Preprint Multimodal Molecular Imaging Reveals Tissue-Based T Cell Activation and Viral RNA Persistence for Up to Two Years Following COVID-19, 2023, Peluso +

Multimodal Molecular Imaging Reveals Tissue-Based T Cell Activation and Viral RNA Persistence for Up to Two Years Following COVID-19
Michael J Peluso; Dylan M Ryder; Robert Flavell; Yingbing Wang; Jelena Levi; Brian H LaFranchi; Tyler-Marie M Deveau; Amanda M Buck; Sadie E Munter; Kofi A Asare; Maya Aslam; Walter Koch; Gyula Szabo; Rebecca Hoh; Monika Deswal; Antonio Rodriguez; Melissa Buitrago; Viva Tai; Uttam Shrestha; Scott Lu; Sarah A Goldberg; Thomas Dalhuisen; Matthew S Durstenfeld; Priscilla Y Hsue; J D Kelly; Nitasha Kumar; Jeffrey N Martin; Aruna Gambhir; Ma Somsouk; Youngho Seo; Steven G Deeks; Zoltan G Laszik; Henry F VanBrocklin; Timothy J Henrich

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 for in situ hybridization 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.

Link | PDF (Preprint: MedRxiv)

 

With the caveat that tissue biopsies were only looking at Long-Covid patients, this study looks very substantial. I don't recall a similar PET study in post-Ebola, if someone knows of one, could they please direct me to it to see how well they line up?

 

My own experience of Covid and continuing symptoms makes me think that residual virus maybe in gut is very plausible. I am not sure how it explains feeling terrible but it might have to do with T cells.

I am a bit worried about the methodology here though. It says pre-pandemic controls. For PET I think you need simultaneous control data and blinding because it is so easy for sensitivity to shift. I am also surprised by a T cell signal in brain stem and spinal cord, where T cells do not normally traffic in any number. Gut is always full of lymphocytes in comparison.

RNA is also maybe a tricky way to document persistent virus but techniques may be more reliable now.

 

Small study of 24 total individuals only 6 of which are pre pandemic controls - and whose images are obtained separate from the work in this paper. They say their dye [18F]F-AraG works by becoming phosphorylated by cytoplasmic deoxycytidine kinase (dCK) and deoxyguanosine kinase (dGK) - markers of activated T cells - therefore getting trapped in the cells. They report big differences in uptake of [18F]F-AraG in lots of places eg brain stem and spinal cord, heart, gut wall. Everything is multiple test corrected with benjamini-hochberg, SUVmax means maximum Standardised Uptake Value of [18F]F-AraG:



They then compare those with and without long covid symptoms, and those pre and post 90 days since covid infection - these comparisons shouldn't be affected by the problems of differential sensitivity of the equipment over years as @Jonathan Edwards suggests could be the case for the above comparisons. There are no statistically significant differences in any of the regions of interest between long covid and non long covid patients, although across the board there appears to be slightly higher [18F]F-AraG uptake in long covid. Similarly just one significant result observed between pre and post 90 days (reduction in uptake in right colon wall at post 90 days), though with a possible slight reduction in uptake across the board in the post 90 days group:

 

Interesting why is that? I'm familiar with in situ hybridisation from developmental biology where it is a routine way of looking at expression domains. Why is it a problem with viruses? low copy number or maybe the RNA being bound up in viral assembly proteins? In the lab I formerly worked in we used single molecule FISH to get incredible sensitivity by using multiple probes each with different fluorophores that plaster the RNA along its whole length, allowing you detect even just a single molecule of RNA (as the name suggests). Again this was in a developmental biology context.

Seems like they're using standard in situ hybridisation here on colon biopsies from control and post covid ( not necessarily long covid) patients:

Spike protein RNA lighting up in green - CD68 and CD3 are markers I believe for macrophages and T cells respectively. They say they see Spike protein RNA in all 5 of the patients they looked at and none of the controls:

 

SUV is Standard Uptake Value.

*That ref is SARS-CoV-2 infection and persistence in the human body and brain at autopsy (2022, Nature)

ETA: a quick hunt around gives a couple of recent papers that discuss T Cells in the CNS —

Peripherally induced brain tissue–resident memory CD8+ T cells mediate protection against CNS infection (2020, Nature Immunology)
Tissue-resident memory T cells populate the human brain (2018, Nature Communications)

 

Also posted a thread for Tissue-resident memory T cells invade the brain parenchyma in multiple sclerosis white matter lesions (2020, Brain)

 

Just that in the days when I was involved in chasing nucleic acids with PCR specificity was a big issue. Specificity with fluorescence staining is also a big issue if you are not careful. I realise that these things can work well when done carefully but these days so much data seems to turn out to be substandard, even if techniques have improved.

If there is a bandwagon, people will get on.

 

Appreciating this UCSF group's work. We have most already in threads —

• A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection (2023, Nature)
• Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients (2023, JCI Insight)
• Reduced Exercise Capacity, Chronotropic Incompetence, and Early Systemic Inflammation in Cardiopulmonary Phenotype Long Coronavirus Disease 2019 (2023, The Journal of Infectious Diseases)
• Chronic viral coinfections differentially affect the likelihood of developing long COVID (2023, The Journal of Clinical Investigation)
• Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2 (2023, Preprint: BioRxiv)
• Use of Cardiopulmonary Exercise Testing to Evaluate Long COVID-19 Symptoms in Adults: A Systematic Review and Meta-analysis (2022, JAMA Network Open)
• SARS-CoV-2 and Mitochondrial Proteins in Neural-Derived Exosomes of COVID-19 (2022, Annals of Neurology)
• Long-term SARS-CoV-2-specific immune and inflammatory responses in individuals recovering from COVID-19 with and without post-acute symptoms (2021, Cell Reports)
• Characterization and Biomarker Analyses of Post-COVID-19 Complications and Neurological Manifestations (2021, Cells)

 

Michael Peluso interviewed on The Long Covid Sessions podcast, discusses this pre-print at 35:36.