COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2

Dutta, Debashis; Naiyer, Sarah; Mansuri, Sabanaz; Soni, Neeraj; Singh, Vandana; Bhat, Khalid Hussain; Singh, Nishant; Arora, Gunjan; Mansuri, M Shahid

doi:10.3390/diagnostics12061503

Cited by 57 publications

(36 citation statements)

References 140 publications

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“…29 A comparison of mutational maps among the Omicron sublineages is displayed in Figure 2. 31,32 Of note, the COVID-19 diagnosis was confirmed by the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), 33,34 and various modifications of this assay could be used to predict an infection by the Omicron variant, particularly in low-to middle-income countries that lacked next-generation sequencing (NGS) facilities. One of those modified assays was the RT-qPCRbased SGTF assay because a Δ69-70 deletion in most sublineages of the Omicron (i.e., BA.1, BA.1.1, BA.3, BA.4, and BA.5) would hinder a detection of the spike gene but not of other genes.…”

Section: The Emergence and Hallmarks Of The Omicron Variantmentioning

confidence: 99%

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

Vidian¹,

Dikson²,

Litanto³

et al. 2022

Explor Res Hypothesis Med

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The world is now in the third year of the COVID-19 pandemic. As such, enormous volumes of virological, immunological, and epidemiological knowledge pertaining to the SARS-CoV-2 infection have been obtained during these years. The SARS-CoV-2 Omicron variant is currently causing the latest wave of infection globally presumably due to its ability to transmit with ease among individuals and to escape from the existing neutralizing antibodies. Fortunately, numerous treatment agents as well as prophylactic vaccines are now available, thus providing people with a better chance to control this infectious disease. This review will discuss the Omicron variant of concern as well as the available treatments and vaccines for COVID-19.

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Section: The Emergence and Hallmarks Of The Omicron Variantmentioning

confidence: 99%

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

Vidian¹,

Dikson²,

Litanto³

et al. 2022

Explor Res Hypothesis Med

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“…The knowledge of a complete new CoV genomic sequence (available at GISAID and GenBank (accession number MN908947) (Cao et al, 2020;Lu et al, 2020)), designated as Wuhan-Human 1 CoV (Wuhan-Hu-1 or WHCV) (Ackermann et al, 2020), allowed the rapid development of probes, reagents and tools for specific and sensitive detection of viral sequences in the patients infected by SARS-CoV-2 (Cheng et al, 2020a;Corman et al, 2020;Dutta et al, 2022). One of the first epidemiological parameters that these tools helped to assess was the basic reproduction number or R 0 (R naught) value for virus community transmission, estimated from 2.2 to 2.68 for the ancestral Wuhan-Hu-1 strain (Liu et al, 2020e).…”

Section: Virosurveillance: Genomics To Trace Sars-cov-2mentioning

confidence: 99%

“…As presented above, the Chinese authorities published in GenBank and in the GISAID portal database the complete genome of SARS-CoV-2. Thanks to this contribution, the microbiological diagnosis of COVID-19 has been based on the detection of the viral genetic material (RNA+) of SARS-CoV-2 from the collection of respiratory samples from patients with compatible symptoms (Corman et al, 2020;Dutta et al, 2022). Various laboratories began development for the detection of SARS-CoV-2 in accordance with WHO guidelines, which initially published five protocols for diagnosis using RT-qPCR (Corman et al, 2020;Dutta et al, 2022).…”

Section: Point-of-care: Rapid Diagnosis and Control Of Outbreaks In T...mentioning

confidence: 99%

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

Valenzuela-Fernandez

Cabrera-Rodríguez

Ciuffreda

et al. 2022

Front. Bioeng. Biotechnol.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.

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“…As of June 23, 2022, there were more than 539 million confirmed cases of COVID-19 and over 6.3 million deaths recorded worldwide ( https://covid19.who.int/ , accessed on 24 June 2022). Although COVID-19 cases are declining, the world is still grappling with the virus; the virus continues to infect new individuals consistently and causing new infection clusters [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Acridone Alkaloids: In-Silico Investigation Against SARS-CoV-2 Main Protease

et al. 2022

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that causes COVID-19 disease is still a major public health concern around the world. The main protease encoded by SARS-CoV-2 is a promising target for COVID-19 therapeutic development since it plays a crucial role in the virus’s life cycle. Repurposing known bioactive molecules is an effective strategy to fast-track the delivery of hits and leads in drug discovery. In this regard, this study assesses in-silico , 17 acridone-based alkaloids for their activity against SARS-CoV-2 main protease. The quantum chemical computations imply that the acridone alkaloids will interact better in the active sites of the enzymes due to their low energy gap. They also have good oral bioavailability as rationalized by “no rule of five violation" and favorable pharmacokinetics parameters. From the docking results, many of the alkaloids displayed a higher binding affinity than nirmatrelvir, an authorised protease inhibitor. Compound 3 (5-hydroxynoracronycine alcohol), with the better binding affinities (6W63, − 7.094 kcal/mol; 5R82, − 5.839 kcal/mol) and unique structural features is a viable candidate that could be investigated further for development of a novel target specific chemotherapeutic agent to stop SARS-CoV-2 invasion.

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COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2

Cited by 57 publications

References 140 publications

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

Acridone Alkaloids: In-Silico Investigation Against SARS-CoV-2 Main Protease

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