Expert Review of Molecular Diagnostics | 2021
Are T cell repertoires useful as diagnostics for SARS-CoV-2 infection?
Abstract
Conventional diagnostic tests for SARS-CoV-2 infection include PCR-based tests to measure viral RNA and various serologic tests to measure antibodies arising from the infection [1]. Much of the testing that has been put in place as part of measures to design isolation and social distancing strategies during the COVID-19 pandemic is based on PCR tests. Among them, the CDC s 2019 Novel Coronavirus (2019nCoV) Real-Time Reverse Transcriptase (RT)–PCR Diagnostic Panel detects the SARS-CoV-2 virus in both nasal and bronchial lavage specimens. The test is designed to be used with existing RT-PCR instruments used to test for other RNA virus infections. Point of care (POC) PCR tests have been and are being developed for rapid testing at airports and other locations. Commercially available PCR tests detect at least two virus targets by using three primer–probe mixes including probes for the virus nucleocapsid gene and include a control for RNA integrity. These PCR tests are highly reliable and sensitive but, owing to their high sensitivity, can suffer from issues including persistently low-level-positive results with no clear correlation with the clinical picture and most importantly, with the real infectiousness of the patients. False negative results also occur owing to poor sampling and/or very low virus titers in some infected individuals. Serological tests measuring anti-virus antibodies are generally a good marker of virus infection and typically arise 1 to 3 weeks after infection . SARS-CoV-2 first induces IgM responses which are then rapidly replaced by IgG and subsequently IgA. The two major virus proteins to which antibodies are generally raised and measured are the spike (S) protein and the immunodominant nucleocapsid (N) protein. The tests are designed to test either binding or neutralizing antibodies. Binding assays are usually in the ELISA format, although POC lateral flow assays are available to measure both IgM and IgG. Neutralizing antibody tests can either measure inhibition of the binding of the RBD domain of the S protein to the ACE-2 receptor or can measure inhibition of viral replication in vitro. Antibody tests are useful for measuring levels of immunity in the population (herd immunity) but are particularly important for assessing vaccine efficacy. Neutralization assays using pseudotyped virus (usually based on VSV and MLV) are also used to determine neutralizing antibody levels but are not performed routinely. The efficacy of the different vaccines being developed against SARS-CoV-2 was initially assessed by measuring their ability to raise antibodies in animals before any human vaccine trial could take place [2]. Only once this has been demonstrated in humans in Phase I and II trials will event-based Phase III trials take place: for example those that were completed with the mRNA-based vaccines and now with the DNA based spike encoding vaccines. There are currently no routine assays used to unequivocally determine the level of protection conferred by any of the vaccines in use or in development. This is determined in Phase 3 trials or by the collection of real world data. Most infected individuals will raise antibodies to virus proteins but, owing to highly variable pathology, going from asymptomatic disease in children and younger people to very serious disease and death in older patients, the actual antibody levels vary considerably. It is also presently unclear how long antibodies and protective immunity last in infected or vaccinated individuals, with some reports of short-lasting antibody responses after mild disease [3,4]. The role of T cells in SARS-CoV-2 infections and their importance for vaccines is now much more appreciated than at the beginning of the pandemic. In many virus infections, T cells potentially target all virus antigens and contribute significantly and, in some cases, exclusively to virus clearance and protection even in the absence of antibody responses. T cells are also likely major mediators of long-term protective memory and persist much longer than antibodies [5]. Many groups worldwide have analyzed T cells from PBMCs and BAL from both convalescent and acutely infected SARS-CoV-2 patients [6–8]. Both CD4 and CD 8 T cells are found in patients and recognize epitopes from most viral proteins. This was predicated to some extent by what was seen when examining T cell responses to infection with the original SARS-CoV causing the 2002/2003 SARS epidemic. Here, specific T cells were recognized for their ability to respond to peptide pools derived from viral proteins [9]. T cells recognized mostly N, M, and S proteins. CD8 T cell responses were more common than CD4 T cell responses. There was also profound lymphodepletion in patients with severe disease. This is almost exactly what is now seen in SARS-CoV-2 infections. Additional data also suggest that aberrant features of T cell responses correlate with disease severity. The reasons for these aberrations are presently unclear [5].