Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection

Gut Month 2022 Vol 0 No 0 Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infectionWe read with great interest the recent article by Yeoh et al, demonstrating an altered stool microbiome composition in patients with COVID-19 compared with controls, with greater dysbiosis correlating with elevated inflammatory markers. 1 Additionally, dysbiosis was seen after disease resolution. 1 To our knowledge, gut microbiome studies in young children with COVID-19 have not been reported.Critically, the developing gut microbiome of very young children differs from adults and establishes immune and inflammatory pathways. 2 3Moreover, children with COVID-19 can subsequently develop autoimmune and autoinflammatory diseases including Multisystem Inflammatory Syndrome in Children (MIS-C) 4 5 , which may in part be microbiome mediated, given recent findings by Yeoh et al. 1 It is difficult to study this in young children, as many with SARS-CoV-2 infection are asymptomatic and rarely tested. 6o address this, knowing that SARS-CoV-2 can be detected in stool, 7 we used an established study collecting longitudinal stool samples from before and throughout the pandemic to investigate the prevalence and associated microbiome changes of SARS-CoV-2 in very young children.We ran the CDC 2019-Novel Coronavirus Real-Time RT-PCR Diagnostic Panel assay on 769 serial stool samples from 595 children aged 0-24 months collected from February 2020 to February 2021.The prevalence of SARS-CoV-2 in faeces was 1.7% (13 samples from 13 separate children) with prevalence at <2 days and 2, 6, 12 and 24 months of 0% (0/1), 0% (0/21), 2.6% (4/156), 2.0% (7/357) and 0.9%,(2/234), respectively.Prevalence by month is shown in online supplemental figure 1A, with the first positive sample detected 31 days before the first reported case of COVID-19 regionally.No samples were positive in controls collected prior to the pandemic in 2019 (n=97 samples from 66 individuals).Of 13 positive children, 12 were asymptomatic with no personal or family history of SARS-CoV-2 (table 1A).Of 13 children, 1 was symptomatic with COVID-19 diagnosed 21 days before stool was collected.Hispanic