Laotian Bat Sarbecovirus BANAL-236 Uses ACE2 to Infect Cells by an Unknown Mechanism

TL;DR

This study analyzes the unique genomic features of bat sarbecovirus BANAL-236, revealing non-canonical UTR structures that suggest it employs an unknown mechanism for replication and infectivity, distinct from other coronaviruses.

Contribution

It uncovers unprecedented UTR structures in BANAL-236, indicating a novel replication and infectivity mechanism in sarbecoviruses.

Findings

BANAL-236 has non-canonical, highly stable duplex RNA structures in UTRs.

It lacks eight obligate cis-acting elements essential for known coronavirus replication.

BANAL-236 likely uses an entirely new mechanism for replication and infectivity.

Abstract

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.