scholarly journals Quantification of SARS-CoV-2 viral copy number in saliva mouthwash samples using digital droplet PCR

2020 ◽  
Author(s):  
Lisa Oberding ◽  
Jia Hu ◽  
Byron Berenger ◽  
Abu Naser Mohon ◽  
Dylan R. Pillai
Keyword(s):  
Viral Load ◽  
Copy Number ◽  
Clinical Samples ◽  
Digital Droplet Pcr ◽  
Viral Copy Number ◽  
Droplet Pcr ◽  
Precise Quantification ◽  
Viral Copy ◽  
Mouth Wash

AbstractSaliva samples were collected through a simple mouth wash procedure and viral load quantified using a technology called digital droplet PCR. Data suggest ddPCR allows for precise quantification of viral load in clinical samples infected with SARS-CoV-2.

Infection with antiretroviral-susceptible HIV in an individual adherent to pre-exposure prophylaxis: strategies for treatment initiation

2021 ◽  
pp. 095646242097112
Author(s):  
Jessica M Hughes ◽  
Darrell HS Tan ◽  
Peter Anderson ◽  
Janani Bodhinayake ◽  
Paul A MacPherson
Keyword(s):  
Viral Load ◽  
Copy Number ◽  
Case Reports ◽  
Pharmacy Records ◽  
Treatment Regimens ◽  
Viral Copy Number ◽  
Low Copy Number ◽  
Viral Copy ◽  
Exposure Prophylaxis ◽  
Tenofovir Diphosphate

HIV pre-exposure prophylaxis (PrEP) is effective at preventing sexual acquisition of HIV, and failures in clinical trials are largely attributable to medication nonadherence. We report here a case of infection with a fully susceptible strain of HIV in an individual adherent to PrEP as demonstrated by pharmacy records and intracellular tenofovir diphosphate levels. At diagnosis, the viral load was 90 copies/mL precluding initial genotype testing due to low copy number. While PrEP failure is rare, this case underscores the importance of regular HIV testing for patient on PrEP and prompts discussion regarding the approach to treatment following failure where an initial genotype is not yet available or not possible due to low viral load. Few other case reports of PrEP failure exist in the literature and approaches to treatment varied widely. We suggest the initial viral copy number may guide next steps and discuss the risks and benefits of stopping PrEP, escalating therapy with integrase inhibitors or boosted protease inhibitors, or switching to non-nucleoside antiretroviral treatment regimens.

scholarly journals Effect of lyophilization on infectivity and viral load of Adenovirus

2015 ◽  
Vol 3 (1) ◽  
pp. 15-21
Author(s):  
Bimlesh Kumar Jha ◽  
Birendra Prasad Gupta ◽  
Prashanna Maharjan ◽  
Somila Kakshapati ◽  
Nabin Narayan Munankarmi
Keyword(s):  
Viral Load ◽  
Copy Number ◽  
Virus Stock ◽  
Log Reduction ◽  
Viral Copy Number ◽  
Significant Difference ◽  
Viral Copy ◽  
Viral Load Assay ◽  
Temperature And Pressure ◽  
And Storage

Freeze drying (Lyophilization) performed at temperature and pressure below the triple point is being practiced for the preservation of virus stocks for longer periods. The present study is aimed to lyophilize adenovirus strain to study its effects on infectivity and viral load. In-house adenovirus reference strain (stock virus) was propagated in Hep-2 cell line in 25cm2 cell culture flasks. In 24-well plates the serial dilutions of stock virus from 10-1 to 10-7 (100μl inoculum) was inoculated in each well with Hep-2 cells for TCID50 titer and viral DNA was extracted separately to determine viral load by Taqman Real Time PCR. Stock virus was lyophilized in 3 lots and stored at RT (25±2°C) and 4°C separately for 1, 4 and 6 months and subjected to TCID50 (for viral infectivity) and viral load assay (for total viral genome copies). Following lyophilisation and storage of adenoviral strains at RT and 4°C separately did not affect significantly on the viral stability, infectivity as well as viral copy number till 4 months. However, storage at RT for 6 months resulted in 1 log reduction in viral copy number. Thus, storage of even lyophilized virus stock would necessitate a temperature of at least 4°C for prolonged periods. The present study could successfully lyophilize adenovirus and retain its infectivity over a period of 6 months when stored at RT and 4°C. No significant difference in the infectivity or TCID50 titer was observed in the lyophilized virus as compared to the stock virus. However, the viral load was observed to increase with lyophilization of the virus over 6 months when stored at 4°C which possibly is due to the concentration of the virus on freeze-drying.Nepal Journal of Biotechnology. Dec. 2015 Vol. 3, No. 1: 15-21

scholarly journals Initial Analysis of Viral Dynamics and Circulating Viral Variants During the mRNA-1273 Phase 3 COVE Trial

2021 ◽  
Author(s):  
Rolando Pajon ◽  
Yamuna Paila ◽  
Bethany Girard ◽  
Groves Dixon ◽  
Katherine Kacena ◽  
...  
Keyword(s):  
Viral Load ◽  
Severe Acute Respiratory Syndrome ◽  
Copy Number ◽  
Respiratory Viruses ◽  
Viral Dynamics ◽  
Phase 3 ◽  
Viral Copy Number ◽  
The Us ◽  
Viral Copy ◽  
The Impact

This analysis assessed the impact of mRNA-1273 vaccination on the viral dynamics of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in the ongoing Coronavirus Efficacy (COVE) trial. mRNA-1273 vaccination significantly reduced SARS-CoV-2 viral copy number (95% confidence interval [CI]) by 100-fold on the day of diagnosis (4.1 [3.4-4.8] versus placebo (6.2 [6.0-6.4] log10 copies/ml). Median times to undetectable viral copies were 4 days for mRNA-1273 and 7 for placebo. Vaccination also reduced the burden of disease and infection scores. Vaccine efficacies (95% CI) during the trial against SARS-CoV-2 variants circulating in the US were 82.4% (40.4%-94.8%) for Epsilon and Gamma, and 81.2% (36.1%-94.5%) for the Epsilon variants. The detection of other respiratory viruses during the trial was similar between groups. In those who became SARS-CoV-2 infected, the reduction of viral load after mRNA-1273 vaccination is potentially correlated to the risk of transmission, which has not been assessed in this study.

scholarly journals SARS-CoV-2 Delta variant saliva viral load is 15-fold higher than wild-type strains

2021 ◽  
Author(s):  
Kenichi Imai ◽  
Ryo Ikeno ◽  
Hajime Tanaka ◽  
Norio Takada
Keyword(s):  
Viral Load ◽  
Copy Number ◽  
Null Distribution ◽  
Host Cells ◽  
Wild Type ◽  
Copy Numbers ◽  
Whole Saliva ◽  
Viral Copy Number ◽  
Viral Copy ◽  
Type Strains

The emergence of SARS-CoV-2 Delta variants has escalated COVID-19 cases globally due to their high transmissibility. Since saliva is crucial for SARS-CoV-2 transmission, we hypothesized that a higher viral load of Delta variants in saliva than their parental wild-type strains contributed to the high transmissibility in the first place. However, studies have not reported this particular comparison done with viral copy numbers. Twenty-two genetically confirmed -positive saliva samples for wild-type strain and 32 Delta variants were statistically compared for viral copy number per milliliter determined by real-time qPCR combined with synthesized viral RNA and Poisson's null distribution equation between the groups of wild and variant strains and between whole saliva and centrifugal supernatant in each group. We found that the copy number of the Delta variants was 15.1 times higher than wild-type strains of the whole saliva. In addition, the viral load of both strains in the whole saliva was higher than the pertinent supernatant, indicating that most viruses in the whole saliva are associated with host cells. Meanwhile, more than a million virions per milliliter of the viral load of the variants in the supernatants were 4.0 times higher but not significant than wild-type strains. Humanity must share our findings; the simple but concrete note that Delta variant viral load is abundant in the saliva is critical for preventing the spread of infection.

Activation-Induced CD4+ T Cell Death in HIV-Positive Individuals Correlates with Fas Susceptibility, CD4+ T Cell Count, and HIV Plasma Viral Copy Number

1999 ◽  
Vol 15 (17) ◽  
pp. 1509-1518 ◽  
Author(s):  
D. H. Dockrell ◽  
A. D. Badley ◽  
A. Algeciras-Schimnich ◽  
M. Simpson ◽  
R. Schut ◽  
...  
Keyword(s):  
Cell Death ◽  
T Cell ◽  
Cell Count ◽  
Copy Number ◽  
Cd4 T Cell ◽  
Hiv Positive ◽  
Viral Copy Number ◽  
Viral Copy ◽  
Cd4 T Cell Count

Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number

2021 ◽  
Author(s):  
Everardo González-González ◽  
Itzel Montserrat Lara-Mayorga ◽  
Iram Pablo Rodríguez-Sánchez ◽  
Yu Shrike Zhang ◽  
Sergio O. Martínez-Chapa ◽  
...  
Keyword(s):  
Copy Number ◽  
Quantitative Method ◽  
Diagnostic Performance ◽  
Cost Effective ◽  
Isothermal Amplification ◽  
Quantitative Detection ◽  
Loop Mediated Isothermal Amplification ◽  
Viral Copy Number ◽  
Viral Copy

Colorimetric LAMP for COVID-19 intensified diagnostics: a simple and quantitative method comparable in diagnostic performance to RT-qPCR.

CD8 + T‐cell attenuation of cutaneous herpes simplex virus infection reduces the average viral copy number of the ensuing latent infection

2008 ◽  
Vol 86 (8) ◽  
pp. 666-675 ◽  
Author(s):  
Linda M Wakim ◽  
Claerwen M Jones ◽  
Thomas Gebhardt ◽  
Christopher M Preston ◽  
Francis R Carbone
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Virus Infection ◽  
Copy Number ◽  
Herpes Simplex Virus Infection ◽  
Latent Infection ◽  
Cd8 T Cell ◽  
Viral Copy Number ◽  
Viral Copy ◽  
Simplex Virus

scholarly journals Low-Coverage Whole Genome Sequencing Using Laser Capture Microscopy with Combined Digital Droplet PCR: An Effective Tool to Study Copy Number and Kras Mutations in Early Lung Adenocarcinoma Development

2021 ◽  
Vol 22 (21) ◽  
pp. 12034
Author(s):  
Elizabeth A. Mickler ◽  
Huaxin Zhou ◽  
Tzu L. Phang ◽  
Mark W. Geraci ◽  
Robert S. Stearman ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Kras Mutations ◽  
Digital Droplet Pcr ◽  
Laser Capture Microscopy ◽  
Droplet Pcr ◽  
Low Coverage ◽  
Laser Capture

Defining detailed genomic characterization of early tumor progression is critical to identifying key regulators and pathways in carcinogenesis as potentially druggable targets. In human lung cancer, work to characterize early cancer development has mainly focused on squamous cancer, as the earliest lesions are more proximal in the airways and often accessible by repeated bronchoscopy. Adenocarcinomas are typically located distally in the lung, limiting accessibility for biopsy of pre-malignant and early stages. Mouse lung cancer models recapitulate many human genomic features and provide a model for tumorigenesis with pre-malignant atypical adenomatous hyperplasia and in situ adenocarcinomas often developing contemporaneously within the same animal. Here, we combined tissue characterization and collection by laser capture microscopy (LCM) with digital droplet PCR (ddPCR) and low-coverage whole genome sequencing (LC-WGS). ddPCR can be used to identify specific missense mutations in Kras (Kirsten rat sarcoma viral oncogene homolog, here focused on Kras Q61) and estimate the percentage of mutation predominance. LC-WGS is a cost-effective method to infer localized copy number alterations (CNAs) across the genome using low-input DNA. Combining these methods, the histological stage of lung cancer can be correlated with appearance of Kras mutations and CNAs. The utility of this approach is adaptable to other mouse models of human cancer.

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