SARS-CoV-2 viral shedding characteristics and potential evidence for the priority for faecal specimen testing in diagnosis

Abstract

This study aimed to identify the specimen type that has high positivity and its proper sampling time for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing to promote diagnostic efficiency. All SARS-CoV-2-infected patients with a laboratory-confirmed diagnosis in Zhoushan City were followed up for viral shedding in respiratory tract specimens and faecal samples. Positivity was analysed both qualitatively and quantitatively by proper statistical approaches with strong testing power. Viral shedding in respiratory tract and faecal specimens was prolonged to 45 and 40 days after the last exposure, respectively. The overall positive rate in respiratory tract specimens was low and relatively unstable, being higher in the early-to-mid stage than in the mid-to-late stage of the disease course. Compared with respiratory tract specimens, faecal samples had a higher viral load, higher overall positive rate, and more stable positivity in different disease courses and varied symptomatic status. Faecal specimens have the potential ability to surpass respiratory tract specimens in virus detection. Testing of faecal specimens in diagnosis, especially for identifying asymptomatic carriers, is recommended. Simultaneously, testing respiratory tract specimens at the early-to-mid stage is better than testing at the mid-to-late stage of the disease course. A relatively small sample size was noted, and statistical approaches were used to address it. Information was missing for both specimen types at different stages of the disease course due to censored data. Our research extends the observed viral shedding in both specimen types and highlights the importance of faecal specimen testing in SARS-CoV-2 diagnosis. Healthcare workers, patients, and the general public may all benefit from our study findings. Disposal of sewage from hospitals and residential areas should be performed cautiously because the virus sheds in faeces and can last for a long time.

Fig 1. Cycle threshold (Ct) values of fluorogenic real-time quantitative polymerase chain reaction (RT-qPCR) assay targeting the ORF1ab and N regions of SARS-CoV-2 on days after the last exposure for 10 independent cases.

Marks in the grey area indicate specimens with equivocal results, and those in the yellow area indicate specimens with negative results. Negative specimens with no accurate Ct values were assigned to random numbers from 40 to 43 only for better visualisation. A, Gathered scatter plot. Numbers on the upper right or top of the marks represent individual case number. Different shapes represent the ORF1ab and N genes respectively and distinct colours represent specimen types, namely, respiratory secretions, faeces, urine and serum. B, Individual scatter plot.

Fig 2. Differences in Cycle threshold (Ct) values between specimens of respiratory secretions and faeces in 10 independent cases.

The boxes and whiskers show the median, interquartile, and full range of Ct values. Boxes in blue represent respiratory secretions, and boxes in red represent faecal specimen. Jittered grey dots represent specimens with corresponding Ct values, and signs on the top illustrate statistical significance. **, statistically significant on level of 0.0010.05. A, Overall comparison with Ct values in both the ORF1ab and N regions. With P = 0.002 analysed by Wilcoxon rank-sum test, the Ct value of faecal samples is lower than that of respiratory secretions; hence, the viral load is higher in faecal specimens than in respiratory secretions. B, Comparison for each individual targeted region of SARS-CoV-2. With P = 0.006 analysed using Wilcoxon rank sum test, the Ct value of faecal specimens is lower than that of respiratory secretions for the N region.

Fig 3. Cumulative positive rates of specimen collected on days backward/forward after the last exposure from SARS-CoV-2 infections for 10 independent cases.

The boxes and whiskers show the median, interquartile and full range of cumulative positive rates. Boxes in red represent cumulative positive rates of days backward (cut-off value included), and boxes in blue represent rates of days forward (cut-off value excluded). ***, statistically significant on a level of 0.00010.05. For respiratory secretions, cumulative positive rates are continually higher in the first 6th to 28th days (as the day after the last exposure) backward compared with cumulative positive rates on the corresponding day forward, with P values of 0.006, 0.006, 0.014, 0.006, 0.002, 0.002, 0.0009, 0.0009, 0.002, 0.002, 0.0008, 0.002, 0.005, 0.013, 0.0099, 0.02, 0.001, 0.003, 0.003, 0.005, 0.005, 0.041, and 0.041 corresponding to days 6–28. No statistically significant difference is found in faeces. All analyses were based on the method of Wilcoxon signed-rank test.