BREAKING! COVID-19 News: Discovery Of SARS-CoV-2 Short RNAs By Scientist From John Hopkins Is A Big Gamechanger In Terms Of Pathogenesis And Long COVID!

COVID-19 News: Scientist from John Hopkins University-USA along with researchers from the German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)-Germany along with Heidelberg Biolabs GmbH-Germany have discovered the presence of distinct and unique viral short RNAs in the SARS-CoV-2 RNA transcriptome and this new startling discovery could have major ramifications in terms in what we had earlier assumed we have known about the pathogenesis of the virus and also about the development of various issues during COVID-19 infections and also in Long COVID!


 
Past studies have already shown that short RNAs of other viruses also play a role as modulators of host gene expression and also in the pathogenesis.
https://www.frontiersin.org/articles/10.3389/fmicb.2020.614231/full
 
Past research has also validated the involvement of small RNAs in various cancers, disorders of neuronal development, cardiac hypertrophy, and skin diseases such as psoriasis. 
https://pubmed.ncbi.nlm.nih.gov/19119093/
 
We at Thailand Medical News in our past COVID-19 News coverage in September 2022 and also in or earlier articles since early 2020 had warned about the presence of such viral peptides and small RNAs that are not part of the genomic structure of the virus but are still spawned by the virus during replication and other processes that can also affect the human host cellular machinery, genes and critical proteases but as usual, many racist white researchers from the United Kingdom and United States dismissed our hypothesis!
https://www.thailandmedical.news/news/breaking-long-covid-is-a-misnomer-the-conditions-are-being-caused-by-viral-persistence-and-viral-peptides-similar-to-retrotransposons-and-introns
 
RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs (svRNAs) generated by SARS-CoV-1 and SARS-CoV-2 remained largely unexplored, mainly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing.
 
The study team from John Hopkins and DKFZ/ DKTK by analyzing publicly available small RNA-seq datasets, observed that human cells infected by SARS-CoV-1 or SARSCoV-2 produce multiple short viral RNAs (svRNAs), ranging in size from 15 to 26 nt and deriving predominantly from (+) RNA strands.
 
More importantly, the study team discovered the presence of the five most abundant SARS-CoV-2 svRNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by qPCR.
 
The copy number of the observed SARS-CoV-2 svRNAs dramatically exceeded the expression of previously reported viral miRNAs in the same cells.
 
The study team hypothesize that the reported SARS- CoV-2 svRNAs could also serve as biomarkers for early infection stages due to their high abundance.
 
The study findings also showed that both SARS-CoV-1 and SARS-CoV-2 infection induced up- and down-regulation of multiple endogenous human short RNAs that align predominantly to protein-coding and lncRNA transcripts.
 
Interestingly, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various hg38 sequences, suggesting opportunities to investigate regulatory roles of svRNAs during infection.
 
The study team stressed that further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.
 
Hopefully the discovery of these small RNAs or viral peptides by researchers from Joh Hopkins will pave the way for more research as to how they also play a role in pathogenesis and during COVID-19 infection and in Long COVID.
 
The study findings were published on a preprint server and are currently being peer reviewed.
https://www.biorxiv.org/content/10.1101/2022.12.27.522023v1
 
To date, the ongoing COVID-19 pandemic has resulted in widespread mortality and morbidity across the globe. . There is still so much that is not known about the virus and its pathogenesis etc and also about the molecular perturbations associated with COVID-19.
 
Many past studies of the SARS-CoV-2 transcriptome involve long RNA biotypes, while small RNAs need further research.
 
Furthermore, according to the study team, the known comparative stability of small RNAs could prove useful in developing prognostic and diagnostic tools for SARS-CoV-2 detection in samples for timely diagnosis. 
 
The study team reported small RNA expression perturbations observed after SARS-CoV-2 and SARS-CoV-1 infection.
 
In order to assess the characteristics of short viral RNAs (svRNAs), the study team studied small RNA-sequencing datasets derived from Calu-3 cells that were either SARS-CoV-2 or SARS-CoV-1-infected. Small RNA-sequencing reads observed in the mock as well as infected cells, were first cut from adapters before they were selected according to size and aligned as per the related viral reference genome.
 
The study team also calculated the count-per-million (CPM) values associated with the reads mapped for each reference.
 
The study team also estimated the distribution pattern associated with viral short RNA (vsRNA) reads and detected virus-specific fragments mapped to different locations.
 
The study team said that this was achieved by extracting reads that aligned to either SARS-CoV-2 or SARS-CoV-1 genomes after eliminating overlapping fragments. Furthermore, RNA from uninfected and uninfected A549 ACE-2 cells was used to analyze the detection of five selected small RNAs.
 
The study team performed reverse transcription and polyadenylation before real-time quantitative polymerase chain reaction (qPCR). The research team also assessed three negative control primers that were annealed to regions within the SARS-CoV-2 genome. Additionally, differential expressions analysis was conducted for mock-infected control cells versus SARS-CoV-2 and SARS-CoV-2-infected cells 24 hours after infection.      
 
Interestingly, the study findings showed that infection with SARS-CoV-2 or SARS-CoV-1 resulted in the significant proliferation of short RNA fragments which were obtained from reverse as well as forward viral RNA genome strands 4-, 12-, and 24-hours post-infection of the Calu-3 cells. Also, the number of reads that were mapped as per the forward viral RNA strands was almost 20 times more than those that were aligned as per the reverse strands. This could be a result of higher protection of positive genome strands by either ribosomes or other related proteins.
 
The study team also noted that the viral sequences, which were a perfect match within the small RNA fractions of infected Calu-3 cells, were 2.83% of the total SARS-CoV-1-infected and 1.51% of the total SARS-CoV-2-infected cells. This approximately two-fold distinction could be because of the remarkably higher cytotoxicity associated with SARS-CoV-2.
 
The study team also noted that several reads aligned to single positions in the SARS-CoV-2 or SARS-CoV-1 genomes.
 
Importantly, five putative forward-strand svRNAs showed a significantly increased signal of infected cells in comparison to the background. Furthermore, the influence of the poly(A) tails addition to the small RNAs suggested that the detected vsRNAs had amplification from small RNA templates instead of full-length viral RNAs.
 
It was also found that for two of the forward-strand svRNAs, a similar signal was observed for the uninfected and infected cells. Moreover, the third negative control was found to be induced within the infected cells. Yet, the study team noted that amplification was found later than that in the putative SARS-CoV-2 small RNA having the most recent amplification.
 
Significantly, this implied that the SARS-CoV-2 genome could encode small RNA fragments having a discrete size. 
Importantly, differential expression analysis showed that a significantly higher number of small RNA transcripts displayed differential expression in SARS-CoV-2 as compared to that in SARS-CoV-1 infection.
 
Among the 14,747 transcripts that remained post-low-expression filtering, zero down- and 12 up-regulated sequences were detected in the SARS-CoV-1 infection. On the other hand, 120 down- and 268 up-regulated sequences were detected in the SARS-CoV-2 infection.
 
The research findings also highlighted significantly different reactions of small RNA expressions when Calu-3 cells were infected with SARS-CoV-2 and SARS-CoV-1.
 
It was noted that SARS-CoV-2 elicited differential expression of a huge number of small RNAs in comparison to that in SARS-CoV-1 infection. Furthermore, the small RNA fragments aligned primarily to IncRNA and protein-coding genes.
 
Also, while substantial alterations were observed in small RNA expression, a few micro RNAs (miRNAs) were impacted, which suggested the limited function of host miRNAs in infection progression.
 
The study team believes that further detailed research is warranted to assess the mechanisms involved in the biological function as well as the biogenesis of svRNAs.
 
The study team also noted that it is possible that svRNAs derived from SARS-CoV-2 could serve as novel ultrasensitive biomarkers for early COVID-19 diagnosis or identification of persistent infection.
 
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