Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19

Abstract

Background Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection in patients with Coronavirus Disease 2019 (COVID-19) prominently manifests with pulmonary symptoms histologically reflected by diffuse alveolar damage (DAD), excess inflammation, pneumocyte hyperplasia and proliferation, and formation of platelet aggregates or thromboemboli. However, the mechanisms mediating these processes remain unclear. Methods We performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections. Findings The lung parenchyma showed severe DAD with thromboemboli in all cases. SARS-CoV-2 infection was found in an extensive range of cells including alveolar epithelial type II/pneumocyte type II (AT2) cells (HT2-280), ciliated cells (tyr-α-tubulin), goblet cells (MUC5AC), club-like cells (MUC5B) and endothelial cells (CD31 and CD34). Greater than 90% of infiltrating immune cells were positive for viral proteins including macrophages and monocytes (CD68 and CD163), neutrophils (ELA-2), natural killer (NK) cells (CD56), B-cells (CD19 and CD20), and T-cells (CD3ε). Most but not all infected cells were positive for the viral entry receptor angiotensin-converting enzyme-2 (ACE2). The numbers of infected and ACE2-positive cells correlated with the extent of tissue damage. The infected tissues exhibited low numbers of B-cells and abundant CD3ε+ T-cells consisting of mainly T helper cells (CD4), few cytotoxic T cells (CTL, CD8), and no T regulatory cell (FOXP3). Antigen presenting molecule HLA-DR of B and T cells was abundant in all cases. Robust interleukin-6 (IL-6) expression was present in most uninfected and infected cells, with higher expression levels observed in cases with more tissue damage. Interpretation In lung tissues from severely affected COVID-19 patients, there is evidence for broad SARS-CoV-2 cell tropisms, activation of immune cells, and clearance of immunosuppressive cells, which could contribute to severe tissue damage, thromboemboli, excess inflammation and compromised adaptive immune responses.

Attenuated activation of pulmonary immune cells in mRNA-1273–vaccinated hamsters after SARS-CoV-2 infection

“…Viral gene reads were detected only in MI hamsters (Figure 4A, Supplemental Figure 10, A and B), consistent with the clearance of infection in the lungs of the VI hamsters that was observed by qRT-PCR (Figure 2C). Several MI samples with higher overall viral reads had virus gene expression detected in a broad selection of cell types in the lungs, including lymphoid and myeloid cells (Figure 4A) which is consonant with other studies sampling bronchoalveolar lavage fluid (BALF) ( 26), blood or post-mortem lung tissues (27,28) from severe infections in humans. Macrophages and granulocytes had the highest average viral read counts (Supplemental Figure 10E).…”

SARS‐CoV‐2 pseudovirus infectivity and expression of viral entry‐related factors ACE2, TMPRSS2, Kim‐1, and NRP‐1 in human cells from the respiratory, urinary, digestive, reproductive, and immune systems

“…RNAseq has demonstrated high ACE2 expression in diverse types of cells including pulmonary AT2, respiratory epithelial, myocardial, digestive tract epithelial, nasal goblet secretory and kidney cells, ileal absorptive enterocytes, and salivary glands 37,43,44 . IFA staining has revealed wide expression of ACE2 protein in different parenchymal and immune cell types 10 . ACE2 protein is present in a different part of the kidney and has a high expression level, 45,46 explaining why SARS‐CoV‐2 kidney infection had a significantly higher risk of in‐hospital death 47 …”

“…On the other hand, we found a statistically significant positive correlation of SARS‐CoV pseudovirus infectivity with the levels of gly‐ACE2 protein but not ungly‐ACE2 protein. Hence, compared with SARS‐CoV, SARS‐CoV‐2 infection is less dependent on gly‐ACE2, which might explain its promiscuous broad tropism and more infectious nature 10 . In fact, the dual nature of human ACE2 glycosylation in binding to SARS‐CoV‐2 spike has been reported 49 .…”

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

“…lung AT2 cells, macrophages, cardiomyocytes, adrenal gland stromal cells, stromal cells in testis, ovary and thyroid cells) [83,84]. Further, different types of immune cells can be infected, including granulocytes [85] which have been reported to be key modulators in SARS-CoV-2 immune response [84];…”