Researchers from Washington State University-USA and Tulane University School of Medicine, Louisiana_USA are warning that the newly discovered Khosta-2 which belongs to the same family of sarbecoviruses as the SARS-CoV-2 virus, is not only able to infect human using the same receptors but will be resistant to all current vaccines and monoclonal therapeutics and will be more far more worse in terms of disease severity.
The study findings were published in the peer reviewed journal: PLOS Pathogens.
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010828
Khosta 1 and 2 viruses are most closely related to other clade 3 RBD viruses, which have been found across a much wider geographic range than the clade 1 viruses [1,13,33,34].
As the researchers who initially discovered the Khosta viruses note with their findings: the Khosta bat sarbecoviruses are genetically distinct from human SARS-CoVs in that they lack genetic information encoding for some of the genes thought to antagonize the immune system and contribute to pathogenicity, such as Orf8 [12].
In the presence of trypsin, both Khosta-1 and -2 RBDs and spike were capable of infecting human cells, with Khosta-1 performing notably stronger than Khosta 2, however in our receptor-specific assays, only Khosta 2 could infect cells expressing human ACE2 without exogenous protease (Figs 1D–1G and 3).
In contrast to our earlier results with African clade 3 sarbecovirues on receptor-transfected BHKs, both the Uganda and Rwanda viruses were able to utilize human ACE2 in cells stably overexpressing the receptor [13] (Fig 1G). The approximate 10-fold entry signal measured in our assay is identical in strength to recent findings reporting that the Uganda virus RBD could use human ACE2 [9].
Thus, while BHK cells transfected with host receptors represent an effective method to distinguish the obvious receptor preference for coronaviruses, transduced human cell lines allow for improved detection of low-affinity interactions. Taken together, these findings from our study and others demonstrate low level human ACE2 usage across the RBD clade 3 sarbecoviruses.
A recent study has demonstrated a single point mutation, T498W, can be introduced into some clade 3 sarbecovirus spike RBDs, including Khosta 1, that broadens viral species tropism from bat to human ACE2 [10]. Curiously, we observed that while Khosta 1 spike was capable of infecting human cells in the presence of protease, Khosta 1 RBD failed to efficiently transduce cells over-expressing human ACE2 (Figs 1F, 1G and 3).
We have previously shown that a small number of clade 2 RBDs, such as As6526 and Rs4081, also exhibit protease-mediated, ACE2-independent entry, and similar phenotypes have been described for other bat coronaviruses [1,35]. Analogous to Khosta 1, the completely ACE2-independent RBD clade 2 sarbecovirus, Rs4081, also efficiently infects Huh-7 cells in the presence of trypsin [36].
Because not all of the RBD clade 2 and 3 sarbecoviruses exhibit trypsin-dependent entry in our comparative assays with chimeric spikes, these findings collectively suggest that some coronaviruses may infect human cells through a presently unknown receptor. Sarbecoviruses have been shown to co-circulate in bats, so this variation in receptor usage among closely related viruses may even represent an evolutionary strategy for viral persistence within the reservoir host population [2].
Current universal sarbecovirus vaccines in development include mostly clade 1 viruses and one of the clade 2 viruses but do not include any members from clade 3 [37,38]. Our results suggest there is little cross-reactivity between clade 1 and clade 3 RBDs that use human ACE2, even though their interactions are likely very similar (Figs 2 and 4C).
More concerning was our observation that serum from vaccinated individuals was less effective at neutralizing pseudotypes when just the SARS-CoV-2 RBD was replaced with the Khosta 2 RBD (Fig 4D–4G). These findings are not too surprising given that the Khosta 2 RBD only shares about 60% sequence identity with SARS-CoV-2, and the neutralizing antibodies elicited by the vaccines from Moderna or Pfizer are directed primarily toward the RBD [39] (Fig 4E and 4F).
Bamlanivimab makes contact with 17 residues on SARS-CoV-2 Wuhan strain, and Khosta2 shares only 10 or the 17 residues. Moreover, loss of bamlanivimab binding has been mapped to E484A and Q493R in Omicron [40,41]; Khosta2 encodes a G435 at a position analogous to E484 on SARS-CoV-2, providing a possible basis for escape from bamlanivimab.
Curiously, the Khosta 2 RBD is least similar to the currently circulating Omicron variant of SARS-CoV-2; with each new variant of concern decreasing in similarity to Khosta 2 (Fig 4H). Given that natural infection or vaccination with a whole spike raises antibodies directed at other regions of spike, it is still possible that new sarbecoviruses or recombinant SARS-CoV-2 would be neutralized by serum from some individuals.
Our findings with chimeric, SARS-CoV-2 spike show that just replacing the RBD is sufficient to reduce efficacy of SARS-CoV-2 spike-directed vaccines (Fig 4). However, sarbecovirus recombination in nature typically occurs via template switching resulting in acquisition of regions larger than the NTD [42].
Thus, a naturally recombinant virus with Khosta 2 may actually acquire more Khosta 2 spike, which as we show here with full protein, is also infectious against human cells and ACE2 (Fig 3). Taken together, our findings with the Khosta viruses underscore the urgent need to develop broader-protecting universal Sarbecovirus vaccines.
