A potential new recombinant echovirus 18 strain detected in a 4-year-old child with encephalitis in China in 2019


The species Enterovirus B includes diverse serotypes that can cause a wide spectrum of human diseases, such as aseptic encephalitis, myocarditis, and paralysis. In this study, a 4-year-old child was diagnosed with viral encephalitis, but the causative agent could not be identified using routine immunological tests. Using metagenomic RNA sequencing, a novel strain of enterovirus B, strain PC06, was identified, and its genome sequence was determined by RT-PCR and Sanger sequencing. The viral genome sequence was most similar to that of echovirus E18 strain E18-HeB15-54498/HeB/CHN/2015 (GenBank accession MG720261), with 87.73% nucleotide sequence identity, while the viral proteins shared 96.98% amino acid sequence identity with those of E18 strain Jena/AN1365/10 (GenBank accession no. KX139452). Phylogenetic analysis based on the VP1 and 3D genes revealed discrepant placement of PC06 in the two trees. In the 3D tree, PC06 formed a separate branch together with other recombinant E18 strains. Further recombination tests revealed that PC06 had possibly undergone recombination at a site between the structural and non-structural regions during its evolutionary history. Based on the analysis of VP1 phylogeny and using online genotyping tools, this potential recombinant is tentatively considered a strain of echovirus 18. This information might contribute to the diagnosis and prevention of related diseases.

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This work was financially supported by the Medical Innovation Team of Jiangsu Province (Grant no. CXTDB2017016) and Top Talent Support Program for young and middle-aged people of Wuxi Health (Grant no. HB2020087).

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Correspondence to Jun Qian or Pengwei Zhu.

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This study was approved by the Ethics Committee of the Affiliated Wuxi Children's Hospital of Nanjing Medical University (number: WXCH2019-03-001).

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Kang, Y., Hua, Y., Sun, M. et al. A potential new recombinant echovirus 18 strain detected in a 4-year-old child with encephalitis in China in 2019. Arch Virol 166, 1231–1236 (2021). https://doi.org/10.1007/s00705-020-04907-w

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