Characterization of a Sabin-like type 2/3 recombinant poliovirus with a triple nucleotide deletion in the VP1 region isolated from sewage

Nucleotide (nt) deletions in the VP1 region of poliovirus are extremely rare. However, as early as 2012, we detected a natural type 2 poliovirus strain in sewage, originating from the Sabin 2, which exhibited such deletions. Whole-genome analysis revealed that the virus genome is 7,436 nt in length, with three nucleotide deletions in positions 16-18 of the VP1 region (2,497-2,499 nt), resulting in a deletion of the amino acid at position six of the VP1 capsid protein. Notaly, the missing amino acids are not located at known attenuation or neutralization sites. In addition, the important attenuated sites at positions 481 and 2,909 remained unchanged. Only one substitution was observed at the known neutralizing antigen site: VP3-61 (Arg to Lys) on NAg3a. Recombinant analysis showed that the virus is a type 2/3 recombinant virus, with the crossover site located between nucleotides 6,981 and 7,439, spanning the 3D^pol region and the 3' untranslated region (UTR). The protein structure simulation showed that VP1 capsid protein of the PV-2 deletion variant was very similar to Sabin 2. In the VP1 region, the PV-2 deletion variant has only a triple nucleotide deletion, with no other mutations, indicates that the virus was in an early stage of evolution before being isolated from sewage. Furthermore, this variant is only a type 2/3 recombinant, not recombined with other non-polio enteroviruses, suggesting a short transmission and circulation time of the virus in the population. Therefore, we speculate that the nucleotide deletion in VP1 region of poliovirus may occur in the early evolutionary stage. Although the virus has not yet spread widely among humans, these findings highlight the importance of continuous environmental monitoring of poliovirus.