COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

Colorimetric isothermal nucleic acid detection of SARS-CoV-2 with dye combination

RT-LAMP detection of SARS-CoV-2 has been demonstrated to be a valuable diagnostic method for the diagnosis of COVID-191,2, which can rapidly screen carriers of the virus to effectively control the spread of the SARS-CoV-2. Here, we present a combination of dyes for isothermal detection of SARS-CoV-2 as a commercial alternative, with expanded colorimetric spectrum. We compared them with commercial reagents and proved their suitability and sensitivity through clinical RNA samples. In addition, together with commercial single dye indicators, we believe the expanded color spectrum developed here as an indicator of rapid detection will promote the diagnosis of COVID-19.

Rapid and sensitive multiplex molecular diagnosis of respiratory pathogens using plasmonic isothermal RPA array chip

The current clinically available multiplex molecular diagnostic technologies are difficult to apply to onsite diagnostic platforms due to their large and sophisticated instrumentation, long amplification times and limited number of simultaneous detections. We developed a plasmonic isothermal recombinase polymerase amplification (RPA) array chip for rapid and sensitive multiplex molecular detection. The 3D plasmonic substrate composed of Au nanoparticles (NPs) on dense Au nanopillars (NPOP) showed highly enhanced plasmon-enhanced fluorescence (PEF) of RPA products with long DNA amplicons (~200 bp). The plasmonic 4-plex RPA array chip successfully detected bacterial DNA within 30 min and viral RNA within 40 min; the sensitivity of the plasmonic RPA array chip was comparable to or 10-fold higher than that of the 4-pelx liquid-phase RPA and 4-plex liquid-phase PCR techniques. Additionally, no cross-reactivity was observed. The 4-plex plasmonic RPA array chip was preliminary evaluated using clinical respiratory viral-positive nasopharyngeal swab samples. This approach enables rapid, sensitive and high-multiplex molecular detection and can be used in the realization of a simplified and miniaturized platform for onsite multiplex molecular diagnostics.

COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools

Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.

Laboratory diagnosis of COVID-19: current status and challenges

The magnitude and pace of global affliction caused by Coronavirus Disease-19 (COVID-19) is unprecedented in the recent past. From starting in a busy seafood market in the Chinese city of Wuhan, the virus has spread across the globe in less than a year, infecting over 76 million people and causing death of close to 1.7 million individuals worldwide. As no specific antiviral treatment is currently available, the major strategy in containing the pandemic is focused on early diagnosis and prompt isolation of the infected individuals. Several diagnostic modalities have emerged within a relatively short period, which can be broadly classified into molecular and immunological assays. While the former category is centered around real-time PCR, which is currently considered the gold standard of diagnosis, the latter aims to detect viral antigens or antibodies specific to the viral antigens and is yet to be recommended as a stand-alone diagnostic tool. This review aims to provide an update on the different diagnostic modalities that are currently being used in diagnostic laboratories across the world as well as the upcoming methods and challenges associated with each of them. In a rapidly evolving diagnostic landscape with several testing platforms going through various phases of development and/or regulatory clearance, it is prudent that the clinical community familiarizes itself with the nuances of different testing modalities currently being employed for this condition.

Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: Challenges and opportunities

The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In fact, statistical reports of diagnostic tools show that their accuracy, specificity and sensitivity in the detection of COVID hampered by some challenges that can be eliminated by using nanoparticles (NPs). In this study, we aimed to present an overview on the most important ways to diagnose different kinds of viruses followed by the introduction of nanobiosensors. Afterward, some methods of COVID-19 detection such as imaging, laboratory and kit-based diagnostic tests are surveyed. Furthermore, nucleic acids/protein- and immunoglobulin (Ig)-based nanobiosensors for the COVID-19 detection infection are reviewed. Finally, current challenges and future perspective for the development of diagnostic or monitoring technologies in the control of COVID-19 are discussed to persuade the scientists in advancing their technologies beyond imagination. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors.

Summary of the Available Molecular Methods for Detection of SARS-CoV-2 during the Ongoing Pandemic

Since early 2020, the COVID-19 pandemic has caused an excess in morbidity and mortality rates worldwide. Containment strategies rely firstly on rapid and sensitive laboratory diagnosis, with molecular detection of the viral genome in respiratory samples being the gold standard. The reliability of diagnostic protocols could be affected by SARS-CoV-2 genetic variability. In fact, mutations occurring during SARS-CoV-2 genomic evolution can involve the regions targeted by the diagnostic probes. Following a review of the literature and an in silico analysis of the most recently described virus variants (including the UK B 1.1.7 and the South Africa 501Y.V2 variants), we conclude that the described genetic variability should have minimal or no effect on the sensitivity of existing diagnostic protocols for SARS-CoV-2 genome detection. However, given the continuous emergence of new variants, the situation should be monitored in the future, and protocols including multiple targets should be preferred.

The Main Molecular and Serological Methods for Diagnosing COVID-19: An Overview Based on the Literature

Diagnostic tests have been considered as the main alternative for the control of coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a correct diagnosis allows for decision making when facing the disease, particularly as there is a lack of effective therapeutic protocols and vaccines. Thus, in this review, we summarized the main diagnostic approaches currently available for the diagnosis of SARS-CoV-2 infection in humans based on studies available in article databases. The tests can be organized into two main categories: nucleic acid-based tests, recommended for the initial detection of the virus, and serological tests, recommended for assessing the disease progression. The studies have shown that the performance of diagnostic methods depends on different factors, such as the type of samples and the characteristics of each assay. It was identified that the positivity of the tests is mainly related to the onset of symptoms. We also observed that point-of-care diagnoses are considered as one of the main trends in this area, due to the low-cost and simplicity of the assay; however, the analytical performance must be critically analyzed. Thus, the COVID-19 pandemic has highlighted the critical role of diagnostic technologies in the control of infectious diseases.

Summary of the Detection Kits for SARS-CoV-2 Approved by the National Medical Products Administration of China and Their Application for Diagnosis of COVID-19

The on-going global pandemic of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been underway for about 11 months. Through November 20, 2020, 51 detection kits for SARS-CoV-2 nucleic acids (24 kits), antibodies (25 kits), or antigens (2 kits) have been approved by the National Medical Products Administration of China (NMPA). Convenient and reliable SARS-CoV-2 detection assays are urgently needed worldwide for strategic control of the pandemic. In this review, the detection kits approved in China are summarised and the three types of tests, namely nucleic acid, serological and antigen detection, which are available for the detection of COVID-19 are discussed in detail. The development of novel detection kits will lay the foundation for the control and prevention of the COVID-19 pandemic globally.

Rapid, Sensitive, and Specific Severe Acute Respiratory Syndrome Coronavirus 2 Detection: A Multicenter Comparison Between Standard Quantitative Reverse-Transcriptase Polymerase Chain Reaction and CRISPR-Based DETECTR

Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity.

Here we compare DETECTR with qRT-PCR to diagnose COVID-19 on 378 patient samples.

Patient sample dilution assays suggest a higher analytical sensitivity of DETECTR compared to qRT-PCR, however, this was not confirmed in this large patient cohort, were we report 95% reproducibility between the two tests. These data showed that both techniques are equally sensitive in detecting SARS-CoV-2 providing additional value of DETECTR to the currently used qRT-PCR platforms. For DETECTR, different gRNAs can be used simultaneously to obviate negative results due to mutations in N-gene. Lateral flow strips, suitable as a point of care test (POCT), showed a 100% correlation to the high-throughput DETECTR assay. Importantly, DETECTR was 100% specific for SARS-CoV-2 relative to other human coronaviruses.

As there is no need for specialized equipment, DETECTR could be rapidly implemented as a complementary technically independent approach to qRT-PCR thereby increasing the testing capacity of medical microbiological laboratories and relieving the existent PCR-platforms for routine non-SARS-CoV-2 diagnostic testing.

Recent biotechnological tools for diagnosis of corona virus disease: A review

Recently, a corona virus disease (COVID-19) caused by a novel corona virus (sevier acute respiratory syndrome corona virus 2; SARS-CoV-2), rapidly spread throughout the world. It has been resulted an unprecedented public health crisis and has become a global threat. WHO declared it as a pandemic due to rapid transmission and severity of the disease. According to WHO, as of 22nd of August 2020, the disease spread over 213 countries of the world having 22,812,491 confirmed cases and 795,132 deaths recorded worldwide. In the absence of suitable antiviral drugs and vaccines, the current pandemic has created an urgent need for accurate diagnostic tools that would be helpful for early detection of the patients. Many tests including classical and high-throughput techniques have developed and obtained U.S. Food and drug administration (FDA) approval. However, efforts are being made to develop new diagnostic tools for detection of the disease. Several molecular diagnostic tests such as real-time-polymerase chain reaction, real-time isothermal loop-mediated amplification (RT-LAMP), full genome analysis by next-generation sequencing, clustered regularly interspaced short palindromic repeats technique and microarray-based assays along with other techniques such as computed tomography scan, biomarkers, biosensor, nanotechnology, serological test, enzyme-linked immunosorbent assay (ELISA), isolation of viral strain in cell culture are currently available for diagnosis of COVID-19 infection. This review provides a brief overview of promising high-throughput techniques currently used for detection of SARS-CoV-2, along with their scope and limitations that may be used for effective control of the disease.

Development of a tablet PC-based portable device for colorimetric determination of assays including COVID-19 and other pathogenic microorganisms

There has been a strong and urgent demand to diagnose community transmission-driven coronavirus disease 2019 (COVID-19) after it crossed borders. A large number of rapid and accurate tests and diagnoses are required at drive-through test stations, community clinics and hospitals. Isothermal amplification technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), provides excellent alternatives for resource limited test environments. LAMP has been shown to be comparable with polymerase chain reaction (PCR) and can be performed in less than 30 min by non-laboratory staff without ribonucleic acid (RNA) extractions commonly associated with PCR. LAMP tests on assays with SARS-CoV-2 and other pathogenic microorganisms, such as Dengue, Malaria, and Influenza viruses and Helicobacter pylori show color changes allowing test results to be interpreted by the color change of the assays. However, visual inspection of a large number of assays is prone to human error and manual record keeping makes test result tracking for an epidemiologic investigation very difficult and inefficient. The epidemiologic investigation is an essential part of the fight against community transmission-driven viruses. We have developed a very accurate and reliable, human error free, tablet PC-based portable device for colorimetric determination of assays including SARS-CoV-2 and other pathogenic microorganisms.