Viable SARS-CoV-2 Omicron sub-variants isolated from autopsy tissues

Abstract

IntroductionPulmonary and extrapulmonary manifestations have been described after infection with SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The virus is known to persist in multiple organs due to its tropism for several tissues. However, previous reports were unable to provide definitive information about whether the virus is viable and transmissible. It has been hypothesized that the persisting reservoirs of SARS-CoV-2 in tissues could be one of the multiple potentially overlapping causes of long COVID.MethodsIn the present study, we investigated autopsy materials obtained from 21 cadaveric donors with documented first infection or reinfection at the time of death. The cases studied included recipients of different formulations of COVID-19 vaccines. The aim was to find the presence of SARS-CoV-2 in the lungs, heart, liver, kidneys, and intestines. We used two technical approaches: the detection and quantification of viral genomic RNA using RT-qPCR, and virus infectivity using permissive in vitro Vero E6 culture.ResultsAll tissues analyzed showed the presence of SARS-CoV-2 genomic RNA but at dissimilar levels ranging from 1.01 × 102 copies/mL to 1.14 × 108 copies/mL, even among those cases who had been COVID-19 vaccinated. Importantly, different amounts of replication-competent virus were detected in the culture media from the studied tissues. The highest viral load were measured in the lung (≈1.4 × 106 copies/mL) and heart (≈1.9 × 106 copies/mL) samples. Additionally, based on partial Spike gene sequences, SARS-CoV-2 characterization revealed the presence of multiple Omicron sub-variants exhibiting a high level of nucleotide and amino acid identity among them.DiscussionThese findings highlight that SARS-CoV-2 can spread to multiple tissue locations such as the lungs, heart, liver, kidneys, and intestines, both after primary infection and after reinfections with the Omicron variant, contributing to extending knowledge about the pathogenesis of acute infection and understanding the sequelae of clinical manifestations that are observed during post-acute COVID-19.

Prevalence of persistent SARS-CoV-2 in a large community surveillance study

“…Although the link between viral persistence and long COVID may not be causal, these results suggest that persistent infections could be contributing to the pathophysiology of long COVID 10 , 45 , as also evidenced by the observation of circulating SARS-CoV-2 S1 spike protein in a subset of patients with long COVID months after first infection 46 . There is also a growing body of evidence of the persistence of replication-competent virus throughout the body months after the start of an infection 47 , 48 , and very recently that this persistence is strongly associated with higher risk of long COVID 49 .…”

Unveiling the Pathological Mechanisms of Death Induced by SARS-CoV-2 Viral Pneumonia

“…Similar results have been highlighted in the specialized literature. A study from Argentina observed increased positivity and persistence of the viral genome in the study cohort for up to 22 days from onset [ 46 ]. A cohort study demonstrates the presence of the viral genome in the lungs even after 67 days [ 26 ].…”

SARS-CoV-2 Omicron variant infection affects blood platelets, a comparative analysis with Delta variant

“…Additionally, it is plausible to suggest that platelets, and megakaryocytes ( 23 ), may contribute to the dissemination of the virus, which first affects the lungs and then spreads via the blood stream, infecting various organs and tissues. A recent study has shown that Omicron can indeed spread to multiple tissue locations after primary infection ( 54 ). The mechanisms by which the virus enters platelets and megakaryocytes remain unclear, but besides a low ACE2 expression, several candidates for SARS-CoV-2 receptors have been proposed ( 34 ), including GPIb ( 55 ) and CD147 ( 49 ).…”