Datasets

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.

This study investigates the duration of norovirus excretion and the viral load in elderly patients with norovirus gastroenteritis. Conducted in aged-care facilities, the study involved 13 elderly patients aged 60-98 years. A total of 63 fecal samples were collected and analyzed using real-time quantitative polymerase chain reaction assays. The study found that the average period of norovirus excretion was 14.3 days, with viral loads varying significantly over time. The findings suggest that monitoring viral load around 16 days after symptom onset could be useful for managing norovirus infections in such settings.

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.

This study investigates the magnitude and duration of Norwalk virus shedding in feces following experimental human infection. Conducted at Baylor College of Medicine from September 2004 to October 2006, the study involved 16 healthy adults aged 18-50 who were inoculated with Norwalk virus. Participants were monitored for clinical signs and symptoms, and fecal samples were collected and analyzed using RT-PCR and ELISA methods. The study found that virus shedding began as early as 18 hours post-inoculation and lasted a median of 28 days, with peak virus titers occurring after symptom resolution. The study provides insights into the prolonged fecal excretion of norovirus and its implications for transmission.

Retrospective analysis of a prophylactic seasonal RT-PCR screening program (Dec 2016 to Apr 2017) for influenza A/B and RSV among hospitalized asymptomatic patients on pediatric and adult hemato-oncological wards at Hannover Medical School (Germany). Respiratory specimens (mostly nasopharyngeal swabs; some pharyngeal lavage/oral wash) were tested by real-time RT-PCR and viral load changes were assessed semi-quantitatively using PCR cycle threshold (Ct) values. The CSV-provided data include longitudinal Ct values over days after the initial positive screening timepoint for 6 asymptomatic patients (5 influenza A; 1 RSV).

Longitudinal RSV viral load study in 51 naturally infected, hospitalized RSV-PCR+ infants (<1 year old) during the 2014–2015 RSV season. Quantitative nasal aspirate/nasal wash samples were collected serially during hospitalization and follow-up visits up to ~1 month after symptom onset. Viral load was measured using TaqMan-based real-time qRT-PCR targeting the RSV N gene with subtype-specific primers (RSV-A and RSV-B), and results were reported as plaque-forming unit equivalents per mL.

Prospective cohort of 25 high-risk contacts of clade IIb monkeypox virus (MPXV) cases recruited in Antwerp, Belgium (June 24–July 31, 2022). Participants performed daily self-sampling (anorectal, genital, saliva) and attended weekly clinic visits (blood, oropharyngeal, etc.). Samples were tested by an in‑house MPXV PCR (targeting the MPXV-TNF receptor gene) on an Applied Biosystems QuantStudio. Study documents presymptomatic MPXV DNA detection (Ct values) and culture of replication-competent virus from presymptomatic anorectal samples.

Prospective birth community-cohort study in Manguinhos, Rio de Janeiro, Brazil (2014–2018) following infants through <1 year of age who received Rotarix (RV1) oral rotavirus vaccine. Stool samples were collected and screened for rotavirus A shedding using RT-qPCR (Ct), with RV1 G1P[8] characterization and VP8* sequencing (including F167L mutation). This extraction captures individual Ct values and days post-vaccination (or pre-dose/non-vaccinated sampling) from the provided CSV/table for Le(a+b+) secretor children.

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/YWAN446/cdc2024nhphrn/tree/main/).

This study evaluates the use of Rotarix™ as a live-attenuated challenge agent in a cohort of 22 Zambian infants. The infants received two standard doses of the vaccine at 6 and 10 weeks of age. The study aimed to assess stool shedding of rotavirus using NSP2 qPCR, with samples collected on days 0, 3, 5, 7, 14, and 28 following each dose. The primary outcome was the viral shedding index, calculated as the average natural logarithm of viral copies per gram of stool. The study found that viral shedding was high after the first dose but reduced after the second dose, indicating the induction of mucosal immunity. The study supports the use of Rotarix as a live-attenuated infection challenge model.

Hospital-based observational study in adults admitted to Foch hospital (Suresnes, France) between Jan 1 and Mar 31, 2021. Systematic nasopharyngeal swab testing using the Alinity M RESP-4-Plex RT-PCR assay identified 8 RSV-positive adults (patients A–H). This extraction captures RSV RT-PCR cycle threshold (Ct) values over time from a figure-derived CSV; symptomatic participants are timed from symptom onset, and asymptomatic participants are timed from first positive PCR (confirmation date).

This study describes the first 12 COVID-19 patients identified in the United States, tracking their clinical progression and virological characteristics. SARS-CoV-2 was detected by real-time reverse transcriptase PCR in stool, urine, serum, sputum, oropharyngeal and nasopharyngeal swabs for 2 to 3 weeks after symptom onset. Results were reported in cycle threshold (Ct) values.

This study investigates the shedding and replication of the RV3-BB human neonatal rotavirus vaccine in a phase IIa trial conducted in Dunedin, New Zealand, from January 2012 to April 2014. The trial involved 96 healthy, full-term neonates who were randomly assigned to receive three doses of the RV3-BB vaccine or placebo. The study aimed to characterize rotavirus shedding in stool samples collected on days 3-7 post-vaccination using VP6 RT-PCR. The trial included neonatal and infant vaccination schedules, with the first dose administered at 0-5 days or 8 weeks after birth, respectively. The study found significant rotavirus shedding in both schedules, with >70% of participants shedding the vaccine virus. The study used quantitative qRT-PCR to measure stool viral load and assessed the relationship between viral load and serological response.

Virological and immunological study of patients hospitalized in Ho Chi Minh City (2004–2005) comparing 18 individuals with influenza A(H5N1) (13 fatal, 5 non-fatal) and 8 patients with human influenza (H3N2/H1N1). Pharyngeal (throat) and nasal swabs, rectal swabs and blood were collected; viral RNA was quantified by real-time PCR targeting a conserved region of the influenza A matrix gene (results expressed as cDNA copies per ml of viral transport medium). The study reports higher pharyngeal viral loads and frequent detection of viral RNA in blood and rectum in H5N1 cases, and elevated plasma cytokine/chemokine levels that correlated with pharyngeal viral load.

Randomized, single-blind, placebo-controlled RSV-A (Memphis 37b) human challenge study in healthy adult volunteers (18–55 years). Participants were inoculated intranasally on study day 0 and received nebulized PC786 (5 mg) or placebo twice daily for 5 days starting ~12 hours after RSV detection or on day 6. RSV viral load was monitored in nasal wash samples by Simplexa RT-qPCR; this extraction includes individual-level measurements digitized to CSV (PatientID, day, value, treatment).

Observational study of previously healthy children <2 years old with naturally acquired RSV infection; RSV load in respiratory secretions was measured by fresh quantitative culture over serial hospital days to evaluate viral dynamics and associations with disease severity outcomes (eg, length of hospitalization, ICU requirement, respiratory failure).

Prospective cohort study of 20 infants (four twin pairs and twelve singletons) admitted to the neonatal intensive care unit at Fujita Health University Hospital (Japan), born Nov 2018–Jun 2020, receiving two doses of Rotarix (RV1). Stool was collected daily from vaccination day (day 0) through day 8 after each dose to quantify fecal RV1 vaccine-strain shedding by RV1-specific qRT-PCR (reported here as gene copies per PCR reaction from figure-derived CSV).

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.

Comparative study of RSV shedding in adult volunteers experimentally challenged with RSV A2, comparing quantitative real-time RT-PCR results with viral culture across multiple postinfection days (0-12 and day 28). CSV-provided measurements represent a time series per subject (PatientID 1-5) with values recorded by day relative to infection/challenge.

Observational substudy of the Influenza Resistance Information Study (IRIS) in immunocompromised patients with influenza. Nasal and throat swabs were analysed by RT-PCR on day 1 and then every 3 days until patients were virus-free to assess viral shedding and emergence of oseltamivir resistance (H275Y). Of 42 enrolled patients, 29 were influenza RT-PCR positive on day 1 (18 adults, 11 children). Resistance (H275Y) was detected in some post-baseline samples; clinical and virological outcomes were described.

Longitudinal cohort study (San Francisco Bay Area, Sep 2020–Oct 2021) comparing nasal SARS-CoV-2 RNA and infectious virus shedding in 84 non-hospitalized adults (52 unvaccinated, 32 fully vaccinated). Participants self-collected anterior nasal swabs daily for up to 14 days and intermittently to day 28. RT-qPCR quantified N and E gene copies/mL using plasmid standards; viral culture (CPE) and plaque assays on Vero-hACE2-TMPRSS2 cells assessed infectious virus. Time values are reported relative to symptom onset. The provided CSV contains per-participant quantitative RT-qPCR measurements for N and E (copies/mL) and vaccination category.

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.

Prospective cohort study of hospitalized infants (<12 months) with acute bronchiolitis at Soroka Medical Center. For each infant, paired respiratory specimens were collected at hospital admission (day 0) and ~48 hours later (day 2): nasopharyngeal swabs and nasal lavage (nasal wash) fluid, each placed in two different transport media (UTM and VCM). Quantitative RT-PCR viral load results (reported as virus particles per mL, vp/mL) are provided here from figure-derived CSV data, stratified by specimen type and transport medium; RSV subtype (A or B) is available per patient in the CSV.

This study investigates a nosocomial outbreak of acute gastroenteritis caused by rotavirus and norovirus at a pediatric hospital in Rio de Janeiro, Brazil, in May 2019. The outbreak affected 30 individuals, including children and hospital staff. Nine stool samples were analyzed using RT-qPCR to detect and quantify the viruses. The study identified the circulation of equine-like G3P[8] DS-1-like rotavirus and GII.4 Sydney[P16] norovirus. The study emphasizes the importance of active surveillance and prevention measures to control nosocomial infections in hospital settings.

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.

Prospective NICU study (Oct 2014–Dec 2015) assessing fecal shedding and dissemination of rotavirus vaccine strains after oral vaccination with RotaTeq (RV5) or Rotarix (RV1). Nineteen vaccinated infants (9 RV5, 10 RV1) and 49 nearby unvaccinated infants were enrolled; stool (and some rectal swab) samples were serially collected and tested by vaccine-strain specific real-time RT-PCR. Vaccine-strain shedding was detected in all vaccinated infants but no vaccine genomes were detected in any samples from unvaccinated infants. The provided CSV contains cycle-threshold (Ct) time-series (days after vaccination) extracted from Figure 2 for RV5-vaccinated infants.

Study of 14 patients with novel influenza A H7N9 admitted to Shanghai Public Health Clinical Centre in April 2013. Viral RNA was quantified sequentially in throat (oropharyngeal) swabs, stool, serum, and urine; viral sequencing of neuraminidase (NA) was performed to assess emergence of resistance. Paper links reduction in viral load after antivirals with improved outcome and reports persistent high viral load and emergence of NA Arg292Lys resistance in some patients. The provided CSV contains 69 measurements from patients with IDs 1, 2, and 3 across the four specimen types.

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 investigates the differentiation between wild-type Group A rotaviruses (RVA) and vaccine strains in cases of suspected horizontal transmission and adverse events following vaccination. Conducted in Germany, the study involved 74 patients, including 68 vaccinated children and 6 cases of suspected horizontal transmission, from 2009 to 2019. The study utilized a PCR-based algorithm to distinguish between vaccine-like and wild-type RVA strains in stool samples. The study found that vaccine-like virus was detected in 46 samples, wild-type RVA in 6 samples, and mixed infections in 3 samples. The study also explored co-infections with other pathogens and the shedding of vaccine strains in immunocompromised patients.

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.

This study conducted a survey of hepatitis A virus (HAV) and hepatitis E virus (HEV) in patients and sewage in Cairo, Egypt. The study found that HAV (genotype IB) was predominant over HEV (genotype 3) and was circulating in the population and the environment. The study involved analyzing patient samples for HAV viral load and genotype, as well as measuring bilirubin levels. The reference event for the measurements was symptom onset or diagnosis.

Outbreak investigation of pandemic (H1N1) 2009 among hospital-associated retreat attendees in Seattle (September 2009). Sixteen health care personnel with laboratory-confirmed infection provided serial self-collected nasal wash specimens (every Mon/Wed/Fri) and symptom logs; specimens were tested by real-time RT-PCR (quantified as RNA copies/mL) and rapid culture. Study evaluated duration of viral RNA detection and culture positivity relative to symptom onset and fever, and found RT-PCR detection lasted longer (3–13 days) than culture (3–10 days). All infected HCP received oseltamivir early in illness.

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 investigates the role of vomiting in norovirus transmission using data from human challenge studies with GI.1 Norwalk virus, GII.2 Snow Mountain virus, and a pilot study with GII.1 Hawaii virus. The study involved healthy adult subjects who were challenged with norovirus and monitored for symptoms, including vomiting. Emesis samples were collected and analyzed for viral titers using strain-specific quantitative RT-PCR. The study found that vomiting is a common symptom in norovirus infection and contributes significantly to environmental contamination and transmission risk. The study provides quantitative data on virus titers in emesis, which is critical for risk assessment and control measures.

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 followed 68 people (90% male) during the NBA 2019 to 2020 season with frequent RT-qPCR to map SARS-CoV-2 viral RNA trajectories and 46 had acute infections. A single low Ct (<30) strongly indicates acute infection, and a second PCR within 48 hours helps tell whether someone is early (proliferation) or late (clearance) in infection.

Study of influenza virus shedding in pediatric patients treated with laninamivir during the 2011-2012 influenza season in Niigata Prefecture, Japan. Nasal discharge samples were collected at three visits (before treatment, 3-5 days after first visit, and 5-9 days after first visit) and assessed by virus culture (TCID50) and quantitative real-time PCR targeting the M gene. The paper enrolled 28 children (7 infected with influenza A(H3N2) and 21 with influenza B) and evaluated duration of fever, virus isolation, viral RNA detection rates, and antiviral susceptibility. The CSV data provided contain quantitative viral RNA measurements (genome-equivalent copies) for a subset of participants.

Hospital-based observational study in Delft, The Netherlands (Nov 2017–Apr 2020) of 6 hospitalized infants (0–2 years) with laboratory-confirmed RSV-B infection (two with rhinovirus co-infection). Longitudinal RSV (and RV where applicable) RNA detection was performed by qRT-PCR (Ct values; Ct>40 negative) on nasopharyngeal aspirates from infants and nose/throat swabs from parents; air sampling around infants used a six-stage Andersen cascade impactor with subsequent qRT-PCR, and infectious RSV was assessed by culture (TCID50) on HEp-2 cells (not extracted here because no individual-level TCID50 values were provided in the supplied CSV/table extraction). Times in the provided figure-derived CSV are treated as days relative to symptom onset (reference event).

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.

Prospective post-marketing study of faecal shedding after oral Lanzhou lamb rotavirus vaccine (LLR) in children in China (September–November 2011/2012). 114 children provided 1,184 stool samples collected for 15 days post-vaccination. Shedding was assessed by enzyme immunoassay (EIA, Oxoid Prospect ELISA kit, EIA positive threshold OD=0.21) and by real-time RT-PCR targeting the NSP3 gene (quantified by plasmid standard curve). Viral loads in PCR-positive samples ranged from <1.0×10^3 to 1.9×10^8 copies/g stool. Reference time for all measurements is days post-vaccination.

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.

This study, conducted from November 2002 to November 2003, investigated the presence of hepatitis A virus (HAV) RNA in saliva and serum samples from six acutely infected patients with HAV viremia. The study was conducted at a hospital in France, and the participants were aged between 15 and 47 years. The study aimed to explore the potential of using saliva samples for outbreak investigations due to the ease of collection. HAV RNA was detected in the saliva of five out of six patients, with viral loads in saliva being 2 logs lower than in serum. The study utilized RT-PCR and real-time PCR assays for detection and quantification, with a focus on the VP1/2A junction of the HAV genome. The study also included phylogenetic analysis to determine HAV genotypes.

This study investigated the shedding of porcine circovirus type 1 (PCV-1) DNA and Rotavirus group A (RVA) RNA in 33 infants aged approximately 2 months following the first dose of Rotarix® vaccine. Stool samples were collected serially post-vaccination and analyzed using molecular methods. The study found that 21% of infants did not shed RVA RNA beyond day 3, suggesting a lack of vaccine virus replication in some cases. The study was conducted in Atlanta, Georgia, and involved both full-term and preterm infants. The analysis used quantitative real-time RT-PCR and qPCR assays to detect viral RNA and DNA in stool samples.

Prospective surveillance in a foster home setting assessing shedding and transmission of rotavirus vaccine strains. Stool samples were collected and tested by quantitative real-time RT-PCR. The study included 4 RV-vaccinated infants (160 samples) and 23 unvaccinated infants (766 samples). Vaccine-strain RNA was persistently detected in stool from the four vaccine recipients and in one unvaccinated infant (who had been vaccinated prior to enrollment). Quantitative RT-PCR data showed a peak RNA load about 1 week after vaccination followed by gradual decrease. Study suggests limited transmission of vaccine strains in close-contact environment.

This study investigates the duration of viral shedding in patients from two outbreaks and four sporadic cases of norovirus (NoV) infections. The research highlights the longest period of viral shedding into feces, which was 173 days in an inpatient from one outbreak case. The study also examines the VP1 sequence from two long-term viral shedding cases, revealing several mutations. The findings suggest that the long-term carrier state of norovirus infection contributes to the generation of escape mutants by host immunoselection.

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 investigates norovirus (NoV) infections in Toyama Prefecture, Japan, during fiscal year 2006, focusing on viral shedding in feces. The study involved 30 individuals from a local hotel outbreak in May 2006, with stool specimens collected and analyzed using real-time PCR. Two employees exhibited long-term viral shedding, with single base substitutions in the NoV capsid region observed. The study highlights the potential for NoV evolution in the gastrointestinal tract, with genetic changes occurring during the infectious course. The research was supported by a Health Labor Sciences Research Grant from the Japanese Ministry of Health, Labor, and Welfare.

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.

Methods/assay standardization study that developed and analytically validated an RT-qPCR absolute quantification assay for influenza A (M gene target) using a plasmid DNA standard. The assay (WHO 2009 M-gene RT-qPCR) was applied to clinical respiratory specimens from a cohort at Hospital de Clínicas, Universidade Federal do Paraná (Curitiba, Brazil). Serial viral-load measurements were obtained for 19 hospitalized SARI patients with two collections (timed by days from symptom onset), including immunocompetent and immunosuppressed participants, to assess viral-load dynamics.

Prospective monocentric observational study in Bologna, Italy (IRCCS Policlinico di Sant’Orsola) enrolling previously healthy infants (≤1 year) hospitalized for a first episode of RSV bronchiolitis (Mar 2019–Nov 2021). Nasopharyngeal aspirates were collected at admission (d0) and every 48 hours during hospitalization; RSV-positive-only samples were quantified retrospectively by RT-qPCR targeting the RSV matrix gene and normalized to human DNA (reported as log10 copies/ng hDNA). This extraction uses the provided figure-derived CSV time series (PatientID-level) with time in days from hospital admission.

Hospital-based study in Italy during the 2011–2012 influenza season assessing influenza A(H3N2) viral kinetics and emergence of oseltamivir resistance. Sequential respiratory samples were analyzed from treated and untreated patients; neuraminidase (NA) sequencing and clonal analysis were performed in patients unresponsive to oseltamivir, identifying resistant mutations including R292K, E119V, N294S, and Del247–250. Figure-derived quantitative viral load time series are available for multiple patients by immune status and treatment, and Table 1 reports clonal proportions of NA mutations over time for two immunocompromised oseltamivir-unresponsive patients (Pavia/14 and Pavia/27).

This study investigates a gastroenteritis outbreak in 2013 in a low-income community in Rio de Janeiro, Brazil, focusing on the presence of enteric viruses. The study involved nine patients, with stool samples collected and analyzed for various viruses, including adenovirus. The outbreak was characterized by symptoms such as fever and diarrhea, and adenovirus A12 was identified as the primary pathogen. The study utilized TaqMan real-time PCR to assess viral loads in stool samples, revealing high viral loads in patients with adenovirus A12. The research highlights the importance of identifying unique viral agents in regions with routine RVA vaccination.

Study of H1N1pdm09 viral load (VL) in respiratory samples collected 2009-2013 at a tertiary hospital in São Paulo, Brazil. Samples from asymptomatic (AS), symptomatic outpatients (OP) and hospitalised patients (HP) were tested by quantitative one-step real-time RT-PCR targeting the M gene; VL reported as Log10 RNA copies/mL in the paper. A subset of 10 hospitalised patients treated with oseltamivir were followed longitudinally and serial VL measurements (days of treatment) are provided (Fig.2 / CSV).

Dose-escalation controlled human infection study (Feb 2024–Mar 2025) evaluating aerosolized inoculation of influenza A/Perth/16/2009 (H3N2) using two devices (FMAG and a medical nebulizer) in 14 healthy adults (aged 18–49). Participants were challenged in an inpatient unit and monitored daily; molecular (qPCR) and infectious (plaque assay) viral loads were measured at multiple upper airway sites (nasopharynx, anterior nares, buccal, oropharynx, saliva). Study assessed viral shedding kinetics, symptom development (MMID), safety, and seroconversion.

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.

Human RSV challenge study in adults analyzing high-resolution viral kinetics using mathematical models. Figure-derived CSV data provide RSV RNA concentrations (gc/mL) and infectious virus titers (pfu/mL) over days post-exposure for individual participants (PatientID). The study report the specimen as nasal samples, and we consider these to be nasopharyngeal aspirates based on the methods description. The study does not provide assay details for the viral RNA or infectious virus measurements.

Retrospective single-season (2010/2011) cohort study of lung transplant recipients at Zurich University Hospital. Laboratory-confirmed influenza A or B infections (22 infections in 21 patients) were diagnosed by nasopharyngeal swab and real-time RT-PCR. Patients received empirical oseltamivir and serial weekly swabs were performed until virologic results were negative. Study reports Ct values from nasopharyngeal swabs (used here as cycle-threshold measurements relative to symptom onset). Prolonged viral shedding (>=7 days) was common.

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.

Controlled human infection study (Emory University Hospital, July–September 2022) in which eight adults were intranasally inoculated with influenza A/Perth/16/2009 (H3N2). Viral shedding was measured in nasopharyngeal swabs, saliva, nasal lavage fluid, stool, urine, exhaled breath aerosols, and environmental surface swabs. Six of eight participants became PCR-positive; infectious virus was measured by plaque assay (MDCK cells) in NP swabs, saliva, and nasal lavage fluid. Respiratory particle emissions were sampled during breathing and speaking and analyzed by ddPCR for viral RNA. Clinical symptom scores and serology (HAI, MN) were also collected.

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.

Longitudinal study of norovirus GII.4 faecal shedding during four nosocomial outbreaks (2009-2011) in a tertiary-care hospital and three nursing homes in The Netherlands. Real-time quantitative RT-PCR was used to measure norovirus genome concentrations in stool from symptomatic and asymptomatic patients and healthcare workers. The study includes 102 subjects with 230 faecal samples overall; data provided here include the CSV subset of 74 sampled measurements (with both Ct and concentration values). Ct readings were done once and calibrated against an RNA standard; Ct=40 was considered the diagnostic detection limit. The analysis compared shedding dynamics (peak, time-to-peak, duration, AUC) between symptomatic and asymptomatic infections.

This study investigates the duration and level of hepatitis A virus (HAV) excretion in blood and feces of 27 patients with acute hepatitis A, with a median age of 33 years, over a period of up to 26 weeks. The study also includes single blood donations from 55 other patients with acute HAV, with a median age of 32 years. Virus loads were quantified using competitive nested RT-PCR. The study found that HAV was excreted in feces for a median period of 81 days after disease onset, with high levels of excretion in the first month. Viraemia was detected for a median period of 42 days. The study highlights the potential for prolonged infectiousness and the need for awareness in blood banks regarding viraemia persistence.

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.

This study investigates norovirus genogroup II excretion during an outbreak of gastroenteritis in an aged-care facility in New South Wales, Australia, in June 2003. The outbreak affected 28 patients and 43 staff members. Stool specimens were collected from 14 volunteers (6 males and 8 females, median age 85 years) every 3 to 7 days from the onset of illness until the second consecutive negative result. The study aimed to determine the duration of viral excretion and the viral load decay rate using quantitative PCR assays. The average duration of viral shedding was 28.7 days, with a viral decay rate of 0.76 per day.

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.

Observational study of RSV infection in adults (Rochester, New York; winters 2005–2008) including outpatients (mild disease) and hospitalized patients (severe disease). RSV RNA was detected by real-time RT-PCR and viral titers were quantified by quantitative RT-PCR and expressed as PFU equivalents per mL. Serial respiratory specimens were collected during illness (daily when possible) until two consecutive RT-PCR negative samples; additional planned follow-ups occurred around days 12–16 and 25–32 after symptom onset. Figure-derived CSV data provide individual-level PFU/mL viral load measurements over time for a subset of participants. The data used here were extracted from Supplementary Figures 3 of “Relating In Vivo Respiratory Syncytial Virus Infection Kinetics to Host Infectiousness in Different Age Groups,” which digitized and re-plotted the original viral-load curves from this study.

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.

This study, conducted between May 2008 and February 2009 at the Broadway Practice of the Ambulatory Care Network of New York-Presbyterian Hospital, examined fecal shedding of the pentavalent rotavirus vaccine (RV5) in infants aged 6 to 12 weeks following their first dose. The study involved 198 enrolled infants, with 103 returning stool collection kits. Rotavirus antigen was detected in 21.4% of the kits. The study used enzyme immunoassay (EIA) and RT-PCR to detect vaccine-type rotavirus in stool samples collected over 9 days post-vaccination. The findings suggest potential for horizontal transmission of vaccine virus, particularly in households with immunocompromised individuals.

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.