Smartphone Screen Testing, a novel pre-diagnostic method to identify SARS-CoV-2 infectious individuals

The COVID-19 pandemic will likely take years to control globally, and constant epidemic surveillance will be required to limit the spread of SARS-CoV-2, especially considering the emergence of new variants that could hamper the effect of vaccination efforts. We developed a simple and robust - Phone Screen Testing (PoST) - method to detect positive SARS-CoV-2 individuals by RT-PCR testing of smartphone screen swab samples. We show that 81.3-100% of individuals with high-viral load SARS-CoV-2 nasopharyngeal positive samples also test positive for PoST, suggesting this method is effective in identifying COVID-19 contagious individuals. Furthermore, we successfully identified polymorphisms associated with SARS-CoV-2 Alpha, Beta and Gamma variants, in SARS-CoV-2 positive PoST samples. Overall, we report that PoST is a new non-invasive, cost-effective, and easy to implement smartphone-based smart alternative for SARS-CoV-2 testing, which could help to contain COVID-19 outbreaks and identification of variants of concern in the years to come.

Download Full-text

Prolonged Detection of SARS CoV2 RNA in Extracellular Vesicles in Nasal Swab RT-PCR Negative Patients

10.1101/2021.12.16.21267912 ◽

2021 ◽

Author(s):

P Debishree Subudhi ◽

Sheetalnath Rooge ◽

Swati Thangriyal ◽

Reshu Aggarwal ◽

Ekta Gupta ◽

...

Keyword(s):

Endothelial Cells ◽

Viral Load ◽

Liver Disease ◽

Chronic Liver Disease ◽

Extracellular Vesicles ◽

Nasal Swab ◽

High Viral Load ◽

Chronic Liver ◽

Rt Pcr ◽

Route Of Transmission

Background: There is a prolonged RT PCR positivity seen in COVID-19 infected patients up to 2 to 3 months. It is assumed that this virus is usually non-infective but there are hardly any study on the reactivation of this virus within the respiratory tract. We aim to investigate the presence of viral particles inside Extracellular vesicles (EV) and its role in underlying liver disease patients. Methods: SARS CoV2 nasal and throat swab RT-PCR positive n=78 {n=24(66.6%) chronic liver disease (CLD); n=52 (81.3%) non liver disease} n=5 RT PCR negative subjects (HC) were studied. SARS CoV2 patients were also followed up for day (d) 7, 14 and 28. Nasal swab [collected in viral transport media (VTM)] and plasma samples were investigated at each time point. Extracellular vesicles were isolated using differential ultracentrifugation. SARS CoV2 RNA was measured using qRT-PCR by Altona Real Star kit. Cellular origin of EV was confirmed using epithelial cells (Epcam+ CK19+ CDh1+), endothelial cells (CD31+CD45-), and hepatocytes (ASGPR+) surface markers by Flow cytometry. Results: The COVID19 patients {Mean age 54±23 years; 41 males} were having severity between moderate to severe. In patients with cirrhosis, the most common aetiology of liver disease was alcohol (MELD 22±8). In baseline RT-PCR positive patients, SARS-CoV2 RNA inside the EV was present in 64/74 (82%) patients with comparable viral load between VTM and EV (mean 1/CT 0.033±0.005 vs. 1/CT 0.029±0.014, p=ns). On follow-up at day 7, of the 24 patients negative for COVID19, 10 (41%) had persistence of virus in the EV (1/CT 0.028±0.004) and on day 14, 14 of 40 (35%) negative RT-PCR had EVs with SARS CoV2 RNA (1/CT 0.028±0.06). The mean viral load decreased at day7 and day14 in nasal swab from baseline (p=0.001) but not in EV. SARS-CoV2 RNA otherwise undetectable in plasma, was found to be positive in EV in 12.5% of COVID19 positive patients. Interestingly, significantly prolonged and high viral load was found in EV at day 14 in CLD COVID19 patients compared to COVID19 alone (p=0.002). The high cellular injury was seen in CLD COVID19 infected patients with significant high levels of EV associated with endothelial cells and hepatocytes than COVID19 alone (p=0.004; 0.001). Conclusion: Identification of SARS-CoV2 RNA in EV, in RT-PCR negative patients indicates persistence of infection for and likely recurrence of the infection. It is suggestive of another route of transmission as EV harbour SARS CoV2 RNA. EV associated RNA may determine the ongoing inflammation and clinical course of subjects with undetectable SARS-CoV2 virus and this may also have relevance in management of chronic liver disease patients.

Download Full-text

Rapid Diagnosis of SARS-CoV-2 Pneumonia on Lower Respiratory Tract Specimens

10.21203/rs.3.rs-684790/v1 ◽

2021 ◽

Author(s):

Vanessa De Pace ◽

Patrizia Caligiuri ◽

Valentina Ricucci ◽

Nicola Nigro ◽

Barbara Galano ◽

...

Keyword(s):

Intensive Care ◽

Viral Load ◽

Respiratory Tract ◽

Intensive Care Units ◽

Lower Respiratory Tract ◽

Clinical Decision Making ◽

High Viral Load ◽

Rt Pcr ◽

Predictive Values ◽

Rapid Pcr

Abstract Background: The ongoing pandemic of SARS-CoV-2 requires the availability of accurate and rapid diagnostic tests, especially in some clinical settings like emergency and intensive care units. The objective of this study was to evaluate the diagnostic performances of rapid PCR kit Vivalytic SARS-CoV-2 in lower respiratory tract (LRT) specimens.Methods: A consecutive sample of LRT specimens (bronchoalveolar lavage and bronchoaspirates) was collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples were tested in RT-PCR by using Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). Based on RT-PCR results, specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤30] and positive with low viral load (Ct of 31–35). A quota 1:1:1 sampling was used to achieve a sample size of 75. Then, all specimens were tested in the rapid PCR assay Vivalytic SARS-CoV-2 (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of the rapid PCR against RT-PCR was assessed through calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values.Results: The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%) with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). The sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. Samples with high viral loads had a sensitivity of 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: P=0.070) with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35), respectively (Figure 1). NPV and PPV was 92.6% and 100%, respectively.Conclusions: This study shows Vivalytic SARS-CoV-2 can be used following the sample liquefaction on LRT specimens. It’s a feasible and highly accurate molecular procedure especially in high viral load samples. This assay allows having a result in about 40 min and therefore may accelerate the clinical decision making in urgent/emergency situations.

Download Full-text

Viral load and antibody levels in patients with COVID-19

GSC Advanced Research and Reviews ◽

10.30574/gscarr.2021.8.3.0180 ◽

2021 ◽

Vol 8 (3) ◽

pp. 010-018

Author(s):

Iva Christova ◽

Iva Trifonova ◽

Teodora Gladnishka ◽

Elena Dragusheva ◽

Georgi Popov ◽

...

Keyword(s):

Viral Load ◽

High Viral Load ◽

Igg Antibodies ◽

Rt Pcr ◽

Serum Samples ◽

Weekly Basis ◽

Specific Antibody Response ◽

Viral Loads ◽

Antibody Levels ◽

Kinetics Of

Relations between viral load, antibody levels and COVID-19 severity are not well studied and results from such investigations are controversial. In this study, we investigated kinetics of viral load and antibody responses to SARS-CoV-2 in 20 patients with COVID-19 and analysed the association with disease severity. The patients were followed on weekly basis within the first month after the onset and then once per month for the next 4 months. Serum samples were tested for IgA, IgM, and IgG antibodies against SARS-CoV-2 using ELISA tests. SARS-CoV-2 viral load in nasopharyngeal swabs was measured by quantitative Realtime RT-PCR. For vast majority of the patients, the viral loads were at their highest levels at presentation and then declined gradually. Despite development of specific antibody response 7-11 days after the onset of COVID-19, SARS-CoV-2 RNA was still detected in nasopharyngeal swabs of most of the patients. There was no direct link between viral load and severity of COVID-19: some of mild and some of severe cases started with a high viral load. There was a relationship between the time from the onset of the disease and the viral load: the highest viral load was in the first days. In more severe cases, there was a tendency for slower reduction in viral load and longer detection of SARS-CoV-2 virus. Levels of the specific antibodies increased earlier and to higher levels and were present for longer time in patients with more severe manifestations of COVID-19 than in those with milder disease.

Download Full-text

Saliva: Both a Threat and an Opportunity in Covid-19 Pandemic

Pakistan Journal of Medical Sciences ◽

10.12669/pjms.37.4.4263 ◽

2021 ◽

Vol 37 (4) ◽

Author(s):

Ismail Serhat Sadıkoğlu ◽

Mehmet Gagari Caymaz

Keyword(s):

Viral Load ◽

Diagnostic Technique ◽

High Viral Load ◽

Rt Pcr ◽

Creative Commons ◽

Aerosol Exposure ◽

Cochrane Database ◽

Dental Practitioners ◽

Day By Day ◽

Open Access Article

Covid-19 pandemic, continues all over the world with the increasing number of confirmed cases and performed tests day by day. It has been shown that collecting nasopharyngeal samples, as the most commonly prefered method to perform RT-PCR, has disadvantages like causing discomfort and bleeding in patients. Sample collecting procedure also renders healthcare professionals by exposing them to the risk of transmission of the virus related to the direct contact with patients. These disadvantages make this procedure undesirable for the researchers and forces them to search for an alternative technique. At this point, saliva appears as an opportunity, regarding its high viral load. On the other hand, this high viral load poses a threat, especially for professions such as dental practitioners, with too much aerosol exposure. Since dentistry is a branch of health that constantly needs direct operations, it is necessary to be protected from the virus as much as possible while caring for the patient. A literature review was done using electronic databases “PubMed,” “Google Scholar,” and “Cochrane Database,” on January 2021. Studies have proposed many different preventive measures in this regard. Therefore, the purpose of this review is to draw attention to the saliva by bringing together the recent research and also to provide information and a perspective to dental clinicians about both prevention and a potential diagnostic technique. doi: https://doi.org/10.12669/pjms.37.4.4263 How to cite this:Sadikoglu IS, Caymaz MG. Saliva: Both a Threat and an Opportunity in Covid-19 Pandemic. Pak J Med Sci. 2021;37(4):---------. doi: https://doi.org/10.12669/pjms.37.4.4263 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download Full-text

Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco

10.1101/2020.11.02.20223891 ◽

2020 ◽

Cited By ~ 2

Author(s):

Genay Pilarowski ◽

Paul Lebel ◽

Sara Sunshine ◽

Jamin Liu ◽

Emily Crawford ◽

...

Keyword(s):

Viral Load ◽

San Francisco ◽

High Viral Load ◽

Performance Characteristics ◽

Viral Rna ◽

Antigen Test ◽

Rt Pcr ◽

Detection Assay ◽

Community Transmission ◽

Testing Site

ABSTRACTWe evaluated the performance of the Abbott BinaxNOW™ Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6×104-4.3×104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.

Download Full-text

Age and Sex Modulate SARS-CoV-2 Viral Load Kinetics: A Longitudinal Analysis of 1735 Subjects

Journal of Personalized Medicine ◽

10.3390/jpm11090882 ◽

2021 ◽

Vol 11 (9) ◽

pp. 882

Author(s):

Valerio Caputo ◽

Andrea Termine ◽

Carlo Fabrizio ◽

Giulia Calvino ◽

Laura Luzzi ◽

...

Keyword(s):

Viral Load ◽

Healthcare Professionals ◽

High Viral Load ◽

Digital Pcr ◽

Original Strain ◽

Rt Pcr ◽

Subgenomic Rna ◽

Slow Decay ◽

Male Sex ◽

Age And Sex

The COVID-19 pandemic caused by SARS-CoV-2 represents a public health emergency, which became even more challenging since the detection of highly transmissible variants and strategies against COVID-19 were indistinctly established. We characterized the temporal viral load kinetics in individuals infected by original and variant strains. Naso-oropharyngeal swabs from 33,000 individuals (admitted to the IRCCS Santa Lucia Foundation Drive-in, healthcare professionals and hospitalized patients who underwent routinary screening) from November 2020 to June 2021 were analyzed. Of them, 1735 subjects were selected and grouped according to the viral strain. Diagnostic analyses were performed by CE-IVD RT-PCR-based kits. The subgenomic-RNA component was assessed in 36 subjects using digital PCR. Infection duration, viral load decay speed, effects of age and sex were assessed and compared by extensive statistical analyses. Overall, infection duration and viral load differed between the groups (p < 0.05). Male sex was more present among both original and variant carriers affected with high viral load and showing fast decay speed, whereas original strain carriers with slow decay speed resulted in older (p < 0.05). Subgenomic-RNA was detected in the positive samples, including those with low viral load. This study provides a picture of the viral load kinetics, identifying individuals with similar patterns and showing differential effects of age and sex, thus providing potentially useful information for personalized management of infected subjects.

Download Full-text

Viral load of SARS-CoV-2 in adults during the first and second wave of COVID-19 pandemic in Houston, TX: the potential of the super-spreader

The Journal of Infectious Diseases ◽

10.1093/infdis/jiab097 ◽

2021 ◽

Author(s):

Vasanthi Avadhanula ◽

Erin G Nicholson ◽

Laura Ferlic-Stark ◽

Felipe-Andres Piedra ◽

Brittani N Blunck ◽

...

Keyword(s):

Viral Load ◽

Contingency Table ◽

Social Dynamics ◽

High Viral Load ◽

Rt Pcr ◽

Median Viral Load ◽

Viral Shedding ◽

The Social ◽

Second Wave ◽

Index Cases

Abstract Background During the COVID-19 pandemic, a minority of index cases are associated with a majority of secondary cases suggesting that super-spreaders could drive the pandemic. We identified a phenotype in individuals with extremely high viral load who could act as super-spreaders. Methods Data were analyzed from individuals tested for SARS-CoV-2 from March 18 through August 15, 2020. Outcomes were compared using contingency table and quantile regression to test the equality of medians between the pandemic waves and by viral load groups. Results Of the 11,564 samples tested, 1,319 (11.4%) were positive for SARS-CoV-2. An increase in weekly median viral load occurred in the second wave of the SARS-CoV2 pandemic. This population was more likely to be women, outpatients, symptomatic and have an extremely high or high viral load. In patients with multiple RT-PCR positive tests, the duration of viral shedding was comparable between individuals with asymptomatic/mild and mild/moderate illness severity. Conclusions We detected a small group of individuals with extremely high SARS-CoV-2 viral load with mild illness. We believe that these individuals’ characteristics could be consistent with the super-spreader phenomenon and that greater awareness of the social dynamics of these individuals is needed to understand the spread of SARS-CoV-2.

Download Full-text

Comparative performance study of three Ebola rapid diagnostic tests in Guinea

BMC Infectious Diseases ◽

10.1186/s12879-020-05339-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Zelda Moran ◽

William Rodriguez ◽

Doré Ahmadou ◽

Barré Soropogui ◽

N’ Faly Magassouba ◽

...

Keyword(s):

Viral Load ◽

Diagnostic Tests ◽

High Viral Load ◽

Rapid Diagnostic Tests ◽

Local Health ◽

Performance Study ◽

Rt Pcr ◽

Effective Response ◽

Ct Value ◽

Panel Test

Abstract Background The 2014/15 Ebola outbreak in West Africa resulted in 11,000 deaths and massive strain on local health systems, and the ongoing outbreak in Democratic Republic of Congo has afflicted more than 3000 people. Accurate, rapid Ebola diagnostics suitable for field deployment would enable prompt identification and effective response to future outbreaks, yet remain largely unavailable. The purpose of this study was to assess the accuracy of three novel rapid diagnostic tests (RDTs): an Ebola, an Ebola-Malaria, and a Fever Panel test that includes Ebola, all from a single manufacturer. Methods We evaluated the three RDTs in 109 Ebola-positive and 96 Ebola-negative stored serum samples collected during the outbreak in Guinea in 2014/15, and tested by real-time polymerase chain reaction (RT-PCR). Sensitivity, specificity, and overall percent agreement were calculated for each RDT using RT-PCR as a reference standard, stratified by Ct value ranges. Results All tests performed with high accuracy on samples with low Ct value (high viral load). The Fever Panel test performed with the highest accuracy, with a sensitivity of 89.9% and specificity of 90.6%. The Ebola and Ebola-Malaria tests performed comparably to each other: sensitivity was 77.1 and 78% respectively, and specificity was 91.7% for the Ebola test and 95.8% for the Ebola-Malaria test. Conclusions This study evaluated the accuracy of three novel rapid diagnostic tests for Ebola. The tests may have significant public health relevance, particularly the Fever Panel test, which detects seven pathogens including Ebola. Given limitations to the study resulting from uncertain sample quality, further evaluation is warranted. All tests performed with highest accuracy on samples with low Ct value (high viral load), and the data presented here suggests that these RDTs may be useful for point-of-care diagnosis of cases in the context of an outbreak. Restrictions to their use in non-severe Ebola cases or for longitudinal monitoring, when viral loads are lower, may be appropriate. Highlighting the challenge in developing and evaluating Ebola RDTs, there were concerns regarding sample integrity and reference testing, and there is a need for additional research to validate these assays.

Download Full-text

Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco

The Journal of Infectious Diseases ◽

10.1093/infdis/jiaa802 ◽

2021 ◽

Author(s):

Genay Pilarowski ◽

Paul Lebel ◽

Sara Sunshine ◽

Jamin Liu ◽

Emily Crawford ◽

...

Keyword(s):

Viral Load ◽

San Francisco ◽

High Viral Load ◽

Performance Characteristics ◽

Viral Rna ◽

Antigen Test ◽

Rt Pcr ◽

Detection Assay ◽

Community Transmission ◽

Testing Site

Abstract We evaluated the performance of the Abbott BinaxNOW TM Covid-19 rapid antigen test (Binax-CoV2) to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured SARS-CoV-2 yielded a human observable threshold between 1.6x10 4-4.3x10 4 viral RNA copies (cycle threshold (Ct) of 30.3-28.8). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.

Download Full-text

Pooled Saliva Specimens for SARS-CoV-2 Testing

Journal of Clinical Microbiology ◽

10.1128/jcm.02486-20 ◽

2020 ◽

Author(s):

Bidisha Barat ◽

Sanchita Das ◽

Valeria De Giorgi ◽

David K. Henderson ◽

Stacy Kopka ◽

...

Keyword(s):

Viral Load ◽

Screening Program ◽

High Viral Load ◽

Load Cycle ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Viral Loads ◽

Viral Transport ◽

Average Loss ◽

Positive Agreement

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The percent positive agreement increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion®, and Roche COBAS® 6800. The average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

Download Full-text