Sample types and their reliability for etiology surveillance
During 2019-2022, a total of 2296 samples were collected from HFMD cases for etiology surveillance, clinicians tended to collect throat swabs (75.7%) other than anal swabs (16.6%) and stool (7.7%) (Figure 8A). We found comparable positive rates of EVs from throat swabs (46.6-68.8%), anal swabs (57.9-80.0%) and stool (58.0-71.1%) (Figure 8B). Generally, throat swabs or anal swabs had higher viral loads than stool, and viral loads of CVA6- or CVA10-infected cases were higher than that of CVA16- or UEV-infected cases (Figure 8C-F). Considering the convenience of sampling, storage, ages of the patients and seasonality of HFMD, throat swab seems convenient and reliable enough for etiology surveillance. However, it’s worthy to continuously collect multiple types of samples from inpatient cases to explore dynamics of virus shedding in the future.