For enterovirus serotype determination based on the obtained sequences generated by viral mNGS, we used a publicly available genotyping tool (10). To determine the relationship between enterovirus strains we sequenced and global strains, we first performed pairwise alignment by using the ClustalW tool in Geneious 8.1.5, and then reconstructed a maximum-likelihood phylogenetic tree by using IQ Tree 1.4.3 (11). A similar phylogenetic approach was used for other viruses. The generated sequences of this study were submitted to GenBank (accession no. PRJNA561465).

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