Isolation of a recombinant type 3/type 2 poliovirus with a chimeric capsid VP1 from sewage in Shandong, China

The genetic and phenotypic characterization of poliovirus strain P3/Jinan/1/09, isolated from sewage sample in Jinan city, Shandong province, China, was described. The strain had a Sabin type 3/type 2/type 3 recombinant genome, with the first crossover site located in capsid VP1 coding region between nucleotide positions 3293 and 3294 (numbering according to Sabin 3), and the second crossover site in 3D region between positions 6374 and 6378. The recombinant had introduced six Sabin 2-derived amino acids into the carboxyl terminus of Sabin 3 VP1 capsid protein. The complete genome of the isolate revealed eight nucleotide substitutions in Sabin 3 region with two substitutions resulting in amino acid alteration, and two missense substitutions in the Sabin 2 region. An estimation based on the evolution rate of the P1 coding region of Sabin 3 background suggested that evolution time of strain P3/Jinan/1/09 might be 76–80 days. The person who excreted the recombinant was not known and no evidence was obtained for its circulation in population via acute flaccid paralysis surveillance. The virus showed Sabin 3 serological characterization in neutralization test, and it did not lose temperature sensitivity phenotype at 40 °C. The significance of environmental surveillance and the presence of natural capsid recombinant poliovirus strain in the context of the global polio eradication initiative are discussed.