Considerations for diagnostic COVID-19 tests

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Abstract

During the early phase of the coronavirus disease 2019 (COVID-19) pandemic, design, development, validation, verification and implementation of diagnostic tests were actively addressed by a large number of diagnostic test manufacturers. Hundreds of molecular tests and immunoassays were rapidly developed, albeit many still await clinical validation and formal approval. In this Review, we summarize the crucial role of diagnostic tests during the first global wave of COVID-19. We explore the technical and implementation problems encountered during this early phase in the pandemic, and try to define future directions for the progressive and better use of (syndromic) diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks. Continuous global improvement in diagnostic test preparedness is essential for more rapid detection of patients, possibly at the point of care, and for optimized prevention and treatment, in both industrialized countries and low-resource settings.

Abstract

In this Review, Vandenberg et al. explore the crucial role of diagnostic tests during the first global wave of coronavirus disease 2019 (COVID-19) and the technical and implementation problems encountered during the early phase of the pandemic, and they define future directions for the progressive and better use of diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks.

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Most cited references 161

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A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu, Dingyu Zhang, Wenling Wang … (2020)

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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Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

Dawei Wang, Bo Hu, Fangfang Zhu … (2020)

In December 2019, novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of affected patients is limited.

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Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Roujian Lu, Xiang Zhao, Juan Li … (2021)

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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Contributors

Olivier Vandenberg: olivier.vandenberg@lhub-ulb.be

Alex van Belkum:

ORCID: http://orcid.org/0000-0001-8545-5108

alex.vanbelkum@biomerieux.com

Journal

Journal ID (nlm-ta): Nat Rev Microbiol

Journal ID (iso-abbrev): Nat Rev Microbiol

Title: Nature Reviews. Microbiology

Publisher: Nature Publishing Group UK (London )

ISSN (Print): 1740-1526

ISSN (Electronic): 1740-1534

Publication date (Electronic): 14 October 2020

Pages: 1-13

Affiliations

[1 ]GRID grid.4989.c, ISNI 0000 0001 2348 0746, Innovation and Business Development Unit, , Laboratoire Hospitalier Universtaire de Bruxelles — Universitair Laboratorium Brussel, Université Libre de Bruxelles, ; Brussels, Belgium

[2 ]GRID grid.4989.c, ISNI 0000 0001 2348 0746, Center for Environmental Health and Occupational Health, School of Public Health, , Université Libre de Bruxelles, ; Brussels, Belgium

[3 ]GRID grid.83440.3b, ISNI 0000000121901201, Division of Infection and Immunity, Faculty of Medical Sciences, , University College London, ; London, UK

[4 ]GRID grid.4989.c, ISNI 0000 0001 2348 0746, Department of Microbiology, , Laboratoire Hospitalier Universtaire de Bruxelles — Universitair Laboratorium Brussel, Université Libre de Bruxelles, ; Brussels, Belgium

[5 ]GRID grid.424167.2, ISNI 0000 0004 0387 6489, Strategic Intelligence, Corporate Business Development, , bioMérieux, ; Chemin de L’Orme, France

[6 ]GRID grid.424167.2, ISNI 0000 0004 0387 6489, Open Innovation and Partnerships, , bioMérieux, ; La Balme Les Grottes, France

[7 ]GRID grid.17703.32, ISNI 0000000405980095, Laboratory Services and Biobank Group, , International Agency for Research on Cancer, World Health Organization, ; Lyon, France

Author information

Olivier Rochas http://orcid.org/0000-0003-0940-5146

Alex van Belkum http://orcid.org/0000-0001-8545-5108

Article

Publisher ID: 461

DOI: 10.1038/s41579-020-00461-z

PMC ID: 7556561

PubMed ID: 33057203

SO-VID: 068aa2ef-6d4f-4a67-a46d-2fe72134f3b3

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This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

Considerations for diagnostic COVID-19 tests

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Most cited references 161

A Novel Coronavirus from Patients with Pneumonia in China, 2019

Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

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