Extended Data Fig. 4: Colocalization analysis of SARS-CoV-2 N protein in glial or vascular brain cells.

a-c, High-resolution Z-projection confocal images from the cortex of a SARS-CoV-2 infected K18-hACE2 mouse (6 dpi), after immunohistological detection of SARS-CoV-2 N protein (green and GFAP (red). The insets are depicted at higher magnification, in b and c, exhibiting single confocal planes (z = 14 and 3 in b; z = 4 in c) of 405 nm z-depth optic resolution and the orthogonal projections. Note the absence of colocalization between green (SARS-CoV-2 N protein) and red (GFAP) fluorescence signals. Arrows in c indicates an example of a GFAP+ process without SARS-CoV-2+ fluorescence signal. d, Cortical confocal images from a SARS-CoV-2 infected K18-hACE2 mouse (6 dpi) immunostained with SARS-CoV-2 N protein (green) and a vascular (IB4; red) marker. Note the presence of a discrete dot of green fluorescence signal (SARS-CoV-2 N protein+) in vascular IB4+ cell, pointed by the arrow and showed by the YZ-orthogonal projection in the left (merge) panel. e, High-resolution Z-projection confocal images from the cortex of SARS-CoV-2 infected K18-hACE2 mouse (6 dpi) immunolabelled with SARS-CoV-2 N protein (green) and the microglial marker IBA1 (red), the inset is showed at higher magnification in h. f,g. High resolution confocal image and 3D reconstructions showing the phagocytic activity of IBA1+ cells on a SARS-CoV-2 infected neuron (f) or brain vascular cells marked by arrows in g. h. High resolution confocal image of the region marked by the inset in e. Arrows and insets show the presence of discrete dots of green fluorescence signal (SARS-CoV-2 N protein+) inside of a microglial cell. These are exhibited at higher magnification in h’ and h’ as single confocal planes (z = 3 and z = 17, respectively; 401 nm z-depth optic resolution) and orthogonal projections. The immunofluorescence stainings were performed in 3 independent experiments obtaining similar results, analyzing SARS-CoV-2 infected mice at 6 dpi, n = 6 (3 females and 3 males).