18147 biomarker measurements for 1630 participants from 30 studies. And counting.

Clinical characteristics of pediatric SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19) in Kuwait

Identifier

alsharrah2020clinical

Participants

29

Measurements

75

Biomarkers

SARS-CoV-2

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.

Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage

Identifier

arts2023longitudinal

Participants

48

Measurements

1502

Biomarkers

SARS-CoV-2 PMMoV crAssphage

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.

SARS-CoV-2 viral load is associated with increased disease severity and mortality

Identifier

fajnzylber2020sars

Participants

88

Measurements

434

Biomarkers

SARS-CoV-2

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.

Hydroxychloroquine and azithromycin as a treatment of COVID-19:results of an open-label non-randomized clinical trial

Identifier

gautret2020hydroxychloroquine

Participants

19

Measurements

126

Biomarkers

SARS-CoV-2

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.

Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study

Identifier

hakki2022onset

Participants

50

Measurements

1428

Biomarkers

SARS-CoV-2

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.

Sequential Analysis of Viral Load in a Neonate and Her Mother Infected With Severe Acute Respiratory Syndrome Coronavirus 2

Identifier

han2020sequential

Participants

2

Measurements

51

Biomarkers

SARS-CoV-2

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.

Quantitative analysis of fecal sapovirus shedding: identification of nucleotide substitutions in the capsid protein during prolonged excretion

Identifier

iwakiri2009quantitative

Participants

17

Measurements

41

Biomarkers

sapovirus

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.

Daily Longitudinal Sampling of SARS-CoV-2 Infection Reveals Substantial Heterogeneity in Infectiousness

Identifier

ke2022daily

Participants

60

Measurements

1699

Biomarkers

SARS-CoV-2

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.

Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea

Identifier

kim2020viral

Participants

2

Measurements

170

Biomarkers

SARS-CoV-2

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.

Viral kinetics of SARS-CoV-2 in asymptomatic carriers and presymptomatic patients

Identifier

kimse2020viral

Participants

13

Measurements

61

Biomarkers

SARS-CoV-2

The authors measured SARS-CoV-2 in longitudinal oropharyngeal swab samples collected from 71 COVID-19 patients between February 4 and April 7, 2020.

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo

Identifier

lavezzo2020suppression

Participants

141

Measurements

526

Biomarkers

SARS-CoV-2

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

Clinical and virological data of the first cases of COVID-19 in Europe: a case series

Identifier

lescure2020clinical

Participants

5

Measurements

42

Biomarkers

SARS-CoV-2

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.

Longitudinal Fecal Shedding of SARS-CoV-2, Pepper Mild Mottle Virus, and Human Mitochondrial DNA in COVID-19 Patients

Identifier

liu2024longitudinal

Participants

42

Measurements

465

Biomarkers

SARS-CoV-2 PMMoV mtDNA

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.

Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19

Identifier

lui2020viral

Participants

11

Measurements

43

Biomarkers

SARS-CoV-2

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.

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection

Identifier

natarajan2022gastrointestinal

Participants

113

Measurements

7563

Biomarkers

SARS-CoV-2

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.

Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study

Identifier

peiris2003clinical

Participants

14

Measurements

42

Biomarkers

SARS

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.

Epidemiological Correlates of Polymerase Chain Reaction Cycle Threshold Values in the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Identifier

salvatore2020epidemiological

Participants

93

Measurements

223

Biomarkers

SARS-CoV-2

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.

Assessing Viral Shedding and Infectivity of Tears in Coronavirus Disease 2019 (COVID-19) Patients

Identifier

seah2020assessing

Participants

17

Measurements

134

Biomarkers

SARS-CoV-2

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.

Distribution of Transmission Potential During Nonsevere COVID-19 Illness

Identifier

shrestha2020distribution

Participants

230

Measurements

528

Biomarkers

SARS-CoV-2

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).

Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients

Identifier

tan2021early

Participants

12

Measurements

82

Biomarkers

SARS-CoV-2

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.

Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States

Identifier

team2020clinical

Participants

12

Measurements

121

Biomarkers

SARS-CoV-2

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.

Individual Correlates of Infectivity of Influenza A Virus Infections in Households

Identifier

tsang2016individual

Participants

478

Measurements

1154

Biomarkers

influenza

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.

Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in COVID-19: a Case Series

Identifier

vetter2020daily

Participants

5

Measurements

74

Biomarkers

SARS-CoV-2

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.

Fecal viral shedding in COVID-19 patients: Clinical significance, viral load dynamics and survival analysis

Identifier

wang2020fecal

Participants

11

Measurements

112

Biomarkers

SARS-CoV-2

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

Virological assessment of hospitalized patients with COVID-2019

Identifier

woelfel2020virological

Participants

9

Measurements

382

Biomarkers

SARS-CoV-2

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.

Prolonged viral shedding in feces of pediatric patients with coronavirus disease 2019

Identifier

xing2020prolonged

Participants

1

Measurements

36

Biomarkers

SARS-CoV-2

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.

Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding

Identifier

xu2020characteristics

Participants

8

Measurements

107

Biomarkers

SARS-CoV-2

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.

Laboratory Diagnosis and Monitoring the Viral Shedding of SARS-CoV-2 Infection

Identifier

yang2020laboratory

Participants

28

Measurements

361

Biomarkers

SARS-CoV-2

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.

Upper Respiratory Tract Levels of Severe Acute Respiratory Syndrome Coronavirus 2 RNA and Duration of Viral RNA Shedding Do Not Differ Between Patients With Mild and Severe/Critical Coronavirus Disease 2019

Identifier

yilmaz2020upper

Participants

54

Measurements

349

Biomarkers

SARS-CoV-2

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.

Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore

Identifier

young2020epidemiologic

Participants

18

Measurements

216

Biomarkers

SARS-CoV-2

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).