The authors present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, pepper mild mottle virus (PMMoV) RNA, and crAss-like phage (crAssphage) DNA from 48 COVID-19 patients. Abundances were quantified using (RT)-ddPCR assays targeting the N and ORF1a genes. The data were obtained from supplementary material.

The paper quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 disease severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infections. Blood was collected from hospitalized participants, non-hospitalized symptomatic individuals seeking care at a respiratory infection clinic, and participants who had recovered from known COVID-19 disease. Nasopharyngeal swabs, oropharyngeal swabs, sputum, and urine were collected from hospitalized participants. Data were obtained from the supplementary materials.

The authors present viral load kinetics for the first two confirmed COVID-19 patients with mild to moderate illness in Korea. Swabs, sputum, serum, plasma, urine, and stool samples were collected throughout the illness. Cycle threshold (Ct) values were quantified using rRT-PCR targeting the RdRp and E genes. Data were obtained from the supplementary material.

The authors measured SARS-CoV-2, pepper mild mottle virus (PMMoV), and human mitochondrial DNA (mtDNA) in longitudinal stool samples collected from 42 COVID-19 patients for up to 42 days after the first sample collection date. Abundances were quantified using Digital PCR assays targeting the N1 genes. The symptom data (e.g., fever, cough, short of breath, diarrhea, headache, loss of smell, loss of taste, etc.) is currently not included in this data.

Lui et al. report on a prospective cohort study of patients with variable disease severity. Viral loads for positive samples were extracted from Tbl. 1 in the supplementary material, and negatives were extracted manually from Fig. 1 and a figure in the supplementary material. The level of quantification was extracted from methods in the supplementary material. Data for other specimen types, including nasopharyngeal swabs, sputum, plasma, and urine, are also available in the source but have not yet been included here.

Fecal samples were collected from 113 participants “in a randomized controlled study of Peg-interferon lambda-1a versus a placebo control for the treatment of mild to moderate COVID-19.” A total of 7,563 measurements were taken for 679 samples using seven distinct assays; assays were typically run in duplicates.

Samples were initially collected using OMNIGene GUT collection tubes (OG) but subsequently replaced with Zymo DNA/RNA shield fecal collection tubes (ZY) because of better performance. There are consequently 14 analytes following the naming convention {target gene E, RdRP, N1, or N2}-{genomic RNA (gRNA) or subgenomic RNA (sgRNA)}-{quantification method RT-qPCR or ddPCR}-{collection tube OG or ZY}.

The reference event for temporal offsets in days is the day of enrollment.

This study evaluated the transmission potential of COVID-19 by examining viral load over time. Over six weeks, 230 healthcare personnel underwent 528 tests at the Cleveland Clinic. Cycle threshold (Ct) values were obtained using RT-PCR targeting the N gene, and viral loads were calculated. Data were obtained from the combined dataset in the supplementary materials of Challenger et al. BMC Medicine (2022) 20:25 (https://doi.org/10.1186/s12916-021-02220-0).

The authors conducted a virological analysis of nine linked cases of COVID-19 in Munich in early 2020. They quantified SARS-CoV-2 RNA gene copies in throat swabs and RNA concentrations in stool and sputum samples. Abundances were quantified using RT-qPCR assays targeting the E and RdRP genes as described in 10.2807/1560-7917.ES.2020.25.3.2000045. Values were programmatically extracted from the figure, resulting in a number of significant figures far exceeding the performance of the assays. The demographic data, including age and sex, are derived from the Challenger et al. BMC Medicine (2022) 20:25 https://doi.org/10.1186/s12916-021-02220-0 supplement combined dataset.