SCABR2 serving as a cellular receptor plays an important role in co-infections of EV71 and CVA16, and has-miR-3605-5p regulates the high expression of SCARB2. We found that differentially expressed miRNA target genes were mainly concentrated in the ECM-receptor interaction and circadian rhythm pathways, which may be related to clinical symptoms of patients infected with CVA16, such as aphthous ulcers, cough, myocarditis and somnolence of meningoencephalitis. This evidence concerns the gene SCARB2 and meningoencephalitis.