Hello! I'm Xiaofang Jiang from National Library of Medicine. I'm excited to tell you the work
done by Yiyan, Keith, and Rafa in our group. In this work, we identified and characterized
the putative host-derived insertions in the genomes of circulating SARS-CoV-2 variants.
Throughout the COVID-19 pandemic, analysis of SARS-CoV-2 genomes has revealed the presence
of the insertions in multiple globally circulating lineages, including the Omicron variant.
The human genome has been suggested to be the source of some of the large insertions in the
SARS-CoV-2 genomes, but the evidence for this was lacking. In this study,
we attempted to address this important scientific question:
Could SARS-CoV-2 insertions be derived from host genetic material?
In detail, we managed to answer the following three sub-questions:
Do host-virus chimeric reads exist? Do chimeric reads have any patterns?
Do long insertions originate from host RNAs? To investigate if host-virus chimeric
reads existed, we utilized Nanopore Direct RNA-sequencing, DRS, data from 30 SARS-CoV-2
infected cell line samples. Compared with other sequencing technology, DRS can avoid chimera
formation during sample preparation, allowing us to identify real host-viral chimeric RNAs.
[P3] In total, 1366 Host-viral chimeric reads were detected in 16 samples. These chimeric reads were
rare, making up 0.206% of only one sample, but less than 0.06% of the other 15 samples.When
available, paired end sequencing data was used to corroborate the presence of these chimeric reads
confirming that they were rare, but present in the samples. These results suggested that
host-viral chimeric RNA formation was rare and likely the result of stochastic processes.
[P4] We then examined the reads to see if there were any patterns in how they were formed. Both
viral to host and host to viral chimeric sequences were identified in nearly equal proportions across
the samples, suggesting that the chimeric RNAs don’t have a preference for either organization.
We also found that the junction sites of the chimeric reads tend to be in the dense coding
region near the 3’ end of the SARS-CoV-2 genome and tend to form in non-base paired segments of
the viral RNA. [P5]
An examination of the types of human geneS found in the chimeric sequences revealed an
enrichment of highly expressed genes. Most notably was a significant enrichment for long non-coding
RNAs (lncRNAs), which were forming parts of the chimeric reads at a much higher abundance compared
to their presence in the human genome. [P6]
Lastly, we attempted to answer whether long inserts could be originating from
host RNAsm by systematically analyzing millions of SARS-CoV-2 genomes in GISAID, we identified
36 large insertions of high confidence. After verification, only 2 insertions of putative
host origin were further investigated. [P7] One of them is a 27 nt long insert,
found in seven SARS-CoV-2 genomes forming a monophyletic group belonging to the AY.103
group of the 21J delta lineage. It is a 100% match to the human 28S rRNA, and located at the
Nsp3 protein of SARS-CoV-2 genome. [P8] Another insert is 24 nt long and
found in 2 genomes in a clade belonging to the B.1.1.7 group of the 20I alpha lineage.
It may be originated from human 18s rRNA and located at the SARS-CoV-2 ORF7a protein.
In summary, our results provided the direct evidence for the formation of
viral-host chimeric sequences and a integration of host genetic material in SARS-CoV-2 genomes.
This highlights the potential role of host-derived insertions in viral evolution.