Detailed methods for stool viral RNA extraction, RT-PCR, and sequencing.

(DOCX)</p

SARS-CoV-2 serology and stool viral RNA results over calendar time.

Results of SARS-CoV-2 serology and quantitative real-time PCR testing of stool samples from Linda Kizazi participants that first tested seropositive and had ≥1 available stool sample collected between May 1-December 31, 2020. Anonymized ID numbers on y-axis for mothers (M) and infants (B). Grey circles indicate date of last seronegative serology test and orange circles indicate date of first seropositive sample. White triangles represent SARS-CoV-2 RNA-negative and red triangles represent RNA-positive stool samples. Calendar time is on the x-axis.</p

SARS-CoV-2 antibody levels over time in mother-infant Pairs.

OD ratios show SARS-CoV-2 antibody levels over time in pairs where both mother and infant were first SARS-CoV-2 positive at the same visit and had ≥1 sample available after initial antibody detection. Increased levels of antibody denoted by darker purple shading as shown in key. Positive antibody levels denoted by filled circle, equivocal levels by X, and levels below the limit of detection by empty circles. Mother-infant pairs in which the mother was living with HIV are shown on top with bold red IDs; HIV-uninfected and -unexposed pairs are shown below with black IDs. (TIF)</p

SARS-CoV-2 genomes sequenced from Kenyan stool samples.

Complete SARS-CoV-2 genomes were sequenced from six RNA-positive stool samples. (A) Phylogenetic analyses of 500 randomly selected SARS-CoV-2 global sequences, the Wuhan1 reference, and the two Kenyan stool-derived genomes (indicated in red) are shown. Clade labels are shown. (B) Next-generation sequencing data statistics of the six Kenyan stool samples. (TIF)</p

Detection of SARS-CoV-2 antibody among mothers and infants over time.

(A) SARS-CoV-2 antibody levels over time relative to the first seropositive time point (0 months). Individual patterns in infants (top) and mothers (bottom) are shown in grey. Grouped by maternal HIV status, running means are shown for HIV-uninfected women or HIV-unexposed infants in black and women living with HIV or HIV-exposed infants in red. Limit of detection denoted by dashed vertical line. (B) and (C) are Kaplan-Meier hazard functions for participants’ estimated time to loss of detectable antibodies stratified by maternal HIV status and infant HIV exposure, respectively. HEU = HIV-exposed uninfected, HUU = HIV-unexposed uninfected. The risk period for loss of detectable antibody begins at the participant’s first positive serology test and ends either at the time of loss of detectable antibodies (estimated as the midpoint between the last positive test and first negative test after a positive test) or at the time of the most recent positive test.</p

Incidence of SARS-CoV-2 infection in postpartum Kenyan women and their infants from May 1, 2020 to February 1, 2022.

Incidence of SARS-CoV-2 infection in postpartum Kenyan women and their infants from May 1, 2020 to February 1, 2022.</p