Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities
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ORIGINAL ARTICLE
Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities Horllys Gomes Barreto 1 & Flávio Augusto de Pádua Milagres 1 Matheus Martins Daúde 1 & Vagner Augusto Benedito 2
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Gessi Carvalho de Araújo 1
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Received: 9 July 2020 / Revised: 5 October 2020 / Accepted: 7 October 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The world is currently facing a novel viral pandemic (SARS-CoV-2), and large-scale testing is central to decision-making for the design of effective policies and control strategies to minimize its impact on the global population. However, testing for the presence of the virus is a major bottleneck in tracking the spreading of the disease. Given its adaptability regarding the nucleotide sequence of target regions, RT-qPCR is a strong ally to reveal the rapid geographical spreading of novel viruses. We assessed PCR variations in the SARS-CoV-2 diagnosis taking into account public genome sequences and diagnosis kits used by different countries. We analyzed 226 SARS-CoV-2 genome sequences from samples collected by March 22, 2020. Our work utilizes a phylogenetic approach that reveals the early evolution of the virus sequence as it spreads around the globe and informs the design of RT-qPCR primers and probes. The quick expansion of testing capabilities of a country during a pandemic is largely impaired by the availability of adequately trained personnel on RNA isolation and PCR analysis, as well as the availability of hardware (thermocyclers). We propose that rapid capacity development can circumvent these bottlenecks by training medical and nonmedical personnel with some laboratory experience, such as biology-related graduate students. Furthermore, the use of thermocyclers available in academic and commercial labs can be promptly calibrated and certified to properly conduct testing during a pandemic. A decentralized, fast-acting training and testing certification pipeline will better prepare us to manage future pandemics. Keywords COVID-19 . Coronavirus . Infrastructure . Polymerase chain reaction . Testing
Introduction The World Health Organization (WHO) received notification on December 31, 2019 of pneumonia cases of unknown etiology in Wuhan, China. On January 11, 2020, the Chinese authorities identified a new type of coronavirus, which was isolated on January 7, 2020, which allowed its rapid
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00109-020-01992-x) contains supplementary material, which is available to authorized users. * Vagner Augusto Benedito [email protected] 1
Molecular Analysis Laboratory, Department of Health Sciences, Faculty of Medicine, Federal University of Tocantins (UFT), Palmas, TO, Brazil
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Genetics and Developmental Biology Program, West Virginia University, Morgantown, WV, USA
sequencing and the public data deposition on January 12 to help with the development of diagnostic kits [1]. WHO declared on March 11, 2020, a pandemic the coronav
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