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

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.

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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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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

Journal of Clinical Microbiology ◽

10.1128/jcm.01785-21 ◽

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.

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

10.21203/rs.3.rs-41867/v1 ◽

2020 ◽

Cited By ~ 1

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.

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Quantifying human and environmental viral load relationships amidst mitigation strategies in a controlled chamber with participants having COVID-19

10.21203/rs.3.rs-940891/v1 ◽

2021 ◽

Author(s):

Hooman Parhizkar ◽

Leslie Dietz ◽

Andreas Olsen-Martinez ◽

Patrick Horve ◽

Liliana Barnatan ◽

...

Keyword(s):

Viral Load ◽

Disease Transmission ◽

Particle Deposition ◽

Near Field ◽

Health And Safety ◽

Field Measurements ◽

Mitigation Strategies ◽

Far Field ◽

Ambient Conditions ◽

Viral Loads

Abstract Several studies indicate that COVID-19 is primarily transmitted within indoor spaces. Therefore, environmental characterization of SARS-CoV-2 viral load with respect to human activity, building parameters, and environmental mitigation strategies is critical to combat disease transmission. We recruited 11 participants diagnosed with COVID-19 to individually occupy a controlled chamber and conduct specified physical activities under a range of environmental conditions; we collected human and environmental samples over a period of three days for each participant. Here we show that increased viral load, measured by lower RNA cycle threshold (CT) values, in nasal samples is associated with higher viral loads in environmental aerosols and surfaces captured in both the near field (1.2 m) and far field (3.5 m). At ambient conditions with ~ 0 Air Changes per Hour (ACH), near field measurements showed a higher particulate matter abundance and carbon dioxide (CO2) concentration as compared to far field measurements. We also found that aerosol viral load in far field is correlated with the number of particulates within the range of 1 µm -2.5 µm. Furthermore, increased ventilation and filtration are associated with lower environmental viral loads, and higher relative humidity is associated with lower aerosol viral loads and higher surface viral loads, consistent with an increased rate of particle deposition. Data from near field aerosol trials with high expiratory activities suggest that respiratory particles of smaller sizes (0.3 µm -1 µm) best characterize the variance of near field aerosol viral load. Moreover, our findings indicate that building operation practices such as ventilation, filtration, and humidification substantially reduce the environmental aerosol viral load, and therefore inhalation dose, and should be prioritized to improve building health and safety.

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

10.1101/2020.03.16.20037135 ◽

2020 ◽

Cited By ~ 26

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

10.1101/2021.04.02.21254771 ◽

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.

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Comparison and correlation of commercial SARS-CoV-2 real-time-PCR assays, Ireland, June 2020

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.6.2002079 ◽

2021 ◽

Vol 26 (6) ◽

Author(s):

Anne Carroll ◽

Eleanor McNamara

Keyword(s):

Viral Load ◽

Real Time ◽

Real Time Pcr ◽

Viral Loads ◽

Viral Culture ◽

Pcr Assays ◽

Result Interpretation

We report the performance of a variety of commercially available SARS-CoV-2 PCR kits, used in several different sites across Ireland to determine if Ct values across platforms are comparable. We also investigate whether a Ct value, a surrogate for calculated viral loads in the absence of viral culture of > 34 can be used to exclude SARS-CoV-2 infection and its complications. We found a variation in Ct values from different assays for the same calculated viral load; this should be taken into consideration for result interpretation.

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Duration of viral shedding and culture positivity with post-vaccination breakthrough delta variant infections

10.1101/2021.10.14.21264747 ◽

2021 ◽

Author(s):

Mark J. Siedner ◽

Julie Boucau ◽

Rebecca Gilbert ◽

Rockib Uddin ◽

Jonathan Luu ◽

...

Keyword(s):

Viral Load ◽

Additional Data ◽

Post Vaccination ◽

Replication Competent Virus ◽

Viral Shedding ◽

Viral Culture ◽

Culture Positivity ◽

Nasal Swabs ◽

Ambulatory Patients ◽

Viral Load Quantification

Isolation guidelines for SARS-CoV-2 are largely derived from data collected prior to emergence of the delta variant. We followed a cohort of ambulatory patients with post-vaccination breakthrough SARS-CoV-2 infections with longitudinal collection of nasal swabs for SARS-CoV-2 viral load quantification, whole genome sequencing, and viral culture. All delta variant infections (8/8, 100%) in our cohort were symptomatic, compared with 64% (9/14) of non-delta variant infections. Delta variant breakthrough infections were characterized by higher initial viral load, longer duration of virologic shedding by PCR (median 13.5 vs 4 days, hazard ratio [HR] 0.45, 95%CI 0.17-1.17), greater likelihood of replication competent virus at early stages of infection (6/8 [75%] vs 3/14 [23%], P=0.03), and longer duration of culturable virus (median 7 vs 3 days, HR 0.38, 95%CI 0.14-1.02) compared to non-delta variants. Nonetheless, no individuals with delta variant infections had replication competent virus by day 10 after symptom onset or 24 hours after resolution of symptoms. These data support current US Center for Disease Control isolation guidelines and reinforce the importance of prompt testing and isolation among symptomatic individuals with delta variant breakthrough infections. Additional data are needed to evaluate these relationships among asymptomatic and more severe delta variant breakthrough infections.

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