key: cord-0962665-u2j1ng8p
authors: Mattoo, Sameer-ul-Salam; Myoung, Jinjong
title: T cell responses to SARS-CoV-2 in humans and animals
date: 2022-02-14
journal: J Microbiol
DOI: 10.1007/s12275-022-1624-z
sha: a23938d6daf4e8953af36a8ab601a785b1d2ab3f
doc_id: 962665
cord_uid: u2j1ng8p

SARS-CoV-2, the causative agent of COVID-19, first emerged in 2019. Antibody responses against SARS-CoV-2 have been given a lot of attention. However, the armamentarium of humoral and T cells may have differing roles in different viral infections. Though the exact role of T cells in COVID-19 remains to be elucidated, prior experience with human coronavirus has revealed an essential role of T cells in the outcomes of viral infections. Moreover, an increasing body of evidence suggests that T cells might be effective against SARS-CoV-2. This review summarizes the role of T cells in mouse CoV, human pathogenic respiratory CoV in general and SARS-CoV-2 in specific.

Coronaviridae, a family of enveloped single-stranded RNA viruses, consists of two sub-families Orthocoronavirinae and Letovirinae (Pillaiyar et al., 2021; Zhou et al., 2021) . Orthocoronavirinae is divided into four genera: Alpha, Beta, Gamma, and Deltacoronavirus. Betacoronavirus includes mouse corona virus (mouse-CoV or mouse hepatitis virus, MHV), severe acute respiratory syndrome coronavirus corona virus 1 (SARS-CoV-1), Middle East respiratory syndrome-CoV (MERS-CoV) and SARS-CoV-2. Mouse-CoV has been adopted as a model to study human CoV (Körner et al., 2020) . The infection with the human CoV is commonly associated with mild respiratory symptoms. However, the emergence of beta subgroup CoV strains, including SARS-CoV-1, MERS-CoV, and SARS-CoV-2, highlights the potential of CoV to cause severe respiratory and systemic disease (Van Der Hoek et al., 2004; Sariol and Perlman, 2020; Grabherr et al., 2021) . SARS-CoV-1-infected individuals were first reported in 2002 with approximately 8100 reported cases (Peng et al., 2003; Zhao et al., 2003; Sariol and Perlman, 2020) . MERS-CoV was identified in 2012 with approximately 2,500 confirmed cases (Zaki et al., 2012) . Recently on December 31, 2019, pneumonia caused by an unknown cause was stated to world health organization (WHO), which was later called Coronavirus disease 2019 , of which causative agent is SARS-CoV-2 , a highly contagious novel CoV (Hartley et al., 2020) . In January 2020, World Health Organization declared COVID-19 an international public health emergency. As of November 29, 2021, more than 260 million people have been infected and more than 5.0 million deaths have been reported worldwide (WHO, 2021) . All these three strains, including SARS-CoV-1, MERS-CoV, and SARS-CoV-2, can cause severe pneumonia (Cleri et al., 2010; Naeem, 2013; Wang et al., 2020; Yang et al., 2020) . However, SARS-CoV-1 and MERS-CoV have limited person-to-person transmission, eventually resulting in a lower number of confirmed cases (Sariol and Perlman, 2020) , compared with SARS-CoV-2. Antibody responses induced in patients previously infected with influenza A virus or SARS-CoV-1 tends to be short-lived (Tang et al., 2011) . In contrast, memory T cells can be detected even after 6 years of infection in SARS-CoV-1 recovered patients. An understanding of SARS-CoV-2-specific T cell responses and more importantly how this particular arm of immune system can be improved to develop more efficient vaccines is the need of the hour.

This review provides a brief summary of roles of CD4 + and CD8 + T cells in mouse-CoV, MERS-CoV and SARS-CoV-1, and then explores roles of different T cells in SARS-CoV-2 in animal models and humans.

mice, resistant to mouse-CoV, possess dominant mouse-CoV (MHV-1) specific CD8 + T cells both in the breadth and magnitude (Khanolkar et al., 2010) , predicting the protective role of CD8 + T cells. Moreover, in CD8 + T cell-depleted mice, antibody response plays a minimal role in controlling the infection (Williamson and Stohlman, 1990) . CD8 + T cells expressing CCR7 sense the expression of CCR7 ligands at the site of inflammation (central nervous system) induced by challenging C57BL/6 intranasally with mouse-CoV (MHV A59) (Cupovic et al., 2016) . Moreover, polyfunctional CD8 + T cells were demonstrated to be critical for the successful elimination of the virus. On the other hand, CD4 + T cells provide crucial helper functions in optimizing activation and antiviral properties of CD8 + T cells (Phares et al., 2012) and resistance to mouse-CoV (MHV-3) requires Th1 development (Liu et al., 1998) . However, in some strains of mouse-CoV, elevated immune response can be deleterious. For example, in contrast to MHV-A59 and MHV-JHM, MHV-1 induced severe lung damage, which correlated better to the elevated inflammatory immune responses than to viral replication in the lung, predicting that the damage is mainly immunopathological (Leibowitz et al., 2010) .

Protective role of T cells against SARS-CoV-1 has been analyzed (Zhao et al., 2010; Channappanavar et al., 2014) . CD4 + T cell-depleted BALB/c mice show delayed clearance of SARS-CoV-1 from the lungs (Chen et al., 2010) . Although SARS-CoV-1-specific CD4 + T cells and antibody responses were necessary for complete protection, CD8 + T cell response was critical to protect C57BL/6 mice from lethal SARS-CoV-1 (MA15, mouse-adapted strain) infection (Channappanavar et al., 2014) . Adoptive transfer of serum from vaccinated (Venezuelan equine encephalitis replicon particles expressing MERS-CoV spike [S]-protein, VRP-S) BALB/c mice to naive mice 1-day before challenge significantly reduced the viral load as early as 1-day post-challenge (DPC) . However, in contrast to B cell knockout (μMT), T cell knockout (TCRα-/-KO) or SCID BALB/c mice did not clear MERS-CoV, suggesting a more important role played by T cells in the protection against viral infection. SARS-CoV-1-specific T cell responses have been analyzed in peripheral blood mononuclear cells (PBMCs) of human convalescents by using overlapping peptides covering the whole proteome of the virus (Li et al., 2008) . These specific T cells were shown to be essential for the clearance of infected cells, especially in the lungs (Gu et al., 2005) . In contrast to waning antibody and memory B cell responses, durable and long-lived memory T cell responses has been detected in recovered patients (Chen et al., 2005; Peng et al., 2006; Yang et al., 2006 Yang et al., , 2007 Fan et al., 2009; Oh et al., 2011; Tang et al., 2011; Da Guan et al., 2015; Ng et al., 2016) . A strong MERS-CoV S-protein-specific T cell response was described in a patient on the 24th-day post symptom onset (PSO) (Da Guan et al., 2015) . Th1-associated cytokines (IL-2 and IFN-γ) have been reported to decrease in a fatal case compared to a patient who survived the infection (Faure et al., 2014) , implying the importance of the development of effective T cell responses in combating the disease.

Parts of antigens that are specifically recognized by lymphocytes are called determinants or epitopes. HLA class I and HLA class II restricted epitopes are generally 8 or 11 and 13-17 residues long, respectively, although longer and shorter epitopes have also been defined. In the context of SARS-CoV-2, a variety of screening methodologies have been used to identify specific epitopes, including varying size of epitopes, evaluation of responses either directly ex vivo or after an in vitro culture re-stimulation, and various readout types (ELISA, ELISpot, AIM, ICS, tetramer staining, or mass spectrometry) Pan et al., 2021) . A detailed Fig. 1 . SARS-CoV-2 specific CD4 + and CD8 + T cell immunodominant epitopes in humans. The dominant epitopes (≥ 50% individuals responded to a specific epitope in a particular study, and at least 3 individuals responded) were summarized from multiple studies (Keller et al., 2020; Shomuradova et al., 2020; Nelde et al., 2021; Nielsen et al., 2021; Saini et al., 2021; Tarke et al., 2021) . Text in italics and bold represents frequently reported immunodominant epitopes in the literature. $ review of SARS-CoV-2 human T cell epitopes has been done . Numerous peptides have been reported to be immunodominant in several studies mainly because each study used different subjective criteria of immunodominance. For example, epitopes frequently targeted by T cells in 6 or more of the 34 participants (Peng et al., 2020) , 3 of 13 participants , immune responses induced in ≥ 50% of tested (Nelde et al., 2021; Saini et al., 2021) and so on. Of note, 3 peptides (open reading frame ORF1; TTDPSFLGRY, S; YLQPRTFLL, nucleocapsid N; SPRWY-FYYL) have been reportedly confirmed to be immunodominant in various studies Wellington et al., 2021) . Herein, we briefly summarize the dominant epitopes in SARS-CoV-2 as per the following definition (Nelde et al., 2021; Saini et al., 2021) : T cell reactivity to an epitope in ≥ 50% clinical samples (Fig. 1) .

In infected individuals, CD4 + T cells have been shown to recognize a range of SARS-CoV-2 antigens (Braun et al., 2020; Grifoni et al., 2020; Le Bert et al., 2020; Lucas et al., 2020; Peng et al., 2020; Thieme et al., 2020; Nelde et al., 2021; Sette and Crotty, 2021) . Overall, S, M, and N proteins contain higher numbers of CD4 + T cell epitopes than other viral proteins when assayed on PBMCs from SARS-CoV-2-infected subjects (Fig. 1A) . It is also worthy to note that the response was also directed against other viral proteins as well: nonstructural protein (Nsp)3, Nsp4, ORF3a, ORF8, ORF7a, and Nsp12. Similarly, CD8 + T cells are specific for a range of SARS-CoV-2 antigens (Braun et al., 2020; Gangaev et al., 2020; Grifoni et al., 2020 Grifoni et al., , 2021 Le Bert et al., 2020; Peng et al., 2020; Nelde et al., 2021; Saini et al., 2021) ( Fig. 1 ). In addition, polyfunctional CD8 + T cell responses directed against membrane/nucleocapsid (M/N)-proteins were broader than S protein (Peng et al., 2020) . Recently, Pan et al. (2021) identified CD8 + T cell epitopes in Nsp13 by using mass spectrometry. Of note, Nsp13 peptide-specific CTLs observed in the peripheral blood were able to recognize and lyse SARS-CoV-2-infected target cells. Although this study was not extensive, the identified epitopes are highly conserved, immunogenic, and presented by highly prevalent allelotypes. Furthermore, additional epitopes to these and other nonstructural proteins need to be sought, broadening the panel for T cellbased responses which would facilitate the development of effective subunit vaccines and T cell therapy in the future (Pan et al., 2021) . The pattern of SARS-CoV-2 antigens recognized (evaluated by IFN-γ ELISpot) appears to be similar (non-significant difference) during acute, convalescent, and memory phases (Rydyznski Moderbacher et al., 2020) . However, interestingly ORF7/8 specific cells may be more selective for acute phase than convalescent phase . The increased immunogenicity of ORF7/8 during early active phase of infection might be investigated further as the mechanism is not clearly understood, which can be due to accelerated selective expansion, preexisting immunity or some other reasons.

Presently different animal models are used to evaluate immune responses and pathogenicity of SARS-CoV-2, including mice expressing human angiotensin I-converting enzyme 2 (hACE2) (Muñoz-Fontela et al., 2020) and mice expressing mRNA-induced hACE2 receptor. Upon infection, hACE2 expressing mice showed CD4 + IFN-γ + and CD8 + IFN-γ + cells in the blood during a prime-boost infection (Hassert et al., 2020) . Mice vaccinated with VRPs expressing four structural proteins (S, N, M, or E), six accessory proteins (ORF3a, ORF6, ORF7a, ORF8, ORF9b, or ORF9c) or various T cell epitopes, showed that SARS-CoV-2-specific T cells (CD4 + and CD8 + T cells) were polyfunctional and were able to lyse peptideloaded target cells in vitro . In bronchoalveolar lavage (BAL) dominant CD4 + T cell epitopes were found in N protein and ORF3a in BALB/c (N351-365, ILLNKHIDAYKTFPP) and C57BL/6 mice (ORF3a266-280, EPIYDEPTTTTSVPL), respectively . In contrast, dominant CD8 + T cell epitopes were identified in S-protein in both BALB/c (S535-543, KNKCVNFNF) and C57BL/6 (S538-546, CVNFNFNGL) mice. In addition, VRPs expressing only immunodominant T cell epitopes partially protected the mice in the absence of neutralizing antibodies, hinting on the protective roles of T cells. For example, IFNγ + CD4 + /CD8 + T cells induced by VRP-N351-365 or VRP-S-538-546 vaccination partially protected mice from severe disease and these cells peaked at 8-10 DPC in airway, lung tissue, draining lymph nodes (DLNs) and spleens. On the other hand, in rhesus macaques, CD4 + central memory T cells were significantly induced at 5 days post re-challenge (DPR) in lymph nodes compared with 5 days post-infection (5 DPI) (Deng et al., 2020) . Moreover, activated CD8 + T cells were significantly increased in blood at 14 DPI and 28 DPI compared to 0 DPI, when they were re-challenged. On rechallenging Macaques mulatta, which have been depleted of CD8 + T cells after primary challenge, displayed breakthrough virus shedding in nasal swabs irrespective of CD8α or CD8β depletion. These data demonstrate virus-specific T cells responses play a protective role against the virus (Mc-Mahan et al., 2021) .

SARS-CoV-2-specific CD4 + T cells have been shown to differentiate into Th1 and Tfh T cells Neidleman et al., 2020; Weiskopf et al., 2020) . Th1 have antiviral properties and Tfh are specialized in providing help to B cells and thus are pivotal for the development of neutralizing antibodies and memory B cells. While Th2 cells are associated with lung immunopathology in SARS-CoV-1 infection (Deming et al., 2006; Yasui et al., 2008) , the dominant cytokine produced by SARS-CoV-2-specific CD4 + T cells was IFN-γ followed by TNF and IL-2 which is a signature of canonical Th1 cell activation Weiskopf et al., 2020) . It was further demonstrated that virus-specific CD4 + and CD8 + T cells were detectable in approximately 100% and 70-80% of convalescents . A similar trend in CD4 + and CD8 + T cells has been seen in acute cases. For example, a study of 10 COVID-19 patients with moderate to severe ARDS, requiring invasive mechanical ventilation, SARS-CoV-2 S-protein-specific CD4 + and CD8 + T cells were detected in 10 and 8 patients, respectively . CD4 + T cell responses were predominantly Th1 type, however, relatively lower Th2 and Th17 cytokines were also detected. In contrast, reported negligible Th2-or Th17-related cytokines in convalescents. In consistent with notion, a study (n = 9), which detected SARS-CoV-2-specific T cells with CyTOF, demonstrated that S-specific peripheral Th2 and Th17 cells were not detected in convalescents from mild disease (Neidleman et al., 2020) . SARS-CoV-2-specific CD8 + T cells possess high levels of effector molecules, including IFN-γ, granzyme B, perforin, and CD107a (Rydyznski Moderbacher et al., 2020; Sekine et al., 2020; Schulien et al., 2021) . Early after the emergence of COVID-19, several studies reported an exhausted phenotype, including programmed cell death protein-1 (PD-1) expressing CD8 + T cells in COVID-19 patients Diao et al., 2020; Mahmoudi et al., 2020) . However, PD-1, a T cell inhibitory receptor, can be upregulated by T cell receptor-induced activation, which likely reflects activation rather than functional exhaustion (Wherry and Kurachi, 2015; Singer et al., 2016; . Other studies demonstrated that in COVID-19 T cells are activated rather than exhausted (Sekine et al., 2020; Jung et al., 2021; . T cells in asymptomatic, mild and moderate COVID-19: SARS-CoV-2-specific T cells were functionally superior in asymptomatic individuals compared with symptomatic COVID-19 patients (Le . For example, T cells secreted higher levels of IFN-γ and IL-2 and a well-coordinated production of pro-inflammatory (IL-6, TNF-α, IL-1β) and regulatory cytokines (IL-10) than T cells from symptomatic COVID-19 patients. In a recent study, it was shown that preexisting replication transcription complex (RTC: Nsp7, Nsp12, and Nsp13)-specific T cells were enriched and expanded in vivo in seronegative health care workers (SN-HCW, repeatedly remained negative by PCR, antibody binding, and neutralization tests) with abortive infection (confirmed by interferoninducible transcript IFI27 in the blood, a robust early innate signature of SARS-CoV-2) (Swadling et al., 2021) . SN-HCW had memory T cells more frequently directed against the RTC, in contrast to structural protein-dominated responses in individuals with detectable infection. By contrast, the group with serologically confirmed infection showed no significant increase in RTC-specific T cells. The presence of virus-specific CD8 + T cells has been associated with better COVID-19 outcomes Rydyznski Moderbacher et al., 2020; Neidleman et al., 2021; Sette and Crotty, 2021) . Compared to S-protein, M/N-specific specific polyfunctional (IFNγ, TNF, and IL-2) CD8 + T cells were considerably higher in proportion in mild cases than in severe cases (Peng et al., 2020) . Another study showed that SARS-CoV-2 specific CD4 + and CD8 + T cells both were associated with less severe disease (Rydyznski Moderbacher et al., 2020) . Moreover, one COVID-19 patient resolved infection without hospitalization, who had no detectable neutralizing antibodies, but SARS-CoV-2-specific CD4 + and CD8 + T cells were present. Another study showed that recovered individuals had elevated and increasing numbers of SARS-CoV-2-specific T cells capable of homeostatic proliferation compared with individuals who succumbed (Neidleman et al., 2021) .

The number of CD4 + and CD8 + T cells were lower in severe COVID-19 cases than in moderate cases . Lower frequencies of IFN-γ-secreting cells in both early stages (day 1-15) and late stages (day 15-30) were reported in moderate/severe COVID-19 patients compared with mild cases . Moreover, one patient who died had no detectable IFN-γ-secreting cells until day 26 when stimulated with the different peptide pools. In contrast, studies have also shown that magnitude of T cells was not associated with recovery in critical COVID-19 cases (Schub et al., 2020; Weiskopf et al., 2020) . SARS-CoV-2 specific T cells in severe COVID-19 may have restricted functionality despite high magnitude. For example, the total percentage of SARS-CoV-2-specific polyfunctional CD4 + T cells (producing IFN-γ, TNF-α, and IL-2) was significantly lower in ICU patients than convalescents (Schub et al., 2020) (Fig. 3) . In contrast, it was also observed that CD4 + and CD8 + T cell responses of deceased or critical COVID-19 patients were robust and comparable or even higher than patients with moderate disease (Thieme et al., 2020) . A severe infection with a more robust immunogenic environment provided by a higher viral burden and inflammatory bystander activation might lead to a higher magnitude and functionality of the T cell (Thieme et al., 2020) . Marked Lymphopenia is a more prominent feature in patients with severe COVID-19 Zhang et al., 2021) . It is believed that T cells might be more robustly recruited to the lungs in severe COVID-19. In this context, T cells in lungs and blood might be analyzed in parallel from the same patients at specific time points. Lung residential memory T cells (T RM ) were shown to be critical mediators for protection against secondary viral infections (Schenkel and Masopust, 2014) . For example, Influenza A virus-specific lung T RM provided potent protection against heterosubtypic influenza challenge, although transient (Pizzolla and Wakim, 2019) . In the context of COVID-19 little is known about T RM . However, studies have reported functional T RM in the lung and nasal tissue (Liao et al., 2020; Grau-Expósito et al., 2021; Roukens et al., 2021; Szabo et al., 2021) . In COVID-19 patients, airway T cells characterized by a resident memory T cells phenotype exhibited protective profiles (Szabo et al., 2021) . Higher frequencies of these cells were seen in younger individuals who survived the infection compared to older who succumbed (Liao et al., 2020) . Additionally, in severe cases of COVID-19, 'immunological misfiring' might result in maladapted immune responses associated with severe clinical outcomes and poor prognosis (Lucas et al., 2020) . Moreover, there are indications of alterations in T cell activation and/or differentiation. Firstly, increased expression levels of exhaustion markers (PD-1, TIM3, LAG3, CTLA4, NKG2A, and CD39) have been reported in patients with COVID-19, particularly in those with severe disease Diao et al., 2020; Laing et al., 2020; Song et al., 2020; Zheng et al., 2020a Zheng et al., , 2020b . However, the expression of these receptors could also indicate recent activation (reviewed by Rha and Shin [2021] ). Briefly, reported that PD-1 expressing S269-specific memory CD8 + T cells were active and not exhausted in acute or convalescent cases, regardless of disease severity. Other studies reported hyper-activated CD8 + T cells with increased cytotoxicity rather than inhibited in severe cases. For example, in mild, severe, and critical cases, peripheral CD8 + T cells decreased in number with a compensatory increase in their cytotoxic potential (evaluated by granzyme A, granzyme B, and perforin expression) (Jiang et al., 2020) . Another study, which employed single-cell RNA sequencing on nasopharyngeal and bronchial samples, reported that critical disease severity correlated with stronger interaction between epithelial cells and hyper-activated CD8 + likely contributing to aggravated epithelial cell death (Chua et al., 2020) . Neidleman et al. (2021) reported that escalation of activated lung homing bystander CD4 + /CD8 + CXCR4 + was associated with fatal COVID-19 outcomes. In contrast, a larger proportion of CD8 + T cells with T RM characteristics were present in BAL from patients with moderate disease compared to severe COVID-19 (Liao et al., 2020) . These studies demonstrate that peripheral blood and lung residential T cells might function in a coordinated manner against SARS-CoV-2 (Fig.  3) . However, the exact differential role of T cells in asymptomatic, mild, moderate, and severe/critical cases remains to be elucidated.

On infection DCs uptake virus/viral particles during their migration to lung-draining lymph node a). Mature and activated DCs activate Tnaive to TE b) and c). TE migrate to the lung d). TE can further differentiate into TRM and TEM e). Where ND = not determined, TE = effector T cell, TEM = effector memory T cell and TRM = residential memory T cell.

body responses (B cell) leads to an effective clearance of SARS-CoV-2. CD4 + and CD8 + T cells peak in the acute phase of infection after which the frequency of cells decreases and maintains a stable level in the memory phase. Memory T cells have been reported to be polyfunctional, able to synthesize IFN-γ, IL-2 or TNF-α on re-stimulation. These cells can supplement memory B cells, which peak for at least 4-8 months before reaching a plateau, for effective formation of plasma cells. The memory phase cells might be strongly responsive to re-infection, ultimately limiting the viral replication and disease progression. Recall response? has not been evaluated yet in the context of COVID-19. Where dotted gray and purple lines represent that the specific memory B and T cells have not been evaluated after 8 and 12 months, respectively.

: SARS-CoV-2 T cells have been detected as early as Day 1 PSO (evaluated by MHCtetramer staining) (Schulien et al., 2021) with other studies (assessed by IFN-γ producing T cells by ELISpot) reporting 3-5 days PSO Tan et al., 2021 ). An early induction (< 10 days PSO) of SARS-CoV-2-specific T cells has been reported in milder cases . CD4 + and CD8 + T cells show differential kinetics in the contraction phase: CD8 + T cells display signs of progressive reduction after viral clearance while CD4 + T cells were more stable during 1-3 months PSO (Rydyznski . However, after an initial contraction phase , polyfunctional (IFN-γ, IL-2, and/or TNF-α-secreting) T cells remained detectable for at least 6-12 months PSO (Breton et al., 2021; Cohen et al., 2021; Dan et al., 2021; Le Bert et al., 2021; Lu et al., 2021) . Polyfunctional T cells have been observed more frequently in convalescents with milder symptoms while severe and critical patients tend to have restricted functional T cells (1-2 months PSO) (Schub et al., 2020) . On re-infection, memory T and B cells can be responsive and supplement each other in the viral clearance (Fig. 2) . Immunological memory provides rapid protection against re-infection. Memory T cells can be classified as T residential memory (T RM , CCR7 + CD45RA -, reside at the site of infection), T central memory (T CM , CCR7 + CD45RA -, circulate in the blood and home in lymphoid organs), T effector memory (T EM , CCR7 -CD45RA -, circulate in the blood and home in non-lymphoid organs) and effector memory re-expressing CD45RA (T EMRA , CCR7 -CD45RA + , circulate in the blood ) (Seder and Ahmed, 2003; Tian et al., 2017; Gray et al., 2018; Martin and Badovinac, 2018) . In contrast to T RM , which might be playing an important role in the clearance of SARS-CoV-2 (discussed in section 'T cells in asymptomatic, mild and moderate COVID-19'), several studies have been performed on peripheral blood T cell subsets in COVID-19 individuals. These cells are composed of naive (Tnaive), T CM , T EM , and T EMRA phenotypes (Breton et al., 2021; Cohen et al., 2021; Dan et al., 2021; Lu et al., 2021; Schulien et al., 2021) , and early (CD27 + CD28 + ) or intermediate (CD27 + CD28 − ) differentiation phenotypes (Peng et al., 2020) . The presence of a minor Tnaive subset fraction (median, 3.9%) of CD8 + T cells supports the notion that most of these cells have been efficiently primed during the infection (Schulien et al., 2021) . Another study reported that SARS-CoV-2-specific MHC-I tetramer + CD8 + T cells exhibited an early differentiated memory phenotype (CCR7 + CD127 + CD45RA -/+ TCF1 + ) in convalescents (Sekine et al., 2020) . This phenotype of cells was associated with stem cell-like properties. Of note, stem celllike memory T cells (T SCM ) have the ability of self-renewal and multipotency to repopulate the broad spectrum of memory and effector T cell subsets (Gattinoni et al., 2011 (Gattinoni et al., , 2017 . Moreover, T SCM (CCR7 + CD45RA + CD95 + ) cells in COVID-19 convalescents displayed poly-functionality and proliferation capacity during a 10-month follow-up period (Jung et al., 2021) , suggesting that these memory T cells might be longliving. Moreover, in this study SARS-CoV-2-specific T cell memory was maintained regardless of disease severity. In a study comparing T cell responses in prolonged SARS-CoV-2 positive (PP) clinically recovered (CR) and healthy donors, the CD8 + T E /T EM cell frequency and number was significantly lower in PP compared with CR patients . The suppressed CD8 + T cell differentiation in PP was likely to be associated with prolonged infection, demonstrating the importance of CD8 + T cells in virus clearance. Moreover, SARS-CoV-2 N protein-specific IFN-γ + T cell response in the PP cohort was significantly weaker than that in the CR cohort. Whether T cell kinetics vary among SARS-CoV-2 strains, and different proteins/epitopes induce different T cell kinetics remains to be evaluated. As described previously, Tan et al. (2021) reported that in mild cases, T cells specific for ORF7 and OFR8 were induced early and were more robustly detected in the early phase of infection. Nevertheless, these claims need to be evaluated in a larger population to reach a sound conclusion. Summary of different methodologies used to evaluate the T cells in acute and convalescent individuals having asymptomatic, mild moderate severe or critical COVID-19 has been provided in Table 1 .

In mRNA (Sahin et al., 2020) , adenovirus vector-based vaccines (Swanson et al., 2021) , and protein subunit vaccines (Keech et al., 2020) a Th1-skewed response with little to no Th2 cytokine profile has been detected, while Tfh and CD8 + T cells have also been detected in vaccinated individuals (Sahin et al., 2020; Koutsakos et al., 2021; Painter et al., 2021; Sette and Crotty, 2021) . T cell responses in COVID-19 mRNA vaccinees showed memory phenotypes, with a preference for T CM and T EM for CD4 + and T EM and T EMRA for CD8 + T cells (Guerrera et al., 2021; Tarke et al., 2021) , which were detectable for at least 6-months-PSO (Guerrera et al., 2021) . Moreover, vaccination also induced CD4 + and CD8 + T SCM . T cell responses induced by vaccines are supposed to recognize SARS-CoV-2 variants (Geers et al., 2021; Tarke et al., 2021) . For example, the CD4 + /CD8 + T cell reactivity in vaccinated individuals was not significantly reduced by mutations in B.1.1.7 and P.1 (Jordan et al., 2021; Tarke et al., 2021) . However, decreases of 14% and 22% were observed with the B.1.351 S-pools for CD4 + and CD8 + T cells, respectively. As discussed somewhere, multiple T cell epitopes are distributed across viral proteins including structural, nonstructural, and accessory proteins which makes evasion of viruses from T cell responses more difficult than neutralizing antibody responses (Noh et al., 2021) . The vast majority of CD4 + and CD8 + T cell epitopes were not affected by mutations found in different SARS-CoV-2 variants (Tarke et al., 2021) . Neutralizing antibodies, on the other hand, tend to target a restricted protein domain exposed on the virus surface, such as the S-protein of SARS-CoV-2. Currently, mRNA, adenovirus vector-based, and protein subunit vaccines rely on the S-protein as immunogen. Vaccines with multiple targets, including but not limited to the SARS-CoV-2 S-protein, are currently being developed and should elicit broad T cell responses (Noh et al., 2021) . These include a) protein-based vaccine, incorporating multiple CD4 + and CD8 + T cell epitopes selected from SARS-CoV-2 M, S2, and N proteins (NCT04683224); b) DNA platform vaccine, expressing S and N proteins (NCT04715997) or S and ORF3a proteins (NCT-04673149); c) adenovirus vector vaccines expressing S and N proteins (NCT04843722 and NCT04563702); d) chim-panzee adenovirus and self-amplifying mRNA vector vaccines expressing S-protein and additional T cell epitopes (NCT04776317); e) synthetic modified viral vectored vaccine, encoding S and N proteins (NCT04977024); f) peptide vaccines, using CD4 + or CD8 + T cell epitopes (NCT04885361 and NCT04954469).

Currently, most of the vaccines adopt the S-protein as immunogen for inducing immune responses against SARS-CoV-2 in humans (Corbett et al., 2020; Sahin et al., 2020; Liu et al., 2021) . However, CD8 + T cell immunodominant epitopes are also found in ORF1 and ORF3, their inclusion in the vaccines needs to be considered (Swadling et al., 2021; Wellington et al., 2021) . Moreover, in humans recovered from mild cases, multiple cytokine (IFN-γ, TNF or IL-2)-producing CD8 + T cells specific for M/N-proteins were higher in proportion compared with S-protein-specific cells, necessitating inclusion of M/N-proteins/epitopes for future vaccine studies (Peng et al., 2020) . A large body of evidence has been accumulated on the role of T cells in coronavirus infections both in mice and in humans. However, the role of T cells in combating SARS-CoV-2 needs to be further investigated in depth in animal models due to difficulty and scarcity of human tissue samples for analysis. Additionally, whether the presence of SARS-CoV-2-specific T cells forebode a bad prognosis in severe and critical cases need to be carefully investigated.

Currently, cell-mediated immune responses against SARS-CoV-2 have been studied mostly in peripheral blood. As such, detailed analysis of the role(s) of tissue resident T cells in the context of SARS-CoV-2 infections would shed light on their relative importance in viral clearance and/or pathology.

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19

Persistent cellular immunity to SARS-CoV-2 infection

Virus-specific memory CD8 T cells provide substantial protection from lethal severe acute respiratory syndrome coronavirus infection

Response of memory CD8 + T cells to severe acute respiratory syndrome (SARS) coronavirus in recovered SARS patients and healthy individuals

Cellular immune responses to severe acute respiratory syndrome coronavirus (SARS-CoV) infection in senescent BALB/c Mice: CD4 + T cells are important in control of SARS-CoV infection

Clinical and immunological features of severe and moderate coronavirus disease 2019

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis

Severe acute respiratory syndrome (SARS)

Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

Central nervous system stromal cells control local CD8 + T cell responses during virus-induced neuroinflammation

Characteristics of traveler with Middle East respiratory syndrome

Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection

Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

Vaccine efficacy in senescent mice challenged with recombinant SARS-CoV bearing epidemic and zoonotic spike variants

Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques

Reduction and functional exhaustion of T cells in patients with coronavirus disease 2019 (COVID-19)

Characterization of SARS-CoV-specific memory T cells from recovered individuals 4 years after infection

Distinct immune response in two MERS-CoV-infected patients: Can we go from bench to bedside?

Abstract S05-01: Profound CD8 T-cell responses towards SARS-CoV-2 OFR1ab in COVID-19 patients. AACR Virtual Meeting: COVID-19 and Cancer

A human memory T cell subset with stem cell-like properties

T memory stem cells in health and disease

SARS-CoV-2 variants of concern partially escape humoral but not T cell responses in COVID-19 convalescent donors and vaccine recipients

Insights into coronavirus immunity taught by the murine coronavirus

Peripheral and lung resident memory T cell responses against SARS-CoV-2

The roles of resident, central and effector memory CD4 T-cells in protective immunity following infection or vaccination

SARS-CoV-2 human T cell epitopes: adaptive immune response against COVID-19

Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals

Multiple organ infection and the pathogenesis of SARS

BNT162b2 vaccination induces durable SARS-CoV-2 specific T cells with a stem cell memory phenotype

Rapid generation of durable B cell memory to SARS-CoV-2 spike and nucleocapsid proteins in COVID-19 and convalescence

2020. mRNA induced expression of human angiotensin-converting enzyme 2 in mice for the study of the adaptive immune response to severe acute respiratory syndrome coronavirus 2

COVID-19 pneumonia: CD8 + T and NK cells are decreased in number but compensatory increased in cytotoxic potential

T cell immune responses to SARS-CoV-2 and variants of concern (Alpha and Delta) in infected and vaccinated individuals

SARS-CoV-2-specific T cell memory is sustained in COVID-19 convalescent patients for 10 months with successful development of stem cell-like memory T cells

Phase 1-2 trial of a SARS-CoV-2 recombinant spike protein nanoparticle vaccine

SARS-CoV-2-specific T cells are rapidly expanded for therapeutic use and target conserved regions of the membrane protein

T cell epitope specificity and pathogenesis of mouse hepatitis virus-1-induced disease in susceptible and resistant hosts

Of mice and men: the coronavirus MHV and mouse models as a translational approach to understand SARS-CoV-2

T follicular helper cells in the humoral immune response to SARS-CoV-2 infection and vaccination

A dynamic COVID-19 immune signature includes associations with poor prognosis

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection

SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

Genetic determinants of mouse hepatitis virus strain 1 pneumovirulence

T cell responses to whole SARS coronavirus in humans

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

Predicted cellular immunity population coverage gaps for SARS-CoV-2 subunit vaccines and their augmentation by compact peptide sets

Resistance of naive mice to murine hepatitis virus strain 3 requires development of a Th1

Durability of SARS-CoV-2-specific T cell responses at 12-months post-infection

Longitudinal analyses reveal immunological misfiring in severe COVID-19

Immunologic features in coronavirus disease 2019: functional exhaustion of T cells and cytokine storm

Defining memory CD8 T cell

Correlates of protection against SARS-CoV-2 in rhesus macaques

Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity

Animal models for COVID-19

Middle East respiratory syndrome (MERS): an update

SARS-CoV-2-specific T cells exhibit phenotypic features of helper function, lack of terminal differentiation, and high proliferation potential

Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19

SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition

Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection

SARS-CoV-2 elicits robust adaptive immune responses regardless of disease severity. EBioMedicine 68, 103410. Noh

Engineering T cells specific for a dominant severe acute respiratory syndrome coronavirus CD8 T cell epitope

Rapid induction of antigen-specific CD4 + T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination

Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs

Epidemiological study on severe acute respiratory syndrome in Guangdong province

Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

Long-lived memory T lymphocyte responses against SARS coronavirus nucleocapsid protein in SARSrecovered patients

CD4 T cells promote CD8 T cell immunity at the priming and effector site during viral encephalitis

The recent outbreaks of human coronaviruses: a medicinal chemistry perspective

Memory T cell dynamics in the lung during influenza virus infection

PD-1-expressing SARS-CoV-2-specific CD8 + T cells are not exhausted, but functional in patients with COVID-19

Activation or exhaustion of CD8 + T cells in patients with COVID-19

Prolonged activation of nasal immune cell populations and development of tissue-resident SARS-CoV-2 specific CD8 + T cell responses following COVID-19

Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity

COVID-19 vaccine BNT162b1 elicits human antibody and T H 1T cell responses

SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8 + T cell activation in COVID-19 patients

Lessons for COVID-19 immunity from other coronavirus infections

Tissue-resident memory T cells

High levels of SARS-CoV-2-specific T cells with restricted functionality in severe courses of COVID-19

Similarities and differences in CD4 + and CD8 + effector and memory T cell generation

Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

Adaptive immunity to SARS-CoV-2 and COVID-19

SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors

A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

Immunological and inflammatory profiles in mild and severe cases of COVID-19

Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2

T-cell mediated immunity after AZD1222 vaccination: A polyfunctional spike-specific T H 1 response with a diverse TCR repertoire

Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19

Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients

Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study

Lack of peripheral memory B cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study

Impact of SARS-CoV-2 variants on the total CD4 + and CD8 + T cell reactivity in infected or vaccinated individuals

Robust T cell response toward spike, membrane, and nucleocapsid SARS-CoV-2 proteins is not associated with recovery in critical COVID-19 patients

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA

Identification of a new human coronavirus

Clinical characteristics of patients with severe pneumonia caused by the SARS-CoV-2 in Wuhan

Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome

Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol

Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2

Molecular and cellular insights into T cell exhaustion

COVID-19) Dashboard. Geneva: World Health Organization

Effective clearance of mouse hepatitis virus from the central nervous system requires both CD4 + and CD8 + T cells

Production of mice from a lethal coronavirus infection in the central nervous system by adoptive transfer of virus-specific T cell clones

Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients

Persistent memory CD4 + and CD8 + T-cell responses in recovered severe acute respiratory syndrome (SARS) patients to SARS coronavirus M antigen

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a singlecentered, retrospective, observational study

Characteristics of T-cell responses in COVID-19 patients with prolonged SARS-CoV-2 positivity -a cohort study

Prior immunization with severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) nucleocapsid protein causes severe pneumonia in mice infected with SARS-CoV

Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia

Peripheral T cell lymphopenia in COVID-19: potential mechanisms and impact

Rapid generation of a mouse model for Middle East respiratory syndrome

Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR

T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice

Functional exhaustion of antiviral lymphocytes in COVID-19 patients

Elevated exhaustion levels and reduced functional diversity of T cells in peripheral blood may predict severe progression in COVID-19 patients

The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Mapping and role of T cell response in SARS-CoV-2-infected mice

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2017R1A6A1-A03015876).

The authors declare that there are no conflicts of interest.