Detection of SARS-CoV-2 genome and whole transcriptome sequencing in frontal cortex of COVID-19 patients

Abstract

SARS-Cov-2 infection is frequently associated with Nervous System manifestations. However, it is not clear how SARS-CoV-2 can cause neurological dysfunctions and which molecular processes are affected in the brain. In this work, we examined the frontal cortex tissue of patients who died of COVID-19 for the presence of SARS-CoV-2, comparing qRT-PCR with ddPCR. We also investigated the transcriptomic profile of frontal cortex from COVID-19 patients and matched controls by RNA-seq analysis to characterize the transcriptional signature. Our data showed that SARS-CoV-2 could be detected by ddPCR in 8 (88%) of 9 examined samples while by qRT-PCR in one case only (11%). Transcriptomic analysis revealed that 11 genes (10 mRNAs and 1 lncRNA) were differential expressed when frontal cortex of COVID-19 patients were compared to controls. These genes fall into categories including hypoxia, hemoglobin-stabilizing protein, hydrogen peroxide processes. This work demonstrated that the quantity of viral RNA in frontal cortex is minimal and it can be detected only with a very sensitive method (ddPCR). Thus, it is likely that SARS-CoV-2 does not actively infect and replicate in the brain; its topography within encephalic structures remains uncertain. Moreover, COVID-19 may have a role on brain gene expression, since we observed an important downregulation of genes associated to hypoxia inducting factor system (HIF) that may inhibit the capacity of defense system during infection and oxigen deprivation, showing that hypoxia, well known multi organ condition associated to COVID-19, also marked the brain.

Multi-Data Integration Towards a Global Understanding of the Neurological Impact of Human Brain Severe Acute Respiratory Syndrome Coronavirus 2 Infection

“…Also, we found four common deregulated genes (INP5D, PRKCA, LRP1, and FCGR2A) in another study focused on the following brain regions: the dorsolateral prefrontal cortex, the medulla oblongata, and the choroid plexus GSE164485 ( Gagliardi et al, 2021 ). We also found other representatives of the same family for others genes.…”

“…The HIF3A, RGS5, and HBA2 genes were validated by quantitative PCR (qPCR) method. In addition, Gagliardi et al (2021) (Fullard et al, 2021 ) considered that these genes are the most deregulated (mRNA encoding the HBA hemoglobin subunits upregulated, and the SLC14A1, HIF3A, and RGS5 genes downregulated), and they are associated with hypoxia and inflammation.…”

SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19

“…In our comprehensive survey ( 154 ) of 16 brain regions of 20 COVID-19 cases, SARS-CoV-2 RNA was detected in only 2.5% (7/320) of sampled brain regions, and in only 4 of 20 cases (20%). However, differing PCR protocols have differing sensitivity and specificity ( 16 , 19 , 40 , 158–161 ) and therefore the true prevalence of viral brain entry may be difficult to establish. When we repeated our RT-PCR screening on OB, AMY and ENT with additional primers and probes for the E, N1, N2, RdRp, and S genes, we found more cases with Ct 40 or lower in OB, for a total of 8/21 (38%), but no additional new positive regions.…”

Investigating underlying human immunity genes, implicated diseases and their relationship to COVID-19

“…The genomic and transcriptomic basis of the complications associated with COVID-19 has not yet been fully determined [ 107 ]. We speculate that COVID-19 patients with inborn errors of IFNAR1 , IFNAR2 , TLR3 , IRF7 and IRF3 may also be indicative of viral hepatitis.…”