Evaluation and modelling of the performance of an automated SARS-CoV-2 antigen assay according to sample type, target population and epidemic trends

The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patient or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR.

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SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame

10.1101/2021.10.06.21263384 ◽

2021 ◽

Author(s):

Wanda G.H. Han ◽

Arno Swart ◽

Axel Bonacic Marinovic ◽

Dirk Eggink ◽

Johan Reimerink ◽

...

Keyword(s):

Symptom Onset ◽

Symptom Severity ◽

Oral Fluid ◽

Probability Of Detection ◽

Serological Response ◽

Sample Type ◽

Sampling Frame ◽

Rt Pcr ◽

Specific Antibodies ◽

Viral Loads

AbstractThis study investigated the dynamics of SARS-CoV-2 infection and diagnostics in household members of different ages and with different symptom severity after SARS-CoV-2 exposure during the early phase of the pandemic. Households with a SARS-CoV-2 confirmed positive case and at least one child in the Netherlands were followed for 6 weeks. Naso (NP)- and oropharyngeal (OP) swabs, oral fluid and feces specimens were analyzed for SARS-CoV-2 RNA and serum for SARS-CoV-2-specific antibodies. The dynamics of the presence of viral RNA and the serological response was modeled to determine the sampling time-frame and sample type with the highest sensitivity to confirm or reject a SARS-CoV-2 diagnosis. Transmission of SARS-CoV-2 between adults and children within a household was correlated with symptom severity of index cases. In children higher viral loads compared to adults were detected at symptom onset. Early in infection, higher viral loads were detected in NP and OP specimens, while RNA in especially feces were longer detectable. SARS-CoV-2-specific antibodies have a 90% probability of detection from 7 days (total Ig) and 18 days (IgG) since symptom onset. In conclusion this study has shown that on average, children carry higher loads of virus as compared to adults early after infection. For highest probability of detection in SARS-CoV-2 diagnostics early in infection, RT-PCR on NP and OP specimens are more sensitive than on oral fluid and feces. For SARS-CoV-2 diagnostics late after infection, RT-PCR on feces specimens and serology are more valuable.

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COVID-19 Viral Load Not Associated with Disease Severity: Findings from A Retrospective Cohort Study

10.21203/rs.3.rs-144590/v1 ◽

2021 ◽

Author(s):

Abdulkarim Abdulrahman ◽

Saad Mallah ◽

Manaf AlQahtani

Keyword(s):

Cohort Study ◽

Viral Load ◽

Disease Severity ◽

Odds Ratio ◽

Retrospective Cohort ◽

Statistical Significance ◽

Rt Pcr ◽

Cross Sectional ◽

Viral Loads ◽

Using Data

Abstract Background: Being able to use COVID-19 RT-PCR Ct values as simple markers of disease outcome or prognosis would allow for the easy and proactive identification and triaging of high-risk cases. This study’s objective was thus to assess whether a correlation exists between COVID-19 viral loads, as indicated by RT-PCR Ct values, and disease severity, as indicated by respiratory indices Results: A multi-centre cross-sectional retrospective study was conducted, using data obtained from Bahrain’s National COVID-19 Task force’s centralised database. The study period was from May 2, 2020 to July 31, 2020. A multivariable logistic regression was used to assess for a correlation. The covariates adjusted for included sex, age, presentation, and comorbidities. In our cohort, Ct value showed no statistical significance for an association with requirement for oxygenation on admission (Odds ratio 1.046; 95%CI 0.999 to 1.096, p=0.054). Conclusion: Viral load, as indicated by Ct values, did not seem to be associated with requirement for oxygenation on admission in our cohort. We postulate however that time since onset of symptom may have acted as an unaccounted-for confounder.

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Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

Clinical Infectious Diseases ◽

10.1093/cid/ciaa345 ◽

2020 ◽

Vol 71 (15) ◽

pp. 793-798 ◽

Cited By ~ 184

Author(s):

Fengting Yu ◽

Liting Yan ◽

Nan Wang ◽

Siyuan Yang ◽

Linghang Wang ◽

...

Keyword(s):

Viral Load ◽

Target Genes ◽

Single Gene ◽

Clinical Staging ◽

N Gene ◽

Quantitative Detection ◽

Imaging Data ◽

Rt Pcr ◽

Viral Loads ◽

Nasal Swabs

Abstract Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 323 samples from 76 COVID-19–confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based 2 target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. Results In 95 samples that tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy number of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). Four (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral loads ranging from 11.1 to 123.2 copies/test. The viral load of respiratory samples was then compared and the average viral load in sputum (17 429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, P < .001) and nasal swabs (651 ± 501 copies/test, P < .001). Furthermore, the viral loads in the early and progressive stages were significantly higher than that in the recovery stage (46 800 ± 17 272 vs 1252 ± 1027, P < .001) analyzed by sputum samples. Conclusions Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.

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COVID-19 viral load not associated with disease severity: findings from a retrospective cohort study

BMC Infectious Diseases ◽

10.1186/s12879-021-06376-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Abdulkarim Abdulrahman ◽

Saad I. Mallah ◽

Manaf Alqahtani

Keyword(s):

Viral Load ◽

Disease Severity ◽

Retrospective Cohort ◽

Statistical Significance ◽

Clinical Markers ◽

Rt Pcr ◽

Clinical Tool ◽

Cross Sectional ◽

Viral Loads ◽

Using Data

Abstract Background Being able to use COVID-19 RT-PCR Ct values as simple clinical markers of disease outcome or prognosis would allow for the easy and proactive identification and triaging of high-risk cases. This study’s objective was thus to explore whether a correlation exists between COVID-19 viral loads, as indicated by RT-PCR Ct values, and disease severity, as indicated by respiratory indices. Results A multi-centre cross-sectional retrospective study was conducted, using data obtained from Bahrain’s National COVID-19 Task force’s centralised database. The study period ranged from May 2, 2020 to July 31, 2020. A multivariable logistic regression was used to assess for a correlation using data from a total of 1057 admitted COVID-19 cases. The covariates adjusted for included sex, age, presentation, and comorbidities. In our cohort, Ct value showed no statistical significance for an association with requirement for oxygenation on admission (Odds ratio 1.046; 95%CI 0.999 to 1.096, p = 0.054). Conclusion Viral load, as indicated by Ct values, did not seem to be associated with requirement for oxygenation on admission in our cohort. We postulate however that time since onset of symptom may have acted as an unaccounted-for confounder. As such, RT-PCR Ct values may not be a useful prognostic clinical tool in isolation.

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Evaluation of viral loads in patients with SARS-CoV-2 Delta variant infection: Higher loads do not translate into different testing scenarios

10.1101/2021.10.14.21265031 ◽

2021 ◽

Author(s):

Juan Luis Gomez Marti ◽

Ashley Mays ◽

Melissa McCullough ◽

Alan Wells ◽

Tung Phan

Keyword(s):

Viral Load ◽

Upper Airway ◽

The Elderly ◽

Rt Pcr ◽

Allegheny County ◽

Viral Loads ◽

The Third ◽

Age Related ◽

Significant Difference ◽

Fourth Wave

The Delta SARS-CoV-2 variant is very infectious, and it is spreading quickly during this pandemic. In the study, we compared viral loads in surging cases infected with the SARS-CoV-2 Delta variant in the fourth wave of COVID-19 with the three prior waves. The data comprised viral loads from positive cases detected within the UPMC health care system in Allegheny County, Pennsylvania. A total of 2,059 upper airway samples were collected and tested for SARS-CoV-2 positive by RT-PCR during March 2020-September 2021. We did not observe significant difference in viral load difference between the third (December 2020 - January 2021) and fourth (June 2021 - September 2021) waves; however, they had the higher viral load than the first (March 2020 - June 2020) and second waves (June 2020 - August 2020). We did find an age-related effect with the elderly presenting with lower viral loads, which was also seen in the earlier waves. However, the level of viral load in the fourth wave was not sufficient higher to qualitatively change our expected detected rates using various testing modalities.

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A novel RT-LAMP workflow for rapid salivary diagnostics of COVID-19 and effects of age, gender and time from symptom onset

10.1101/2021.06.07.21258288 ◽

2021 ◽

Author(s):

Gerson Shigeru Kobayashi ◽

Luciano Abreu Brito ◽

Danielle De Paula Moreira ◽

Angela May Suzuki ◽

Gabriella Shih Ping Hsia ◽

...

Keyword(s):

Viral Load ◽

Symptom Onset ◽

Clinical Performance ◽

Point Of Care ◽

Rapid Diagnostics ◽

Rt Pcr ◽

Point Of Care Testing ◽

Viral Loads ◽

Peak Viral Load ◽

Salivary Diagnostics

Objectives: Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP workflow for viral detection in saliva, and to provide more information regarding its potential in COVID-19 diagnostics. Methods: Clinical and contrived specimens were used to screen/optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate clinical performance (n = 90) and to characterize saliva based on age, gender and time from onset of symptoms (n = 49). Results: The devised workflow achieved 93.2% sensitivity, 97% specificity, and 0.895 Kappa for salivas containing >102 copies/μL. Further analyses in saliva showed peak viral load in the first days of symptoms and lower viral loads in females, particularly among young individuals (<38 years). NOP RT-PCR data did not yield relevant associations. Conclusions: This novel saliva RT-LAMP workflow can be applied to point-of-care testing. This work reinforces that saliva better correlates with transmission dynamics than NOP specimens, and reveals gender differences that may reflect higher transmission by males. To maximize detection, testing should be done immediately after symptom onset, especially in females.

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Viral load and antibody levels in patients with COVID-19

GSC Advanced Research and Reviews ◽

10.30574/gscarr.2021.8.3.0180 ◽

2021 ◽

Vol 8 (3) ◽

pp. 010-018

Author(s):

Iva Christova ◽

Iva Trifonova ◽

Teodora Gladnishka ◽

Elena Dragusheva ◽

Georgi Popov ◽

...

Keyword(s):

Viral Load ◽

High Viral Load ◽

Igg Antibodies ◽

Rt Pcr ◽

Serum Samples ◽

Weekly Basis ◽

Specific Antibody Response ◽

Viral Loads ◽

Antibody Levels ◽

Kinetics Of

Relations between viral load, antibody levels and COVID-19 severity are not well studied and results from such investigations are controversial. In this study, we investigated kinetics of viral load and antibody responses to SARS-CoV-2 in 20 patients with COVID-19 and analysed the association with disease severity. The patients were followed on weekly basis within the first month after the onset and then once per month for the next 4 months. Serum samples were tested for IgA, IgM, and IgG antibodies against SARS-CoV-2 using ELISA tests. SARS-CoV-2 viral load in nasopharyngeal swabs was measured by quantitative Realtime RT-PCR. For vast majority of the patients, the viral loads were at their highest levels at presentation and then declined gradually. Despite development of specific antibody response 7-11 days after the onset of COVID-19, SARS-CoV-2 RNA was still detected in nasopharyngeal swabs of most of the patients. There was no direct link between viral load and severity of COVID-19: some of mild and some of severe cases started with a high viral load. There was a relationship between the time from the onset of the disease and the viral load: the highest viral load was in the first days. In more severe cases, there was a tendency for slower reduction in viral load and longer detection of SARS-CoV-2 virus. Levels of the specific antibodies increased earlier and to higher levels and were present for longer time in patients with more severe manifestations of COVID-19 than in those with milder disease.

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Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium

PLoS ONE ◽

10.1371/journal.pone.0259908 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0259908

Author(s):

Laura Heireman ◽

Steven Abrams ◽

Peggy Bruynseels ◽

Reinoud Cartuyvels ◽

Lize Cuypers ◽

...

Keyword(s):

Viral Load ◽

Respiratory Tract ◽

Age Group ◽

Test Results ◽

Rt Pcr ◽

Median Viral Load ◽

Viral Loads ◽

Asymptomatic Patients ◽

Positivity Ratio ◽

Second Wave

Introduction The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. Materials/Methods We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020–31 March 2021). Results In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20–30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20–40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. Conclusion There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20–30 year old individuals, indicating they could have been the hidden drivers of this wave.

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Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco

10.1101/2020.11.02.20223891 ◽

2020 ◽

Cited By ~ 2

Author(s):

Genay Pilarowski ◽

Paul Lebel ◽

Sara Sunshine ◽

Jamin Liu ◽

Emily Crawford ◽

...

Keyword(s):

Viral Load ◽

San Francisco ◽

High Viral Load ◽

Performance Characteristics ◽

Viral Rna ◽

Antigen Test ◽

Rt Pcr ◽

Detection Assay ◽

Community Transmission ◽

Testing Site

ABSTRACTWe evaluated the performance of the Abbott BinaxNOW™ Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6×104-4.3×104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.

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Noninvasive Detection of New Simian Immunodeficiency Virus Lineages in Captive Sooty Mangabeys: Ability To Amplify Virion RNA from Fecal Samples Correlates with Viral Load in Plasma

Journal of Virology ◽

10.1128/jvi.77.3.2214-2226.2003 ◽

2003 ◽

Vol 77 (3) ◽

pp. 2214-2226 ◽

Cited By ~ 34

Author(s):

Binhua Ling ◽

Mario L. Santiago ◽

Sreelatha Meleth ◽

Bobby Gormus ◽

Harold M. McClure ◽

...

Keyword(s):

Genetic Diversity ◽

Viral Load ◽

Simian Immunodeficiency Virus ◽

Sooty Mangabey ◽

Rt Pcr ◽

Noninvasive Methods ◽

Fecal Samples ◽

Viral Loads ◽

Immunodeficiency Virus ◽

In The Wild

ABSTRACT The sooty mangabey (SM) (Cercocebus atys) is the natural host of a simian immunodeficiency virus, termed SIVsm, which gave rise to human immunodeficiency virus type 2. Data on the geographic distribution, prevalence, and genetic diversity of SIVsm in the wild remains limited. To address this issue, noninvasive strategies based on screening SM fecal and urine specimens for SIVsm-specific antibodies and virion RNA (vRNA) were developed, and the results were correlated with viral loads in plasma. Twenty-three SIVsm-infected and 27 uninfected SMs were evaluated. Time-matched urine, fecal and plasma samples were collected over a 2-month period from 16 captive naturally infected SMs. The remaining 7 infected and 27 uninfected SMs were sampled once. Each specimen was subjected to enhanced chemiluminescence-Western blot analysis and nested reverse transcriptase (RT) PCR. The results showed that urine was highly sensitive (96%) and specific (100%) for detection of SIVsm antibodies, while fecal detection was much less sensitive (16%). Conversely, vRNA detection was more sensitive in feces (50%) than in urine (2%) samples. Fecal-vRNA detection correlated with viral loads in plasma (P < 0.002). SMs with detectable fecal vRNA had a mean viral load in plasma of 458,006 copies/ml, while those with undetectable fecal vRNA had a mean viral load in plasma of 29,428 copies/ml. Moreover, for every log increase in the viral load in plasma, the odds of detecting virus in fecal samples increased 87-fold. Genetic diversity of SIVsm in the SM colony was characterized by sequencing partial gag (846 bp) and gp43 (439 bp) fragments. Surprisingly, four new SIVsm lineages were identified, two of which were initially detected by fecal RT-PCR. This study documents the suitability of noninvasive methods for the detection and molecular characterization of new SIV variants. These assays will be useful for studying the phylogeny and epidemiology of SIVsm infections in the wild, and they hold promise as tools for investigating natural SIV infections in endangered nonhuman primates.

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