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

Abstract

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.

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.

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.

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.

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.