Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies

Guaman-Bautista, Linda P; Moreta-Urbano, Erick; Oña-Arias, Claudia G; Arias, Marbel Torres; Kyriakidis, Nikolaos C; Malcı, Koray; Jonguitud‐Borrego, Nestor; Rios‐Solis, Leonardo; Ramos-Martı́nez, Espiridión; López‐Cortés, Andrés; Barba-Ostria, Carlos

doi:10.3390/diagnostics11111981

Cited by 13 publications

(8 citation statements)

References 148 publications

(179 reference statements)

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“…Another type of test developed for rapid SARS-CoV-2 detection is based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP). Although antigen tests are cheaper, the RT-LAMP is more accurate [ 7 ]. The novelty of this technique lies in the performance of a PCR reaction at a constant temperature by the use of specific DNA polymerase.…”

Section: Introductionmentioning

confidence: 99%

Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit

et al. 2022

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The need for the early identification of SARS-CoV-2 has let to a quest for reliable tests that meet the standards of polymerase chain reaction (PCR) tests, on the one hand, and are low-cost, easy-to-use, and fast, on the other hand. One such test is the Lucira™ Check It COVID-19 Test kit (“Lucira”) (Lucira Health, Inc., Emeryville, CA, USA), which utilizes real-time loop-mediated isothermal amplification technology, developed for at-home use. This study evaluated the clinical sensitivity and specificity of Lucira in identifying the virus in 190 nasopharyngeal samples collected between January and October 2021. Each sample was also subjected to RT-PCR. All negative RT-PCR results were paralleled by a negative Lucira result. Out of 90 participants who had a positive RT-PCR result, 82 (91.1%) tested positive by Lucira. Among the 72 symptomatic participants, 67 (93%) tested positive by Lucira. All samples with a positive RT-PCR result with a threshold cycle (Ct) > 36, yielded a negative Lucira result. In addition, a significant positive correlation was found between Ct and time-to-positivity with Lucira (R = 0.8612, p < 0.0001). The implementation of such a portable and affordable assay may aid in breaking the COVID-19 transmission chain.

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Section: Introductionmentioning

confidence: 99%

Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit

et al. 2022

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“…Even if several methods are being developed to detect SARS-CoV-2 in biological samples, such as reverse transcription loop-mediated isothermal amplification (RT-LAMP), clustered regularly interspaced short palindromic repeats (CRISPR) and droplet digital reverse transcription polymerase chain reaction (ddRT-PCR) [ 7 ], the RT-PCR is currently the gold standard for detecting the new virus from nasopharyngeal, oropharyngeal and nasal swabs and saliva. Among PCR-based methods, syndromic tests are frequently used for patients who exhibit more than one respiratory symptom to improve diagnosis and clinical management and to monitor possible respiratory co-infections [ 8 ].…”

Section: New Advances In Microbiological Diagnosis Of Sars-cov-2 Infe...mentioning

confidence: 99%

Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota

et al. 2022

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Early recognition and prompt management are crucial for improving survival in COVID-19 patients, and after 2 years of the pandemic, many efforts have been made to obtain an early diagnosis. A key factor is the use of fast microbiological techniques, considering also that COVID-19 patients may show no peculiar signs and symptoms that may differentiate COVID-19 from other infective or non-infective diseases. These techniques were developed to promptly identify SARS-CoV-2 infection and to prevent viral spread and transmission. However, recent data about clinical, radiological and laboratory features of COVID-19 at time of hospitalization could help physicians in early suspicion of SARS-CoV-2 infection and distinguishing it from other etiologies. The knowledge of clinical features and microbiological techniques will be crucial in the next years when the endemic circulation of SARS-CoV-2 will be probably associated with clusters of infection. In this review we provide a state of the art about new advances in microbiological and clinical findings of SARS-CoV-2 infection in hospitalized patients with a focus on pulmonary and extrapulmonary characteristics, including the role of gut microbiota.

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“…CRISPR-based diagnostics have been introduced as a feasible method of high-throughput testing. CRISPR techniques are highly adaptable and vary depending on the situation ( 3 ). To automate these systems, it is important to understand some of the key steps needed to be performed in such diagnostic systems: Isothermal amplification method: recombinase polymerase amplification (RPA or reverse-transcription loop mediated isothermal amplification (RT-LAMP) CRISPR enzyme used: Cas9 and Cas12 for DNA detection, Cas13a for RNA detection.…”

Section: Crispr Based Diagnostics For Covid-19mentioning

confidence: 99%

“…Even though vaccination campaigns across the world have been initiated, it will take a long time before most people are vaccinated against SARS-CoV-2. Additionally, manual testing has limited capacity in terms of number of tests processed, while for high-throughput testing it can reach a few thousand tests per day depending on the setup ( 3 ). While vaccine and testing campaigns are ongoing, many companies at the cutting-edge of computer-aided biology like Analytik Jena (Germany), Beckman Coulter (USA), Hamilton (USA) and Tecan (Switzerland) have been donating their time and effort to provide automated testing solutions for SARS-CoV-2 diagnosis, as the crisis is still at a peak in many countries (Computed aided biology, https://www.computeraidedbiology.com/cab-companies-on-covid19 , 03/21/2021).…”

Section: Introductionmentioning

confidence: 99%

High—throughput and automated screening for COVID-19

Jonguitud‐Borrego

Malcı

Anand

et al. 2022

Front. Med. Technol.

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The COVID-19 pandemic has become a global challenge for the healthcare systems of many countries with 6 million people having lost their lives and 530 million more having tested positive for the virus. Robust testing and a comprehensive track and trace process for positive patients are essential for effective pandemic control, leading to high demand for diagnostic testing. In order to comply with demand and increase testing capacity worldwide, automated workflows have come into prominence as they enable highthroughput screening, faster processing, exclusion of human error, repeatability, reproducibility and diagnostic precision. The gold standard for COVID-19 testing so far has been RT-qPCR, however, different SARS-CoV-2 testing methods have been developed to be combined with high throughput testing to improve diagnosis. Case studies in China, Spain and the United Kingdom have been reviewed and automation has been proven to be promising for mass testing. Free and Open Source scientific and medical Hardware (FOSH) plays a vital role in this matter but there are some challenges to be overcome before automation can be fully implemented. This review discusses the importance of automated high-throughput testing, the different equipment available, the bottlenecks of its implementation and key selected case studies that due to their high effectiveness are already in use in hospitals and research centres.

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Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies

Cited by 13 publications

References 148 publications

Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit

Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit

Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota

High—throughput and automated screening for COVID-19

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