  A manuscript identified bat sarbecoviruses with high sequence homology to
SARS-CoV-2 found in caves in Laos that can directly infect human cells via the
human ACE2 receptor (Coronaviruses with a SARS-CoV-2-like receptor binding
domain allowing ACE2-mediated entry into human cells isolated from bats of
Indochinese peninsula, Temmam S., et al.). Here, I examine the genomic sequence
of one of these viruses, BANAL-236, and show it has 5-UTR and 3-UTR secondary
structures that are non-canonical and, in fact, have never been seen in an
infective coronavirus. Specifically, the 5-UTR has a 177 nt copy-back extension
which forms an extended, highly stable duplex RNA structure. Because of this
copy-back, the four obligate Stem Loops (SL) -1, -2, -3, and -4 cis-acting
elements found in all currently known replicating coronaviruses are buried in
the extended duplex. The 3-UTR has a similar fold-back duplex of 144 nts and is
missing the obligate poly-A tail. Taken together, these findings demonstrate
BANAL-236 is missing eight obligate UTR cis-acting elements; each one of which
has previously been lethal to replication when modified individually. Neither
duplex copyback has ever been observed in an infective sarbecovirus, although
some of the features have been seen in defective interfering particles, which
can be found in co-infections with non-defective, replicating viruses. They are
also a common error seen during synthetic genome assembly in a laboratory.
BANAL-236 must have evolved an entirely unique mechanism for replication, RNA
translation, and RNA packaging never seen in a coronavirus and because it is a
bat sarbecovirus closely related to SARS-CoV-2, it is imperative that we
understand its unique mode of infectivity by a collaborative, international
research effort.
