The essentials of understanding SARS-CoV-2 laboratory diagnosis and immunity
One of the hottest topics in COVID-19 disease is the use of diagnostic testing. This topic includes both the identification of active infection as well as serologic testing which may provide evidence of immunity. This is a fast-moving field and work in progress but two brief reports we really like published in JAMA nicely summarize the field.
I will highlight a few points worth reflecting on. First, in terms of diagnosis, we have thus far been relying on PCR which has very high specificity as only small amounts of viral RNA are needed to amplify a signal but the sensitivity of the test is variable. That is important in diagnosis for false negative tests are problematic when trying to manage disease or contagion. While fluid from BAL is a rich source of virus (sensitivity 93%) oral fluid or nasal swab may be as low as 63% which is poor. (See the figure below which gives you a feel of the relative sensitivities from different biologic sources as well as the timeline for positivity.) Many variables contribute to these variations, not the least of which is sample collection. The bottom line is that PCR is highly specific but the sensitivity is modest (akin to rapid flu testing). A second point is that quantitative viral load (which can be inferred from cycle threshold (Ct)) is a semi-quantitative way of telling us how much virus is present. We know that viral load peaks early in the disease course and then declines; we also know that sicker people have poorer control of the virus and thus have higher viral loads. Finally, and most problematic, is that it may take a long time to clear the virus and this confounds clinical decision making. Generally, the virus will clear in about 3 weeks but with PCR even tiny amounts of non-viable RNA can be amplified. Some patients may take up to 6 weeks to clear and such patients, many of whom have been well for weeks, are not likely infectious but therein lies the rub. Accordingly many health care institutions, including ours, are now using a non-testing algorithm to return to work with a minimum of 10 days passing since disease onset, 3 days of total symptom resolution and afebrile (free of antipyretics), returning (with a mask) with no patient contact for 2 weeks. We can arm wrestle about cloth vs surgical masks…. Personally I look forward to the next generation of viral tests which will likely be point-of-care and antigen-based or possibly CRISPER based, which has recently been discussed.
Lastly, what about the antibody test controversy? There are scores of antibody tests and in general SARS-CoV-2 infection is similar to other respiratory viral infections with IgM (which can be a source of cross-reactive results) appearing after 5-7 days and IgG following in the second week. These antibodies are important for viral defense but the story is much more complicated with the potential for both neutralizing and enhancing capabilities. There are now limited data suggesting that rheumatoid factor may not confound test results but this is preliminary. We are hoping that SARS-CoV-2 is similar to other Coronaviruses which generate a long-lasting and protective host defense (IgG response) but that is unknown for now, so we at Cleveland Clinic are only using the test (i.e. now- i.e. today in the COVID era!) for epidemiologic study. Maybe by the next issue of COVID CORNER, this will change. The proposed use of a positive antibody as a license or certificate of immunity is way premature in our opinion.
In conclusion, we urge you to read these two well-written and clear topical summaries on this very important and relevant topic.
COVID-19 and Post infection Immunity
Limited Evidence, Many Remaining Questions
Robert D. Kirkcaldy, MD, MPH; Brian A. King, PhD, MPH; John T. Brooks, MD
JAMA. Published online May 11, 2020. doi:10.1001/jama.2020.7869
Interpreting Diagnostic Tests for SARS-CoV-2
Nandini Sethuraman, MD; Sundararaj Stanleyraj Jeremiah, MD; Akihide Ryo, MD, PhD
JAMA. Published online May 6, 2020. doi:10.1001/jama.2020.8259
Evolving Manifestations of COVID-19: what have we learned from Post-mortem studies
I think we all can agree that the fast pace at which COVID-19 related manuscripts, news stories, and press releases being circulated each day is overwhelming. Every day we are learning something new: cardiovascular manifestations, renal manifestations, “COVID toes”, stroke– you name it, it has been described in patients with COVID-19. While the mechanisms underlying these manifestations remain incompletely understood, our knowledge of immunopathogenesis has been evolving. There are countless reports of patients with hypercoagulable states, venous thromboembolism, and other evidence of vascular damage and it is becoming clear that something is going on at the endothelial level. Unfortunately, much of what has been learned is from post-mortem studies. Two of these studies caught my eye:
Varga et al report a series of post-mortem cases demonstrating endothelial cell involvement across vascular beds of different organs. It is well known that ACE2, the receptor used by SARS-CoV-2 to gain entry to cells, is expressed on alveolar epithelial cells, thereby explaining the lung injury caused by COVID-19, but ACE2 is also widely expressed on other endothelial cells, traversing multiple organs. Post-mortem histopathological analysis revealed evidence of both direct viral infection of endothelial cells and diffuse endothelial inflammation in several organs, which could explain some of the clinical sequel being seen in patients with COVID-19.
The second paper presents autopsy data from 27 patients, demonstrating multi-organ involvement by SARS-CoV-2, in particular renal tropism. The authors quantified SARS-CoV-2 viral load in tissue samples and found highest levels in respiratory tract tissues, however they also detected the virus in kidneys, liver, heart, brain, and blood. Paying particular attention to the kidneys, they detected viral load in all renal compartments, with preferential targeting of renal glomerular cells. The observed that 17 of the 27 patients had a history of two or more chronic conditions, and this was associated with SARS-CoV-2 tropism for the kidneys.
While knowledge we glean from post-mortem studies in no way tells us about what is going on in the days/weeks preceding death, these reports do shed light on possible mechanisms underlying end organ involvement, and we encourage you to read them.
Lastly, we give a shout out to the Director of Pulmonary Pathology at the Cleveland Clinic, Sanjay Mukhopadhyay MD, who in this great video reviews the lung histopathology of COVID-19. https://consultqd.clevelandclinic.org/a-pulmonary-pathologists-perspective-on-covid-19/
Please give us a shout out with any questions!
Leonard H. Calabrese, DO, is the head of the RJ Fasenmyer Center for Clinical Immunology and Vice-Chair of the Department of Rheumatic and Immunologic Diseases at Cleveland Clinic Dr. Calabrese has lectured nationally and internationally on the subjects of immunology, rheumatology, and viral diseases. He is the author of more than 400 published peer-reviewed articles, book chapters, and reviews. @LCalabreseDO
Cassandra Calabrese, DO, is a staff physician in the Department of Rheumatic and Immunologic Diseases and the Department of Infectious Diseases at Cleveland Clinic and directs the combined Rheumatology-Infectious Disease training program. She also directs the Clinic for immune-related adverse events form cancer immunotherapy within the department of Rheumatic and Immunologic Diseases. @CCalabreseDO