  Specific elements of viral genomes regulate interactions within host cells.
Here, we calculated the secondary structure content of >2500 coronaviruses and
computed >100000 human protein interactions with severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are
the most structured elements in the viral genome and the 5 prime end has the
strongest propensity to associate with human proteins. The domain encompassing
nucleotides 23000-24000 is highly conserved both at the sequence and structural
level, while the region upstream varies significantly. These two sequences code
for a domain of the viral protein Spike S that interacts with the human
receptor angiotensin-converting enzyme 2 (ACE2) and has the potential to bind
sialic acids. Our predictions indicate that the first 1000 nucleotides in the 5
prime end can interact with proteins involved in viral RNA processing such as
double-stranded RNA specific editases and ATP-dependent RNA-helicases, in
addition to other high-confidence candidate partners. These interactions,
previously reported to be also implicated in HIV, reveal important information
on host-virus interactions. The list of transcriptional and
post-transcriptional elements recruited by SARS-CoV-2 genome provides clues on
the biological pathways associated with gene expression changes in human cells.
