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      Laboratory tests for the detection of SARS-CoV-2 infection: basic principles and examples Translated title: Labortests zum Nachweis einer SARS-CoV-2-Infektion: Grundprinzipien und Beispiele

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          Abstract

          Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated throughout the world causing the worst pandemic since 1918. All efforts have been marshalled towards testing different treatment approaches, obtaining clinical and epidemiological information, developing suitable diagnostic tests, and developing new vaccines. New ribonucleic acid (RNA)-based and viral vector-based vaccines have been developed and licensed under emergency use in many countries; however, there is a huge demand for vaccines, and it will take some time before a sufficient number of people are vaccinated to stop the circulation of the virus. Therefore, the proper diagnosis and identification of infected individuals are crucial for the isolation and treatment of these patients and tracing of their contacts. Many diagnostic tests and diag-nostic kits have been developed in a relatively short time. This review summarizes the principles of the available laboratory assays that are in use for the detection of SARS-CoV-2 RNA, antigens, or antibodies.

          Zusammenfassung

          Das Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), das sich weltweit ausgebreitet hat, ist für eine der größten Pandemien seit 1918 verantwortlich. Seit Beginn der Pandemie laufen weltweit zahlreiche klinische und epidemiologische Studien, um mögliche effektive Behandlungsansätze zu testen und geeignete diagnostische Testverfahren zu entwickeln. Obwohl in einigen Ländern bereits einige RNA- und Vektorimpfstoffe gegen das Virus entwickelt und zugelassen wurden, ist die Nachfrage nach Impfstoffen in vielen Ländern immer noch groß. Aus diesem Grund und bis eine ausreichende Zahl von Menschen weltweit geimpft ist, bleibt eine schnelle Diagnose die entscheidende Maßnahme, um infizierte Personen zu identifizieren und das Infektionsgeschehen zurückzuverfolgen. In relativ kurzer Zeit wurden viele diagnostische Testverfahren und diagnostische Kits entwickelt, die den Nachweis von SARS-CoV-2-RNA, -Antigenen oder -Antikörpern ermöglichen. Dieser Review-Artikel gibt eine Übersicht über verfügbare diagnostische COVID-19-Tests, ihre Prinzipien und Einsatzmöglichkeiten.

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          A Novel Coronavirus from Patients with Pneumonia in China, 2019

          Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)
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            Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

            Summary Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. Methods We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus. Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues. Interpretation 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation. Funding National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
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              A new coronavirus associated with human respiratory disease in China

              Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
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                Author and article information

                Journal
                Ger Med Sci
                Ger Med Sci
                GMS Ger Med Sci
                GMS German Medical Science
                German Medical Science GMS Publishing House
                1612-3174
                27 May 2021
                2021
                : 19
                : Doc06
                Affiliations
                [1 ]Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
                Author notes
                *To whom correspondence should be addressed: Khaled R. Alkharsah, Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), 31441 Dammam, Saudi Arabia, Phone: +966 13 333 1053, E-mail: kalkharsah@ 123456iau.edu.sa
                Article
                000293 Doc06 urn:nbn:de:0183-0002936
                10.3205/000293
                8167375
                5da0c2d2-a038-4d29-a282-2eb3b3d81c69
                Copyright © 2021 Alkharsah

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License. See license information at http://creativecommons.org/licenses/by/4.0/.

                History
                : 29 October 2020
                : 04 February 2021
                Categories
                Article

                Medicine
                covid-19,sars-cov-2,coronavirus,laboratory test,molecular assay,immunoassay
                Medicine
                covid-19, sars-cov-2, coronavirus, laboratory test, molecular assay, immunoassay

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