How the Novel Coronavirus Attacks the Brain

Presentations of patients infected with SARS-CoV-2 are varied and unique in their neurological manifestations, including loss of smell, confusion, and altered mental status, when the course of the novel coronavirus disease (COVID-19) is complicated by insults to the neurological system. The nasopharynx and nasal cavities are reservoirs for high viral load and olfactory tissue contains key receptors and proteases that may facilitate viral entry and replication at the cellular level. Downstream mechanisms of brain cellular invasion and integration remain poorly understood, particularly how SARS-CoV-2 may be instigating diffuse neurological effects. Patients with COVID-19 sustain a severe cytokine storm, the interplay between inflammation and coagulation combined with endothelial damage, may lead to thrombo-embolic events, and microglia activation leading to neuronal damage. Patients also present with long-term brain sequela of COVID-19, including "brain fog," difficulties concentrating, impaired short-term and working memory, fatigue, headache, dysautonomia, and insomnia, and the neuropathological bases of these symptoms are unknown. Appropriate evaluation of specific brain regions from deceased patients with COVID-19 who did and did not present with neurological symptoms will allow for improved comprehension of possible targets to limit brain damage. Additionally, lessons from how SARS-CoV-2 affects the brain may provide insight into generalizable mechanisms for effects of neuroinflammation on neurodegenerative diseases. We aim to determine: 1. Whether COVID-19 patients with neurological presentations at the time of intake (NP-COVs) have altered brain expression of genes regulating inflammation and coagulation compared to those without (COVs) and non-COVID-19 age and sex matched controls (CONT). We will map the whole transcriptome in the entire brain tissue section using single nuclei RNA sequencing (sn-RNA-seq, 10X Genomics). We will validate and quantify candidate mRNAs expression on neurons, glia, and vasculature-associated cells, using Duplex RNAscope® (ACDBio), as we successfully performed in CONT. 2. Whether NP-COVs have elevated brain pro-inflammatory markers. We will run a Human Cytokine/Chemokine/Growth Factor Panel (48 Plex Kit, Milliopre) and quantify cytokines, chemokines and growth factors. We will map their expression on neurons and glia, using double immunohistochemistry (IHC), as we piloted in CONT. 3. If NP-COVs have elevated brain microglia activation. Using double-IHC for microglia markers TSPO (translocator protein), CD11b, Iba1 (Ionized calcium binding adaptor molecule), and neuronal markers, and stereology for cell quantification, we will compute activated (amoeboid) and resting (small cell body and elaborated thin processes) microglia, and map spatial relationship to neurons. 4. If NP-COVs have reduced neuronal density and dendrite arborization. Using double-IHC for neuronal marker NeuN and neurofilament, Stereoinvestigator and Neurolucida (MBF Inc.), will quantify neuron density, dendrite length and arborization, as in our pilot studies.