Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

Abstract

Clinical observations indicate that COVID-19 is a systemic disease. An investigation of the viral distribution within the human body and its correlation with tissue damage can aid in understanding the pathophysiology of SARS-CoV-2 infection. We present a detailed mapping of the viral RNA in 61 tissues and organs of 11 deceased patients with COVID-19. The autopsies were performed within the early postmortem interval (between 1.5 and 15 hr, mean: 5.6 hr) to minimize the bias due to viral RNA and tissue degradation. Very high viral loads (>10⁴copies/ml) were detected in most patients' lungs, and the presence of intact viral particles in the lung tissue could be verified by transmission electron microscopy. Interestingly, viral RNA was detected throughout various extrapulmonary tissues and organs without visible tissue damage. The dissemination of SARS-CoV-2-RNA throughout the body supports the hypothesis that there is a maladaptive host response with viremia and multiorgan dysfunction.

Keywords: COVID-19; SARS-CoV-2; autopsy; early post-mortem interval; histology; immunology; infectious disease; inflammation; microbiology; transmission electron microscopy; virus.

Figure 1.. Overview of SARS-CoV-2 vRNA throughout the human body.

Postmortem determination of SARS-CoV-2 RNA with qRT-PCR of homogenized organs and tissues in copies/ml represented as decadic logarithm of 11 patients with mean value and standard deviation (SD) of the following systems: respiratory system, lymphatic system, gastrointestinal tract, urinary tract, nervous system, cardiovascular system, hematological tissues, reproductive system, and endocrine system. Intensity of colors describes the amount of vRNA. Abbrev.: bdl (below detection limit), UL (upper lobe), ML (middle lobe), LL (lower lobe), LV (left ventricle), sr (suprarenal), VS (ventricular septum), RV (right ventricle), aw (anterior wall), pw (posterior wall), bp (basal part), ap (apical part), paraaort. (paraaortal).

Figure 1—figure supplement 1.. Individual vRNA load of the respiratory system, the lymphatic system, the cardiovascular system, and hematological tissues.

Postmortem determination of SARS-CoV-2 RNA with qRT-PCR of homogenized organs and tissues in copies/ml represented as decadic logarithm of 11 patients. Abbrev.: bdl (below detection limit), UL (upper lobe), ML (middle lobe), LL (lower lobe), LV (left ventricle), sr (suprarenal), VS (ventricular septum), RV (right ventricle), aw (anterior wall), pw (posterior wall), bp (basal part), ap (apical part), nd (not determined), np (not present). Intensity of colors describes the amount of RNA.

Figure 1—figure supplement 2.. Individual vRNA load of the gastrointestinal tract, the endocrine system, the urinary tract, the nervous system, and the reproductive system.

Postmortem determination of SARS-CoV-2 RNA with qRT-PCR of homogenized organs and tissues in copies/ml represented as decadic logarithm from patient 1–11. Abbrev.: bdl (below detection limit), nd (not determined), np (not present). Intensity of colors describes the amount of vRNA.

Figure 2.. Transmission electron microscopic image of the lung tissue of patient 3.

(a) Alveolar septum showing intact capillaries with erythrocytes (asterisk) and the air space (cross). The blood-air barrier is damaged as the pneumocytes are missing and the basal membrane is exposed to air (arrowheads). (b–e) Close-ups of the four boxed regions in (a) from left to right showing SARS-CoV-2 virus particles encased in plasmatic vesicles of alveolar fibrocytes. (f) Reference image of SARS-CoV-2 virus particles proliferated in cell culture (Vero76).

Figure 3.. Proinflammatory and prothrombotic factors.

Blood analysis of patients 1–11 by using Legendplex Panel (Biolegend, CA, USA) of the proinflammatory cytokines Interleukin (IL)−6 (a) and IL-8 (b) as well as tissue plasminogen activator (tPa) (c), P-Selectin (d), D-Dimer (e), Plasminogen activator inhibitor-1 (PAI) (f), soluble (s) CD40ligand(L) (g), Factor IX (h), and the P-selectin glycoprotein ligand 1 (PSGL-1) (i) in pg/ml compared to the mean of five controls (Control, healthy volunteers). Unpaired t-test, Mann-Whitney test p<0.005 ***; p<0.05 **; ns=not significant.

Figure 4.. Macromorphology findings of COVID-19 patients.

(a) Pneumonectomy of patient one showed strong congestion with liquids and hemorrhages. The tissue consistency was fragile. (b) Cut surface of lung tissue in higher magnification as shown in (a). The pleura shows further hemorrhages. (c) Pneumonectomy of patient seven showed a more solid lung tissue without congestion. The tissue consistency was very firm. (d) Cut surface of lung tissue in higher magnification as shown in (c). Lung tissue was retracted adjacent to the bronchus. (e) Pale pleura visceralis of the lung of patient 6 with disseminated hemorrhages and signs of disturbed ventilation. (f) Nodular transformation of lung tissue as phenomenon of fungal superinfection in patient 3. (g) Hemorrhagic lung infarct in patient 4 due to a thrombembolus in a pulmonary artery branch. (h) Anemic spleen infarct due to a clotted small artery in patient 4. (i) Fulminant stasis and thromboses in the periprostatic plexus in patient 4. (j) Cerebellar infarction (hemorrhagic) in patient 9.

Figure 5.. Micromorphology lung findings of COVID-19 patients.

(a) Destroyed lung tissue with intraalveolar hemorrhagia and aggregates of prominent epithelial cells resembling squamous metaplasia (patient 1; HE). (b) Strong architectural damage of lung alveolar tissue with disruption of the epithelial barrier and intraalveolar accumulation of enlarged cells with prominent nuclei and visible nucleoli. Initial syncytial pattern is given (patient 2; HE). (c) Lung tissues with multinucleated giant cells admixed with only few lymphocytes (patient 4; HE). (d) Alveolar unit with band-like desquamation of the alveolar epithelial cells in the alveolar space partially filled with liquids, erythrocytes and few lymphocytes (patient 5; HE). (e) Multinucleated giant cell in an alveolar space is strongly positive for keratins (patient 4; immunostaining AE1/3). (f) Serial section of (e), the multinucleated giant cell after immunostaining against TTF1 (patient 4; immunostaining TTF1). (g) Lung tissue with interstitial fibrosis (patient 8; EvG). (h) Lung tissue with interstitial and intraalveolar fibrosis (patient 8; EvG).

Figure 6.. Micromorphology lung findings of COVID-19 patients.

(a) Lung tissue with minimal emphysematous changes derived from the upper lobes without detectable viral loads (patient 2; HE). (b) Severe hemorrhagic pneumonia in specimens from the lower lobes with high viral loads (patient 2; HE). (c) Vasculitis-like changes around pulmonary artery branches (patient 4; HE). (d) Damaged lung tissue with hemostasis and inflammatory changes adjacent to the pulmonary artery branch (patient 4; HE). (e) Strong lymphocytic-predominant infiltration of lung tissues with hemorrhagic and interstitial edema (patient 7; HE). (f) Higher magnification of the lymphocytic-predominant infiltrate (patient 7; HE). (g) Lung tissue with a large nucleated cell in an alveolar capillary, suggestive for a megakaryocyte (arrow; patient 9; HE). (h) The same tissue after immunostaining against CD61 (patient 9; immunostaining CD61).

Figure 7.. Extrapulmonary micromorphology findings of COVID-19 patients.

(a) Overview of a mediastinal lymphnode with some nodular aggregates of lymphocytes, but destroyed lymphofollicular structures (patient 5; HE). (b) Bone marrow with prominent hemophagocytosis (arrow) and maturating cells of the hematopoiesis (patient 9; HE). (c) Myocardial tissue of the left ventricle (patient 1; HE). (d) Myocardial tissue of the left ventricle in higher magnification with a minimal increase in cellularity indicating for an activated cardiomesenchyme (patient 1; HE). (e) Thoracic aorta with a low number of non-inflammatory nucleated cells in an unsuspicious matrix (patient 5; HE). (f) Tissue from the thoracic aorta in higher magnification. The endothelium is labeled with an asterisk (patient 5; HE). (g) Colon mucosa with a crypt lined by goblet cells and enterocytes without any strong intraepithelial inflammation (patient 3; HE). (h) Exocrine pancreas tissue with structural intact acini without inflammatory cells (patient 9; HE).