Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques.

SARS-CoV-2 infection presents clinical manifestations ranging from asymptomatic to fatal respiratory failure. Despite the induction of functional SARS-CoV-2-specific CD8+ T-cell responses in convalescent individuals, the role of virus-specific CD8+ T-cell responses in the control of SARS-CoV-2 replication remains unknown. In the present study, we show that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques. Eight macaques were intranasally inoculated with 105 or 106 TCID50 of SARS-CoV-2, and three of the eight macaques were treated with a monoclonal anti-CD8 antibody on days 5 and 7 post-infection. In these three macaques, CD8+ T cells were undetectable on day 7 and thereafter, while virus-specific CD8+ T-cell responses were induced in the remaining five untreated animals. Viral RNA was detected in nasopharyngeal swabs for 10-17 days post-infection in all macaques, and the kinetics of viral RNA levels in pharyngeal swabs and plasma neutralizing antibody titers were comparable between the anti-CD8 antibody treated and untreated animals. SARS-CoV-2 RNA was detected in the pharyngeal mucosa and/or retropharyngeal lymph node obtained at necropsy on day 21 in two of the untreated group but undetectable in all macaques treated with anti-CD8 antibody. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but our results indicate possible containment of subacute viral replication in the absence of CD8+ T cells, implying that CD8+ T-cell dysfunction may not solely lead to viral control failure.

Introduction

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread resulting in a major pandemic [1]. SARS-CoV-2 transmission occurs via the respiratory route, and the average incubation period from infection to symptom onset has been estimated to be 5 days [2]. SARS-CoV-2 infection presents a wide spectrum of clinical manifestations ranging from asymptomatic to fatal respiratory failure [3]. Multiple cofounding factors such as age and underlying diseases are associated with COVID-19 severity [4-8]. For instance, auto-antibodies against type I interferon have been reported to be associated with life-threatening COVID-19 pneumonia [9,10]. However, the exact determinants for failure in viral control and/or fatal disease progression have not been elucidated fully.

Most non-fatal COVID-19 cases show a limited period of detectable virus production in pharyngeal swabs peaking at around one week post-infection [11]. Host acquired as well as innate immune responses are involved in the control of viral replication [8,12-14]. Anti-SARS-CoV-2 neutralizing antibodies are induced in most infected individuals [13-16]. Recent clinical studies including those on convalescent plasma and/or monoclonal antibody administration have indicated efficacy of neutralizing antibodies against SARS-CoV-2 infection [17-20]. Animal studies have confirmed in vivo efficacy of neutralizing antibodies against infection [21-25]. Also, SARS-CoV-2-specific T-cell responses are induced in most non-fatal COVID-19 cases [26-28]. Current studies have indicated induction of functional virus-specific CD8+ T-cell responses in convalescent COVID-19 individuals, implying suppressive pressure of CD8+ T cells on SARS-CoV-2 replication [29,30]. Thus, both acquired immune effectors, antibodies and CD8+ T cells, are considered to contribute to viral control. However, it remains unknown whether a deficiency in either of these two arms is directly linked to failure in the control of SARS-CoV-2 replication. It has been reported that COVID-19 patients with agammaglobulinemia controlled disease progression, suggesting viral control even in the absence of antibody responses [31].

A previous study of anti-CD8 antibody administration prior to re-infection in rhesus macaques has indicated partial contribution of CD8+ T cells to protection against SARS-CoV-2 re-infection [25]. However, the requirement of CD8+ T cells for the control of virus replication after the establishment of infection remains unclear. In the present study, we investigated the effect of CD8+ cell depletion by monoclonal anti-CD8 antibody administration in the subacute phase on SARS-CoV-2 replication in cynomolgus macaques. Unexpectedly, our analysis revealed no significant impact of CD8+ cell depletion on viral replication, indicating that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells.

Results

Kinetics of SARS-CoV-2 infection in cynomolgus macaques after intranasal inoculation

Previous studies have shown that intranasal and intratracheal inoculation with 105 TCID50 (50% tissue culture infective doses) of SARS-CoV-2 results in the establishment of infection in rhesus macaques, with viral RNA detectable for more than a week post-infection in pharyngeal swabs [32,33]. In the present study, we first examined whether intranasal SARS-CoV-2 inoculation only can result in viral infection in cynomolgus macaques. In the first experiment, cynomolgus macaques were intranasally inoculated with 106 (exactly 7.5 x 105 in macaque N011), 105 (exactly 7.5 x 104 in macaques N012 and N013), or 104 (exactly 7.5 x 103 in macaque N014) TCID50 of SARS-CoV-2 (Table 1). Macaques N011, N012, and N013 showed similar levels of viral RNA in nasopharyngeal swabs on day 2, at the peak (Fig 1A). Viral RNA was also detected in throat swabs with a lower peak (Fig 1B). Viral RNA in nasopharyngeal swabs was detectable for approximately two weeks (up to: day 17 in N011, day 12 in N012, and day 14 in N013) after virus inoculation (Fig 1A, 1C and 1D). Subgenomic RNAs (sgRNAs) were also detected in nasopharyngeal and throat swabs, indicating viral replication (Fig 2A and 2B). SARS-CoV-2 sgRNAs were detected in nasopharyngeal swabs until day 9 in N011, day 7 in N012, and day 5 in N013 (Fig 2A, 2C and 2D). However, in macaque N014, which was inoculated with 104 TCID50 of SARS-CoV-2, sgRNAs were undetectable, and viral RNAs were detectable albeit at lower levels, only until day 5 in nasopharyngeal swabs (Figs 1A and 2A), indicating that 104 TCID50 is below the virus inoculum threshold to consistently induce detectable viral replication. N014 was subsequently excluded from further analyses.

Table 1

Macaque experimental protocol.

Group	Experimenta	Macaques	Gender	Age(yrs)	SARS-CoV-2 doseb(TCID50)	anti-CD8 AbTxc	Necropsyd
N	1	N011	male	6	106	NT	d21
N	1	N012	male	6	105	NT	d21
N	1	N013	male	6	105	NT	d21
-e	1	N014	male	6	104	NT	d21
N	2	N021	female	3	106	NT	d14
N	2	N022	female	3	105	NT	d21
D	2	D023	male	6	106	d5 & d7	d21
D	2	D024	male	6	105	d5 & d7	d21
D	2	D025	female	3	105	d5 & d7	d21

aTwo sets of experiments were performed using the same SARS-CoV-2 inoculum stock.

bMacaques were intranasally inoculated with the indicated doses (106 [exactly 7.5 x 105], 105 [exactly 7.5 x 104], or 104 [exactly 7.5 x 103] TCID50) of SARS-CoV-2 on day 0.

cMacaques in Group D were treated intravenously with anti-CD8 antibody on days 5 and 7 post-infection. NT, not treated.

dMacaques were euthanized and necropsied on day 14 or 21 post-infection.

eN014 was excluded from comparisons between groups N and D.

Fig 1

Viral RNA levels in swabs.

(A-D) Changes in viral RNA levels in nasopharyngeal (A, C, D) and throat (B) swabs after SARS-CoV-2 infection in all animals (A, B) or those infected with 106 (C) or 105 (D) TCID50 of SARS-CoV-2. The lower limit of detection was approximately 3 x 103 copies/swab. (E) Comparison of viral RNA levels in nasopharyngeal swabs at day 5 post-infection between 106 TCID50-infected and 105 TCID50-infected macaques. No significant difference was observed. (F) Comparison of viral RNA levels in nasopharyngeal swabs at days 5 (left), 7 (middle), and 9–12 (right) post-infection between Group N and D animals infected with 106 or 105 TCID50 of SARS-CoV-2. No significant difference was observed.

Fig 2

Viral subgenomic RNA levels in swabs.

Changes in viral sgRNA levels in nasopharyngeal (A, C, D) and throat (B) swabs after SARS-CoV-2 infection in all animals (A, B) or those infected with 106 (C) or 105 (D) TCID50 of SARS-CoV-2. The lower limit of detection was approximately 3 x 103 copies/swab.

In the second experiment, two (N021 and D023) and three (N022, D024, and D025) macaques were intranasally inoculated with 106 and 105 TCID50 of SARS-CoV-2, respectively (Table 1). Monoclonal anti-CD8 antibody was administered intravenously on days 5 and 7 to three (D023, D024, and D025 in Group D) of the five macaques. All of the five macaques in the second experiment showed comparable levels of viral RNAs and sgRNAs in nasopharyngeal swabs on day 2 compared to the three macaques inoculated with 106 or 105 TCID50 of SARS-CoV-2 in the first experiment (Figs 1A and 2A). Indeed, no significant difference in RNA levels in nasopharyngeal swabs on day 5 was observed between the first three and the second five animals (Fig 1E). No clear difference in viral loads in either nasopharyngeal or throat swabs on days 2 and 5 was observed between macaques inoculated with 106 (n = 3) and 105 (n = 5) TCID50 of SARS-CoV-2 (Figs 1C, 1D, 2C and 2D). Viral RNA in nasopharyngeal swabs was detectable until day 14 in N021 and day 10 in N022 following inoculation (Fig 1A, 1C and 1D). SARS-CoV-2 sgRNAs in nasopharyngeal swabs were detected until day 5 in N021 and day 7 in N022 following inoculation (Fig 2A, 2C and 2D). Collectively, in the first and second experiments, intranasal inoculation of cynomolgus macaques with 106 or 105 TCID50 of SARS-CoV-2 resulted in viral replication with viral RNA detectable for 10–17 days in nasopharyngeal swabs.

Kinetics of SARS-CoV-2 infection after CD8+ cell depletion

We then investigated the effect of CD8+ cell depletion on viral replication in the subacute phase of SARS-CoV-2 infection. In the three Group D macaques administered with anti-CD8 antibody on days 5 and 7, CD8+ T cells were undetectable in peripheral blood on day 7 and thereafter (Fig 3). These three macaques showed comparable levels of viral RNA in nasopharyngeal swabs before (day 5) and after (day 7) anti-CD8 antibody treatment compared to the five untreated Group N macaques (Fig 1F). Viral RNA in nasopharyngeal swabs was detectable until day 10 in D025 and day 14 in macaques D023 in D024 after virus inoculation (Fig 1A, 1C and 1D). Viral sgRNAs in nasopharyngeal swabs were detected until day 2 in D023, day 5 in D024, and day 7 in D025 (Fig 2A, 2C and 2D). Collectively, no clear difference in viral RNA levels in swabs was observed for the three anti-CD8 antibody-treated Group D versus the five untreated Group N macaques.

Fig 3

Peripheral blood B- and T-cell frequencies.

Changes in %CD3+, %CD3+CD4+, %CD3+CD8+, and %CD3-CD20+ T cells in macaque PBMCs after SARS-CoV-2 infection.

We also examined whether virus could be recovered from individual swab samples (Table 2). SARS-CoV-2 was recovered from nasopharyngeal and throat swabs from all eight animals intranasally inoculated with either 106 or 105 TCID50. Virus was recovered for 2–12 days in anti-CD8 antibody-untreated macaques (until day 2 in N021, day 5 in N013 and N022, day 7 in N011, and day 12 in N012) and for 2–7 days in anti-CD8 antibody-treated macaques (until day 2 in D024 and day 7 in D023 and D025). There was no indication of enhanced virus recovery after CD8 cell depletion.

Table 2

Virus recovery from pharyngeal swabs after SARS-CoV-2 infection.

Macaques	Virus recovery from swabsa
	d0	d2	d5	d7	d9/10	d12	d14	d17	d21
N011	-	+	+	+	-	-	-	-	-
	-	+	+	-	-	-	-	-	-
N012	-	+	+	+	-	+	-	-	-
	-	+	-	-	-	-	-	-	-
N013	-	+	-	-	-	-	-	-	-
	-	+	+	-	-	-	-	-	-
N014	-	-	-	-	-	-	-	-	-
	-	+	-	-	-	-	-	-	-
N021	-	+	-	-	-	-	-	-	-
	-	+	-	-	-	-	-	-	-
N022	-	+	+	-	-	-	-	-	-
	-	+	-	-	-	-	-	-	-
D023	-	+	-	+	-	-	-	-	-
	-	+	-	-	-	-	-	-	-
D024	-	+	-	-	-	-	-	-	-
	-	+	-	-	-	-	-	-	-
D025	-	+	+	+	-	-	-	-	-
	-	+	+	-	-	-	-	-	-

aSwab samples were added to Vero E6/TMPRSS2 cell culture to recover infectious virus. + indicates successful virus recovery from nasopharyngeal (upper row) or throat (lower row) swabs for each animal.

Macaque N021 was euthanized on day 14, while the remaining animals were euthanized on day 21 post-infection (Table 1). Examination of body temperature showed transient slight fever in some animals (on day 2 in N021 and D025; on day 6 in D023 and D024; on days 13–19 in N012) (S1 Fig). Histopathological analysis of the lung obtained at necropsy on day 14 in macaque N021 revealed mild or moderate pulmonary inflammation (S2 Fig), whereas no significant pathology in the lung was detected on day 21 in other animals.

RNA was extracted from the pharyngeal mucosa, retropharyngeal lymph nodes (RPLN), lung, intestine, and spleen obtained at necropsy, and subjected to RT-PCR for detection of viral RNA (Table 3). Viral RNA was undetectable in tissues from macaques N012, N014, N021, D023, and D024. However, viral RNA was detected in the RPLN of N011, in the pharyngeal mucosa, RPLN, and spleen of N013, and in the spleens of N022 and D025. Additionally, viral sgRNAs were also detectable in pharyngeal mucosa, RPLN, and spleen of N013. There was no evidence of enhanced viral replication in anti-CD8 antibody-treated macaques.

Table 3

Detection of viral RNA in tissues obtained at necropsy.

Macaques	Autopsy	Detection of viral RNA in tissuesa
		Pharyngeal mucosa	Retropharyngeal lymph node	Lung	Intestine	Spleen
N011	d21	-	+	-	-	-
N012	d21	-	-	-	-	-
N013	d21	+	+	-	-	+
N014	d21	-	-	-	-	-
N021	d14	-	-	-	-	-
N022	d21	-	-	-	-	+
D023	d21	-	-	-	-	-
D024	d21	-	-	-	-	-
D025	d21	-	-	-	-	+

aRNA was extracted from individual tissues and subjected to RT-PCR to detect SARS-CoV-2 RNA. + indicates detection of viral RNA.

Antibody and T-cell responses in macaques after intranasal SARS-CoV-2 inoculation

Anti-SARS-CoV-2 neutralizing antibody (NAb) responses were induced in all the macaques after intranasal SARS-CoV-2 inoculation (Fig 4) NAb responses were detected on day 7 in macaques N021 and D025 only, and in all animals on day 14. Macaques D025 and D024 exhibited the highest and lowest NAb titers, respectively. No clear difference in NAb responses was observed between the three anti-CD8 antibody-treated and the five untreated macaques.

Fig 4

SARS-CoV-2-specific neutralizing antibody responses.

Changes in plasma anti-SARS-CoV-2 neutralizing antibody titers post-infection in all animals (left) or those infected with 106 (middle) or 105 (right) TCID50 of SARS-CoV-2.

Finally, we examined CD8+ T-cell responses specific for SARS-CoV-2 spike (S), nucleocapsid (N), and membrane-and-envelope (M&E) antigens in the five anti-CD8 antibody-untreated macaques inoculated with 106 or 105 TCID50 of SARS-CoV-2. In the analysis using peripheral blood mononuclear cells (PBMCs), SARS-CoV-2-specific CD8+ T-cell responses were undetectable in macaque N013 but detected in the remaining four macaques (Fig 5A and 5B). Macaque N022 exhibited CD8+ T-cell responses on day 7 while the remaining three macaques (N011, N012, and N021) showed initial SARS-CoV-2 specific responses on day 14. Analysis using submandibular lymph nodes (SMLN) obtained at necropsy found SARS-CoV-2-specific CD8+ T-cell responses in macaques N011, N013, and N021 (Fig 5C). Interestingly, SARS-CoV-2-specific CD8+ T-cell responses were undetectable in PBMCs but detected in SMLN in macaque N013. Thus, SARS-CoV-2-specific CD8+ T-cell responses were detected in all the five anti-CD8 antibody-untreated Group N macaques inoculated with 106 or 105 TCID50 of SARS-CoV-2. Finally, CD8+ T-cell depletion was confirmed in SMLN obtained at necropsy from the anti-CD8 antibody-treated macaques (S3 Fig).

Fig 5

SARS-CoV-2-specific CD8+ T-cell responses.

(A) Representative gating schema for detection of IFN-γ induction after stimulation with overlapping M&E peptide pools in macaque N012 on day 14 post-infection. (B) Frequencies of CD8+ T cells targeting S, N, and M&E in PBMCs on days 7, 14, and 21 post-infection in Group N animals infected with 106 (middle) or 105 (right) TCID50 of SARS-CoV-2. (C) Frequencies of CD8+ T cells targeting S, N, and M & E in submandibular lymph nodes obtained at necropsy in macaques N011, N013, N021, and N022. Samples were unavailable for analysis in macaque N012.

Discussion

Host T-cell and B-cell responses have been reported to contribute to the control of SARS-CoV-2 replication [8,12,13,28]. In a murine model of infection with a mouse-adapted strain of SARS-CoV, depletion of CD4+ T cells resulted in reduced neutralizing antibody responses and delayed virus clearance from the lung [34]. Furthermore, SARS-CoV replication was controlled in the absence of CD4+ T and B cells, implicating CD8+ T cells in viral control [35]. Recent studies in humans have shown that functional virus-specific CD8+ T-cell responses are induced in convalescent COVID-19 individuals [29,30]. These reports suggest contribution of CD8+ T cells in the control of SARS-CoV-2 replication. However, it remains unclear whether SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells. In the present study, we investigated the impact of depletion of CD8+ cells (including CD8+ T cells) by anti-CD8 antibody administration on SARS-CoV-2 replication in the subacute phase after establishment of virus infection. Our results on viral RNA and virus recovery from pharyngeal swabs (Fig 2 and Table 2) indicate that viral replication was not contained when animals were treated with anti-CD8 antibody, while viral replication was controlled after the CD8+ cell depletion. We found no significant enhancement of viral replication or delay in viral clearance after CD8+ cell depletion, indicating that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells.

Our findings do not deny the contribution of CD8+ T cells in the control of SARS-CoV-2 replication or the possibility of viral protection by vaccine-induced CD8+ T cells. Virus-specific CD8+ T-cell responses were mostly undetectable at week 1 and became detectable at week 2 post-infection in the present study, which is consistent with a recent report on T-cell responses in the acute phase after onset in COVID-19 patients [29]. Thus, CD8+ T-cell responses may not play a central role in the control of peak viral load but could have a large impact on the containment of viral replication and/or disease progression after that in primary SARS-CoV-2 infection. Contribution of CD8+ T-cell responses to protection against re-infection has been suggested [25], implying that vaccine-induced CD8+ T-cell responses may enhance viral control in the acute phase. What is indicated in the present study is that CD8+ T-cell dysfunction is not directly linked to failure in viral control, possibly implying that there may be multiple arms of host immune mechanisms involved in containing primary SARS-CoV-2 replication.

An animal model for SARS-CoV-2 infection is necessary for analysis of pathogenesis and transmission and the evaluation of vaccines and anti-viral drugs. Non-human primate models are recognized as being the most clinically relevant because of their genetic and physiological similarities to humans. Recent studies have shown that rhesus and cynomolgus macaques can be infected with SARS-CoV-2 and exhibit clinical manifestations resembling human COVID-19 [32,36-38]. Both macaque species present mild to moderate forms of COVID-19, which is observed in the majority of the human population. We thus used a model of SARS-CoV-2 infection in cynomolgus macaques for analysis of the effect of CD8+ cell depletion on virus replication.

We attempted SARS-CoV-2 inoculation via the intranasal route only without intratracheal inoculation, because it may more closely reflect viral transmissions in humans. The geometric means of peak viral RNAs and sgRNAs in nasopharyngeal swabs (on day 2) were 2.7 x 108 (range: 1.1 x 108 to 5.2 x 108) and 1.0 x 106 (range: 1.8 x 105 to 1.8 x 106) copies/swab, respectively, which are equivalent to those in rhesus macaques inoculated both intranasally and intratracheally with 105 TCID50 of SARS-CoV-2 [32,33]. In macaques inoculated with 105 TCID50 (1.4 x 108 RNA copies) of SARS-CoV-2, viral RNA copies in nasopharyngeal swabs on day 2 were comparable (N012) to or greater (N013, N022, D024, and D025) than the total viral RNA copies in the inoculum, confirming viral replication in macaques even with 105 TCID50. The three macaques inoculated with 106 TCID50 showed similar levels of viral RNA in nasopharyngeal swabs on days 2 and 5 compared to the five macaques with 105 TCID50. All the eight macaques intranasally inoculated with 106 or 105 TCID50 of SARS-CoV-2 developed efficient anti-SARS-CoV-2 NAb responses, and the five anti-CD8 antibody-untreated macaques induced SARS-CoV-2-specific CD8+ T-cell responses. Taken together, our results show that intranasal inoculation of cynomolgus macaques with 106 or 105 TCID50 of SARS-CoV-2 results in viral replication in the pharyngeal mucosa. Containment of viral replication in the pharyngeal mucosa would be important for the control of further viral transmission as well as disease progression.

Our cynomolgus macaque model of intranasal but not intratracheal SARS-CoV-2 inoculation is considered to represent asymptomatic or mild COVID-19. However, histopathological analysis of the lung detected pulmonary inflammation in one animal (N021) on day 14 post-infection (S2 Fig), suggesting the potential of intranasal SARS-CoV-2 inoculation to induce moderate pulmonary diseases. Other animals may also have developed mild pulmonary inflammation detectable on day 14, which was resolved by day 21. Macaque N013 showed a unique phenotype with undetectable viral RNAs in swabs after day 14 (Fig 1D) but relatively higher levels of viral RNA in pharyngeal mucosa and submandibular lymph nodes on day 21 post-infection (Table 3). Virus-specific CD8+ T-cell responses were undetectable in PBMCs but efficiently detected in the submandibular lymph nodes on day 21 (Fig 5), suggesting localized virus replication in the pharyngeal mucosa.

The sample size used in this study is relatively limited (three anti-CD8 antibody treated animals and five untreated controls). However, these three animals exhibited similar levels of pharyngeal viral loads before the anti-CD8 antibody treatment, and again showed similar levels of viral loads after CD8+ cell depletion. Neither enhancement of viral replication nor delay in viral control was observed. Regarding the five anti-CD8 antibody untreated macaques, SARS-CoV-2-specific CD8+ T-cell responses were detected in all, although the magnitudes and kinetics of these responses were different. Therefore, this study provides sufficient evidence for our conclusion.

In summary, the present study showed that subacute viral replication can be controlled even in the absence of CD8+ T cells in primary SARS-CoV-2 infection. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but our results suggest that CD8+ T-cell dysfunction does not solely lead to viral control failure or disease progression.

Materials and methods

Ethics statement

Animal experiments were performed in the National Institute of Infectious Diseases (NIID) after approval by the Committee on the Ethics of Animal Experiments in NIID (permission number: 520001) under the guidelines for animal experiments in accordance with the Guidelines for Proper Conduct of Animal Experiments established by the Science Council of Japan (http://www.scj.go.jp/ja/info/kohyo/pdf/kohyo-20-k16-2e.pdf). The experiments were in accordance with the "Weatherall report for the use of non-human primates in research" recommendations (https://royalsociety.org/topics-policy/publications/2006/weatherall-report/). Each macaque was housed in a separate cage and received standard primate feed and fresh fruit daily. Virus inoculation, blood collection, nasopharyngeal and throat swab collection, and anti-CD8 antibody treatment were performed under ketamine anesthesia. Macaques were euthanized by whole blood collection under deep anesthesia on day 14 or 21 post-infection.

Animal experiments

SARS-CoV-2 wk-521 strain [39] (2019-nCoV/Japan/TY/WK-521/2020, GenBank Accession LC522975) was expanded in Vero E6/TMPRSS2 cells [39] and harvested to prepare a virus inoculum stock. Virus infectivity was assessed by detection of cytopathic effect (CPE) on Vero E6/TMPRSS2 cells and determination of endpoint titers. Nine cynomolgus macaques (Macaca fascicularis, 3–6 years old) were intranasally inoculated with the same stock of SARS-CoV-2 wk-521 at a dose of 106 (exactly 7.5 x 105) TCID50 (1.4 x 109 RNA copies) (n = 3), 105 (exactly 7.5 x 104) TCID50 (n = 5), or 104 (exactly 7.5 x 103) TCID50 (n = 1) (Table 1). Three (Group D) of the nine macaques were intravenously administrated with 5 mg/kg body weight of anti-CD8α antibody clone MT807 (NIH Nonhuman Primate Reagent Resource) on days 5 and 7 post-infection. Body temperature was measured with a small implantable thermo logger (DST micro-T; Star-Oddi) that was set intraperitoneally under ketamine anesthesia at least five days prior to virus inoculation. Macaques were euthanized and subjected to necropsy on day 14 or 21 post-infection (Table 1).

Detection of SARS-CoV-2 RNAs

Swab RNA was extracted from 0.2 ml of swab solutions (1ml of DMEM with 2% fetal bovine serum [Cytiva]) using QIAamp Viral RNA Minikit (QIAGEN) and subjected to real-time RT-PCR for viral RNA quantitation [40] using QuantiTect Probe RT-PCR Kit (Qiagen) and QuantStudio 5 (Thermo Fisher Scientific). Swab RNAs were also subjected to real-time RT-PCR for measurement of viral subgenomic RNA (sgRNA) levels [32,33,41] using the following primers: SARS2-LeaderF60 (5’-CGATCTCTTGTAGATCTGTTCTCT-3’), SARS2-N28354R (5’-TCTGAGGGTCCACCAAACGT-3’), and SARS2-N28313Fam (FAM-TCAGCGAAATGCACCCCGCA-TAMRA). Tissue RNAs were extracted from homogenized tissues by using TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) with phenol-chloroform extraction and subjected to real-time RT-PCR for detection of viral RNAs.

Virus recovery from swabs

Vero E6/TMPRSS2 cells in 96-well plates were added with 10-fold serially diluted swab solutions and cultured for 4 days without medium change. Virus recovery was assessed by detection of CPE and determination of endpoint titers. Swab samples with virus titers greater than 1 x 102 TCID50/swab were considered positive.

Analysis of anti-SARS-CoV-2 NAb responses

Plasma samples were heat inactivated for 30 min at 56°C. Serial two-fold dilutions of heat-inactivated plasma were tested in quadruplicate. In each mixture for quadruplicate testing, 40 μl of diluted plasma were incubated with 40 μl of 80 TCID50 SARS-CoV-2 wk-521. After incubation for 45 min at room temperature, 20 μl of the mixture was added to each of four wells (1 x 104 Vero cells/well) in a 96-well plate. Three days later, virus infectivity was assessed by detection of CPE to determine the endpoint titers. The lower limit of detection was 1:10.

Analysis of cell surface markers

Whole blood samples were treated with Lysing Solution (BD) and subjected to surface staining using anti-CD3 APC-Cy7 (SP34-2; BD), anti-CD4 FITC (M-T477; BD), anti-CD8 PerCP (SK1; BD), and anti-CD20 PE (2H7; BD) antibodies. Alternatively, whole blood samples from anti-CD8 antibody-treated animals were stained with anti-CD3 APC-Cy7, anti-CD4 PerCP (L200; BD), anti-CD8 FITC (DK25; FUJIFILM), and anti-CD20 PE. Stained cells were analyzed by BD FACS Canto II.

Analysis of SARS-CoV-2 antigen-specific CD8+ T-cell responses

Virus-specific CD8+ T-cell frequencies were measured by flow cytometric analysis of gamma interferon (IFN-γ) induction after specific stimulation as described previously [42]. PBMCs were prepared from whole blood by density gradient centrifugation using Ficoll-Paque PLUS (Cytiva). Lymph node-derived lymphocytes were prepared from minced lymph nodes by density gradient centrifugation using Ficoll-Paque PLUS. Cells were pulsed and cocultured with peptide pools (at a final concentration of more than 0.1 μM for each peptide) using panels of overlapping peptides spanning the SARS-CoV-2 S, N, M, and E amino acid sequences (PM-WCPV-S-1, PM-WCPV-NCAP-1, PM-WCPV-VME-1, and PM-WCPV-VEMP-1; JPT Peptide Technologies) in the presence of GolgiStop (monensin, BD), 1 μg/ml of anti-CD28 (CD28.2, BD) and 1 μg/ml anti-CD49d (9F10, BD) for 6 hours. Intracellular IFN-γ staining was performed with a CytofixCytoperm kit (BD) and anti-CD3 APC-Cy7, anti-CD4 FITC, anti-CD8 PerCP, and anti-IFN-γ PE (4S.B3; BioLegend). Stained cells were analyzed by BD FACS Lyric. A representative gating schema for flow cytometric analysis is shown in Fig 5A. Specific T-cell frequencies were calculated by subtracting nonspecific IFN-γ+ T-cell frequencies from those after peptide-specific stimulation. Specific T-cell frequencies less than 0.03% of CD8+ T cells were considered negative.

Statistical analysis

Statistical analyses were performed using Prism software (GraphPad Software, Inc.) with significance set at p values of < 0.05. Comparisons were performed by Mann-Whitney U test.

Changes in body temperatures pre- and post-infection in macaques.

(TIF)

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Histopathology of the lung in macaque N021.

Representative histopathology with hematoxylin and eosin staining (H&E) of the lung obtained from macaque N021 at autopsy on day 14 post-infection, indicating mild or moderate pulmonary inflammation. Infiltration of mononuclear cells were observed around blood vessels and bronchiole (upper left panel). Lymphocytes, eosinophils, and macrophages were observed in pulmonary alveoli (upper right and lower panels).

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Click here for additional data file.

CD8+ T-cell frequencies in the submandibular lymph nodes at necropsy.

CD3+CD8+ cell frequencies in the submandibular lymph nodes obtained at autopsy are shown.

(TIF)

Click here for additional data file.

28 Jun 2021

Dear Prof. Matano,

Thank you very much for submitting your manuscript "Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

All three reviewers thought this was a timely and significant study. While the number of animals used is limited, the authors have acknowledged this limitations. I ask that the authors address the minor comments raised by Reviewers #2 and #3. These can be addressed editorially in the text of the revised manuscript.

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Section Editor

PLOS Pathogens

Benhur Lee

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************

Reviewer Comments (if any, and for reference):

Reviewer's Responses to Questions

Part I - Summary

Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship.

Reviewer #1: Nomura et al CD8 deplete 3 macaques 5 days after SARS-CoV-2 infection and show the profile of resolution of infection is similar in these 3 macaques to 5 controls. The work is well done and of interest to the COVID field grappling with a role if any for CD8 T cells in control of COVID.

Comments

Although acknowledged by the authors, the numbers of macaques and groups are very limited. I felt a more definitive data set would have perhaps considered a B cell depletion positive control.

Only one time point of depletion was studied. I felt that day 5 was a reasonable stab at showing the importance of control, but it remains possible it was too late.

The role of CD8 T cells, if any, may be more important in prevention of severe disease, which macaques rarely suffer from. An alternate role may be in control of reinfection, as suggested by Barouch et al (albeit with limited data).

Reviewer #2: This study uses a macaque model with intranasal SARS-CoV-2 exposure to assess the role of CD8+ T-cells in viral control. The results demonstrate that CD8+ T cell depletion does not impact viral clearance during SARS-CoV-2 primary infection. The manuscript is well written, but could be improved by addressing some concerns related to study design and interpretation of the results.

1. The investigators should clarify the apparent timing issue where viral clearance occurs predominantly by 10 days post-infection, while induction of systemic CD8+ T cell responses occurs by 14 days post-infection. Their proposed temporal sequence of T-cell and B-cell activity in the primary infection should be provided in a diagram to illustrate the possible relationship with viral clearance.

2. The investigators should comment on whether there is actual depletion of CD8+ T cells in the tissues, especially at sites of SARS-CoV-2 replication. Looking at tissue specific CD8+T cells responses would be more informative considering where the virus replicates. This is demonstrated by authors own data on animal N013 that has no detectable systemic CD8+T cell responses but has responses as well as viral replication in submandibular lymph nodes.

3. While the investigators find systemic SARS-CoV-2 specific CD8+ T cell responses in untreated macaques, the responses have a wide range. Even in the 5 animals examined, a wide range of responses can be noticed from no response (N013) to some response at d14. Having only 3 animals in the active arm and a wide range of responses in the control animals are two important limitations impacting each other in the interpretation of the results that the investigators should comment on.

4. Since cellular immunity may play a more important role in clearing/preventing subsequent infections and controlling outcome in severe/uncontrolled infections, the investigators should comment on the need for further studies using a reinfection model to assess the role of CD8+ T cell responses in viral clearance.

5. Statements in lines 203-205 and 250-252 need to be adjusted to clearly state that the observations are only relevant for primary, controlled SARS-CoV-2 infections.

Reviewer #3: Nomura and colleagues assess the impact of CD8 T cell depletion on the control of subacute SARS-CoV-2 replication in a small cohort of cynomolgus macaques. They report that when CD8 depletion is performed 5-7 days after SARS-CoV-2 infection, there is no demonstrable impact on viral replication compared to control animals. They correctly surmise in the discussion that while this does not dispute a potential role for vaccine-induced CD8 T cells in protection from infection, the data suggest that CD8 T cells are not strictly required to control low-level viral replication in the pharyngeal mucosa.

The role for T cells in determining COVID-19 severity or vaccine-induced protection is a topic of significant interest, which can be challenging to conclusively assess in human cohorts. While the authors note the limitations of the current study, including the sample size, non-human primate studies are a valuable pre-clinical model to assess the contributions of various immune cells to viral control. The manuscript is well-written and presents the data and conclusions in a clear and concise manner. I have no substantial concerns about the study, but some additional discussion points would enhance its message (see below).

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Part II – Major Issues: Key Experiments Required for Acceptance

Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions.

Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject".

Reviewer #1: see above

Reviewer #2: No additional experiments required

Reviewer #3: None

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Part III – Minor Issues: Editorial and Data Presentation Modifications

Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity.

Reviewer #1: see above

Reviewer #2: (No Response)

Reviewer #3: One of the major considerations for the role of CD8 T cells in controlling viral replication during primary infection versus the contribution of T cells to protection from re-infection includes the kinetics of the T cell response. Based on the data presented in Figure 5, it is relatively clear that primary, subacute infection is unlikely to induce detectable CD8 responses prior to day 14 in most animals. Given how early viral replication peaks in this animal model, it seems likely that the primary CD8 response simply occurs too late to contribute to viral control. I think the discussion could more explicitly point this out, and perhaps report what is known about similar kinetics in humans.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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2 Jul 2021

Submitted filename: Nomura PP_Response to Comments.docx

Click here for additional data file.

6 Jul 2021

Dear Prof. Matano,

We are pleased to inform you that your manuscript 'Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques' has been provisionally accepted for publication in PLOS Pathogens.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens.

Best regards,

Benhur Lee

Section Editor

PLOS Pathogens

Benhur Lee

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************************************************

Reviewer Comments (if any, and for reference):

16 Jul 2021

Dear Prof. Matano,

We are delighted to inform you that your manuscript, "Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques," has been formally accepted for publication in PLOS Pathogens.

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Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens.

Best regards,

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064