SARS-CoV-2 prevalence in feces of very young children, a longitudinal study

Background: Understanding the disease burden of the severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) in young children has been challenging as the majority are asymptomatic or experience mild symptoms and were rarely tested especially near the start of the pandemic. Since children are a potential reservoir of SARS-CoV-2, this is vital epidemiological data to understand. SARS-CoV-2 is traditionally detected through respiratory secretions;however, detection of SARS-CoV-2 has also been reported in feces and shedding may continue for weeks after respiratory samples show resolution. This allows the unique opportunity to examine the prevalence of SARS-CoV-2 in stool samples of young infants collected during the pandemic who may otherwise not be tested for SARS- CoV-2. We examined the prevalence of SARS-CoV-2 in already collected fecal samples from young children through the pandemic as well as associated demographic and clinical factors. Methods: As part of an ongoing longitudinal microbiome study in Northern Virginia, serial stool samples were collected from infants before 2 days of life, 2 months, 6 months, 12 months and 24 months of age before and throughout the Covid-19 pandemic. Stool samples were stored at -80°C without viral preservative. Viral RNA was extracted and reverse transcription quantitative-PCR detecting SARS-CoV-2 nucleocapsid gene in the N1 and N2 regions was performed as per manufacturer guidelines (CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel assay). Positive and negative controls were included on each plate. At each time point, household infectious history particular to SARS-CoV-2 infection and social demographic factors were collected. The characteristics of the study cohort were described and univariate analyses were performed to investigate associations between test results and characteristics of the study cohort. Penalized logistic regression models were developed to evaluate the association between fecal positivity and ethnicity, essential worker status, and other potential risk factors. Results: 769 serial stool samples from 595 infants were included. The overall prevalence of SARS-CoV-2 in infant feces was 1.69 % (13 samples) with a prevalence at delivery, 2 months, 6 months, 12 months and 24 months of 0, 0, 2.56, 1.96, and 0.85 % respectively. There were no positive stool samples collected in 2019 prior to the start of the pandemic. Fecal positivity was first detected 2/3/2020, 31 days before the reported first case of Covid-19 in Northern Virginia;prevalence rates peaked in September at 4.5% (Figure 1). One infant who tested positive was symptomatic and diagnosed with COVID-19 21 days before his stool was collected;no other infant with a positive stool sample was symptomatic or had a personal or family history of a SARS-CoV-2 (Table 1). Of the 13 positive samples, 8 reported Hispanic or Latino ethnicity and 7 reported an essential worker (Table 1). Penalized logistic regression model showed an association between Hispanic ethnicity and testing positive (OR 5.04 (95% CI 1.7 - 15.0)) that persisted after controlling for a household member being an essential worker (OR 4.7 (95% CI 1.6 - 14.0)). Conclusion: Studying infant stool allows a unique glimpse into SARS-CoV-2 burden in an understudied population. Prevalence of SARS- CoV-2 in infant stool correlated with the prevalence of COVID-19 during the pandemic, with higher rates in those of Hispanic ethnicity correlating with regional trends. Fecal positivity in asymptomatic infants even before quarantine restrictions supports the early but silent transmission of SARS-CoV-2. This study likely underestimates fecal positivity and true prevalence rates as stool samples were stored without viral preservative. Although this study suggests an association between Hispanic ethnicity and fecal positivity, there are many socioeconomic factors that predispose to disease while ethnicity may be a mediating or confounding factor.