Characteristics of four natural poliovirus type 1 variants with six-nucleotide deletion (2,783–2,788 nt) in the VP1 region

Since the establishment of the Chinese acute flaccid paralysis (AFP) case surveillance system in 1999, around 7,200 strains of poliovirus (PV) type 1 have been identified and isolated. Among these, the VP1 region of 5,649 strains has been sequenced. Based on the existing VP1 region sequence library, four strains of type 1 PV with six-nucleotide deletion in the VP1 region, identified from AFP cases, healthy children, and environmental sewage samples, were identified, and their biological characteristics were investigated. Whole-genome sequence analysis showed that the similarity with the Sabin 1 strain was 99.5-99.8%, and the mutation rate in the VP1 region was only 0.11-0.55%, indicating that these strains are not vaccine-derived PVs. The missing nucleotide is located at positions 2,783-2,788 in the VP1 region, resulting in the deletion of amino acids 102 and 103 at neutralizing antigen site 1 (N-Ag I) in the BC loop. It is worth noting that the neutralization test results showed that the two strains detected from AFP and healthy children evaded immune recognition, whereas the other two from environmental sewage did not. Molecular docking and neutralization antigen site analyzes indicate that the deletion of nucleotides 2,783-2,788 in N-Ag I is not a critical factor leading to the development of neutralization escape variants.IMPORTANCEInterestingly, we observed that the VP3-60 mutation in N-Ag IIIa may be the main reason for the immune evasion of these two viruses. In addition, based on the temperature sensitivity experiments, the four viruses exhibited similar temperature sensitivity to the Sabin 1 strain and their replication ability at 39.5°C was comparable to vaccine-derived polioviruses. Although variants with six-nucleotide deletion (2,783-2,788 nt) in the VP1 region do not cause significant biological changes, they can still spread in the environment and among populations, posing a certain risk of transmission.