Viral loads in throat and anal swabs in children infected with SARS-CoV-2

Abstract

Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay on anal swabs was recently reported to be persistently positive even after throat testing was negative during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, data about the consistent performance of RT-PCR assay on throat and anal swabs remain limited in paediatric patients. Here, we retrospectively reviewed RT-PCR-testing results of 212 paediatric patients with suspected SARS-CoV-2 infection at Wuhan Children's Hospital. 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 (Kappa value was 0.311, P < 0.0001) in paediatric patients. Furthermore, viral loads detected on both throat and anal swabs also showed no significant difference (P = 0.9511) and correlation (Pearson r = 0.0434, P = 0.8406), and exhibited an inconsistent kinetic change through the course of SARS-CoV-2 infection. Besides, viral loads in the throat and anal swabs were correlated with different types of immune states, immune-reactive phase, and the resolution phase/immunologic tolerance, respectively. These findings revealed that RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune state in paediatric patients.

Keywords: RT-PCR; SARS-CoV-2; diagnostic potential; paediatric patients; viral load.

Figure 1.

The difference and correlation of Ct value between throat and anal swabs-testing. (A) The difference between Ct value obtained by RT-PCR-testing on throat swabs (200 cases) and anal swabs (41 cases). (B) The difference between Ct value obtained by RT-PCR-testing on paired throat swabs and anal swabs in 24 cases. The data were normally distributed and a paired t-test was used to compare statistical differences. (C) The pearson correlation between Ct value obtained by RT-PCR-testing on paired throat swabs and anal swabs in 24 cases.

Figure 2.

Correlation of viral loads to indexes of SARS-CoV-2 infection. (A) The correlation of viral loads to indexes of SARS-CoV-2 infection. Ct values were detected in throat swabs obtained from 200 cases and viral loads were inversely correlated to Ct value. (B) The correlation of viral loads in anal swabs of 41 cases to indexes of SARS-CoV-2 infection. (C) The difference of Ct value detected in throat and anal swabs between males and females.

Figure 3.

Timeline of RT-PCR-testing results from throat and anal swabs through the course of SARS-CoV-2 infection for 13 cases, January to March 2020.