scholarly journals No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups When Infected with SARS-CoV-2 Delta Variant

2021 ◽  
Author(s):  
Charlotte B. Acharya ◽  
John Schrom ◽  
Anthea M. Mitchell ◽  
David A. Coil ◽  
Carina Marquez ◽  
...  
Keyword(s):  
Viral Load ◽  
Substantial Proportion ◽  
Threshold Values ◽  
Cycle Threshold ◽  
Significant Difference

AbstractWe found no significant difference in cycle threshold values between vaccinated and unvaccinated, asymptomatic and symptomatic groups infected with SARS-CoV-2 Delta. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered for all in settings with elevated COVID-19 transmission.

scholarly journals The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients

2021 ◽  
Author(s):  
Elisa Teyssou ◽  
Cathia Soulie ◽  
Benoit Visseaux ◽  
Sidonie Lambert-Niclot ◽  
Valentine Ferre ◽  
...  
Keyword(s):  
Viral Load ◽  
Newly Diagnosed ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
The World

The 501Y.V2 and the 501Y.V1 SARS-CoV-2 variants emerged and spread rapidly into the world. We analysed the RT-PCR cycle threshold values of 643 nasopharyngeal samples of COVID-19 patients at diagnosis and found that the 501Y.V2 variant presented an intermediate viral load between the 501Y.V1 and the historical variants.

scholarly journals Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

2021 ◽  
Author(s):  
Yun Lin ◽  
Bingyi Yang ◽  
Sarah Cobey ◽  
Eric Lau ◽  
Dillon Adam ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Temporal Distribution ◽  
Time Estimation ◽  
Population Level ◽  
Reproductive Number ◽  
Threshold Values ◽  
Illness Onset ◽  
Cycle Threshold ◽  
Viral Loads

Abstract Many locations around the world have used real-time estimates of the time-varying effective reproductive number (\({R}_{t}\)) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of \({R}_{t}\) are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the incubation period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral loads among confirmed cases can provide insights into epidemic trajectory. Here, we analyzed viral load data on confirmed cases during two local epidemics in Hong Kong, identifying a strong correlation between temporal changes in the distribution of viral loads (measured by cycle threshold values) and estimates of \({R}_{t}\) based on case counts. We demonstrate that cycle threshold values could be used to improve real-time \({R}_{t}\) estimation, enabling more timely tracking of epidemic dynamics.

scholarly journals Association of cycle threshold values of CBNAAT with severity and outcome in COVID-19

2021 ◽  
Author(s):  
Kranti Garg ◽  
Karan Sharma ◽  
Aditi Gupta ◽  
Vishal Chopra
Keyword(s):  
Viral Load ◽  
Virus Disease ◽  
Nucleic Acid Amplification ◽  
Clinical Parameters ◽  
Surrogate Markers ◽  
Threshold Values ◽  
Cycle Threshold ◽  
E Gene ◽  
Disease Outcomes

Determination of viral load through cycle threshold (Ct) values may act as a predictor of severity and outcomes in patients with corona virus disease 2019 (COVID-19). However, variable literature is available regarding this relationship. Our study attempted to explore this association and the effect of various socio-demographic and clinical parameters on severity and outcome of COVID-19.  Retrospective analysis of records of 731 patients whose nasopharyngeal/ oropharyngeal swabs were subjected to cartridge based nucleic acid amplification (CBNAAT) on Cepheid Xpert Xpress SARS-Cov-2 was done. Cycle threshold (Ct) values of N2 and E genes were studied in relation to severity and outcome of COVID-19. The viral load as determined by Ct values was classified as high (<25), medium (25.1-32) and low (>32). Association of socio-demographic and clinical parameters with respect to severity and outcome was also studied. Severity and mortality were significantly more in elder individuals, those belonging to the rural background, those with symptoms >7 days in duration before presentation and those with increasing number of co-morbidities (Severity: p<0.001, mortality: p <0.001, 0.005, 0.006 and <0.001 respectively). The Ct values of gene N2 and E inversely correlated with severity and mortality from the disease (N2 gene: p=0.001 for both severity and mortality, E gene: severity: p<0.001, mortality: p=0.016 respectively). The severity of the illness and chances of mortality were significantly lesser when the CT value of N2 gene was >32, in comparison when it was upto 25, and when between 25.1 and 32 (severity: p=0.032 and 0.003 respectively, mortality: p=0.018 and <0.001 respectively). Almost similar trends were seen with respect to E gene (severity: p<0.001 and 0.067 respectively, mortality p=0.175 and 0.005 respectively). Viral load as determined by Ct values of N2 and E genes can act as surrogate markers for prediction of severity and disease outcomes in COVID-19.

scholarly journals Sampling site for SARS-CoV-2 RT-PCR—An intrapatient four-site comparison from Tampere, Finland

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260184
Author(s):  
Dominik Kerimov ◽  
Pekka Tamminen ◽  
Hanna Viskari ◽  
Lauri Lehtimäki ◽  
Janne Aittoniemi
Keyword(s):  
Informed Consent ◽  
Study Design ◽  
Nasal Swab ◽  
Sampling Site ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Significant Difference ◽  
Nasal Swabs ◽  
Written Informed Consent

Background SARS-CoV-2 diagnosis relies on the performance of nasopharyngeal swabs. Alternative sample sites have been assessed but the heterogeneity of the studies have made comparing different sites difficult. Objectives Our aim was to compare the performance of four different sampling sites for SARS-CoV-2 samples with nasopharynx being the benchmark. Study design COVID-19 positive patients were recruited prospectively, and samples were collected and analysed for SARS-CoV-2 with RT-PCR from all four anatomical sites in 43 patients, who provided written informed consent. Results All anterior nasal and saliva samples were positive, while two oropharyngeal samples were negative. There was no significant difference in the cycle threshold values of nasopharyngeal and anterior nasal samples while saliva and oropharynx had higher cycle threshold values. Conclusions Anterior nasal swab performs as good as nasopharynx swab with saliva also finding all the positives but with higher cycle threshold values. Thus, we can conclude that anterior nasal swabs can be used for SARS-CoV-2 detection instead of nasopharyngeal swabs if the situation would require so.

scholarly journals SARS-CoV-2 Viral Load, IFNλ Polymorphisms and the Course of COVID-19: An Observational Study

2020 ◽  
Vol 9 (10) ◽  
pp. 3315
Author(s):  
Emanuele Amodio ◽  
Rosaria Maria Pipitone ◽  
Stefania Grimaudo ◽  
Palmira Immordino ◽  
Carmelo Massimo Maida ◽  
...  
Keyword(s):  
Viral Load ◽  
Observational Study ◽  
Lower Risk ◽  
Nucleotide Polymorphisms ◽  
Threshold Values ◽  
Single Nucleotide ◽  
Cycle Threshold ◽  
Viral Loads ◽  
The Relationship ◽  
Multiorgan Disease

The course of SARS-CoV-2 infection ranges from asymptomatic to a multiorgan disease. In this observational study, we investigated SARS-CoV-2 infected subjects with defined outcomes, evaluating the relationship between viral load and single nucleotide polymorphisms of genes codifying for IFNλs (interferon). The study enrolled 381 patients with laboratory-confirmed SARS-CoV-2 infection. For each patient, a standardized form was filled including sociodemographic variables and clinical outcomes. The host’s gene polymorphisms (IFNL3 rs1297860 C/T and INFL4 rs368234815 TT/ΔG) and RtReal-Time PCR cycle threshold (PCR Ct) value on SARS-CoV-2 were assessed on nasal, pharyngeal or nasopharyngeal swabs. Higher viral loads were found in patients aged > 74 years and homozygous mutant polymorphisms DG in IFNL4 (adj-OR = 1.16, 95% CI = 1.01–1.34 and adj-OR = 1.24, 95% CI = 1.09–1.40, respectively). After adjusting for age and sex, a statistically significantly lower risk of hospitalization was observed in subjects with higher RtReal-Time PCR cycle threshold values (adj-OR = 0.95, 95% CI = 0.91, 0.99; p = 0.028). Our data support the correlation between SARS-CoV-2 load and disease severity, and suggest that IFNλ polymorphisms could affect the ability of the host to modulate viral infection without a clear impact on the outcome of COVID-19.

scholarly journals Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020

2020 ◽  
Vol 25 (32) ◽  
Author(s):  
Anika Singanayagam ◽  
Monika Patel ◽  
Andre Charlett ◽  
Jamie Lopez Bernal ◽  
Vanessa Saliba ◽  
...  
Keyword(s):  
Viral Load ◽  
Severe Acute Respiratory Syndrome ◽  
Respiratory Tract ◽  
Symptom Onset ◽  
Infectious Virus ◽  
Upper Respiratory Tract ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Upper Respiratory

Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus.

scholarly journals Modelling RT-qPCR cycle-threshold using digital PCR data for implementing SARS-CoV-2 viral load studies

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260884
Author(s):  
Fabio Gentilini ◽  
Maria Elena Turba ◽  
Francesca Taddei ◽  
Tommaso Gritti ◽  
Michela Fantini ◽  
...  
Keyword(s):  
Viral Load ◽  
Regression Model ◽  
Case Fatality ◽  
High Specificity ◽  
Digital Pcr ◽  
Public Health Authority ◽  
Load Factor ◽  
Threshold Values ◽  
Cycle Threshold ◽  
Low Sensitivity

Objectives To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/μL. Methods A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset. The model was then used to convert the stored cycle threshold values of a large dataset of 6208 diagnostic samples into copies/μL of SARS-CoV-2. The calculated viral load was used for a single cohort retrospective study. Finally, the cohort was randomly divided into a training set (n = 3095) and an evaluation set (n = 3113) to establish a logistic regression model for predicting case-fatality and to assess its accuracy. Results The model for converting the Ct values into copies/μL was suitably accurate. The calculated viral load over time in the cohort of Covid-19 positive samples showed very low viral loads during the summer inter-epidemic waves in Italy. The calculated viral load along with gender and age allowed building a predictive model of case-fatality probability which showed high specificity (99.0%) and low sensitivity (21.7%) at the optimal threshold which varied by modifying the threshold (i.e. 75% sensitivity and 83.7% specificity). Alternative models including categorised cVL or raw cycle thresholds obtained by the same diagnostic method also gave the same performance. Conclusion The modelling of the cycle threshold values using digital PCR had the potential of fostering studies addressing issues regarding Sars-CoV-2; furthermore, it may allow setting up predictive tools capable of early identifying those patients at high risk of case-fatality already at diagnosis, irrespective of the diagnostic RT-qPCR platform in use. Depending upon the epidemiological situation, public health authority policies/aims, the resources available and the thresholds used, adequate sensitivity could be achieved with acceptable low specificity.

scholarly journals Can Use of Viral Load Improve Norovirus Clinical Diagnosis and Disease Attribution?

2017 ◽  
Vol 4 (3) ◽  
Author(s):  
Kayoko Shioda ◽  
Leslie Barclay ◽  
Sylvia Becker-Dreps ◽  
Filemon Bucardo-Rivera ◽  
Philip J Cooper ◽  
...  
Keyword(s):  
Viral Load ◽  
Diarrheal Disease ◽  
Age Groups ◽  
The United States ◽  
Epidemiological Studies ◽  
Threshold Values ◽  
Characteristic Analysis ◽  
Symptomatic Disease ◽  
Cycle Threshold ◽  
Specimen Collection

Abstract Background Real-time reverse-transcriptase polymerase chain reaction (RT-PCR) is the state-of-the-art diagnostic for norovirus. Cycle threshold (Ct), an indicator of viral load, may be associated with symptomatic disease as well as demographic and outbreak characteristics. Methods Data on (1) outbreak and sporadic cases and (2) asymptomatic controls in the United States and Latin America were analyzed. With multivariate regression models, we assessed relationships between various factors and Ct values, and we calculated odds ratios (ORs) for the presence of symptoms and attributable fractions of norovirus. Receiver-operating characteristic analysis was performed to define an optimal Ct cutoff to identify disease-causing infections. Results Cycle threshold values were lower (ie, higher viral loads) among symptomatic cases (model-adjusted mean ± standard error: 25.3 ± 1.2) compared with asymptomatic controls (28.5 ± 1.4). Cycle threshold values were significantly different across age groups, norovirus genogroups, timing of specimen collection, outbreak settings, and transmission modes. Genogroup II (GII) Ct values were associated with presence of symptoms (OR = 1.1), allowing us to estimate that 16% of diarrheal disease was attributable to norovirus. The optimized Ct cutoff led to poor sensitivity and specificity for genogroup I and GII. Conclusions Cycle threshold values were associated with host, pathogen, and outbreak factors. Cycle threshold values may not effectively distinguish disease-causing infection for individual patients, but they are useful for epidemiological studies aiming to attribute disease.

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