REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-amyloid oligomer	Sigma-Aldrich	Cat#AB9234; RRID: AB_11214948
Rabbit polyclonal anti-human ACE2	Abcam	Cat# ab15348; RRID: AB_301861
Goat polyclonal anti-ACE2	R&D Systems	Cat#AF933; RRID: AB_355722
Guinea pig polyclonal anti-Aquaporin 4	Synaptic Systems	Cat#429004; RRID: AB_2802156
Rat monoclonal anti-human CD66acd (clone YTH71.3)	Bio-Rad	Cat#MCA1147G; RRID: AB_2077339
Rat monoclonal anti-mouse CD8a (clone 53-6.7)	Invitrogen	Cat#14-0081-82; RRID: AB_467087
Rabbit monoclonal anti-Claudin-5 (clone EPR7583)	Abcam	Cat#ab131259; RRID: AB_11157940
Goat polyclonal anti-Collagen Type IV	Sigma-Aldrich	Cat#AB769; RRID: AB_92262
Rabbit polyclonal anti-Myelin basic protein, degraded	Us Biological	Cat#M9758-04; RRID: N/A
Mouse monoclonal anti-dsRNA (clone J2)	SciCons	Cat#10010200; RRID: AB_2651015
Chicken polyclonal anti-GFAP	Abcam	Cat#ab4674; RRID: AB_304558
Rabbit polyclonal anti-Iba1	Fujifilm Wako	Cat#019-19741; RRID: AB_839504
Mouse monoclonal anti-Iba1 (clone NCNP27)	Fujifilm Wako	Cat#013-27593; RRID: N/A
Guinea pig polyclonal anti-MAP2	Synaptic Systems	Cat#188004; RRID: AB_2138181
Rabbit monoclonal anti-human HLA-E (clone JF10-38)	Novus Bio	Cat#NBP2-66946; RRID: N/A
Mouse monoclonal anti-human HLA-DR (clone LN3)	BioLegend	Cat#327002; RRID: AB_893582
Mouse monoclonal anti-human HLA-DR (clone LN3)	Invitrogen	Cat#MA5-11966; RRID: AB_10979984
Human monoclonal anti-myelin basic protein (clone IGX3421)	Abcam	Cat#ab209328; RRID: AB_2818988
Mouse monoclonal anti-human myeloperoxidase (clone 2C7)	Bio-Rad	Cat#MCA1757; RRID: AB_2146467
Guinea pig polyclonal anti-NeuN	Synaptic Systems	Cat#266004; RRID: AB_2619988
Mouse monoclonal anti-NeuN (clone A60)	Sigma-Aldrich	Cat#MAB377; RRID: AB_2298772
Mouse monoclonal anti-Neurofilament H (clone SMI32)	BioLegend	Cat#801701; RRID: AB_2564642
Chicken polyclonal anti-Neurofilament heavy polypeptide	Abcam	Cat#ab4680; RRID: AB_304560
Mouse monoclonal anti-Neurofilament 70 kDa (clone DA2)	Sigma-Aldrich	Cat#MAB1615; RRID: AB_94285
Rabbit polyclonal anti-Olig-2	Sigma-Aldrich	Cat#AB9610; RRID: AB_570666
Mouse monoclonal anti-human Pan-Neuronal Neurofilament (clone TNJ-312)	Creative Diagnostics	Cat#DMAB7133; RRID: AB_2391764
Guinea pig polyclonal anti-Parvalbumin	Synaptic Systems	Cat#195004; RRID: AB_2156476
Goat polyclonal anti-PSD95	Abcam	Cat#ab12093; RRID: AB_298846
Mouse monoclonal anti-SARS/SARS-CoV-2 Nucleocapsid protein (clone E16C)	Invitrogen	Cat#MA1-7403; RRID: AB_1018420
Rabbit polyclonal anti-SARS-CoV-2 Spike Protein	Abcam	Cat#ab272504; RRID: AB_2847845
Human monoclonal anti-SARS-CoV-2 Spike Protein RBD (clone T01KHu)	Invitrogen	Cat#703958; RRID: AB_2866477
Guinea pig polyclonal anti-Synaptophysin 1	Synaptic Systems	Cat#101004; RRID: AB_1210382
Guinea pig polyclonal anti-Tight Junction Protein 1 (ZO-1)	Novus Bio	Cat#NBP1-49669; RRID: AB_10011789
Bacterial and virus strains
SARS-CoV-2 2019-nCoV/USA-WA1/2020	BEI Resources	NR-52352
Biological samples
Rhesus macaque CNS tissues (brain, vessels, leptomeninges, and choroid plexus)	CNPRC, University of California Davis	N/A
Chemicals, peptides, and recombinant proteins
DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)	Invitrogen	Cat#D1306
ProLong Gold antifade reagent	Invitrogen	Cat#P36930
Bovine serum albumin	Sigma-Aldrich	Cat#A9647
Donkey serum	Sigma-Aldrich	Cat#D9663
Goat serum	MP Biomedicals	Cat#2939149
Target Retrieval Solution	Dako	Cat#S1700
Autofluorescence Eliminator Reagent	EMD Millipore	Cat#2160
Experimental models: Organisms/strains
Rhesus macaque (Macaca mulatta)	CNPRC, University of California Davis	N/A
Software and algorithms
ZEN (Blue Edition, version 2.3)	Carl Zeiss	https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html
Imaris (version 9.8)	Bitplane/Oxford Instrumentals	https://imaris.oxinst.com/
Adobe Photoshop 2022	Adobe	https://www.adobe.com/products/photoshop.html
Adobe Illustrator 2022	Adobe	https://www.adobe.com/products/illustrator.html
GraphPad Prism (version 9)	GraphPad/Dotmatics	https://www.graphpad.com/scientific-software/prism/