SARS-CoV-2 Gastrointestinal Shedding in Hospitalized Children Free

We conducted a cross-sectional study from January through July 2021 to determine the proportions of SARS-CoV-2 GI viral shedding in SARS-CoV-2 NP-positive and symptomatic SARS-CoV-2 NP-negative inpatients. We enrolled patients aged 0 to 21 years old at a quaternary care academic children’s hospital in the Bronx, New York who had a positive SARS-CoV-2 NP PCR test or a negative SARS-CoV-2 NP PCR test but who had respiratory and/or GI symptoms within 14 days before admission. We selected 14 days because this is the standard accepted definition of the period during which exposed patients can become symptomatic.¹⁶  Respiratory symptoms were defined as cough, chest tightness, shortness of breath, rhinorrhea, and/or sore throat. GI symptoms were defined as vomiting, diarrhea, and/or abdominal pain. We excluded asymptomatic patients with a negative SARS-CoV-2 NP test because of an extremely low likelihood of stool positivity, as well as patients who tested positive for other respiratory viruses or GI pathogens by PCR testing. Patients were also excluded if their primary language was not English, Spanish, Arabic, or Bengali, if they were in the ICU, or if they were unable to consent or assent (for children ≥7 years old) because of altered mental status or moderate to severe pain (pain score ≥4). This study was approved by the Albert Einstein College of Medicine Institutional Review Board.

All admitted patients were tested for SARS-CoV-2 using NP swabs and the Cepheid Xpert Xpress RT-PCR assay (Cephalid; Sunnyvale, CA), as per hospital protocol. Study personnel approached eligible patients after admission and consented caregivers and/or patients (for those ≥18 years old) to participate in the study; assent was also obtained as appropriate. A convenience sample of approximately equal numbers of SARS-CoV-2 NP-positive and NP-negative patients were enrolled. Demographic and clinical characteristics were obtained via survey (Supplemental Fig 1).

After consent, a stool collection kit was provided, and age-appropriate instructions were given. Consents, surveys, and isolation guidelines were provided in English, Spanish, Arabic, and Bengali, the most common languages spoken by our population. All documents were translated and back-translated by a professional company, Eriksen Translations (Brooklyn, NY). All stool samples were swabbed using an Eswab containing 1 mL of liquid Amies transport media and tested using the Hologic Panther Fusion real-time RT-PCR assay (Hologic, Inc, Marlborough, MA). The Cepheid assay was prioritized for SARS-CoV-2 clinical specimens, whereas the Hologic assay was prioritized for research specimens. Patients who tested positive for SARS-CoV-2 were sent or given a handout on isolation guidelines per Centers for Disease Control and Prevention (CDC) recommendations.¹⁷ 

Descriptive statistics were used to analyze demographic and clinical characteristics. Fisher’s exact test was used to evaluate bivariate associations of stool PCR SARS-CoV-2 positivity with each of the following categorical variables: immunocompromised state, comorbid condition, fever and/or chills, respiratory symptoms, headache and/or myalgias, and anosmia and/or ageusia. Immunocompromised participants were defined as those who met CDC criteria for moderately to severely immunocompromised individuals vulnerable to COVID-19.¹⁸  Comorbid conditions included asthma, chronic lung disease, diabetes, cancer, inflammatory bowel disease, or heart disease.

A total of 67 patients were consented and surveyed; 33 patients were included in the analysis. Of the 34 patients not included, 33 did not provide a stool sample before discharge, and 1 patient’s sample could not be analyzed. Included patients ranged in age from 12 days to 21 years old (Table 1). Most were Hispanic (73%) and Black/African American (52%), reflecting local demographics. Higher percentages of SARS-CoV-2 NP-positive patients were immunocompromised and had comorbid conditions compared with NP-negative patients.

Of the enrolled patients, 17 had a positive SARS-CoV-2 NP test, and 16 had a negative NP test. Eight of the 17 SARS-CoV-2 NP-positive patients had a positive stool PCR test. None of the 16 SARS-CoV-2 NP-negative patients had a positive stool PCR (Fisher’s exact test, P < .01). Of the 17 patients with a positive SARS-CoV-2 NP test, those with GI symptoms were more likely to have a positive stool test (Table 3, P = .05); however, in all 33 enrolled patients, patients with GI symptoms were not found to be more likely to have a positive stool test (Table 2, P = .11). A SARS-CoV-2 positive stool test was not associated with immunocompromised state, comorbid condition, fever and/or chills, respiratory symptoms, headache and/or myalgias, or anosmia and/or ageusia, in either all enrolled patients or NP-positive patients only (Tables 2 and 3).

In this prevalence study, we evaluated stool SARS-CoV-2 positivity in 33 hospitalized children. We discovered that only SARS-CoV-2 NP-positive patients had positive stool PCR tests, with a rate of positivity in this group of 47%. No NP-negative patients had positive stool tests. The prevalence of SARS-CoV-2 GI shedding among our NP-positive patients is similar to an adult study at our institution showing 48% stool PCR positivity.⁹  The results of other pediatric studies revealed higher SARS-CoV-2 GI shedding rates among NP-positive patients (61% [n = 26]⁶ ; 86% [n = 69]¹² ); these studies used rectal swabs and stool samples, whereas we only collected stool samples. It is unclear how the accuracy of these two methods compare. Nevertheless, the results of our study reinforce that GI viral shedding is common in SARS-CoV-2 NP-positive children.

In contrast to previous studies,^9,12  we did not detect GI shedding in any SARS-CoV-2 NP-negative patients. This difference may be explained by our small sample size or a lower COVID-19 community prevalence during our study. We also performed stool testing on symptomatic, hospitalized children with no known past SARS-CoV-2 infection, compared with previous studies that focused on viral shedding after recently confirmed SARS-CoV-2 infection.

The clinical significance of SARS-CoV-2 detection in fecal samples is not understood. Infectivity rates of COVID-19 via fecal-oral transmission remain unknown. Historical outbreaks of SARS linked to fecal-oral spread support the possibility of transmission.^19,20  The results of in vitro studies have revealed SARS-CoV-2 infection of human intestinal cell lines, and those of other studies have identified live viral particles and subgenomic mRNA in fecal samples, suggesting active replication.¹⁰  It is plausible but not yet proven that SARS-CoV-2 may remain infectious in stool.¹⁰ 

Limitations of our study include the small sample size and single-center nature of this study. Symptoms were either parent- or self-reported and subject to recall bias. Additionally, we had a high rate of patients who did not complete the study (51%) because of some patients not providing a stool sample before discharge. However, demographic variables did not differ between those who completed and did not complete the study (Supplemental Table 4).

In conclusion, we found a prevalence of GI shedding in SARS-CoV-2 NP-positive children similar to previous adult and pediatric studies, but we did not detect GI shedding in SARS-CoV-2 NP-negative children. Our small sample does not support SARS-CoV-2 stool testing as an alternate method of diagnosis for COVID-19, although larger studies may be needed to verify this. Nasopharyngeal testing captured all COVID-19–positive patients in this study and resulted in sufficient infection control measures in this cohort. Although SARS-CoV-2 stool testing may not be useful as a primary diagnostic method, it may be an important consideration for patients with GI symptoms after SARS-CoV-2 exposure despite negative NP testing. Further research is needed to investigate the role of SARS-CoV-2 GI shedding in transmission in children, and to define the utility of stool PCR testing in community and hospital settings.

We acknowledge the tremendous work of the following residents and medical students in enrolling participants for this study: Leah Regenbaum, MD, Anna Bitners, MD, Shayon Mottahed, MD, Amanda Orley, MD, Trina Marie Salvador, MS3, Gabrielle Jean-Baptiste, MS4, and Grace Aharon, MS4. We also thank the nursing staff at the Children’s Hospital at Montefiore for their assistance in collecting the samples. Thank you to the Montefiore Departments of Microbiology and Virology for developing a testing pathway for SARS-CoV-2 stool PCR tests, especially Wendy Szymczak, PhD and Yitz Goldstein, MD.