Discussion: -
We have profiled T cell populations during COVID-19 in a longitudinal study cohort, where we followed them from inclusion up to 6-8 months post-recovery, using spectral flow cytometry. We found wide-ranging alterations to the T cell compartment including a rise in effectors and effector memory T cells that lasted for a period of 6 months after discharge from the hospital.
Lymphopenia was observed in many of the COVID-19 patients in our cohort at inclusion (i.e., at hospitalization [11], and is a common clinical observation [12-15] that may be attributed to the cells relocating or dying at this stage of the disease. Indeed, a highly inflammatory form of cell death, i.e., pyroptosis, induced in infected and uninfected cells, appears to be a major contributing factor for the onset of strong inflammatory responses seen globally in many individuals with COVID-19 [8, 16-19]. Furthermore, we and others have shown that the T cell compartment is affected to a higher degree than other immune cells such as B or NK cells [20-23] , which implies that T cell subsets play a paramount role in COVID-19 pathogenesis. Of note, reductions in circulating NKT cells as illustrated by us and others [24], have also been correlated to severe COVID-19 disease and poor outcome [25-26].
Memory T cells, both general and antigen-specific, in the context of SARS-CoV-2 infection have been widely studied, notwithstanding often for shorter time-periods [27-30] with fewer long-term studies, i.e. 8-9 months [31]. Evidence from the SARS-CoV outbreak in 2005 suggests that anti-SARS-CoV antibodies fell below detection limits within two years [32], and SARS-CoV-specific memory T cells were detectable 11 years after the SARS outbreak [33]. Memory T cells are an important and diverse subset of antigen experienced T cells that are sustained long term, and when needed are converted into effector cells during reinfection/ exposure [34, 35]. Depending on their cellular programming and phenotype they are classified into different central and effector memory subtypes. The effector subsets contain the CD45RA+CCR7- TEMRA, which are essentially TEM that re-express CD45RA after antigen stimulation [36]. Not much is known about the functionality of this population, but CD4+ TEMRA are implicated in protective immunity [36].
Furthermore, elevated levels of virus specific CD8+ effectors are maintained after dengue vaccination [37]. We found an elevation of both (CD4+ and CD8+T) effectors T cells and effectors memory T cells that lasted throughout the study, i.e., 6-7 months which contrasted with the CD4+ effectors that remained unaltered by COVID-19 in previous study [38]. Previous studies have shown the CD8+ TEMRA population to be increased at hospitalization [39,40] and sustained for 6 weeks [39]. Currently, the exact role of CD8+ effectors in COVID-19 remains largely ambiguous, but Cohen et al. [31] found an increase in SARS-CoV-2-specific CD8+ effectors over time. In our case, we have explored the whole expanded CD8+ effectors and CD8+ effector memory T cells population and cannot confirm if there was a larger fraction of antigen-exposed, i.e., SARS-CoV-2-specific T cells, among the population.
We found that all COVID-19 patients developed effectors T cells and effector memory T cells, which increased over time. Our findings are in accordance with other studies that have shown that SARS-CoV-2 infection results in increased expansion of antigen-specific CD4+ and CD8+ T cell subsets [41,42]. It is still unclear if the lower antigen-specific responses seen at one month compared to 6-7 months are due to an overall immunosuppression [43] or a natural development of the immune response over time [44].
At present, all immunocompetent individuals develop SARS-CoV-2-specific antibodies, which is also evident in our study. Some studies provide clear evidence that these antibodies are detected only for a few months after infection [45,46], whereas others support the detection for a minimum of 6 months [47,48]. In our cohort, we found that the increase in B cells lasted for 6-8 months post infection, even though there was a drastic decline at some time point after 6 weeks. Our findings are like those by Björkander et al. [42], who have reported that the antibody responses lasted up to 8 months among young adults. Even if the antibody levels are waning, the affinity maturation will continue and the SARS-CoV-2-specific humoral immunity will have the ability to provide protection against severe disease, and these antibodies could have increased potency to neutralize the virus [49].
With the continued burden of the current COVID-19 pandemic on the population, there is still a need for more insight into the SARS-CoV-2-specific immune response elicited during infection. Despite having multiple approved and licensed vaccines, the emergence of variants with multiple mutations [50], and the long list of long-term symptoms following a natural SARS-CoV-2 infection [51-53], are still cause for great concern. Further, given the likely impact of inter-human variations in clinical parameters, more data is needed regarding the durability and sustenance of SARS-CoV-2-specific antibodies and T cells generated during
COVID-19 and their contribution to the quality of immune responses and what is the lasting effect on the immune cell compartment in individuals who that have recovered from COVID-19.
Despite the immensely challenging conditions during the pandemic, we do believe that the cohort presented in this investigation is well characterized and of high quality and value.
Altogether, this study highlights the alterations in the immune response which occur during hospital treated SARS-CoV-2 infection and convalescence. These novel longitudinal data illustrate the substantial changes to the T cell landscape lasting for more than 6 months. Our findings, in combination with others, are valuable in providing insight into SARS-CoV-2 cellular and humoral immunity, and open new avenues to be explored for improved understanding of the long-term alterations described herein in COVID-19 immunopathogenesis.