scholarly journals Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection

2021 ◽  
Author(s):  
Emily S. Savela ◽  
Alexander Winnett ◽  
Anna E. Romano ◽  
Michael K. Porter ◽  
Natasha Shelby ◽  
...  
Keyword(s):  
Viral Load ◽  
Los Angeles ◽  
Nasal Swab ◽  
Sampling Site ◽  
High Sensitivity ◽  
Analytical Sensitivity ◽  
Viral Loads ◽  
Analytical Test ◽  
Nasal Swabs ◽  
High Analytical Sensitivity

Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California area, initially-SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity RT-qPCR and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5 days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva, but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to design optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.

scholarly journals SARS-CoV-2 is detectable using sensitive RNA saliva testing days before viral load reaches detection range of low-sensitivity nasal swab tests

2021 ◽  
Author(s):  
Emily S. Savela ◽  
Alexander Winnett ◽  
Anna E. Romano ◽  
Michael K. Porter ◽  
Natasha Shelby ◽  
...  
Keyword(s):  
Viral Load ◽  
Early Detection ◽  
Nasal Swab ◽  
Limit Of Detection ◽  
High Sensitivity ◽  
Viral Loads ◽  
Test Sensitivity ◽  
Sensitivity Tests ◽  
Nasal Swabs ◽  
Low Sensitivity

Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic spread of COVID-19, curb the spread of viral variants by travelers, and maximize efficacy of therapeutic treatments. We designed a study to evaluate the preferred test sensitivity and sample type (saliva and nasal swab) for detecting early infections of COVID-19. We performed a case-ascertained study to monitor household contacts of individuals recently diagnosed with a SARS-CoV-2 infection. From those individuals, we obtained twice-daily self-collected anterior-nares nasal swabs and saliva samples and quantified SARS-CoV-2 RNA viral loads in those samples using high-sensitivity RT-qPCR and RT-ddPCR assays. We found that SARS-CoV-2 RNA first appears in saliva and then in nasal-swab samples. A high-sensitivity (limit of detection of ~103 copies/mL) RNA test detected SARS-CoV-2 virus in saliva 1.5 to 4.5 days before the viral load in the paired nasal-swab samples exceeded the limit of detection of low-sensitivity tests. It was possible to observe a high (>107-108 copies/mL) viral load in saliva samples while the paired nasal swab was either negative or had low (~103 copies/mL) viral load. Our results indicate that both sampling site and test sensitivity must be considered to ensure early detection of SARS-CoV-2 infection: high-sensitivity tests that use saliva can detect SARS-CoV-2 infection days earlier than low-sensitivity tests that use nasal swabs. Furthermore, early in the infection, low-sensitivity tests that use nasal swabs may miss SARS-CoV-2-positive individuals with very high and potentially infectious viral loads in saliva.

scholarly journals Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection

2021 ◽  
Author(s):  
Julie Boucau ◽  
Kara W Chew ◽  
Manish Chandra Choudhary ◽  
Rinki Deo ◽  
James Regan ◽  
...  
Keyword(s):  
Viral Load ◽  
Disease Transmission ◽  
Treated Group ◽  
Antibody Treatment ◽  
Rapid Reduction ◽  
Viral Loads ◽  
Viral Culture ◽  
Nasal Swabs ◽  
Monoclonal Antibody Treatment ◽  
Viral Load Rebound

Monoclonal antibodies (mAbs) are the treatment of choice for high-risk ambulatory persons with mild to moderate COVID-19. We studied viral culture dynamics post-treatment in a subset of participants receiving the mAb bamlanivimab in the ACTIV-2 trial. Viral load by qPCR and viral culture were performed from anterior nasal swabs collected on study days 0 (day of treatment), 1, 2, 3, and 7. Treatment with mAb resulted in rapid clearance of culturable virus in participants without treatment-emergent resistance. One day after treatment, 0 of 28 (0%) participants receiving mAb and 16 of 39 (41%) receiving placebo still had culturable virus (p <0.0001); nasal viral loads were only modestly lower in the mAb-treated group at days 2 and 3. Recrudescence of culturable virus was detected in three participants with emerging mAb resistance and viral load rebound. The rapid reduction in shedding of viable SARS-CoV-2 after mAb treatment highlights the potential role of mAbs in preventing disease transmission.

scholarly journals Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1184
Author(s):  
Licia Bordi ◽  
Giuseppe Sberna ◽  
Eleonora Lalle ◽  
Pierluca Piselli ◽  
Francesca Colavita ◽  
...  
Keyword(s):  
Viral Load ◽  
Oral Fluid ◽  
Clinical Sample ◽  
High Sensitivity ◽  
Analytical Sensitivity ◽  
Parallel Testing ◽  
Viral Load Monitoring ◽  
Load Monitoring ◽  
High Concordance ◽  
Assay Conditions

Background: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral load and shedding. Methods: Optimal assay conditions and analytical sensitivity were established for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients; 50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were also analysed. Results: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection down to 1 TCID50/mL (corresponding to 4 × 103 copies (cp)/mL) was observed. No crossreaction with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771–0.891), and high correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples, respectively, collected between 60 and 100 DSO. Conclusions: Simplexa™ COVID-19 Direct assays on OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to NPS for diagnosis and monitoring SARS-CoV-2 shedding.

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

2020 ◽  
Vol 71 (15) ◽  
pp. 793-798 ◽  
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 &lt; .001) and nasal swabs (651 ± 501 copies/test, P &lt; .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 &lt; .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.

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 Clinical utility of cycle threshold values in the context of COVID-19

2020 ◽  
Author(s):  
Sonia N. Rao ◽  
Davide Manissero ◽  
Victoria Steele ◽  
Josep Pareja
Keyword(s):  
Viral Load ◽  
Troponin I ◽  
Severe Disease ◽  
Clinical Information ◽  
High Sensitivity ◽  
Clinical Value ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Ct Value ◽  
Viral Culture

Abstract BackgroundThe ability to predict likely prognosis and infectiousness for patients with COVID-19 would aid patient management decisions. Diagnosis is usually via real-time PCR and it is unclear whether the semi-quantitative capability of this method, determining viral load through cycle threshold (Ct) values, can be leveraged.ObjectivesWe aim to review available knowledge on correlations between SARS-COV-2 Ct values and patient- or healthcare-related outcomes to determine whether Ct values provide useful clinical information.SourcesA PubMed search was conducted on 1st June 2020 based on a search strategy of (Ct value OR viral load) AND SARS-CoV-2. Data was extracted from studies reporting on the presence or absence of an association between Ct values, or viral loads determined via Ct value, and clinical outcomes.ContentData from 18 studies were relevant for inclusion. One study reported on the correlation between Ct values and mortality and one study reported on the correlation between Ct values and progression to severe disease; both reported a significant association (p < 0.001 and p = 0.008, respectively). Fourteen studies reported on the correlation between Ct value or viral loads determined via Ct value and disease severity and an association was observed in 8 (57%) studies. Studies reporting on the correlation of viral load with biochemical and haematological markers showed an association with at least one marker, including increased lactate dehydrogenase (n = 4), decreased lymphocytes (n = 3) and increased high-sensitivity troponin I (n = 2). Two studies reporting on the correlation with infectivity showed that lower Ct values were associated with higher viral culture positivity.ImplicationsData suggest that lower Ct values may be associated with worse outcomes, and that Ct values may be useful in predicting the clinical course and prognosis of patients with COVID-19; however, further studies are warranted to confirm clinical value.

scholarly journals Sensitive detection and quantification of SARS-CoV-2 in saliva

2020 ◽  
Author(s):  
Mustafa Fatih Abasiyanik ◽  
Blake Flood ◽  
Jing Lin ◽  
Sefika Ozcan ◽  
Sherin J Rouhani ◽  
...  
Keyword(s):  
Nasal Swab ◽  
Digital Pcr ◽  
Rt Pcr ◽  
Community Screening ◽  
Viral Loads ◽  
Reverse Transcription Pcr ◽  
Testing Facility ◽  
Wide Range ◽  
Nasal Swabs ◽  
Higher Sensitivity

AbstractSaliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

scholarly journals Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples

2021 ◽  
Author(s):  
C. Lam ◽  
K. Gray ◽  
M. Gall ◽  
R. Sadsad ◽  
A. Arnott ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Low Frequency ◽  
Variant Calling ◽  
High Sensitivity ◽  
Viral Escape ◽  
Viral Loads ◽  
Sensitivity Specificity

SARS-CoV-2 genomic surveillance has been vital in understanding the spread of COVID-19, the emergence of viral escape mutants and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low frequency variants. Our analyses highlight that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina respiratory viral oligo panel, and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high quality sequence data from low viral load samples for public health and genomic surveillance purposes.

scholarly journals Sensitive detection and quantification of SARS-CoV-2 in saliva

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mustafa Fatih Abasiyanik ◽  
Blake Flood ◽  
Jing Lin ◽  
Sefika Ozcan ◽  
Sherin J. Rouhani ◽  
...  
Keyword(s):  
Nasal Swab ◽  
Digital Pcr ◽  
Rt Pcr ◽  
Community Screening ◽  
Viral Loads ◽  
Reverse Transcription Pcr ◽  
Testing Facility ◽  
Wide Range ◽  
Nasal Swabs ◽  
Higher Sensitivity

AbstractSaliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

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

2020 ◽  
Author(s):  
Philippe Gautret ◽  
Jean-Christophe Lagier ◽  
Philippe Parola ◽  
Van Thuan Hoang ◽  
Line Meddeb ◽  
...  
Keyword(s):  
Viral Load ◽  
Clinical Presentation ◽  
Open Label ◽  
Virus Elimination ◽  
Viral Loads ◽  
Viral Load Reduction ◽  
Nasal Swabs ◽  
Negative Controls ◽  
To Receive

AbstractBackgroundChloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the role of hydroxychloroquine on respiratory viral loads.Patients and methodsPatients were included in a single arm protocol to receive 600mg of hydroxychloroquine daily and their viral load in nasal swabs was tested daily. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point.ResultsTwenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported of untreated patients in the literature. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination.ConclusionHydroxychloroquine is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin.

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