Table 4.

Advantages and limitations of the methods that have been used to prove SARS-CoV-2 in brain tissues

Method	What is detected?	Advantages	Limitations
Plaque formation (PF)	Replicating virus	Evidence for replication of virus	No cellular localization
RT-qPCR (PCR)	Virus mRNA	Highly sensitive for virus mRNA	Contamination may give false positives, no cellular localization, significance of subgenomic vs. genomic RNA for replication still uncertain
In situ hybridization (ISH)	Virus mRNA	Sensitive for virus mRNA
Immunocytochemistry	Virus protein (antigen)	Cellular localization
For nucleocapsid protein (ICn)	Nucleocapsid protein	Cellular localization	No distinction between shed protein and entire virus
For spike protein (ICs)	Spike protein	Cellular localization	No distinction between shed protein and entire virus
Electron microscopy	Virus	Precise tissue localization	Very difficult identification of virus even with good morphology