This study measured SARS-CoV-2 detected by real-time reverse transcriptase PCR in paired oropharyngeal and nasopharyngeal samples from 33 COVID-19 patients in Jaber Alahmad Hospital (JAH). Cycle threshold (Ct) value for E and RdRP genes were measured using Tib MolBiol’s LightMix.

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 INHERENT study, part of the CDC funded Nursing Home Public Health Response Network (NHPHRN), examined SARSCoV2 shedding in nursing home residents and staff. It characterized the viral shedding kinetics including proliferation, peak, and clearance using qRTPCR, antigen testing, genetic sequencing, and culture. The original dataset is published and updated on their GitHub repository (https://github.com/abtassociates/CDC_NHPHRN/blob/main/).

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.

This study evaluated the effect of hydroxychloroquine on respiratory viral loads. Six patients were asymptomatic, 22 exhibited upper respiratory tract infection symptoms, and eight showed lower respiratory tract infection symptoms. Only 19 patients with a known onset of symptoms were included in the analysis below. Data for the nasopharyngeal swab results were obtained from the combined dataset in the supplementary materials of Challenger et al. (2022). Attributes of drug treatments were sourced from the supplementary materials of the original paper.

Through a prospective, longitudinal, community cohort study that captures the critical growth phase and peak of viral replication, the goal is to characterize the window of SARS-CoV-2 infectiousness and its temporal relationship with symptom onset.

The study reports SARS-CoV-2 viral loads in different specimen types for a neonate and her mother diagnosed on 2020-03-20. The study includes nasopharyngeal, oropharyngeal, stool, plasma, saliva, and urine samples. Viral loads were extracted manually from Figure 1 using WebPlotDigitizer.

This study quantifies Sapovirus (SaV) RNA shedding in stool from two outbreak cases using real-time RT-PCR, revealing that SaV excretion generally declines within two weeks but can persist at high concentrations for up to four weeks in some individuals. The study also identifies nucleotide substitutions in the VP1 gene during prolonged excretion, suggesting potential viral evolution.

This study analyzed viral load data from 25,381 German cases, including 9519 hospitalized patients, 6110 PAMS cases from walk-in test centers, 1533 B.1.1.7 variant infections, and the viral load time series of 4434 (mainly hospitalized) patients. Viral load results were then combined with estimated cell culture isolation probabilities, producing a clinical proxy estimate of infectiousness. Data were obtained from the ‘viral-load-with-negatives.tsv’ dataset in the GitHub repository of Jones et al. (2021). Samples lacking a known onset date or a detected positive test result were filtered out.

The authors studied the dynamics of infectious virus and viral RNA shedding for SARS-CoV-2 during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. Nasal swab and saliva samples were collected daily and tested for University of Illinois at Urbana-Champaign faculty, staff, and students (during the fall of 2020 and spring of 2021) who reported a negative RT-qPCR test result in the past 7 days and were either within 24 h of a positive RT-qPCR result or within 5 days of exposure to someone with a confirmed positive RT-qPCR result.

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 in longitudinal oropharyngeal swab samples collected from 71 COVID-19 patients between February 4 and April 7, 2020.

This study analyzed densely sampled longitudinal RT-qPCR data from 65 individuals infected with SARS-CoV-2, including 7 infected with the B.1.1.7 (Alpha) variant, using each person’s lowest Ct value as the reference event time point. Inclusion criteria required each individual to have at least 5 positive PCR tests (Ct < 40), including at least one with Ct < 35. Ct value were collected using the Roche cobas target 1 assay and converted to estimated RNA viral concentrations via a standard curve and log-linear transformation.

This study was conducted in the Italian municipality of Vo. Lockdown was implemented after first death of pneumonia was reported. Two surveys and virus tests were conducted with the first survey near the start of lockdown and the second one at the end of lockdown

The authors followed five patients admitted to Bichat-Claude Bernard University Hospital (Paris, France) and Pellegrin University Hospital (Bordeaux, France) and diagnosed with COVID-19 by semi-quantitative RT-PCR on nasopharyngeal swabs. We assessed patterns of clinical disease and viral load from different samples (nasopharyngeal and blood, urine, and stool samples), which were obtained once daily for 3 days from hospital admission, and once every 2 or 3 days until patient discharge. Stool samples only have positive and negative results (currently not included in this data). The data was obtained from Goyal et al. 2020 for the nasopharyngeal swab results in 4 patients.

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 examined whether and to what extent SARS-CoV-2 is detectable in the feces of lactating women and their breastfed infants following maternal COVID-19 diagnosis. A total of 57 maternal-infant dyads provided maternal and/or infant fecal samples, including 33 dyads in the COVID-19 group and 24 dyads in the healthy group. Fecal samples were collected from each mother and child in both the groups and telephone surveys administered during the first week following enrollment (1, 2-6 and 7 day) and again around 2, 3, 4, and 8 wk following enrollment for COVID-19 group, and two separate days during the first week after enrollment (1, 7 day) and again around 3 and 8 wk for healthy group. Since the author didn’t provide the specific time information in the paper, we adopted mean value of time period as our data (4d for 2-6d, 11d for 2wk, 18d for 3wk, 25d for 4wk, 53d for 8wk).

This study measured SARS detected by real-time reverse transcriptase PCR in nasopharyngeal samples from 14 patients who admitted to the United Christian Hospital from the Amoy Gardens housing estate who fulfilled the modified WHO definition of SARS, on days 5, 10, and 15 after symptom onset.

This study was conducted in Utah and Wisconsin between 23 March and 13 May 2020, with testing data collected during a prospective household transmission investigation of outpatient and mild coronavirus disease 2019 cases.

This study investigated the potential transmission of SARS-CoV-2 through tears by detecting the virus using viral isolation and quantitative reverse-transcription polymerase chain reaction (RT-PCR) analysis. A total of 17 COVID-19 patients were enrolled in this prospective study in Singapore after obtaining informed consent. Researchers collected 135 nasopharyngeal swab samples and 32 tear samples throughout the study (all tear samples showed negative results for SARS-CoV-2 on viral isolation and RT-PCR). No evidence of SARS-CoV-2 shedding in tears was observed during the course of the disease. In conclusion, the findings suggest that the risk of SARS-CoV-2 transmission through tears is minimal.

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).

Measured SARS-CoV-2 viral load in the upper respiratory tract, along with SARS-CoV-2-specific antibodies and T cell responses, at multiple time points from acute infection through convalescence or until death.

Respiratory, stool, serum, and urine specimens were submitted for SARS-CoV-2 real-time reverse-transcription polymerase chain reaction (rRT-PCR) testing, viral culture, and whole-genome sequencing. Only nasopharyngeal samples were included in this dataset. Data for the nasopharyngeal swab results were obtained from the combined dataset in the supplementary materials of Challenger et al. (2022), while attributes of hospitalized patients were obtained from the original paper.

The community-based study reports the transmission of Influenza A virus within households from February 2008 through December 2012, focusing on viral loads in nasal and throat swabs from index cases and their household contacts.

The author measured SARS-CoV-2 detected by real-time reverse transcriptase PCR in both oropharyngeal (OPS) and nasopharyngeal (NPS) swabs from five COVID-19 patients in Geneva, Switzerland, up to days 7 and 19 after symptom onset. Cellular and humoral SARS-CoV-2-specific adaptive responses and serology data are currently not included in this dataset.

This study investigates the fecal shedding of SARS-CoV-2 in COVID-19 patients, analyzing viral load dynamics, clinical significance, and survival analysis.

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.

This study characterized the dynamic profiles of SARS-CoV-2 shedding in respiratory and fecal specimens in three children with COVID-19. However, complete specimen test value data were available for only one child. A total of 19 oropharyngeal swab specimens and 17 fecal specimens were collected.

This study reported the epidemiological and clinical features of ten children infected with SARS-CoV-2 confirmed by real-time reverse transcription PCR assay of SARS-CoV-2 RNA and tested for evidence of viral excretion through the gastrointestinal and respiratory tracts. A total of 107 samples in both of nasopharyngeal and rectal swabs were collected and ct values were recorded by days after admission. The standard curve of transforming ct value into viral load was calculated based on the concentration provided by the author.

This study involved 3552 clinical samples from 410 COVID-19 patients confirmed by Guangdong CDC. Oropharyngeal swabs, nasopharyngeal swabs and sputum samples were tested for upper respiratory tract infection, while bronchoalveolar lavage fluid (BALF) was tested for lower respiratory tract infection.

The authors reported longitudinal viral RNA loads from the nasopharynx/oropharynx in patients with mild and severe/critical coronavirus disease 2019 (COVID-19). They also investigated whether the duration of symptoms correlated with the duration of viral RNA shedding. A total of 56 patients were included.

Clinical, laboratory, and radiologic data were collected, including PCR cycle threshold values from nasopharyngeal swabs and viral shedding in blood, urine, and stool. The clinical course was summarized, including the requirement for supplemental oxygen, intensive care, and the use of empirical treatment with lopinavir-ritonavir. The numbers of positive stool, blood, and urine samples were small. Data for the nasopharyngeal swab results were obtained from the combined dataset in the supplementary materials of Challenger et al. (2022). The standard curve was calculated based on the concentration provided by Goyal et al. (2020).

This study investigates the shedding of SARS-CoV-2 RNA across multiple specimen types-including stool, respiratory secretions, urine, and serum-in both symptomatic and asymptomatic COVID-19 patients. It evaluates viral load dynamics and time to clearance across specimen types.

The author measured SARS-CoV-2 detected by real-time reverse transcriptase PCR in fecal samples from 15 hospitalized COVID-19 patients in Hong Kong.