A method for campus-wide SARS-CoV-2 surveillance at a large public university

The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.

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Evaluation of sample pooling for screening of SARS CoV-2

PLoS ONE ◽

10.1371/journal.pone.0247767 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0247767

Author(s):

Andargachew Mulu ◽

Dawit Hailu Alemayehu ◽

Fekadu Alemu ◽

Dessalegn Abeje Tefera ◽

Sinknesh Wolde ◽

...

Keyword(s):

Clinical Sample ◽

Diagnostic Testing ◽

Positive Sample ◽

Clinical Samples ◽

Global Public Health ◽

Rt Pcr ◽

Resource Saving ◽

Public Health Importance ◽

Ct Value ◽

Sample Pooling

Background The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. Objectives To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2. Methods We evaluated pooling approach on both direct clinical and NA samples. The standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 was employed targeting the nucleocapsid (N) and open reading frame (ORF1ab) genomic region of the virus. The experimental pools were created using SARS CoV-2 positive clinical samples and extracted RNA spiked with up to 9 negative samples. For the direct clinical samples viral NA was extracted from each pool to a final extraction volume of 200μL, and subsequently both samples tested using the SARS CoV-2 RT-PCR assay. Results We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the cycle threshold (Ct) value of the original sample, corresponding to high, and low SARS CoV-2 viral copies per reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend pooling of 4/5 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 5 in 1 was expected to retain accuracy of the test irrespective of the Ct value samples spiked, and result in a 137% increase in testing efficiency. Conclusions The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community. We recommend clinical sample pooling of 4 or 5 in 1. However, we don’t advise pooling of clinical samples when disease prevalence is greater than 7%; particularly when sample size is large.

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458. Molecular SARS-CoV-2 Testing During the COVID-19 Outbreak: Experiences of a Hospital in Southeast Michigan, USA

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.651 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S296-S297

Author(s):

Trini A Mathew ◽

Jonathan Hopkins ◽

Diane Kamerer ◽

Shagufta N Ali ◽

Daniel Ortiz ◽

...

Keyword(s):

Clinical Features ◽

Diagnostic Testing ◽

Beaumont Hospital ◽

High Capacity ◽

Turnaround Time ◽

Molecular Diagnostic ◽

The Novel ◽

Repeat Testing ◽

Asymptomatic Patients ◽

Novel Coronavirus

Abstract Background The novel Coronavirus SARS CoV-2 (COVID-19) outbreak was complicated by the lack of diagnostic testing kits. In early March 2020, leadership at Beaumont Hospital, Royal Oak Michigan (Beaumont) identified the need to develop high capacity testing modalities with appropriate sensitivity and specificity and rapid turnaround time. We describe the molecular diagnostic testing experience since initial rollout on March 16, 2020 at Beaumont, and results of repeat testing during the peak of the COVID-19 pandemic in MI. Methods Beaumont is an 1100 bed hospital in Southeast MI. In March, testing was initially performed with the EUA Luminex NxTAG CoV Extended Panel until March 28, 2020 when testing was converted to the EUA Cepheid Xpert Xpress SARS-CoV-2 for quicker turnaround times. Each assay was validated with a combination of patient samples and contrived specimens. Results During the initial week of testing there was > 20 % specimen positivity. As the prevalence grew the positivity rate reached 68% by the end of March (Figure 1). Many state and hospital initiatives were implemented during the outbreak, including social distancing and screening of asymptomatic patients to increase case-finding and prevent transmission. We also adopted a process for clinical review of symptomatic patients who initially tested negative for SARS-CoV-2 by a group of infectious disease physicians (Figure 2). This process was expanded to include other trained clinicians who were redeployed from other departments in the hospital. Repeat testing was performed to allow consideration of discontinuation of isolation precautions. During the surge of community cases from March 16 to April 30, 2020, we identified patients with negative PCR tests who subsequently had repeat testing based on clinical evaluation, with 7.1% (39/551) returning positive for SARS- CoV2. Of the patients who expired due to COVID-19 during this period, 4.3% (9/206) initially tested negative before ultimately testing positive. Figure 1 BH RO testing Epicurve Figure 2: Screening tool for repeat COVID19 testing and precautions Conclusion Many state and hospital initiatives helped us flatten the curve for COVID-19. Our hospital testing experience indicate that repeat testing may be warranted for those patients with clinical features suggestive of COVID-19. We will further analyze these cases and clinical features that prompted repeat testing. Disclosures All Authors: No reported disclosures

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Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

Scientific Reports ◽

10.1038/s41598-021-81487-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shan Wei ◽

Esther Kohl ◽

Alexandre Djandji ◽

Stephanie Morgan ◽

Susan Whittier ◽

...

Keyword(s):

Limit Of Detection ◽

Point Of Care ◽

Diagnostic Testing ◽

Rna Extraction ◽

Cost Effective ◽

Clinical Samples ◽

Nasopharyngeal Swab ◽

Percentage Agreement ◽

Testing Method ◽

Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

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Analysis of the tendency of development of biosensors based on GaN

Nanotechnology : the development , application - XXI Century ◽

10.18127/j22250980-202102-02 ◽

2021 ◽

Author(s):

S.I. Agasieva ◽

E.A. Smetanin ◽

A.R. Vechkanov ◽

A.V. Gubanov

Keyword(s):

Clinical Trials ◽

Infectious Diseases ◽

Diagnostic Tests ◽

Diagnostic Testing ◽

Healthcare Systems ◽

Clinical Analysis ◽

Molecular Diagnostic ◽

Economic Damage ◽

Disease Research ◽

Local Healthcare

Statement of the problem of this article - one of the most important problems is protection from especially dangerous infectious diseases. The use of biosensors in clinical trials will significantly reduce the time for obtaining the results of analyzes, thereby speeding up the appointment of treatment to patients. The purpose of the article is to present modern designs of biosensors based on gallium nitride, the possibilities of their application and characteristics. Consider the principles of operation, areas of application and characteristics. As a result, the design of modern biosensors and modern trends in their use from various sources of literature in recent years are shown. Biosensors, principles of their action, areas of application and characteristics are considered, which will reduce the possible socio-economic damage from temporary disability for sick citizens due to the rapid and timely implementation of anti-epidemic measures. Practical value: the proposed biosensors are of interest as devices for detecting diseases. The use of biosensors in clinical disease research has several potential advantages over other clinical analysis methods, including increased analysis speed and flexibility, multipurpose analysis capability, automation, reduced diagnostic testing costs, and the ability to integrate molecular diagnostic tests into local healthcare systems.

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A portable microfluidic platform for rapid molecular diagnostic testing of patients with myeloproliferative neoplasms

Scientific Reports ◽

10.1038/s41598-017-08674-8 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Hua Wang ◽

Xinju zhang ◽

Xiao Xu ◽

Qunfeng Zhang ◽

Hengliang Wang ◽

...

Keyword(s):

Myeloproliferative Neoplasms ◽

Diagnostic Testing ◽

Molecular Diagnostic ◽

Microfluidic Platform ◽

Molecular Diagnostic Testing

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Molecular Diagnostic Testing by eyeGENE: Analysis of Patients With Hereditary Retinal Dystrophy Phenotypes Involving Central Vision Loss

Investigative Opthalmology & Visual Science ◽

10.1167/iovs.14-14359 ◽

2014 ◽

Vol 55 (9) ◽

pp. 5510 ◽

Cited By ~ 8

Author(s):

Akhila Alapati ◽

Kerry Goetz ◽

John Suk ◽

Mili Navani ◽

Amani Al-Tarouti ◽

...

Keyword(s):

Vision Loss ◽

Diagnostic Testing ◽

Retinal Dystrophy ◽

Molecular Diagnostic ◽

Central Vision ◽

Central Vision Loss ◽

Molecular Diagnostic Testing ◽

Hereditary Retinal Dystrophy

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A point-of-care diagnostic for differentiating Ebola from endemic febrile diseases

Science Translational Medicine ◽

10.1126/scitranslmed.aat0944 ◽

2018 ◽

Vol 10 (471) ◽

pp. eaat0944 ◽

Cited By ~ 19

Author(s):

David Sebba ◽

Alexander G. Lastovich ◽

Melody Kuroda ◽

Eric Fallows ◽

Joshua Johnson ◽

...

Keyword(s):

Ebola Virus ◽

Clinical Symptoms ◽

Point Of Care ◽

Hemorrhagic Fever ◽

Diagnostic Methods ◽

Outbreak Detection ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Live Virus ◽

And Control

Hemorrhagic fever outbreaks such as Ebola are difficult to detect and control because of the lack of low-cost, easily deployable diagnostics and because initial clinical symptoms mimic other endemic diseases such as malaria. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need. Although rapid tests such as lateral flow can be broadly deployed, they are typically not well-suited for differentiating among multiple diseases presenting with similar symptoms. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect and differentiate infection with Ebola virus from other more common febrile diseases. Here, we developed and tested an immunoassay technology that uses surface-enhanced Raman scattering (SERS) tags to simultaneously detect antigens from Ebola, Lassa, and malaria within a single blood sample. Results are provided in <30 min for individual or batched samples. Using 190 clinical samples collected from the 2014 West African Ebola outbreak, along with 163 malaria positives and 233 negative controls, we demonstrated Ebola detection with 90.0% sensitivity and 97.9% specificity and malaria detection with 100.0% sensitivity and 99.6% specificity. These results, along with corresponding live virus and nonhuman primate testing of an Ebola, Lassa, and malaria 3-plex assay, indicate the potential of the SERS technology as an important tool for outbreak detection and clinical triage in low-resource settings.

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Detection of LytA Genes in Streptococcus pneumoniae Isolated from sputum pneumonia patients

Biomedika ◽

10.31001/biomedika.v13i1.718 ◽

2020 ◽

Vol 13 (1) ◽

pp. 23-30

Author(s):

Mustika Sari Hutabarat ◽

Firdaus Hamid ◽

Irawaty Djaharuddin ◽

Alfian Zainuddin ◽

Rossana Agus ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

False Negative ◽

Pneumococcal Infection ◽

Diagnostic Methods ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Biochemical Tests ◽

Negative Results ◽

False Negative Results ◽

Polymerase Chain

Streptococcus pneumoniae (pneumococcus) is a Gram-positive facultative anaerobic bacterium that is a major cause of morbidity and mortality worldwide. But the lack of reporting of disease by this bacterium in Indonesia, one of the causes is because the diagnosis of pneumococcal infection is often clinically not typical and conventional methods which are still the standard gold method often give false-negative results. So the purpose of this study was to evaluate the performance of culture and molecular diagnostic methods using the Polymerase Chain Reaction (PCR) technique in detecting Streptococcus pneumoniae in sputum clinical samples using the Autolysin (LytA) gene which is a virulence factor of this bacterium. 57 isolates from 60 samples were confirmed as Streptococcus sp through microscopic identification, culture, and biochemical tests. Then the sensitivity test with an optochin test of 9 (9%) compared the results descriptively with the PCR technique using the Autolysin A (LytA) gene which was obtained more sensitive by 15 (25%).

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Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States

10.1101/2021.02.10.21251540 ◽

2021 ◽

Author(s):

Tara Alpert ◽

Erica Lasek-Nesselquist ◽

Anderson F. Brito ◽

Andrew L. Valesano ◽

Jessica Rothman ◽

...

Keyword(s):

Public Health ◽

United States ◽

New York ◽

Diagnostic Testing ◽

The United States ◽

International Travel ◽

Health Concern ◽

Public Health Response ◽

Community Transmission ◽

The Uk

SummaryThe emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a national public health concern in the United States because of its increased transmissibility. Over 500 COVID-19 cases associated with this variant have been detected since December 2020, but its local establishment and pathways of spread are relatively unknown. Using travel, genomic, and diagnostic testing data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. New York, which receives the most international travel from the UK, is likely one of the key hubs for introductions and domestic spread. Finally, we provide evidence for increased community transmission in several states. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

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