Rectal Shedding of SARS-CoV-2 May Persist for Up to 7 Weeks

The goal of this study was to examine the time sequences of oral and fecal viral shedding in patients with coronavirus disease 2019 (COVID-19).

Study data published in Gastroenterology provide a profile of rectal viral shedding in patients with coronavirus disease 2019 (COVID-19). Data from a cohort in Shenzhen, China, suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may remain in the gastrointestinal tract for up to 7 weeks after diagnosis. In a substantial portion of patients, viral load was significantly higher in rectal swabs compared with respiratory samples. Prolonged fecal shedding of SARS-CoV-2 was independently associated with neutrophil levels and treatment delays.

This retrospective cohort study enrolled 401 patients with laboratory-confirmed COVID-19 who were admitted to Shenzhen Third People’s Hospital. Investigators obtained nasal (respiratory) and rectal swabs and tested them for the presence of viral ribonucleic acid (RNA) of SARS-CoV-2 using quantitative reverse-transcription polymerase chain reaction. They considered samples with a cycle threshold value less than or equal to 37 positive and followed patients for up to 7 weeks, collecting nasal and rectal swabs once weekly. The researchers categorized respiratory and rectal samples collected on the same day as a “pair.” They also obtained demographic and clinical information and performed multivariate logistic regression to identify correlates of prolonged viral shedding in rectal samples (>4 weeks vs ≤4 weeks).

Investigators collected a total of 1758 rectal swabs from 401 patients. Overall, 80 (19.95%) patients tested positive for SARS-CoV-2 in rectal swabs. Pediatric patients (<18 years) had higher rates of rectal swab positivity compared with adults (56.67% vs 16.98%). Clinical characteristics were similar between patients with and without positive rectal swab results. Among patients who had positive rectal swab results at baseline, 44.19% remained positive at 1 week, 30% at 2 weeks, 16.67% at 3 weeks, 12.29% at 4 weeks, 12.3% at 5 weeks, 5.22% at 6 weeks, 0.76% at 7 weeks, and 0 at greater than 7 weeks after illness onset.

Researchers collected a total of 517 respiratory-rectal sample pairs from the 80 patients who tested positive for SARS-CoV-2 RNA on rectal swabs. Overall, 58 (11.8%) pairs were double-positive; 112 (21.7%) were positive in the rectal swab but negative in the respiratory swab; and 40 (7.7%) were positive for the respiratory swab but negative in the rectal swab. Rectal swabs had higher viral loads than respiratory swabs more than half the time. Specifically, at 1, 2, 3, 4, 5, and 6 weeks after disease onset, 11 (61.54%), 9 (56.25%), 9 (64.29%), 4 (51.14%), 3 (50%), and 2 (100%) double-positive pairs had higher viral loads in the rectal samples, respectively.

In multivariate logistic regression models, increased neutrophil levels were associated with greater odds of prolonged viral shedding (odds ratio [OR] 1.549; 95% CI, 1.055-2.405; P =.034). Longer duration between illness onset and initiation of antiviral therapy was also associated with prolonged rectal shedding of viral DNA (OR 1.168; 95% CI, 1.011-2.369; P =.042).

These data elucidate the timeline and risk factors for rectal shedding of SARS-CoV-2 RNA. Viral RNA remained in rectal samples for as long as 7 weeks after diagnosis. The incorporation of rectal swabs into COVID-19 testing may be critical to minimizing false negatives.

“The gastrointestinal viral reservoir is potentially a long-lasting fomite for SARS-CoV-2 transmission even for asymptomatic patients,” investigators wrote.


Zhao F, Yang Y, Wang Z, Li L, Liu L, Liu Y. The time sequences of respiratory and rectal viral shedding in patients with coronavirus disease 2019. Gastroenterology. 2020;159(3):1158-1160.e2.