SARS-CoV-2 Variants of Concern B.1.1.7 and B.1.351 Are Not Associated With Higher Viral Loads in Upper Respiratory Specimens

2021 ◽  
Author(s):  
Chun Huai Luo ◽  
Adannaya Amadi ◽  
C. Paul Morris ◽  
Matthew Schwartz ◽  
Eili Y. Klein ◽  
...  
Keyword(s):  
Viral Loads ◽  
Upper Respiratory ◽  
Respiratory Specimens

scholarly journals Assessment of SARS-CoV-2 infectivity of upper respiratory specimens from COVID-19 patients by virus isolation using VeroE6/TMPRSS2 cells

2021 ◽  
Vol 8 (1) ◽  
pp. e000830
Author(s):  
Souichi Yamada ◽  
Shuetsu Fukushi ◽  
Hitomi Kinoshita ◽  
Makoto Ohnishi ◽  
Tadaki Suzuki ◽  
...  
Keyword(s):  
Virus Isolation ◽  
Laboratory Diagnostics ◽  
Viral Isolation ◽  
Viral Loads ◽  
A Cell ◽  
Blind Passage ◽  
Upper Respiratory ◽  
Novel Coronavirus ◽  
Respiratory Specimens

BackgroundAn outbreak of novel coronavirus (SARS-CoV-2)-associated respiratory infectious diseases (COVID-19) emerged in 2019 and has spread rapidly in humans around the world. The demonstration of in vitro infectiousness of respiratory specimens is an informative surrogate for SARS-CoV-2 transmission from patients with COVID-19; accordingly, viral isolation assays in cell culture are an important aspect of laboratory diagnostics for COVID-19.MethodsWe developed a simple and rapid protocol for isolating SARS-CoV-2 from respiratory specimens using VeroE6/TMPRSS2 cells, a cell line that is highly susceptible to the virus. We also investigated a correlation between isolation of SARS-CoV-2 and viral load detected by real-time RT-PCR (rRT-PCR) using N2 primer/probe set that has been developed for testing of COVID-19 in Japan.ResultsThe SARS-CoV-2 isolation protocol did not require blind passage of inoculated cells and yielded the results of viral isolation within 7 days after inoculation. Specimens with cycle threshold (Ct) values of <20.2, determined by rRT-PCR, were predicted to be isolation-positive. On the other hand, 6.9% of specimens with Ct values >35 were virus isolation-positive, indicating that low viral loads (high Ct values) in upper respiratory specimens do not always indicate no risk of containing transmissible virus.ConclusionIn combination with rRT-PCR, the SARS-CoV-2 isolation protocol provides a means for assessing the potential risk of transmissible virus in upper respiratory specimens.

scholarly journals Clinical evaluation of rapid point-of-care antigen tests for diagnosis of SARS-CoV-2 infection

2021 ◽  
Author(s):  
Johannes G. M. Koeleman ◽  
Henk Brand ◽  
Stijn J. de Man ◽  
David S. Y. Ong
Keyword(s):  
Health Care ◽  
Health Care Workers ◽  
Antigen Test ◽  
Duration Of Symptoms ◽  
Large Variability ◽  
Clinical Sensitivity ◽  
Care Workers ◽  
Upper Respiratory ◽  
Antigen Tests ◽  
Respiratory Specimens

AbstractThe RT-qPCR in respiratory specimens is the gold standard for diagnosing acute COVID-19 infections. However, this test takes considerable time before test results become available, thereby delaying patients from being diagnosed, treated, and isolated immediately. Rapid antigen tests could overcome this problem. In the first study, clinical performances of five rapid antigen tests were compared to RT-qPCR in upper respiratory specimens from 40 patients with positive and 40 with negative RTq-PCR results. In the second study, the rapid antigen test with one of the best test characteristics (Romed) was evaluated in a large prospective collection of upper respiratory specimens from 900 different COVID-19-suspected patients (300 emergency room patients, 300 nursing home patients, and 300 health care workers). Test specificities ranged from 87.5 to 100.0%, and test sensitivities from 55.0 to 80.0%. The clinical specificity of the Romed test was 99.8% (95% CI 98.9–100). Overall clinical sensitivity in the study population was 73.3% (95% CI 67.9–78.2), whereas sensitivity in the different patient groups varied from 65.3 to 86.7%. Sensitivity was 83.0 to 86.7% in patients with short duration of symptoms. In a population with a COVID-19 prevalence of 1%, the negative predictive value in all patients was 99.7%. There is a large variability in diagnostic performance between rapid antigen tests. The Romed rapid antigen test showed a good clinical performance in patients with high viral loads (RT-qPCR cycle threshold ≤30), which makes this antigen test suitable for rapid identification of COVID-19-infected health care workers and patients.

scholarly journals Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Gwynngelle A Borillo ◽  
Ron M Kagan ◽  
Russell E Baumann ◽  
Boris M Fainstein ◽  
Lamela Umaru ◽  
...  
Keyword(s):  
Real Time ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Negative Results ◽  
Single Positive ◽  
Upper Respiratory ◽  
Respiratory Specimens

Abstract Background Nucleic acid amplification testing is a critical tool for addressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Specimen pooling can increase throughput and conserve testing resources but requires validation to ensure that reduced sensitivity does not increase the false-negative rate. We evaluated the performance of a real-time reverse transcription polymerase chain reaction (RT-PCR) test authorized by the US Food and Drug Administration (FDA) for emergency use for pooled testing of upper respiratory specimens. Methods Positive specimens were selected from 3 prevalence groups, 1%–3%, &gt;3%–6%, and &gt;6%–10%. Positive percent agreement (PPA) was assessed by pooling single-positive specimens with 3 negative specimens; performance was assessed using Passing-Bablok regression. Additionally, we assessed the distributions of RT-PCR cycle threshold (Ct) values for 3091 positive specimens. Results PPA was 100% for the 101 pooled specimens. There was a linear relationship between Ct values for pooled and single-tested specimens (r = 0.96–0.99; slope ≈ 1). The mean pooled Ct shifts at 40 cycles were 2.38 and 1.90, respectively, for the N1 and N3 targets. The median Cts for 3091 positive specimens were 25.9 (N1) and 24.7 (N3). The percentage of positive specimens with Cts between 40 and the shifted Ct was 1.42% (N1) and 0.0% (N3). Conclusions Pooled and individual testing of specimens positive for SARS-CoV-2 demonstrated 100% agreement, which demonstrates the viability of pooled specimens for SARS-COV-2 testing using a dual-target RT-PCR system. Pooled specimen testing can help increase testing capacity for SARS-CoV-2 with a low risk of false-negative results.

scholarly journals Fatal Pneumonia Associated With a Novel Genotype of Human Coronavirus OC43

2022 ◽  
Vol 12 ◽  
Author(s):  
Susanna Kar Pui Lau ◽  
Kenneth Sze Ming Li ◽  
Xin Li ◽  
Ka-Yan Tsang ◽  
Siddharth Sridhar ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Respiratory Infections ◽  
Endotracheal Aspirate ◽  
Human Coronavirus ◽  
Genotype I ◽  
Viral Loads ◽  
Pairwise Genetic Distance ◽  
Distinct Cluster ◽  
Upper Respiratory ◽  
Novel Genotype

Since its first discovery in 1967, human coronavirus OC43 (HCoV-OC43) has been associated with mild self-limiting upper respiratory infections worldwide. Fatal primary pneumonia due to HCoV-OC43 is not frequently described. This study describes a case of fatal primary pneumonia associated with HCoV-OC43 in a 75-year-old patient with good past health. The viral loads of the respiratory tract specimens (bronchoalveolar lavage and endotracheal aspirate) from diagnosis to death were persistently high (3.49 × 106–1.10 × 1010 copies/ml). HCoV-OC43 at a 6.46 × 103 copies/ml level was also detected from his pleural fluid 2 days before his death. Complete genome sequencing and phylogenetic analysis showed that the present HCoV-OC43 forms a distinct cluster with three other HCoV-OC43 from United States, with a bootstrap value of 100% and sharing 99.9% nucleotide identities. Pairwise genetic distance between this cluster and other HCoV-OC43 genotypes ranged from 0.27 ± 0.02% to 1.25 ± 0.01%. In contrast, the lowest pairwise genetic distance between existing HCoV-OC43 genotypes was 0.26 ± 0.02%, suggesting that this cluster constitutes a novel HCoV-OC43 genotype, which we named genotype I. Unlike genotypes D, E, F, G, and H, no recombination event was observed for this novel genotype. Structural modeling revealed that the loop with the S1/S2 cleavage site was four amino acids longer than other HCoV-OC43, making it more exposed and accessible to protease, which may have resulted in its possible hypervirulence.

scholarly journals Asymptomatic COVID-19 Adult Outpatients identified as Significant Viable SARS-CoV-2 Shedders 

2021 ◽  
Author(s):  
Marie Glenet ◽  
Anne-Laure Lebreil ◽  
Laetitia Heng ◽  
Yohan N’Guyen ◽  
Ittah Meyer ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Control Measures ◽  
Upper Respiratory Tract ◽  
Rna Detection ◽  
Viral Loads ◽  
Infection Control Measures ◽  
Infected Adult ◽  
Asymptomatic Adult ◽  
Upper Respiratory ◽  
Kinetics Of

Abstract Differential kinetics of RNA loads and infectious viral levels in the upper respiratory tract between asymptomatic and symptomatic SARS-CoV-2 infected adult outpatients remain unclear limiting recommendations that may guide clinical management, infection control measures and occupational health decisions. In the present investigation, 496 (2.5%) of 17,911 French adult outpatients were positive for an upper respiratory tract SARS-CoV-2 RNA detection by a quantitative RT-PCR assay, of which 180 (36.3%) were COVID-19 asymptomatic. Of these adult asymptomatic viral shedders, 84.4% had mean to high RNA viral loads (Ct values<30) which median value was significantly higher than that observed in symptomatic subjects (P=0.029), and 50.6% were positive by cell culture assays of their upper respiratory tract specimens. Our findings indicate that COVID-19 asymptomatic adult outpatients are significant viable SARS-CoV-2 shedders in their upper respiratory tract playing a major potential role as SARS-CoV-2 transmitters in various epidemiological transmission chains, promoting COVID-19 resurgence in populations.

scholarly journals Factors Associated With Viral Load Kinetics of Middle East Respiratory Syndrome Coronavirus During the 2015 Outbreak in South Korea

2020 ◽  
Author(s):  
Jeong-Sun Yang ◽  
Min-Gyu Yoo ◽  
Hye-Ja Lee ◽  
Han Byul Jang ◽  
Hee-Dong Jung ◽  
...  
Keyword(s):  
Viral Load ◽  
Middle East ◽  
Symptom Onset ◽  
Healthcare Workers ◽  
Middle East Respiratory Syndrome ◽  
Viral Loads ◽  
Hospitalization Period ◽  
Using Data ◽  
Kinetics Of ◽  
Respiratory Specimens

Abstract We conducted a retrospective study of Middle East respiratory syndrome coronavirus (MERS-CoV) viral load kinetics using data from patients hospitalized with MERS-CoV infection between 19 May and 20 August 2015. Viral load trajectories were considered over the hospitalization period using 1714 viral load results measured in serial respiratory specimens of 185 patients. The viral load levels were significantly higher among nonsurvivors than among survivors (P = .003). Healthcare workers (P = .001) and nonspreaders (P &lt; .001) had significantly lower viral loads. Viral RNA was present on the day of symptom onset and peaked 4–10 days after symptom onset.

scholarly journals Reduced Pathogenicity of the SARS-CoV-2 Omicron Variant in Hamsters

2022 ◽  
Author(s):  
Katherine McMahan ◽  
Victoria Giffin ◽  
Lisa Tostanoski ◽  
Benjamin Chung ◽  
Mazuba Siamatu ◽  
...  
Keyword(s):  
Weight Loss ◽  
Respiratory Tract ◽  
Lung Parenchyma ◽  
Clinical Disease ◽  
Upper Respiratory Tract ◽  
Viral Loads ◽  
Syrian Golden Hamsters ◽  
The World ◽  
Pulmonary Pathology ◽  
Upper Respiratory

The SARS-CoV-2 Omicron (B.1.1.529) variant has proven highly transmissible and has outcompeted the Delta variant in many regions of the world. Early reports have also suggested that Omicron may result in less severe clinical disease in humans. Here we show that Omicron is less pathogenic than prior SARS-CoV-2 variants in Syrian golden hamsters. Infection of hamsters with the SARS-CoV-2 WA1/2020, Alpha, Beta, or Delta strains led to 4-10% weight loss by day 4 and 10-17% weight loss by day 6, as expected. In contrast, infection of hamsters with two different Omicron challenge stocks did not result in any detectable weight loss, even at high challenge doses. Omicron infection still led to substantial viral replication in both the upper and lower respiratory tracts and pulmonary pathology, but with a trend towards higher viral loads in nasal turbinates and lower viral loads in lung parenchyma compared with WA1/2020 infection. These data suggest that the SARS-CoV-2 Omicron variant may result in more robust upper respiratory tract infection but less severe lower respiratory tract clinical disease compared with prior SARS-CoV-2 variants.

scholarly journals Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eric C. Rouchka ◽  
Julia H. Chariker ◽  
Brian Alejandro ◽  
Robert S. Adcock ◽  
Richa Singhal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Load ◽  
Respiratory Tract ◽  
Disease Severity ◽  
Critical Factor ◽  
Interferon Response ◽  
Upper Respiratory Tract ◽  
Viral Loads ◽  
Antiviral Responses ◽  
Upper Respiratory

AbstractKey elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.

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