BACKGROUND:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a respiratory virus that can cause gastrointestinal (GI) symptoms, with studies demonstrating detection of stool viral RNA weeks after respiratory tract clearance. It is unknown if children who test negative for SARS-CoV-2 on a nasopharyngeal (NP) swab may be shedding the virus in their stool.

OBJECTIVE:

To measure the prevalence of SARS-CoV-2 stool shedding in children with positive and negative SARS-CoV-2 NP polymerase chain reactions (PCR) tests, and to determine clinical factors associated with GI shedding.

METHODS:

In this cross-sectional study, we enrolled hospitalized patients 0 to 21 years old with a positive or a negative SARS-CoV-2 NP PCR test who had respiratory and/or GI symptoms. Participants were surveyed, and stool samples were sent for viral PCR testing. Fisher’s exact test was used to evaluate bivariate associations of stool PCR test positivity with categorical variables.

RESULTS:

Sixty-seven patients were consented; 34 patients did not provide stool samples so 33 patients were included: 17 NP-positive and 16 NP-negative for SARS-CoV-2. Eight of the 17 NP-positive patients had a positive stool PCR test for SARS-CoV-2, while none of the 16 SARS-CoV-2 NP-negative patients had a positive result (P < .01). For the 17 SARS-CoV-2 NP-positive patients, GI symptoms were associated with a positive stool PCR test (P = .05) for SARS-CoV-2, but this association was not found for all 33 patients (P = .11). No associations were found with patients in an immunocompromised state or those with a comorbid condition, fever and/or chills, respiratory symptoms, headache and/or myalgias, or anosmia and/or ageusia.

CONCLUSIONS:

SARS-CoV-2 GI shedding is common and associated with GI symptoms in NP-positive children, with 47% having positive stool PCRs for SARS-CoV-2. GI shedding was not demonstrated in SARS-CoV-2 NP-negative children.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19), causes gastrointestinal (GI) symptoms in a significant percentage of infected children. In a multicenter study of pediatric patients hospitalized with COVID-19, 36% of patients with respiratory disease also reported GI symptoms at admission; many patients required hospitalization for GI symptoms alone.1 

Multiple studies of both adult and pediatric SARS-CoV-2–positive patients have shown that viral RNA can be detected in stool samples and rectal swabs.2,8 A study of adult patients with GI symptoms found that nearly half of those who tested positive for SARS-CoV-2 by nasopharyngeal (NP) swab also had positive stool polymerase chain reaction (PCR) tests,9 similar to high rates in other studies.10,11 In addition, 7% of SARS-CoV-2 NP-negative patients had positive stool PCR tests.9 Fecal SARS-CoV-2 RNA was demonstrated in a recent meta-analysis to be more commonly detected in adult patients with GI symptoms, specifically diarrhea.7 Studies have found that stool PCR test positivity rates in SARS-CoV-2 NP-positive children range from 61% to 86%.6,12 

There is also evidence that stool specimens and rectal swabs remain positive for weeks after respiratory tract clearance.4,12,14 GI shedding persisted after NP swabs became negative in 89% of cases in 1 pediatric review, which also reported mean durations of viral shedding in the respiratory and GI tracts as 11.1 days and 23.6 days, respectively.12 The results of these studies reveal that children who test negative for SARS-CoV-2 on an NP swab may still be shedding the virus in their stool, but to our knowledge there have been no studies comparing the prevalence of GI shedding in both SARS-CoV-2 NP-positive and negative children.

The infectivity of SARS-CoV-2 in stool is unknown,15 although there is evidence that active replication occurs in the GI tract.10 If GI shedding is demonstrated in SARS-CoV-2 NP-negative children, stool PCR testing may be an alternate method of detection, offering potential advantages including increased ease of collection leading to decreased patient anxiety. Our aim was to measure the prevalence of SARS-CoV-2 stool shedding in hospitalized children with positive and negative nasopharyngeal SARS-CoV-2 PCR tests. Our secondary aim was to determine clinical risk factors associated with gastrointestinal viral shedding.

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.

TABLE 1

Demographics of Enrolled Patients (N = 33)a

SARS-CoV-2 NP-Positive (n = 17)SARS-CoV-2 NP-Negative (n = 16)All (n = 33)
Sex assigned at birth    
 Male 10 (59) 8 (50) 18 (55) 
 Female 7 (41) 8 (50) 15 (45) 
Median age, y 2.5 
 Range 12 d–21 y 5 wk–20 y 12 d–21 y 
Ethnicity    
 Hispanic 12 (71) 12 (75) 24 (73) 
 Non-Hispanic 4 (24) 4 (25) 8 (24) 
 No response 1 (6) 1 (3) 
Race    
 Black/African American 9 (53) 8 (50) 17 (52) 
 White 2 (12) 2 (13) 4 (12) 
 Asian 
 American Indian or Alaska native 2 (12) 2 (6) 
 Native Hawaiian or other Pacific Islander 
 Other 3 (18) 5 (31) 8 (24) 
 No response 1 (6) 1 (6) 2 (6) 
Immunodeficiency 6 (35) 2 (13) 8 (24) 
Comorbid condition 8 (47) 3 (19) 11 (33) 
SARS-CoV-2 NP-Positive (n = 17)SARS-CoV-2 NP-Negative (n = 16)All (n = 33)
Sex assigned at birth    
 Male 10 (59) 8 (50) 18 (55) 
 Female 7 (41) 8 (50) 15 (45) 
Median age, y 2.5 
 Range 12 d–21 y 5 wk–20 y 12 d–21 y 
Ethnicity    
 Hispanic 12 (71) 12 (75) 24 (73) 
 Non-Hispanic 4 (24) 4 (25) 8 (24) 
 No response 1 (6) 1 (3) 
Race    
 Black/African American 9 (53) 8 (50) 17 (52) 
 White 2 (12) 2 (13) 4 (12) 
 Asian 
 American Indian or Alaska native 2 (12) 2 (6) 
 Native Hawaiian or other Pacific Islander 
 Other 3 (18) 5 (31) 8 (24) 
 No response 1 (6) 1 (6) 2 (6) 
Immunodeficiency 6 (35) 2 (13) 8 (24) 
Comorbid condition 8 (47) 3 (19) 11 (33) 
a

Values represent n (%) unless otherwise indicated. Because of rounding, percentages do not always add up to 100.

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).

TABLE 2

Stool PCR Results in All Enrolled Patients (N = 33)

SARS-CoV-2 Stool Positive (n = 8)SARS-CoV-2 Stool Negative (n = 25)Pa
Immunocompromised .64 
Comorbid condition .39 
Fever and/or chills 15 .99 
Respiratory symptoms 20 .99 
GI symptoms 13 .11 
Headache and/or myalgias .68 
Anosmia and/or ageusia .99 
SARS-CoV-2 Stool Positive (n = 8)SARS-CoV-2 Stool Negative (n = 25)Pa
Immunocompromised .64 
Comorbid condition .39 
Fever and/or chills 15 .99 
Respiratory symptoms 20 .99 
GI symptoms 13 .11 
Headache and/or myalgias .68 
Anosmia and/or ageusia .99 
a

Two-sided Fisher’s exact test.

TABLE 3

Stool PCR Results in SARS-CoV 2 Nasopharyngeal Positive Patients Only (N = 17)

SARS-CoV2 Stool Positive (n = 8)SARS-CoV-2 Stool Negative (n = 9)Pa
Immunocompromised .34 
Comorbid condition .99 
Fever and/or chills .99 
Respiratory symptoms .47 
GI symptoms .05 
Headache and/or myalgias .99 
Anosmia and/or ageusia .29 
SARS-CoV2 Stool Positive (n = 8)SARS-CoV-2 Stool Negative (n = 9)Pa
Immunocompromised .34 
Comorbid condition .99 
Fever and/or chills .99 
Respiratory symptoms .47 
GI symptoms .05 
Headache and/or myalgias .99 
Anosmia and/or ageusia .29 
a

Two-sided Fisher’s exact test.

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.

FUNDING: This work was supported by the Department of Pediatrics at the Albert Einstein College of Medicine.

Dr Tam conceptualized and designed the research project, coordinated and participated in data collection, analyses, and interpretation, drafted the initial manuscript, and reviewed and revised the manuscript; Dr McNamara participated in data collection, analyses, and interpretation and reviewed and revised the manuscript; Dr Dunbar participated in data collection, analyses, and interpretation and reviewed and revised the manuscript; Dr O’Connor participated in data collection, analyses, and interpretation and reviewed and revised the manuscript; Dr Manzano participated in data interpretation and reviewed and revised the manuscript; Drs Cabana and Hametz conceptualized and designed the research project and reviewed and revised the manuscript; and all authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work.

1
Fernandes
DM
,
Oliveira
CR
,
Guerguis
S
et al
SARS-CoV-2 clinical syndromes and predictors of disease severity in hospitalized children and youth
.
J Pediatr
.
2020
;
230
:
23
31.e10
2
Wang
W
,
Xu
Y
,
Gao
R
et al
Detection of SARS-CoV-2 in different types of clinical specimens
.
JAMA
.
2020
;
323
(
18
):
1843
1844
3
Zhang
W
,
Du
RH
,
Li
B
et al
Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes
.
Emerg Microbes Infect
.
2020
;
9
(
1
):
386
389
4
Xu
Y
,
Li
X
,
Zhu
B
et al
Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding
.
Nat Med
.
2020
;
26
(
4
):
502
505
5
Wang
X
,
Zheng
J
,
Guo
L
et al
Fecal viral shedding in COVID-19 patients: clinical significance, viral load dynamics and survival analysis
.
Virus Res
.
2020
;
289
:
198147
6
Pinninti
SG
,
Pati
S
,
Poole
C
et al
Virological characteristics of hospitalized children with SARS-CoV-2 infection
.
Pediatrics
.
2021
;
147
(
5
):
e2020037812
7
Zhang
Y
,
Cen
M
,
Hu
M
et al
Prevalence and persistent shedding of fecal SARS-CoV-2 RNA in patients with COVID-19 infection: a systematic review and meta-analysis
.
Clin Transl Gastroenterol
.
2021
;
12
(
4
):
e00343
8
Yan
D
,
Zhang
X
,
Chen
C
et al
Characteristics of viral shedding time in SARS-CoV-2 infections: A systematic review and meta-analysis
.
Front Public Health
.
2021
;
9
:
652842
9
Szymczak
WA
,
Goldstein
DY
,
Orner
EP
et al
Utility of stool PCR for the diagnosis of COVID-19: comparison of two commercial platforms
.
J Clin Microbiol
.
2020
;
58
(
9
):
e01369-20
10
Guo
M
,
Tao
W
,
Flavell
RA
,
Zhu
S
.
Potential intestinal infection and faecal-oral transmission of SARS-CoV-2
.
Nat Rev Gastroenterol Hepatol
.
2021
;
18
(
4
):
269
283
11
Cheung
KS
,
Hung
IFN
,
Chan
PPY
et al
Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from a Hong Kong cohort: systematic review and meta-analysis
.
Gastroenterology
.
2020
;
159
(
1
):
81
95
12
Xu
CLH
,
Raval
M
,
Schnall
JA
,
Kwong
JC
,
Holmes
NE
.
Duration of respiratory and gastrointestinal viral shedding in children with SARS-CoV-2: a systematic review and synthesis of data
.
Pediatr Infect Dis J
.
2020
;
39
(
9
):
e249
e256
13
Xing
YH
,
Ni
W
,
Wu
Q
et al
Prolonged viral shedding in feces of pediatric patients with coronavirus disease 2019
.
J Microbiol Immunol Infect
.
2020
;
53
(
3
):
473
480
14
Wu
Y
,
Guo
C
,
Tang
L
et al
Prolonged presence of SARS-CoV-2 viral RNA in faecal samples
.
Lancet Gastroenterol Hepatol
.
2020
;
5
(
5
):
434
435
15
Troisi
J
,
Venutolo
G
,
Pujolassos Tanyà
M
,
Delli Carri
M
,
Landolfi
A
,
Fasano
A
.
COVID-19 and the gastrointestinal tract: source of infection or merely a target of the inflammatory process following SARS-CoV-2 infection?
World J Gastroenterol
.
2021
;
27
(
14
):
1406
1418
16
Lauer
SA
,
Grantz
KH
,
Bi
Q
, et al.
The incubation period of coronavirus disease 2019 (COVID-19) from bublicly reported confirmed cases: estimation and application
.
Ann Intern Med
.
2020
;
172
(
9
):
577
582
17
CDC
. Isolate if you are sick. Available at: https://www.cdc.gov/coronavirus/2019-ncov/if-you-are-sick/isolation.html. Accessed August 2, 2021
18
CDC
. COVID-19 vaccines for moderately to severely immunocompromised people. Available at: https://www.cdc.gov/coronavirus/2019-ncov/vaccines/recommendations/immuno.html. Accessed October 15, 2021
19
Kang
M
,
Wei
J
,
Yuan
J
et al
Probable evidence of fecal aerosol transmission of SARS-CoV-2 in a high-rise building
.
Ann Intern Med
.
2020
;
173
(
12
):
974
980
20
McKinney
KR
,
Gong
YY
,
Lewis
TG
et al
Environmental transmission of SARS at Amoy Gardens
.
J Environ Health
.
2006
;
68
(
9
):
26
30, quiz 51–52

Competing Interests

POTENTIAL CONFLICT OF INTEREST: The authors have indicated they have no conflicts of interest relevant to this article to disclose.

Supplementary data