A cohort autopsy study defines COVID-19 systemic pathogenesis

Abstract

Severe COVID-19 disease caused by SARS-CoV-2 is frequently accompanied by dysfunction of the lungs and extrapulmonary organs. However, the organotropism of SARS-CoV-2 and the port of virus entry for systemic dissemination remain largely unknown. We profiled 26 COVID-19 autopsy cases from four cohorts in Wuhan, China, and determined the systemic distribution of SARS-CoV-2. SARS-CoV-2 was detected in the lungs and multiple extrapulmonary organs of critically ill COVID-19 patients up to 67 days after symptom onset. Based on organotropism and pathological features of the patients, COVID-19 was divided into viral intrapulmonary and systemic subtypes. In patients with systemic viral distribution, SARS-CoV-2 was detected in monocytes, macrophages, and vascular endothelia at blood-air barrier, blood-testis barrier, and filtration barrier. Critically ill patients with long disease duration showed decreased pulmonary cell proliferation, reduced viral RNA, and marked fibrosis in the lungs. Permanent SARS-CoV-2 presence and tissue injuries in the lungs and extrapulmonary organs suggest direct viral invasion as a mechanism of pathogenicity in critically ill patients. SARS-CoV-2 may hijack monocytes, macrophages, and vascular endothelia at physiological barriers as the ports of entry for systemic dissemination. Our study thus delineates systemic pathological features of SARS-CoV-2 infection, which sheds light on the development of novel COVID-19 treatment.

Fig. 1. Profiling of SARS-CoV-2 organotropism in COVID-19 patients.

a Major death causes for the 26 autopsy COVID-19 cases. The major death causes were severe pulmonary injuries (n = 23), including COVID-19-related respiratory failure without (n = 21) or with (n = 2) pulmonary fungal infection. The major death causes for other three cases were pulmonary thromboembolism, dissecting aneurysm rupture, and cardiovascular disorders, respectively. b Schematic model for SARS-CoV-2 organ tropism. LNs, Lymph nodes. c Heatmap showing SARS-CoV-2 distribution groups and viral RNA (Log2) in postmortem organs in 26 autopsy cases with COVID-19. LU, left upper; LL, left lower; RU, right upper; RM; right middle; RL, right lower. d Percentage of COVID-19 autopsy cases in three groups of SARS-CoV-2 distribution. e The correlation between SARS-CoV-2 viral RNA in the lungs and the number of SARS-CoV-2-positive organs. f Comparison of viral infection rate between SARS-CoV-2 based on the current autopsy study and SARS-CoV in the literature in postmortem organs from patients with COVID-19 and SARS.

Fig. 2. SARS-CoV-2-associated pulmonary pathological changes.

a H&E and IHC staining showing SARS-CoV-2 spike protein in pulmonary areas manifesting different features (1, exudation; 2, proliferation; 3, fibrosis) of diffuse alveolar damage (DAD). Scale bars, 250 μm. b–e Proportion of DAD-exudation areas (b), DAD-proliferation areas (c), and DAD-fibrosis areas (d), and the average SARS-CoV-2 RNA (e) in postmortem lungs from 15 COVID-19 autopsy cases. f, g H&E staining showing hyaline membrane formation (f) and bronchiolar-alveolar mucus (g). Scale bars, 100 μm. h The correlation between average bronchiolar-alveolar mucus plug number and PaO₂ level in patients with respiratory failure.

Fig. 3. The presence of SARS-CoV-2 in the endothelia of physiological barriers in the lungs, kidneys, and testes.

a Immunofluorescent staining of SARS-CoV-2 spike protein and CD34 in endothelia of pulmonary vessels using COVID-19 lung tissues (upper panel, Case 1) or control lung tissues from a patient with lung carcinoma (lower panel). Scale bars, 25 μm. b IHC showing that SARS-CoV-2 spike protein was detected in glomeruli with abundant filtrated barriers and convoluted tubular epithelia in the kidneys positive for viral RNA (Case 2). The kidney tissues (Case 16) negative for viral RNA were used as control. Scale bars, 25 μm. c H&E staining and IHC staining showing SARS-CoV-2 spike in endothelia of the blood–testis barrier, seminiferous tubules, and sperms in the epididymis (blue arrows) of the testes from COVID-19 patients (Case 2). Scale bars, 50 μm.

Fig. 4. Evidence of the presence of SARS-CoV-2 in circulating and infiltrating monocytes and macrophages.

a IHC staining of CD68, CK7, and viral spike in alveoli on serial sections. Macrophages are indicated by blue arrows. Scale bars, 50 μm. b, c IHC staining of monocytes/macrophages marked by CD68 and viral spike protein in lymph nodes (b) and the spleen (c) on serial sections from COVID-19 patients. Scale bars, 50 μm. d IHC staining showing viral spike in peripheral blood mononuclear cells (blue arrows) in vessels of the indicated postmortem organs from COVID-19 patients. Scale bar, 50 μm. e U-MAP showing scRNA-seq of 1437 cells on COVID-19 autopsy lung tissues (Case 17). CD8⁺ T, CD8⁺ T cells; CD14⁺ Mono-1/2, CD14⁺ monocyte-1/2; MoAM-1/2, monocyte-derived alveolar macrophages-1/2; AT, alveolar epithelial type 1/2 cells; Erythroid-like, erythroid-like and erythroid precursor cells; EC, endothelial cells; Fibro, fibroblast cells; MKI67⁺, MKI67⁺cells; Plasma, plasma cells. f Detection of SARS-CoV-2 transcripts. Plot shows SARS-CoV-2 ORF_10 or nucleocapsid (N) genes in CD14⁺ monocyte-1 from scRNA-seq. g U-MAP showing the expression of BSG (encoding CD147), TFRC (encoding transferrin receptor-1), NRP1 (encoding neuropilin-1), and ACE2 in the scRNA-seq of COVID-19 lung tissues.