Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns
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 vaccinated children 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. Alarmingly, 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 mutation. Our results suggest that current definitions of cVDPVs may exclude circulating virulent viruses that pose a public health risk and underscore the need for intensive surveillance following OPV use.
- scripts/ includes scripts to reproduce analyses discussed in the paper
- processed/aln/opv1_aln_to_ref.fasta, opv21_aln_to_ref.fasta, opv31_aln_to_ref.fasta: aligned samples to full reference sequence
- data/metadata includes required metadata for analysis and data dictionary
- data/who includes formatted metadata from the WHO extranet (https://extranet.who.int/polis/public/CaseCount.aspx), including both global and country-level reported cases from 2000-2022.