Abstract
Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered. Results: Here we show that genomes from SARS-CoV-2 and from closely related coronaviruses are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.
Highlights
From the beginning of the COVID-19 pandemic, in March 2020, evidence was put forward that the outbreak of novel coronavirus SARS-CoV-2 within the human population was most likely a product of natural evolution[1]
To transform yeast into a synthetic host for viral replication, the scheme has been to co-express viral RNA dependent RNA polymerase (RdRp) and, if necessary for replication, additional viral factors on plasmids under the control of auxotrophic yeast selectable markers (YSM)[16]
To obtain a genome-wide view of this homology signal we stacked together all homologous regions weighted by their individual alignment scores S, which resulted in an accumulated homology profile, Profiled alignment scores (pS)
Summary
From the beginning of the COVID-19 pandemic, in March 2020, evidence was put forward that the outbreak of novel coronavirus SARS-CoV-2 within the human population was most likely a product of natural evolution[1]. The natural evolution hypothesis of SARS-CoV-2 origin is currently not without considerable limitations: first, the difficulty in characterizing the evolutionary origin of the unusual polybasic (RRAR) furin cleavage site at the S1/S2 junction of the SARS-COV-2 spike (S) glycoprotein[4]; second, the discrepancy between an exponentially suppressed tropism of SARS-CoV-2 in Rhinolophus sinicus bat cells[5] and the high susceptibility of SARS-CoV-2 toward cell entry via Rhinolophus sinicus angiotensin-converting enzyme 2, its primary entry receptor[6]; and third, the persistent inability to identify an intermediate ancestral host between human and the horseshoe bat Rhinolophus affinis This species was reported to be the host of coronavirus RaTG137,8, currently the isolate with the highest sequence similarity to the SARS-CoV-2 genome, which is located on the same phylogenetic branch as Rhinolophus sinicus bat coronavirus[9]. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells
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