SARS-CoV-2 infection and persistence in the human body and brain at autopsy【Nature 2022年12月14日】


Coronavirus disease 2019 (COVID-19) is known to cause multi-organ dysfunction during acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with some patients experiencing prolonged symptoms, termed post-acute sequelae of SARS-CoV-2. However, the burden of infection outside the respiratory tract and time to viral clearance are not well characterized, particularly in the brain. Here we carried out complete autopsies on 44 patients who died with COVID-19, with extensive sampling of the central nervous system in 11 of these patients, to map and quantify the distribution, replication and cell-type specificity of SARS-CoV-2 across the human body, including the brain, from acute infection to more than seven months following symptom onset. We show that SARS-CoV-2 is widely distributed, predominantly among patients who died with severe COVID-19, and that virus replication is present in multiple respiratory and non-respiratory tissues, including the brain, early in infection. Further, we detected persistent SARS-CoV-2 RNA in multiple anatomic sites, including throughout the brain, as late as 230 days following symptom onset in one case. Despite extensive distribution of SARS-CoV-2 RNA throughout the body, we observed little evidence of inflammation or direct viral cytopathology outside the respiratory tract. Our data indicate that in some patients SARS-CoV-2 can cause systemic infection and persist in the body for months.


COVID-19 has respiratory and non-respiratory manifestations, including multi-organ failure and shock among patients with severe and fatal disease. Some individuals who survive experience post-acute sequelae of SARS-CoV-2, also known as long COVID. Although autopsy studies of fatal COVID-19 cases support the ability of SARS-CoV-2 to infect multiple organs, extrapulmonary organs often lack histopathological evidence of virally mediated injury or inflammation. The paradox of infection outside the respiratory tract without injury or inflammation raises many pathogen- and host-related questions.

To investigate the cellular tropism, replication competence, persistence and evolution of SARS-CoV-2 in humans, and to look for associated histopathology in infected tissues, we carried out autopsies on 44 COVID-19 cases. Our approach focused on timely, systematic and comprehensive tissue sampling and preservation for complementary analyses. We carried out droplet digital polymerase chain reaction (ddPCR) for detection and quantification of SARS-CoV-2 nucleocapsid (N) gene targets and in situ hybridization (ISH) to validate the ddPCR findings and determine the cellular tropism of SARS-CoV-2. Immunofluorescence (IF) and chromogenic immunohistochemistry (IHC) were used to further validate the presence of SARS-CoV-2 in the brain. We carried out quantitative real-time PCR with reverse transcription (RT–qPCR) to detect subgenomic RNA, a marker suggestive of recent virus replication, and demonstrated replication-competent SARS-CoV-2 in selected respiratory and non-respiratory tissues, including the brain, by virus isolation in traditional and modified Vero E6 cell culture. In six individuals, we measured the diversity and anatomic distribution of intra-individual SARS-CoV-2 spike gene variants using high-throughput, single-genome amplification and sequencing (HT-SGS).

We categorized autopsy cases as early (n = 17), mid (n = 13) or late (n = 14) by illness day (d) at the time of death, being ≤d14, d15–30 or ≥d31, respectively. We defined persistence as the presence of SARS-CoV-2 RNA among late cases. We analysed and described our results in terms of respiratory and non-respiratory tissues to quantify and statistically compare SARS-CoV-2 RNA levels across tissues and cases.