Pathology and Pathogenesis of SARS-CoV-2 Associated with Fatal Coronavirus Disease, United States

Roosecelis B. Martines; Jana M. Ritter; Eduard Matkovic; Joy Gary; Brigid C. Bollweg; Hannah Bullock; Cynthia S. Goldsmith; Luciana Silva-Flannery; Josilene N. Seixas; Sarah Reagan-Steiner; Timothy Uyeki; Amy Denison; Julu Bhatnagar; Wun-Ju Shieh; Sherif R. Zaki


Emerging Infectious Diseases. 2020;26(9):2005-2015. 

In This Article


The clinical distinction between SARS-CoV-2 and other respiratory viral infections is difficult because there are overlapping clinical features characterized by febrile illness with cough that lasts for several days before progressing to acute pneumonia. In addition, persons with SARS-CoV-2 and other respiratory viral infections may have atypical or minimal symptoms.[25–27] Besides respiratory failure, particularly in patients with severe disease, fatigue, myalgia or arthralgia, chills, hepatic and renal dysfunction, lymphocytopenia, leukopenia, thrombocytopenia, and elevated inflammatory biomarkers have been described.[5,28,29]

Histopathologic lesions attributed directly to the virus in these cases were limited to respiratory tissues; the predominant finding was DAD, with various levels of progression and severity. We saw no clear correlation of the pathologic phase of DAD to known symptom duration, which could be the result of underrecognition of early symptoms in elderly residents of LTCFs and underestimation of illness duration. Together, the histopathologic, IHC, and EM findings in this report provide insight into SARS-CoV-2 pathogenesis. IHC testing, including double staining with surfactant, and EM confirmed viral tropism for pulmonary II pneumocytes. The ultrastructural observations are consistent with previous reports of SARS-CoV infection, with the exception that neither double-membrane vesicles nor nucleocapsid inclusions were detected.[15,20] Viral antigen was also seen in respiratory epithelium of conducting airways (trachea, bronchi, and bronchioles) and occasionally in alveolar macrophages; infection of these cell types may be key in viral replication and trafficking. The respiratory epithelium is one of the first cell types encountered by inhaled virus; SARS-CoV-2 antigens were detected by IHC in ciliated epithelial cells from 50% of these case-patients and up to 16 days after known symptom onset. Ultrastructural analysis showed numerous extracellular viral particles along the ciliated surface and within ciliated columnar epithelial cells. These findings corroborate reports of high viral loads in the upper respiratory tract and support the potential for persons infected with SARS-CoV-2 to readily transmit the virus, with prolonged and continued viral shedding in severe cases.[30,31]

Overall pathologic features in these 8 COVID-19 deaths were similar to those seen in SARS-CoV and MERS-CoV infections, and in available COVID-19 reports.[10–15,18,20,32] However, the amount of viral antigen detected by IHC in lung tissue from these cases is more than what we have seen in SARS and MERS[16,18] cases submitted to our laboratory, and its extensive detection in epithelial cells of the upper respiratory tract is unique among these highly pathogenic coronaviruses.[33] In addition to direct viral effects on tissues, the immune response to viral infection likely plays a major role in determining clinical outcome, and acute decline in COVID-19 patients has been linked to an immune-mediated cytokine storm.[34] Preliminary evaluation of immune cell populations in the respiratory tissues from these 8 cases revealed abundant T lymphocytes in the upper airways and lung parenchyma, with B lymphocytes in smaller numbers and predominating in areas of lymphoid aggregates (data not shown). Further investigation into the roles of these cell populations in COVID-19 is needed. In 6 of the 8 case-patients, sinus histiocytosis and hemophagocytosis were seen in hilar lymph nodes. However, SARS-CoV-2 antigens were detected by IHC in hilar lymph node macrophages from only 1 immunosuppressed patient. Lymph nodes are key sites for immune recognition and elimination of respiratory pathogens. Elucidating the immune response to, and the effects of immunosuppression on, SARS-CoV-2 infection is therefore of fundamental importance.

SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor to facilitate viral entry into target cells. ACE2 is expressed in multiple tissues throughout the body, including type II pneumocytes, myocardial cells, cholangiocytes, enterocytes, and oral mucosal epithelium.[5,35,36] However, among these patients, SARS-CoV-2 antigens were not detected in extrapulmonary tissues besides hilar lymph node, and pathologic findings in other tissues were attributable to other underlying concurrent conditions. Some of the underlying conditions in these case-patients (e.g., hypertension, COPD) are associated with upregulation of ACE2 receptors; possible correlation of these conditions with COVID-19 severity warrants further exploration.[5,28,37] COVID-19 cardiomyopathy and acute cardiac death during clinical resolution of pulmonary disease have been described.[24,38] However, we did not observe any evidence of myocarditis or myocardial necrosis in the tissues of the 8 case-patients we examined. Reports have been made of coagulation abnormalities and pulmonary vascular perfusion issues without DAD in some COVID-19 patients,[39,40] and we saw microthrombi in the lung from 1 case-patient who lacked DAD but had severe bacterial bronchopneumonia. These various and potentially severe cardiovascular complications of COVID-19 warrant further investigation into the specific mechanisms of SARS-CoV-2–induced cardiovascular injury, homeostatic derangement, or both.

Clinical studies have reported elevated liver enzymes in patients with COVID-19.[28,29] The lack of viral detection by IHC in the liver in this investigation suggests that for these case-patients, abnormal biomarkers of hepatic injury may not be the result of direct viral infection of hepatocytes. Gastrointestinal symptoms are not typically a prominent feature of COVID-19 but have been reported, and SARS-CoV-2 has been detected in fecal samples.[41–43] However, no histopathologic findings or SARS-CoV-2 antigens were detected in gastrointestinal tissues, and diarrhea was reported for only 1 of these case-patients.

We identified viral co-infections in upper respiratory tract tissues from 3 case-patients, including 2 with parainfluenza virus 3 and 1 with influenza B virus, but the contribution of these co-infections to pulmonary disease and fatal outcomes is unknown. Although we identified streptococcal lower respiratory infections in 3 case-patients, none were caused by Streptococcus pneumoniae, and there was no strict correlation of these infections with mechanical ventilation among these case-patients. Because 7 of 8 case-patients discussed in this report were residents of a LTCF, their exposures and risks for viral and bacterial co-infections may be different from those for other patients. Few community-acquired bacterial infections have been reported in critically ill patients with COVID-19, but co-infections are not frequently reported with SARS and MERS.[17,32,44] Co-infections may play a key role in increasing susceptibility to, and illness from, SARS-CoV-2 infection in a LTCF setting. Further investigation into this association, and characterization of the etiologic agents most commonly involved, is warranted and may contribute to improved overall management of COVID-19 disease.

This report describes the specific cellular and extracellular localization of SARS-CoV-2 in respiratory tissues, without any IHC evidence of the virus in other tissues. Although detection of SARS-CoV-2 RNA in blood or serum has been reported,[34,41] we did not find evidence of systemic virus dissemination in these case-patients. Our findings highlight the importance of underlying conditions and pulmonary co-infections in COVID-19; these factors may potentially delay or confound diagnosis and contribute to adverse outcomes.

A limitation of this study is that 7 of 8 cases were from a single skilled nursing facility; findings may therefore not be representative of community-acquired SARS-CoV-2 infections. However, nosocomial transmission of viruses often parallels community outbreaks, and understanding disease transmission in healthcare settings is crucial.[25,45] None of these case-patients had diagnoses of acute cardiac injury, myocarditis, or cardiomyopathy, so understanding the pathogenesis of cardiac injury with SARS-CoV-2 infection requires additional investigations in fatal cases with evidence of cardiac injury.

No clinical or histopathologic features are specific to SARS-CoV-2 infection. Demonstrating SARS-CoV-2 directly in lung tissue, when taken in context with any other pathology present, is critical to assessing its contribution to mortality. Herein, we establish the utility of IHC as a diagnostic modality for SARS-CoV-2 in FFPE tissues by localizing viral antigens in respiratory tissues from RT-PCR confirmed cases. This diagnostic method is particularly valuable for FFPE specimens from cases in which antemortem or postmortem respiratory swab testing for SARS-CoV-2 was not performed. We also demonstrate virus identification in tissues by EM using various tissue sources (formalin-fixed wet tissue, FFPE blocks, and stained slides). Identification of SARS-CoV-2 cellular tropisms in the respiratory tract represents a crucial step forward in understanding the pathogenesis of SARS-CoV-2 infection and provides some insights relevant to the development of targeted therapeutic and preventive measures to combat COVID-19.