COVID-19 Molecular Testing

Expires: May 4, 2023

  • Presenter

    Matthew Binnicker, Ph.D.
    Director of Clinical Virology
    Professor of Laboratory Medicine and Pathology
    Vice Chair of Practice
    Mayo Clinic, Rochester, Minnesota


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    Transcript and References


    Thanks for joining me for this Hot Topic presentation on molecular testing for COVID-19. I’m Dr. Matt Binnicker, the Director of Clinical Virology and Vice Chair of Practice in the Department of Laboratory Medicine and Pathology at Mayo Clinic.


    Before we begin, I wanted to mention that I serve as an Advisory Board member for DiaSorin molecular.

    So with that, let’s get started.

    Coronaviruses: From the Common Cold to Global Contagion

    As the number of cases continues to increase each day of COVID-19, our knowledge of the virus itself, as well as how we can and should test for COVID-19, is also rapidly evolving. In this presentation, I want to provide a brief overview of the virus, the current testing options, and finally review what factors may influence the performance of molecular testing in patients with possible COVID-19 disease.

    To begin, it’s important to highlight that not all coronaviruses are created equal. Over the past several decades, we know now that four serotypes of coronaviruses—I’ve listed those here on this slide—circulate in the population, and are associated with annual epidemics of mild-to-moderate upper respiratory tract infection. The serotypes listed on this slide are most commonly associated with the common cold.

    However, over the past 20 years, there have been outbreaks of novel or variant coronaviruses that have been associated with more severe disease.

    In 2002, there was an outbreak of respiratory illness in China that was due to severe acute respiratory syndrome coronavirus, or SARS-CoV, and SARS-CoV ultimately was confirmed in about 8,400 cases, and it had a case fatality rate of approximately 10%. A decade later, Middle East Respiratory syndrome coronavirus, or MERS, caused an outbreak effecting around 2,500 people, but MERS was associated with a high-case fatality rate of about 35%. MERS cases have occurred primarily in the Arabian Peninsula and have not shown broad global spread to this point. And now in 2020, we’re in the midst of a global pandemic caused by severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2, which has been determined to be a variant of the 2003 SARS virus. In other words, the current virus is not believed to be a novel virus, but a relative of the original SARS virus from 2003. SARS-CoV-2 has now caused over 3.2 million cases worldwide. It’s killed more than 228,000 people, and that translates to a case fatality rate of about 7%.

    Why do certain coronaviruses cause more severe disease?

    One common question is “Why do certain coronaviruses cause more severe disease?”

    It’s known that coronaviruses are zoonotic in origin, which means that they naturally reside in animal reservoirs. Sequencing and phylogenetic data support the conclusion that many of the coronaviruses infecting humans have bats as their natural reservoir. In fact, we have solid data indicating that SARS from 2003 was transmitted from bats to palm civets, which served as the intermediate host for spillover of SARS into humans.

    Similarly, MERS virus is believed to have been harbored in bats, but the initial transmission of MERS virus into humans occurred through contact with dromedary camels in the Arabian Peninsula. And finally, while much less is known regarding SARS-CoV-2, it is believed that the virus was transmitted from bats to animals that were sold at wet markets in China. Although the intermediate host for SARS-CoV-2 is still undefined, we have sequencing data that suggests that the pangolin or turtles may have facilitated the transmission of SARS-CoV-2 to humans.

    SARS-CoV-2 (COVID-19): Laboratory Testing

    Now that we have reviewed some background information on SARS-CoV-2, let’s turn our attention to laboratory testing. To date, the vast majority of testing for COVID-19 has been performed using a technology called real-time PCR. PCR-based assays detect the viral RNA in clinical samples, and are designed to diagnose active infection with SARS-CoV-2. Recently, there has been a significant amount of attention on serology, or antibody-based assays, for COVID-19. These tests detect antibodies, like IgG, which have been developed by the immune system in response to SARS-CoV-2 infection. Serologic assays are unlikely to play a key role in diagnosis of COVID-19 due to the fact that is requires 10-14 days for antibodies to develop following infection, but serology will be important as a means of determining whether an individual has been exposed to the virus and has developed an antibody response.

    SARS-CoV-2 (COVID-19): Molecular Testing

    With regards to molecular testing for SARS-CoV-2, the majority of the real-time PCR assays that have been developed target a combination of several genes in the SARS-CoV-2 genome. Examples of viral gene targets targeted by these PCR assays include the nucleocapsid, the open reading frame, and the envelope and RNA-dependent RNA polymerase genes.

    As the primary clinical manifestation of COVID-19 is a respiratory illness, PCR tests are generally used to test samples obtained from the upper or lower respiratory tract. Appropriate upper respiratory sample types include a nasopharyngeal swab or a throat swab. If a patient has evidence of a lower respiratory tract infection, or if the patient is in a later stage of the disease, then a clinical specimen such as sputum, bronchoalveolar lavage fluid (BAL fluid), or tracheal secretions may be appropriate for testing.

    There are several questions that are common with regards to molecular testing that I’d like to address. The first is “When is SARS-CoV-2 shed at the highest amount?”

    There is a growing amount of data in the published literature suggesting that the virus is present at peak amounts very early in the disease course. One study that was recently published in Nature Medicine actually showed that peak viral shedding occurs about 24 hours prior to a patient’s onset of symptoms. This is very important, in that it likely explains why we have seen such effective community spread of this virus, since many people are shedding the virus at high amounts before they even know they are infected. Importantly, the viral load tends to decrease in the upper airway after 3-5 days of symptoms.

    Another common question is “What is the sensitivity of PCR tests for COVID-19? Is it really only 60%?”

    At this point, it is important to underscore that most clinical laboratories only know the analytical sensitivity of the molecular PCR tests. In other words, laboratories have determined the limit of detection of these assays using control material and known positive samples. The clinical sensitivity, or the number of times the test will be positive in patients with COVID-19, still needs to be defined. The true clinical sensitivity of COVID-19 PCR tests likely depends on several factors, including when the sample is collected in relation to the patient’s disease course, the sample type, the quality of the sample that is collected, and the performance characteristics of the test itself.

    With regards of sensitivity of PCR, there was a recent study published in the Journal of the American Medical Association that assessed the detection rate of PCR using different sample types in hospitalized patients. The detection rate in these various sample types range significantly, and as you can see on this slide, the highest rate of positive results was achieved when testing BAL fluid and sputum: 93% of the BAL were positive, and 72% of the sputum samples were positive in these patients. However, the number of positive results decreased in sample types such as nasal swabs and throat swabs at 63% and 32% respectively. I think these data are attributing to some of the information of a 60% sensitivity for PCR. But it’s really important to underscore when these patients were tested as these were mainly hospital patients. They were likely further along in their disease course, and we know now from the viral transmission data, again, that the virus tends to decrease in viral load in the upper respiratory tract further along in the disease. So this data actually makes a lot of sense—being that these are hospitalized patients—the virus is likely present at higher amounts in the lower respiratory tract, which we can see by the positivity rates and sample types such as BAL and sputum.

    SARS-CoV-2 (COVID-19): Summary

    In summary, COVID-19 is continuing to cause a worldwide pandemic involving millions of cases. It’s caused by a variant virus called SARS-CoV-2. We now have several laboratory tests for SARS-CoV-2. Real-time PCR is used for acute diagnosis of patients with symptoms, and serology can be used to determine whether an individual has been exposed to the virus and mounted an antibody response.

    Importantly, the sensitivity of PCR testing depends on a number of factors, including the timing of disease, when the test is performed, the type of sample that is collected, the quality of the sample, and finally, the performance characteristics of the test itself.

    Thanks very much for joining me for this Hot Topic on COVID-19 molecular testing, and if you have any questions, you can submit them to Mayo Clinic Laboratories. Thank you.

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    This post was developed by our Education and Technical Publications Team.