-like viruses had ≥1 known reversion mutations in the VP1 gene. Our results are consistent with previous work documenting rapid reversion to virulence of OPV and underscores the need for intensive surveillance following OPV use.

Fig. 1. The increasing global burden of vaccine-derived poliovirus.

a Confirmed cases of paralytic polio were reported to the World Health Organization from 2000-2022. Color indicates source: circulating vaccine derived poliovirus (cVDPV) and wild poliovirus cases. b Map of countries reporting cVDPV cases from 2020-2022; fill indicates number of cVDPV cases identified. Data from the World Health Organization.

Fig. 2. Prospective study of OPV shedding among NHW vaccinees, household members, and community members following a vaccination campaign.

a Map of Mexico with Veracruz State highlighted and Orizaba city, where the study took place, indicated with a red point. b We conducted a prospective observational study of OPV viral shedding following a vaccination campaign. 148 children were enrolled and vaccinated with trivalent OPV. The stool was collected from NHW vaccinees, unvaccinated household members, and community members in unvaccinated households. We extracted RNA from stool samples, tested samples with OPV serotype-specific RT-PCR, and Sanger sequenced positive samples.

Fig. 3. Limited overall genetic diversity in sampled OPV viral capsid protein 1 (VP1) gene following vaccination campaigns.

For each OPV serotype and sampling site, haplotype networks of OPV VP1 represent sampled genetic diversity. Nodes indicate identical haplotypes (VP1 consensus sequences) and node size indicates the number of samples sharing a haplotype. Points on edges between nodes indicate the SNP distance between haplotypes and node colors indicate an individual’s vaccination status. Labels indicate OPV serotype and study site. Site C Capoluca, had 70% vaccination coverage of eligible children, site CG Campo Grande: 30%, site T Tuxpanguillo: 10%. One sample with a distant haplotype (>14 SNPs distant to the Sabin vaccine) was removed from OPV-2 site C, to aid visualization.

Fig. 4. Measurable evolution in the OPV VP1 gene following vaccination campaigns.

Genetic distance of the OPV VP1 gene to the Sabin vaccine strain versus time from vaccination for NHW vaccinees (blue) and not vaccinated study participants, including household contacts and unvaccinated community members (red), for each OPV serotype (a-c). Black lines and grey shading of a linear model for distance to the Sabin strain. Days following vaccination is measured as days from the first vaccination (for NHW vaccinees), day from the first household vaccination (for household members), and days from the first community vaccination (for other community members). Red dashed lines indicate the genetic distance threshold for a VDPV: 10 SNPs distant from the Sabin vaccine for serotypes 1 and 3 and 6 SNPs distant for serotype 2.

Fig. 5. Moderate genetic structure of OPV VP1 gene from samples shed two months following vaccination campaigns.

The proportion of pairs of OPV VP1 sequences within a given, binned pairwise genetic distance for pairs of samples collected longitudinally from the same individual, from the same household, different households within the same community, or outside the community, i.e. pairs of samples from different communities. Facets indicate OPV serotype.

Fig. 6. Loss of OPV attenuating mutations following vaccination.

For each serotype, points indicate the revertant proportion, the proportion of samples with a mutation at a key attenuating position in OPV in the weeks following vaccination. Bars indicate the total number of sequences available for that sampling week. Each serotype has unique attenuating sites.