Breakthrough gastrointestinal COVID and intra-host evolution consequent to combination monoclonal antibody prophylaxis

SARS-CoV-2 is known to infect gastrointestinal tissues, which may be a site for long term viral sequestration. We sequenced virus from three gastrointestinal tissues and from a rectal swab from one week post viral infection in a rhesus macaque that had been treated with a low dose of two monoclonal antibodies intended to prevent infection. We identified viral mutations in two of the four sites, possibly suggestive of compartmentalized replication and evolution. These data confirm reports of gastrointestinal viral infection and suggest this site to be a site for ongoing viral infection and replication and possibly a source of mutation accumulation, which may have important implications for both antiviral treatment and for viral spread within populations.