Analysis of SARS-CoV-2 RT-PCR Testing and Pooling Strategies for Screening of Asymptomatic Individuals - The Philippine Children's Medical Center Experience

Abstract Introduction/Objective SARS-CoV-2 is a pandemic that has required mobilization to meet urgent needs. In this mobilization, emergency use authorizations (EUA) have been issued by the FDA to expedite the deployment of these tests. This has led to a situation whereby sensitivity has not been rigorously studied for any of the assays with EUAs. Estimates can be extrapolated from the limited samples documented by the company in their instructions for use (IFU). Although the nationwide shortage of testing reagents prevent parallel testing of multiple platforms on all specimens, observations of repeat specimens at the Veteran Affairs Medical Center (VAMC) provides the first study in the literature of more complete data for SARS-CoV-2 nucleic acid (RT-PCR) assay on sensitivity on the Abbott (Abbott Park Ill) and Cepheid (Sunnyvale CA) assays. Methods A retrospective search was performed for all test results for SARS-CoV-2 by RT-PCR from 3/1/2020 to 4/14/2020 at Corporal Michael J. Crescenz Medical Center, in order to evaluate the sensitivity on Abbott m2000 and Cepheid platforms. Results across multiple reference laboratories and in-house testing platforms were collated in a table with all patients clinically requiring repeat testing recorded. Results 114/863 patients had repeat testing. The tests were performed initially by outside reference laboratories (25 patients), on the Abbott m2000 (63 patients), and Cepheid Infinity (26 patients). 15/114 (13%) had discordant results on repeat testing. This included 1 test initially done by a reference laboratory. 8 days after the initial result from the reference lab, a positive for the same patient was identified on the Abbott platform. 11 initial Abbott results were discordant on further repeat testing on two platforms - Abbott (6 patients) and Cepheid (5 patients) 1-6 days later. In addition, 3 initial Cepheid were discordant on further repeat testing by the same Cepheid platform (1-16 days later). Conclusion While the instructions for use for both platforms suggest 100% sensitivity and specificity (due to the 100% positive and negative percent agreement in limited specimens), the true sensitivity is less than 100%, particularly early in the course of the infection. In our study, the positive percent agreement (surrogate for sensitivity) was 83% for initial Abbott tests, 88% for initial Cepheid tests, and 95% by Reference laboratory platform.

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Replicative Deformed Wing Virus Found in the Head of Adults from Symptomatic Commercial Bumblebee (Bombus terrestris) Colonies

Veterinary Sciences ◽

10.3390/vetsci8070117 ◽

2021 ◽

Vol 8 (7) ◽

pp. 117

Author(s):

Giovanni Cilia ◽

Laura Zavatta ◽

Rosa Ranalli ◽

Antonio Nanetti ◽

Laura Bortolotti

Keyword(s):

Bombus Terrestris ◽

The Body ◽

Rt Pcr ◽

Deformed Wing Virus ◽

The United Kingdom ◽

Target Organs ◽

Specific Organ ◽

Virus Localization ◽

Juvenile Stages ◽

Asymptomatic Individuals

The deformed wing virus (DWV) is one of the most common honey bee pathogens. The virus may also be detected in other insect species, including Bombus terrestris adults from wild and managed colonies. In this study, individuals of all stages, castes, and sexes were sampled from three commercial colonies exhibiting the presence of deformed workers and analysed for the presence of DWV. Adults (deformed individuals, gynes, workers, males) had their head exscinded from the rest of the body and the two parts were analysed separately by RT-PCR. Juvenile stages (pupae, larvae, and eggs) were analysed undissected. All individuals tested positive for replicative DWV, but deformed adults showed a higher number of copies compared to asymptomatic individuals. Moreover, they showed viral infection in their heads. Sequence analysis indicated that the obtained DWV amplicons belonged to a strain isolated in the United Kingdom. Further studies are needed to characterize the specific DWV target organs in the bumblebees. The result of this study indicates the evidence of DWV infection in B. terrestris specimens that could cause wing deformities, suggesting a relationship between the deformities and the virus localization in the head. Further studies are needed to define if a specific organ could be a target in symptomatic bumblebees.

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Sniffer Dogs as a Screening/Diagnostic Tool for COVID-19: A Proof of Concept Study

10.21203/rs.3.rs-64455/v2 ◽

2021 ◽

Author(s):

Esmaeil Eskandari ◽

Milad Ahmadi Marzaleh ◽

Hassan Roudgari ◽

Ramin Hamidi Farahani ◽

Amir Nezami-Asl ◽

...

Keyword(s):

Medical Center ◽

Diabetic Patients ◽

Rt Pcr ◽

German Shepherd ◽

True Negative ◽

Predictive Values ◽

Male And Female ◽

Medical Centers ◽

Verification Test ◽

Single Blind

Abstract Background: Sniffer dogs are able to detect certain chemical particles and are suggest to be capable of helping diagnose some medical conditions and complications, such as colorectal cancer, melanoma, bladder cancer, and even critical states such as hypoglycemia in diabetic patients. With the global spread of COVID-19 throughout the world and the need to have a real-time screening of the population, especially in crowded places, this study aimed to investigate the applicability of sniffer dogs to carry out such a task.Methods: Firstly, three male and female dogs from German shepherd (Saray), German black (Kuzhi) and Labrador (Marco) breeds had been intensively trained throughout the classical conditioning method for seven weeks. They were introduced to human specimens obtained from the throat and pharyngeal secretions of participants who were already reported positive or negative for SARS-COV-2 infection be RT-PCR. Each dog underwent the conditioning process for almost 1000 times. In the meantime another similar condition process was conducted on clothes and masks of COVID-19 patient using another three male and female dogs from Labrador (Lexi), Border gypsy (Sami), and Golden retriever (Zhico) breeds. In verification test for the first three dogs, 80 pharyngeal secretion samples consisting of 26 positive and 54 negative samples from different medical centers who underwent RT-PCR test were in a single-blind method. In the second verification test for the other three dogs, masks and clothes of 50 RT-PCR positive and 70 RT-PCR negative cases from different medical center were used.Results: In verification test using pharyngeal secretion, the sniffer dogs’ detection capability was associated with a 65% of sensitivity and 89% of specificity and they amanged to identify 17 out of the 26 positive and 48 out of the 54 true negative samples. In the next verification test using patients’ face masks and clothes, 43 out of the 50 positive samples were correctly identified by the dogs. Moreover, out of the 70 negative samples, 65 samples were correctly found to be negative. The sensitivity of this test was as high as 86% and its specificity was 92.9%. In addition, the positive and negative predictive values were 89.6% and 90.3%, respectively.Conclusion: Dogs are capable of being trained to identify COVID-19 cases by sniffing their odour, so they can be used as a reliable tool in limited screening.

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COVID-19 Admission Screening, and Assessment of Infectiousness at an Academic Medical Center, Iowa 2020

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.294 ◽

2021 ◽

pp. 1-19

Author(s):

Mohammed Alsuhaibani ◽

Takaaki Kobayashi ◽

Alexandra Trannel ◽

Stephanie Holley ◽

Oluchi J. Abosi ◽

...

Keyword(s):

Medical Center ◽

Academic Medical Center ◽

Clinical History ◽

Rt Pcr ◽

University Of Iowa ◽

Past Infection ◽

Admission Screening ◽

Academic Medical ◽

The University ◽

Positive Results

Abstract Objective: Patients admitted to the hospital may unknowingly carry SARS-CoV-2 and hospitals have implemented SARS-CoV-2 admission screening. However, because SARS-CoV-2 RT-PCR may remain positive for months after infection, positive results may represent active or past infection. We determined the prevalence and infectiousness of patients who were admitted for reasons unrelated to COVID-19 but tested positive on admission screening. Methods: We conducted an observational study at the University of Iowa Hospitals & Clinics from July 7 to October 25, 2020. All patients admitted without suspicion of COVID-19 infection were included and medical records of those with a positive admission screening test were reviewed. Infectiousness was determined using patient history, PCR cycle threshold (Ct) value, and serology. Results: A total of 5,913 patients were screened and admitted for reasons unrelated to COVID-19. Of these, 101 had positive admission RT-PCR results. Thirty-six patient were excluded because they had respiratory signs/symptoms on admission on chart review. Sixty-five patients (1.1%) did not have respiratory symptoms. A total of 55 patients had Ct values available and were included in this analysis. The median age was 56 years, and (51%) were male. Our assessment revealed that 23 patients (42%) were likely infectious. The median duration of in-hospital isolation was five days for those likely infectious and two days for those deemed non-infectious. Conclusions: COVID-19 infection was infrequent among patients admitted for reasons unrelated to COVID-19. An assessment of the likelihood of infectiousness using clinical history, RT-PCR Ct values, and serology may help discontinue isolation and conserve resources.

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Risk factors, outcomes and mechanisms of tigecycline non-susceptibleKlebsiella pneumoniaebacteremia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01503-16 ◽

2016 ◽

pp. AAC.01503-16 ◽

Cited By ~ 3

Author(s):

Chih-Han Juan ◽

Yi-Wei Huang ◽

Yi-Tsung Lin ◽

Tsuey-Ching Yang ◽

Fu-Der Wang

Keyword(s):

Risk Factors ◽

Risk Factor ◽

Independent Risk Factor ◽

Medical Center ◽

Attributable Mortality ◽

Rt Pcr ◽

Potential Risk Factors ◽

Matched Case ◽

Matched Case Control Study ◽

Control Study

A rise in tigecycline resistance inKlebsiella pneumoniaehas been reported recently worldwide. We aim to identify risk factors, outcomes, and mechanisms for adult patients with tigecycline non-susceptibleK. pneumoniaebacteremia in Taiwan. We conducted a matched case-control study (ratio of 1:1) in a medical center in Taiwan from January 2011 through June 2015. The cases were patients with tigecycline non-susceptibleK. pneumoniaebacteremia, and the controls were patients with tigecycline susceptibleK. pneumoniaebacteremia. Logistic regression was performed to evaluate the potential risk factors for tigecycline non-susceptibleK. pneumoniaebacteremia. Quantitative RT-PCR was performed to analyzeacrA,oqxA,ramA,rarA,andkpgAexpression among these isolates. A total of 43 cases were matched with 43 controls. The 14-day mortality of patients with tigecycline non-susceptibleK. pneumoniaebacteremia was 30.2%, and the 28-day mortality was 41.9%. The attributable mortality of tigecycline non-susceptibleK. pneumoniaeat 14 days and 28 days was 9.3% and 18.6%, respectively. Fluoroquinolone use within 30 days prior to bacteremia was the only independent risk factor for tigecycline non-susceptibleK. pneumoniaebacteremia. Tigecycline non-susceptibleK. pneumoniaewere mostly caused by overexpression of AcrAB and/or OqxAB efflux pumps, together with the upregulation of RamA and/or RarA respectively. One isolate has isolated overexpression ofkpgA. In conclusion, tigecycline non-susceptibleK. pneumoniaebacteremia was associated with high mortality and prior fluoroquinolone use was the independent risk factor for acquisition of tigecycline non-susceptibleK. pneumoniae. The overexpression of AcrAB and/or OqxAB contributes to tigecycline non-susceptibility inK. pneumoniae.

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2704. Molecular Technology to Detect Pneumococcal Colonization in Young Children Reveals Increased Prevalence of Vaccine Serotypes as Compared with Enhanced Culture Methods

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.2381 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S951-S951

Author(s):

Stephen I Pelton ◽

Kim Shea ◽

Yazden Shaik-Dasthagirisaheb ◽

Brent Little

Keyword(s):

Young Children ◽

Medical Center ◽

Pediatric Population ◽

Rt Pcr ◽

Culture Methods ◽

Vaccine Serotypes ◽

Enhanced Sensitivity ◽

Sick Children ◽

Tract Infections ◽

Culture Negative

Abstract Background Human challenge studies demonstrate enhanced sensitivity of molecular technology for identification of vaccine serotype pneumococcal (SP) carriage in PCV13 immunized adults. We hypothesized that PCV13 immunized children would similarly harbor vaccine serotypes in their nasopharynx (NP) that could only be identified by molecular technology. Methods We compared use of enhanced microbiologic culture vs. molecular technology to characterize SP colonization among NP swabs collected from 995 healthy or sick children <5 years old at Boston Medical Center from November 2015 to May 2017. NP specimens were broth enriched for 4 hours and cultured on selective blood agar. Specimens were evaluated for presence of SP using both routine microbiologic methods and RT–PCR. RT–PCR assays targeted the lytA, and piaB (SP membrane permease) genes, and 26 SP serotypes: all serotypes included in 13-valent pneumococcal conjugate vaccine and 13 prevalent non-vaccine serotypes Results A total of 162 (16.3%) NP specimens were positive for SP via enhanced culture, and an additional 163 (16.3%) were SP positive via lytA+ RT–PCR molecular technology. Prevalence of SP carriage was equivalent in children aged 0<2 years and 2≤5 years, but greater in children with respiratory tract infections (RTI) compared with children without RTI (26.5% vs. 9.6% among culture+ specimens only; and 43.2% vs. 25.8% among combined culture+ and molecular+ specimens). Using enhanced culture only, vaccine serotypes (VST) were identified in 4 (1%) of 450 children <2 years and 14 (2.6%) of 545 children 2 ≤5 years; adding molecular positive specimens increased the prevalence of VST to 2.9% in children <2 years and 4.6% in children 2 ≤5 years (table). Serotypes 3 and 19A were the two most commonly identified VST. Conclusion Combining molecular technology with enhanced culture reveals an increased prevalence of vaccine serotype colonization in young children. The ability of sensitive molecular methods to detect vaccine serotypes in culture-negative specimens suggests low-density vaccine serotype carriage persists in a highly immunized pediatric population. The importance of culture negative but RTPCR positive carriage for transmission requires further evaluation. Disclosures All authors: No reported disclosures.

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The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience

Journal of Clinical Microbiology ◽

10.1128/jcm.01416-20 ◽

2020 ◽

Vol 58 (8) ◽

Author(s):

Alexander L. Greninger ◽

Keith R. Jerome

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Real Time ◽

Real Time Pcr ◽

Medical Center ◽

Rt Pcr ◽

University Of Washington ◽

Clinical Laboratories ◽

To Come ◽

The Many ◽

The University

ABSTRACT In early March 2020, the University of Washington Medical Center clinical virology laboratory became one of the first clinical laboratories to offer testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When we first began test development in mid-January, neither of us believed there would be more than 2 million confirmed SARS-CoV-2 infections nationwide or that we would have performed more than 150,000 real-time PCR (RT-PCR) tests, with many more to come. This article will be a chronological summary of how we rapidly validated tests for SARS-CoV-2, increased our testing capacity, and addressed the many problems that came up along the way.

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Performance of SARS-CoV-2 rapid antigen test compared with real-time RT-PCR in asymptomatic individuals

10.1101/2021.02.12.21251643 ◽

2021 ◽

Author(s):

Mónica Peña ◽

Manuel Ampuero ◽

Carlos Garcés ◽

Aldo Gaggero ◽

Patricia García ◽

...

Keyword(s):

Real Time ◽

False Negative ◽

Pivotal Role ◽

Contact Tracing ◽

Antigen Test ◽

Rt Pcr ◽

Asymptomatic Carriers ◽

Asymptomatic Individuals ◽

Pcr Diagnostics

AbstractScreening, testing and contact tracing plays a pivotal role in the control of COVID-19 pandemic. To carry out this strategy it is necessary to increase the testing capacity. Here, we compared a SARS CoV-2 rapid antigen test (RAT) and RT-PCR in 842 asymptomatic individuals from Tarapacá, Chile. We report a sensibility of 69.86%, a specificity of 99.61%, PPV of 94.44% and NPP of 97.22% with Ct values (Ct > 27) that were significantly higher among individuals with false-negative RAT. These results support the fact that RAT might have a significant impact in the identification of asymptomatic carriers in areas that lack well-equipped laboratories to perform SARS-CoV-2 real -time RT-PCR diagnostics or the results take more than 24-48 hours, as well as zones with high traffic of individuals, such as border/customs, airports, interregional bus, train stations or in any mass testing campaign requiring rapid results.

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Validation of rapid antibody (IgG-IgM) test kit for SARS COV-2 infection in Qatar

Journal of Public Health Research ◽

10.4081/jphr.2021.2421 ◽

2021 ◽

Author(s):

Jesha Mundodan ◽

Samina Hasnain ◽

Hayat Khogali ◽

Soha Shawqi Al Bayat ◽

Dina Ali ◽

...

Keyword(s):

Predictive Value ◽

Local Population ◽

Rapid Test ◽

Antibody Test ◽

Molecular Testing ◽

Rt Pcr ◽

Test Kit ◽

Asymptomatic Individuals ◽

Sensitivity Specificity ◽

Rapid Antibody

Background: In response to the growing coronavirus disease 2019 (COVID-19) pandemic and the shortage of laboratory based molecular testing capacity and reagents, multiple diagnostic test manufacturers have developed rapid and easy to use devices to facilitate testing outside laboratory settings. These kits are either based on detection of proteins from SARS-CoV-2 virus or detection of antigen or human antibodies generated in response to the infection. However, it is important to understand their performance characteristics and they must be validated in the local population setting.Design and Methods: The objective is to assess the validity of the rapid test for IgG and IgM immunoglobulins compared to the current gold standard reverse transcription polymerase chain reaction (RT-PCR) test. A total of 16951 asymptomatic individuals were tested by the Ministry of Public Health track-and-trace team using both rapid immunodiagnostic test and RT-PCR as part of screening across various random settings with potential risk of community interaction prior to gradual lifting of restrictions in Qatar. Rapid test was considered to be posiive if both IgG and IgM are positive, while only IgG/IgM positive was considered as rapid test negative. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated.Results: The sensitivity of rapid test kit was found to be 0.9%, whereas the specificity was found to be 97.8%. the PPV was found to be 0.3% whereas the NPV was found to be 99.4%.Conclusion: Based on the outcome and results of the study, it appears that the sensitivity and PPV of the rapid antibody test are low. As such, this test is not recommended for use to assist in taking clinic-based decisions or decisions related to quarantine/isolation.

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An assessment of a rapid SARS-CoV-2 antigen test in Bangladesh

10.1101/2021.10.05.21264551 ◽

2021 ◽

Author(s):

Zannat Kawser ◽

Mohabbat Hossain ◽

Sara Suliman ◽

Shahin Lockman ◽

Jesse Gitaka ◽

...

Keyword(s):

False Positive ◽

Rapid Test ◽

Field Evaluation ◽

Ease Of Use ◽

Large Field ◽

Antigen Test ◽

Rt Pcr ◽

Rapid Antigen Detection Test ◽

Antigen Tests ◽

Asymptomatic Individuals

Early detection of SARS-CoV-2 infection is crucial to prevent the spread of the virus. In this study, we evaluated the performance of a commercial rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against a gold-standard of nasopharyngeal (NP) swab tested by reverse transcription-polymerase chain reaction (RT-PCR) in prospectively recruited adults in Dhaka, Bangladesh. We compared the sensitivity and specificity of the two rapid antigen tests against RT-PCR results in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease-of-use of the BD Veritor test in a subsample of study participants (n=42) and implementers (n=5). The sensitivity of the BD Veritor rapid antigen 66 test was 70% in symptomatic (95% confidence interval [CI]: 51-85%) and 87% (95% CI: 69-96%) in asymptomatic individuals with positive SARSCoV-2 RT-PCR, for overall sensitivity of 78% (95% CI: 66-88%). The sensitivity of the Standard Q rapid antigen test was 63% (95% CI: 44-69 80%) in symptomatic and 73% (95% CI: 54-87%) in asymptomatic individuals. One false positive in BD Veritor test (specificity 99.5) and no false positive in Standard Q tests were observed (specificity 100%). The BD Veritor rapid antigen test was 78% sensitive when compared with RT-PCR irrespective of the cycle threshold (Ct) levels in this evaluation in Bangladesh. The implementation evaluation data showed good acceptability in the field settings. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.

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