Multimodal Molecular Imaging Reveals Tissue-Based T Cell Activation and Viral RNA Persistence for Up to 2 Years Following COVID-19

Abstract

The etiologic mechanisms of post-acute medical morbidities and unexplained symptoms (Long COVID) following SARS-CoV-2 infection are incompletely understood. There is growing evidence that viral persistence and immune dysregulation may play a major role. We performed whole-body positron emission tomography (PET) imaging in a cohort of 24 participants at time points ranging from 27 to 910 days following acute SARS-CoV-2 infection using a novel radiopharmaceutical agent, [18F]F-AraG, a highly selective tracer that allows for anatomical quantitation of activated T lymphocytes. Tracer uptake in the post-acute COVID group, which included those with and without Long COVID symptoms, was significantly higher compared to pre-pandemic controls in many anatomical regions, including the brain stem, spinal cord, bone marrow, nasopharyngeal and hilar lymphoid tissue, cardiopulmonary tissues, and gut wall. Although T cell activation tended to be higher in participants imaged closer to the time of the acute illness, tracer uptake was increased in participants imaged up to 2.5 years following SARS-CoV-2 infection. We observed that T cell activation in spinal cord and gut wall was associated with the presence of Long COVID symptoms. In addition, tracer uptake in lung tissue was higher in those with persistent pulmonary symptoms. Notably, increased T cell activation in these tissues was also observed in many individuals without Long COVID. Given the high [18F]F-AraG uptake detected in the gut, we obtained colorectal tissue forin situhybridization SARS-CoV-2 RNA and immunohistochemical studies in a subset of participants with Long COVID symptoms. We identified cellular SARS-CoV-2 RNA in rectosigmoid lamina propria tissue in all these participants, ranging from 158 to 676 days following initial COVID-19 illness, suggesting that tissue viral persistence could be associated with long-term immunological perturbations.

Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection

“…6 More recently, an autopsy study showed widespread sub-genomic RNA in tissues of decedents up to 6 months post-COVID, 7 and we have reported SARS-CoV-2 spike RNA detection in gut biopsies for up to 2.5 years post-COVID. 9 SARS-CoV-2 antigens, particularly spike protein and its components, are known to be highly immunogenic. 14–16 These antigens have been shown to induce inflammatory cytokine responses as well as dysregulation of fibrinogen, complement proteins, and endothelial cells.…”

“…5 For example, viral RNA or protein persistence has since been identified in a variety of tissues in gut biopsy and autopsy studies for up to 2 years post-infection, although the clinical significance is unclear. [6][7][8][9] Recent studies assessing protein and RNA in plasma reported antigen detection in small cohorts of individuals post-COVID, 10,11 but their conclusions were limited by sporadic detection at or near the assay quantification limit and a lack of comparison to a large number of true negative control samples.…”

“…Use of small and non-representative sample sizes, unclear documentation of complicating vaccination and reinfection histories, and, most importantly, lack of a sizeable true-negative comparator group to assess assay specificity all threaten conclusions about the existence, frequency, and duration of viral persistence. [9][10][11][12][13][14][15][16] To address these limitations, we evaluated the presence of SARS-CoV-2 antigens in plasma in a large, well-characterized group of persons at several time points in the first 14 months of the post-acute phase of SARS-CoV-2 infection, most of whom were studied prior to widespread vaccination or reinfection. To understand the specificity of our findings, we compared them to a large number of persons studied prior to 2020, who, by definition, were SARS-CoV-2-uninfected.…”

Association of nirmatrelvir for acute SARS‐CoV‐2 infection with subsequent Long COVID symptoms in an observational cohort study

“…3,4 Recent studies suggest viral persistence in a subset of individuals with PASC, including prolonged gastrointestinal shedding, ongoing Spike and Nucleocapsid antigen in neuronal and astrocytic exosomes, and evidence of persistent viral RNA or proteins in deep tissues and plasma. [5][6][7][8][9][10] Among high-risk, unvaccinated, nonhospitalized individuals with symptomatic COVID-19, nirmatrelvir, a novel orally-administered SARS-CoV-2 main protease (M pro ) inhibitor in combination with ritonavir reduces viral load and progression to severe disease. 11 Anecdotal reports suggest that nirmatrelvir may improve Long COVID symptoms.…”

“…Higher acute viral load or prolonged shedding may be associated with increased risk 3,4 . Recent studies suggest viral persistence in a subset of individuals with PASC, including prolonged gastrointestinal shedding, ongoing Spike and Nucleocapsid antigen in neuronal and astrocytic exosomes, and evidence of persistent viral RNA or proteins in deep tissues and plasma 5–10 …”