scholarly journals Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2

2020 ◽  
Author(s):  
Cole Anderson ◽  
Fritz Castillo ◽  
Michael Koenig ◽  
Jim Managbanag
Keyword(s):  
Rapid Identification ◽  
Positive Sample ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Global Pandemic ◽  
Recent Emergence ◽  
Single Positive ◽  
High Risk Populations ◽  
Pooling Strategy ◽  
Moderate Complexity

AbstractThe recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.

scholarly journals Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools

2020 ◽  
Vol 71 (16) ◽  
pp. 2073-2078 ◽  
Author(s):  
Idan Yelin ◽  
Noga Aharony ◽  
Einat Shaer Tamar ◽  
Amir Argoetti ◽  
Esther Messer ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
False Negative ◽  
Rna Extraction ◽  
False Negative Rate ◽  
Positive Sample ◽  
Recent Emergence ◽  
Single Positive ◽  
Polymerase Chain ◽  
Pool Test ◽  
Current Screening

Abstract Background The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic of unprecedented scale. Although diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately applicable protocol. Methods RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction, alone or in pools of different sizes (2-, 4-, 8-, 16-, 32-, and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. Results A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, although this may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. Conclusions As it uses the standard protocols, reagents, and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for coronavirus disease 2019 would allow expanding current screening capacities, thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.

scholarly journals Una presentación infrecuente de COVID-19, con diarrea como síntoma inicial, el primer caso diagnosticado en Cartagena, Colombia.

2021 ◽  
Vol 10 (1) ◽  
pp. 65-74
Author(s):  
Germán Enrique Arenas ◽  
Jesús De León Martínez ◽  
Marcela Negrete Vasquez ◽  
Mario Lora ◽  
Martín Carvajal ◽  
...  
Keyword(s):  
World Health ◽  
Nasopharyngeal Swab ◽  
Imaging Data ◽  
Rt Pcr ◽  
Global Pandemic ◽  
First Case ◽  
Initial Symptoms ◽  
The Common ◽  
Severity Of The Disease ◽  
Health Organization

Introduction: the Coronavirus disease 2019 (COVID-19) was declared as a global pandemic by the World Health Organization on March 11, 2020. The clinical presentation and severity of the disease has been described from its most typical symptoms, the common cold, pneumonia and respiratory distress syndrome, to the involvement of other organs and systems such such as the gastrointestinal, renal and cardiovascular. Case report: we describe the first case of COVID-19 diagnosed in Cartagena, Colombia, on March 11, 2020, and its uncommon clinic presentation, which was almost unknown at the time. An 85-year-old woman with week-long initial symptoms of nausea and occasional vomiting, with progression to diarrhea and a 38.5 oC fever during the last three days. The patient came from Oxford, UK, and she had been on a Caribbean cruise excursion since the end of February, 2020. Chest computed tomography showed ground glass opacities in both peripheral and central lung fields, multilobar and predominantly subpleural; without evidence of consolidation or pleural effusion. COVID-19 was confirmed three days after admission, when a RT-PCR molecular test performed on a nasopharyngeal swab sample tested positive for SARS-Cov-2 Conclusion: this first case of COVID-19 diagnosed in Cartagena occurred at a time when our health system was not prepared to face the pandemic. However, despite having manifested with a clinical that had not been described at the time, and thanks to the epidemiological, clinical and imaging data, the case could be adequately approached, diagnosed and treated according to the necessary and recommended measures at the time.

scholarly journals Rapid identification of SARS-CoV-2-infected patients at the emergency department using routine testing

2020 ◽  
Author(s):  
Steef Kurstjens ◽  
Armando van der Horst ◽  
Robert Herpers ◽  
Mick W.L. Geerits ◽  
Yvette C.M. Kluiters-de Hingh ◽  
...  
Keyword(s):  
Respiratory Symptoms ◽  
Demographic Data ◽  
Characteristic Curve ◽  
Rapid Identification ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Validation Population ◽  
Score Model ◽  
Using Data ◽  
Novel Coronavirus

ABSTRACTBackgroundThe novel coronavirus disease 19 (COVID-19), caused by SARS-CoV-2, spreads rapidly across the world. The exponential increase in the number of cases has resulted in overcrowding of emergency departments (ED). Detection of SARS-CoV-2 is based on an RT-PCR of nasopharyngeal swab material. However, RT-PCR testing is time-consuming and many hospitals deal with a shortage of testing materials. Therefore, we aimed to develop an algorithm to rapidly evaluate an individual’s risk of SARS-CoV-2 infection at the ED.MethodsIn this multicenter retrospective study, routine laboratory parameters (C-reactive protein, lactate dehydrogenase, ferritin, absolute neutrophil and lymphocyte counts), demographic data and the chest X-ray/CT result from 967 patients entering the ED with respiratory symptoms were collected. Using these parameters, an easy-to-use point-based algorithm, called the corona-score, was developed to discriminate between patients that tested positive for SARS-CoV-2 by RT-PCR and those testing negative. Computational sampling was used to optimize the corona-score. Validation of the model was performed using data from 592 patients.ResultsThe corona-score model yielded an area under the receiver operating characteristic curve of 0.91 in the validation population. Patients testing negative for SARS-CoV-2 showed a median corona-score of 3 versus 11 (scale 0-14) in patients testing positive for SARS-CoV-2 (p<0.001). Using cut-off values of 4 and 11 the model has a sensitivity and specificity of 96% and 95%, respectively.ConclusionThe corona-score effectively predicts SARS-CoV-2 RT-PCR outcome based on routine parameters. This algorithm provides the means for medical professionals to rapidly evaluate SARS-CoV-2 infection status of patients presenting at the ED with respiratory symptoms.

scholarly journals Pooling for SARS-CoV-2 Control in Care Institutions

2020 ◽  
Author(s):  
Jorge J. Cabrera Alvargonzalez ◽  
Sonia Rey Cao ◽  
Sonia Pérez Castro ◽  
Lucía Martínez Lamas ◽  
Olaia Cores Calvo ◽  
...  
Keyword(s):  
Scale Up ◽  
Positive Sample ◽  
Care Homes ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Average Delay ◽  
Global Rate ◽  
Local Experience ◽  
Expected Performance ◽  
Pooling Strategies

Abstract Background Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources.The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people.Methods 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were tested using RT-PCR. Prevalence and distribution of positive detection in Care Homes was calculated. Pools of 19 negative samples and one positive sample were tested using RT-PCR as well. Prevalence and distribution of positive detection in Care Homes was calculated. Results Distribution of SARS-CoV-2 infection at Care Houses was uneven. As the virus circulation global rate was low in our area, the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on quantification cycle (Cq) values. Conclusions A new surveillance system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Houses, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.

scholarly journals Rapid identification of SARS-CoV-2-infected patients at the emergency department using routine testing

2020 ◽  
Vol 58 (9) ◽  
pp. 1587-1593 ◽  
Author(s):  
Steef Kurstjens ◽  
Armando van der Horst ◽  
Robert Herpers ◽  
Mick W. L. Geerits ◽  
Yvette C. M. Kluiters-de Hingh ◽  
...  
Keyword(s):  
Respiratory Symptoms ◽  
Demographic Data ◽  
Characteristic Curve ◽  
Rapid Identification ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Validation Population ◽  
Score Model ◽  
Using Data ◽  
Novel Coronavirus

AbstractObjectivesThe novel coronavirus disease 19 (COVID-19), caused by SARS-CoV-2, spreads rapidly across the world. The exponential increase in the number of cases has resulted in overcrowding of emergency departments (ED). Detection of SARS-CoV-2 is based on an RT-PCR of nasopharyngeal swab material. However, RT-PCR testing is time-consuming and many hospitals deal with a shortage of testing materials. Therefore, we aimed to develop an algorithm to rapidly evaluate an individual’s risk of SARS-CoV-2 infection at the ED.MethodsIn this multicenter retrospective study, routine laboratory parameters (C-reactive protein, lactate dehydrogenase, ferritin, absolute neutrophil and lymphocyte counts), demographic data and the chest X-ray/CT result from 967 patients entering the ED with respiratory symptoms were collected. Using these parameters, an easy-to-use point-based algorithm, called the corona-score, was developed to discriminate between patients that tested positive for SARS-CoV-2 by RT-PCR and those testing negative. Computational sampling was used to optimize the corona-score. Validation of the model was performed using data from 592 patients.ResultsThe corona-score model yielded an area under the receiver operating characteristic curve of 0.91 in the validation population. Patients testing negative for SARS-CoV-2 showed a median corona-score of 3 vs. 11 (scale 0–14) in patients testing positive for SARS-CoV-2 (p<0.001). Using cut-off values of 4 and 11 the model has a sensitivity and specificity of 96 and 95%, respectively.ConclusionsThe corona-score effectively predicts SARS-CoV-2 RT-PCR outcome based on routine parameters. This algorithm provides the means for medical professionals to rapidly evaluate SARS-CoV-2 infection status of patients presenting at the ED with respiratory symptoms.

scholarly journals No SARS-CoV-2 detection in the German CAPNETZ cohort of community acquired pneumonia before COVID-19 peak in March 2020

Infection ◽  
2020 ◽  
Vol 48 (6) ◽  
pp. 971-974
Author(s):  
Marcus Panning ◽  
◽  
Julius Wiener ◽  
Kathrin Rothe ◽  
Jochen Schneider ◽  
...  
Keyword(s):  
Real Time ◽  
Community Acquired Pneumonia ◽  
Positive Sample ◽  
Nasopharyngeal Swab ◽  
Study Cohort ◽  
Respiratory Pathogens ◽  
Rt Pcr ◽  
Viral Pathogens ◽  
Geographic Regions ◽  
Positive Results

Abstract Purpose The first SARS-CoV-2 cases in Europe were reported in January 2020. Recently, concern arose on unrecognized infections before this date. For a better understanding of the pandemic, we retrospectively analyzed patient samples for SARS-CoV-2 from the prospective CAPNETZ study cohort. Methods We used nasopharyngeal swab samples from a cohort of well characterized patients with community acquired pneumonia of the CAPNETZ study group, recruited from different geographic regions across Germany, Austria, the Netherlands, and Switzerland between 02nd December 2019 and 28th April 2020. Multiplex real-time RT-PCR for a broad range of respiratory pathogens and SARS-CoV-2 real-time RT-PCR were performed on all samples. Results In our cohort, respiratory pathogens other than SARS-CoV-2 were detected in 21.5% (42/195) of patients with rhinovirus as the most frequently detected pathogen. The detection rate increased to 29.7% (58/195) when SARS-CoV-2 was included. No SARS-CoV-2 positive sample was detected before end of March 2020. Conclusions Respiratory viral pathogens accounted for a considerable number of positive results but no SARS-CoV-2 case was identified before the end of March 2020.

scholarly journals Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care

2021 ◽  
Author(s):  
Jerome Le Goff ◽  
Solen Kerneis ◽  
Caroline Elie ◽  
Severine Mercier Delarue ◽  
Nabil Gastli ◽  
...  
Keyword(s):  
Point Of Care ◽  
False Negative ◽  
Lamp Assay ◽  
Rapid Identification ◽  
Ambulatory Setting ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Rt Pcr ◽  
A Prospective Study ◽  
Antigen Testing

Background: The rapid identification of SARS-CoV-2 infected individuals is a cornerstone in strategies for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Objectives and methods: We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) specifically designed for the detection of SARS-CoV-2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR as reference test, saliva RT-PCR and nasopharyngeal antigen testing. Results: Overall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Sensitivities of saliva RT-PCR and nasopharyngeal antigen test were 93% (95% Confidence Interval (95%CI): 86-97) and 85% (95%CI: 77-91), respectively. The sensitivity and specificity of the RT-LAMP assay in saliva were 34% (95%CI: 26-44) and 97% (95%CI: 96-98). The performance was similar in symptomatic and asymptomatic participants and whatever the reference standard considered. Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p=0.028). Conclusion: In the ambulatory setting, the detection of SARS-CoV-2 from crude saliva samples with the RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.

scholarly journals Evaluation of COVID-19 RT-qPCR test in multi-sample pools

2020 ◽  
Author(s):  
Idan Yelin ◽  
Noga Aharony ◽  
Einat Shaer Tamar ◽  
Amir Argoetti ◽  
Esther Messer ◽  
...  
Keyword(s):  
Diagnostic Tests ◽  
False Negative ◽  
False Negative Rate ◽  
Positive Sample ◽  
Testing Laboratories ◽  
Recent Emergence ◽  
Single Positive ◽  
Pool Test ◽  
Current Screening ◽  
A Current

AbstractThe recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented levels. Though diagnostic tests are fundamental to the ability to detect and respond, many health systems are already experiencing shortages of reagents associated with this test. Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts.

scholarly journals Validation of saliva sampling as an alternative to oro-nasopharyngeal swab for detection of SARS-CoV-2 using unextracted rRT-PCR with the Allplex 2019-nCoV assay

2021 ◽  
Vol 70 (8) ◽  
Author(s):  
Marco Andres Bergevin ◽  
Wesley Freppel ◽  
Guylaine Robert ◽  
Georges Ambaraghassi ◽  
Dany Aubry ◽  
...  
Keyword(s):  
Detection Efficiency ◽  
Rna Extraction ◽  
Positive Sample ◽  
Proteinase K ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Specialized Equipment ◽  
Potential Alternative ◽  
Proteinase K Treatment ◽  
Alternative Specimen

Introduction. The current severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) pandemic has stressed the global supply chain for specialized equipment, including flocked swabs. Hypothesis. Saliva could be a potential alternative specimen source for diagnosis of SARS-CoV-2 infection by reverse-transcriptase PCR (RT-PCR). Aim. To compare the detection efficiency of SARS-CoV-2 RNA in saliva and oro-nasopharyngeal swab (ONPS) specimens. Methodology. Patients recruited from hospital provided paired saliva and ONPS specimens. We performed manual or automated RT-PCR with prior proteinase K treatment without RNA extraction using the Seegene Allplex 2019 nCoV assay. Results. Of the 773 specimen pairs, 165 (21.3 %) had at least one positive sample. Additionally, 138 specimens tested positive by both sampling methods. Fifteen and 12 cases were detected only by nasopharyngeal swab and saliva, respectively. The sensitivity of ONPS (153/165; 92.7 %; 95 % CI: 88.8–96.7) was similar to that of saliva (150/165; 90.9 %; 95 % CI: 86.5–95.3; P=0.5). In patients with symptoms for ≤ 10 days, the sensitivity of ONPS (118/126; 93.7 %; 95 % CI: 89.4–97.9) was similar to that of saliva (122/126; 96.8 %; 95 % CI: 93.8–99.9 %; P=0.9). However, the sensitivity of ONPS (20/22; 95.2 %; 95 % CI: 86.1–100) was higher than that of saliva (16/22; 71.4 %; 95 % CI: 52.1–90.8) in patients with symptoms for more than 10 days. Conclusions. Saliva sampling is an acceptable alternative to ONPS for diagnosing SARS-CoV-2 infection in symptomatic individuals displaying symptoms for ≤ 10 days. These results reinforce the need to expand the use of saliva samples, which are self-collected and do not require swabs.

scholarly journals Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care

2021 ◽  
Author(s):  
Jérôme LeGoff ◽  
Solen Kernéis ◽  
Caroline Elie ◽  
Séverine Mercier Delarue ◽  
Nabil Gastli ◽  
...  
Keyword(s):  
Point Of Care ◽  
False Negative ◽  
Lamp Assay ◽  
Rapid Identification ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Rt Pcr ◽  
Registration Number ◽  
A Prospective Study ◽  
Antigen Testing

Abstract Background Rapid identification of SARS-Cov-2 infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Methods We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV™) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Results Overall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97% respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. Conclusion The detection of SARS-CoV-2 from crude saliva samples with a RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration number : NCT04578509

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