This retrospective study found inconsistent results of RT-PCR-testing using throat and anal swabs for monitoring SARS-CoV-2 infection.

• RT-PCR assay on throat and anal swabs were simultaneously tested in 212 of 2138 pediatric patients with suspected SARS-CoV-2 infection in Wuhan Children’s Hospital. 78 of 212 patients were confirmed with SARS-CoV-2 infection according to the positive results obtained from either throat or anal swabs
• Of the 78 patients, 17 were positive on anal swabs and 37 were positive on throat swabs, as well as 24 were double positive.
• The diagnostic potential of these two types of specimens showed significant difference (positive rate: 78.2% on throat swabs vs. 52.6% on anal swabs, McNemar Test P = 0.0091) and exhibited a weak positive consistency with Kappa value was 0.311 (P < 0.0001).
• Viral loads showed no difference and correlation between throat and anal swabs.
• Further research is needed to determine if there is a fecal-oral route of transmission for SARs-CoV-2