Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2

Abstract

The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

“…While not routinely used for SARS-CoV-2 diagnostic testing in clinical laboratories, genome sequencing of SARS-CoV-2-positive specimens with NGS technologies has paved the way for numerous applications, including investigations of disease pathogenesis, epidemiology, virus phylogenetics, SARS-CoV-2 evolution, and the impact of viral evolution on diagnostic testing or interventions like therapeutics and vaccines ( 420 – 424 ). For example, Meredith et al used SARS-CoV-2 nanopore sequencing on PCR-positive specimens combined with epidemiological data to help identify nosocomial transmission events and inform infection control interventions ( 418 ).…”

“…The establishment of a correlate of protection first requires an in-depth understanding of whether nAbs are produced, the extent to which they are produced, whether they provide protection, and the duration of these responses and then analyzing these data in large population studies to correlate a level of nAbs that may confer protection against subsequent infection ( 514 ). The quantification of nAbs in serum or plasma is performed using target- and immunoglobulin isotype-specific neutralization assays 9like plaque reduction neutralization tests (PRNTs) ( 41 , 241 , 424 , 515 ). Briefly, PRNTs rely on the ability of nAbs to effectively prevent SARS-CoV-2 from infecting cultured cells that would otherwise cause cytopathic effects (i.e., cell death/lysis) ( 41 , 241 , 511 , 515 – 517 ).…”

“…Despite MN, FRNTs are amenable to moderate-throughput testing, and alternatives have been developed using fluorescence detection and luminescence to increase sensitivity. On the other hand, MN tests and FRNTs share a challenge similar to that with PRNTs: they all rely on SARS-CoV-2 propagation in cell culture, which requires laboratory facilities with higher levels of biological containment (i.e., biosafety level 3 [BSL3] in Canada or physical containment level 3 [PC3] as defined by the WHO) ( 424 ). These practices are not common outside reference laboratories ( 241 ).…”

Diagnostic Potential of a Luminex-Based Coronavirus Disease 2019 Suspension Immunoassay (COVID-19 SIA) for the Detection of Antibodies against SARS-CoV-2

“…Although PCR-diagnosis of acute SARS-CoV-2 infections is highly efficient, specific serology is a valuable complement due to the limited time of viral RNA-positivity [7]. During the spring of 2020, several commercial serological assays such as various rapid tests and enzyme immunoassays (EIA) also became available, for a review see [8]. Previous approaches to serologic detection of infection with emerging coronaviruses, including SARS and MERS, focused on the S and N proteins, which are considered the immunodominant antigens for these viruses [9].…”

Disease Prevalence Matters: Challenge for SARS-CoV-2 Testing

“…However, in addition to testing frequency, it is important to understand how prevalence influences the performance of these tests, especially in low-prevalence situations. In previous articles that explore diagnostic methods of COVID-19 testing [ 11 , 12 , 13 , 14 , 15 , 16 , 17 ], this important concept is not elaborated upon, or only explained in brief. Thus, in this article, we explain the concepts of PPV/NPV and the influence of disease prevalence.…”