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

Jie Lin, Lei Zhou, Chenglin Zhu, Jichen Li, Wei Zhang, Shuangli Zhu, Dongyan Wang, Xiaolei Li, Hui Zhu, Qian Yang, Tianjiao Ji, Jinbo Xiao, Lan Yang, Kaitao Xiao, Kexin Shao, Yong Zhang, Dongmei Yan

Journal: Virology journal 2025;22(1):387

PMID: 41316283

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Abstract

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.

Address: National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; National Laboratory for Poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; National Health Commission Key Laboratory of Microbial Genomics, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.; GuangDong Center for Disease Control and Prevention, Guangzhou, China.; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].; National Laboratory for Poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].; National Health Commission Key Laboratory of Microbial Genomics, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].; National Laboratory for Poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].; National Health Commission Key Laboratory of Microbial Genomics, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [email protected].

DOI: 10.1186/s12985-025-03014-z

MeSH Terms: Sewage, Poliovirus, Capsid Proteins, Sequence Deletion, Genome, Viral, Recombination, Genetic, Humans, Phylogeny