VP1 molecular evolution of type 2 immunodeficiency-related vaccine-derived polioviruses (iVDPV2) in a patient with primary immunodeficiency disease (PID)

Vaccine-derived polioviruses (VDPVs) arising after use of oral poliovirus vaccine (OPV) are an important impediment to the polio endgame, particularly in settings with low population immunity or prolonged infections in immunodeficient individuals.If immunocompromised individuals such as patients with primary immunodeficiency (PID) receive OPV, the live attenuated vaccine virus will replicate in their intestinal tract and chronically shed in the stool. Long-term proliferation of the vaccine virus in the enteric cells of the PID patients causes several mutations, which eventually culminates in the emergence of immunodeficiency-associated VDPVs (iVDPVs). Therefore, screening the PID patients for poliovirus excretion is of great importance during the last years of polio eradication.During the above-mentioned screening, Iran National Polio Laboratory detected iVDPV2 in a PID case who was suffering from severe combined immune deficiency (SCID). To meet the World Health Organization (WHO) standards and protocols, the lab received several follow-up stool specimens from the patient to check whether the patient was continuously shedding or cleared the mutated poliovirus, i.e., iVDPV2. All the follow-up specimens were positive for iVDPV2.The aim of this study is to investigate the genomic and amino acid changes in 24 sequential iVDPV2 isolates from the mentioned PID excretor during a 108-month period.Complete sequences of VP1 region of the genome of the isolated iVDPV2 were analyzed. The VP1 was amplified by one-step RT-PCR and the PCR product was purified. Then, the purified PCR product was sequenced using at least 4 sequencing bidirectional primers by Sanger sequencing method. The raw sequences were edited and assembled with Sequencher 5.4.6 software. Finally, after alignment and translation, phylogenetic tree was constructed by comparing to the reference strain, Sabin OPV2, using Geneious Prime software.The result of this study showed that out of 903 nucleotide positions in the VP1, 86 positions had substitutions (85% transition and 15% transversion). The estimated mutation rate was 1.0% per year. In total, 824 mutations were occurred in 108 months. The percentage of ambiguous nucleotide changes ranged from 3 to 70%, indicating high quasi-species diversity in iVDPV2 isolates. Amino acid changes were observed in 19 positions. Significantly, a neuro-pathogenesis single mutation (I143T) was observed in all isolates. Additionally, the last twelve isolates had amino acid changes in the main antigenic site (between residues 94 and 99 of VP1). Phylogenetic tree showed two distinct lineages and four sub-lineages had emerged during the 108-month shedding of the iVDPV2.The results of this study showed that Sabin-like poliovirus vaccines are excreted for an extended period in PID patients and exhibit high genomic variation. These extensive genomic changes can transform the Sabin-like vaccine strain into a neurovirulent form capable of causing paralysis in non-immune individuals, posing a potential risk to the polio eradication endgame.