BREAKING! Brazil Study Involving Detailed Epitranscriptomic Analysis Shockingly Reveals That SARS-CoV-2 Alters RNA Of Infected Host Cells!

COVID-19 News: Shocking findings of a new study by researchers from the Center for Medical Bioinformatics and the Department of Microbiology, Immunology and Parasitology at Escola Paulista de Medicina, UNIFESP (Federal University of São Paulo)-Brazil has revealed that the SARS-CoV-2 also alters the RNA of infected host cells!


 
The study findings have numerous implications for the pathogenesis and also for issues seen in Long COVID manifestations.
 
The detailed study involving epitranscriptomics of the SARS-CoV-2 infected cell reveals its response to viral replication. Among various types of RNA nucleotide modifications, the m6A is the most common and is involved in several crucial processes of RNA intracellular location, maturation, half-life and translatability. This epitranscriptome contains a mixture of viral RNAs and cellular transcripts.
 
In a previous study, the research team presented the analysis of the SARS-CoV-2 RNA m6A methylation based on direct RNA sequencing and characterized DRACH motif mutations in different viral lineages.
https://pubmed.ncbi.nlm.nih.gov/34834915/
 
In this current study, the research team presented the analysis of the m6A transcript methylation of Vero cells (derived from African Green Monkeys) and Calu-3 cells (human) upon infection by SARS-CoV-2 using direct RNA sequencing data.
 
Detailed analysis of these data by nonparametric statistics and two computational methods (m6anet and EpiNano) showed that m6A levels are higher in RNAs of infected cells.
 
Subsequently, functional enrichment analysis revealed increased m6A methylation of transcripts involved in translation, peptide and amine metabolism. This analysis allowed the identification of differentially methylated transcripts and m6A unique sites in the infected cell transcripts.
 
The study findings presented indicate that the cell response to viral infection not only changes the levels of mRNAs, as previously shown, but also its epitranscriptional pattern. Also, transcriptome-wide analysis shows strong nucleotide biases in DRACH motifs of cellular transcripts, both in Vero and Calu-3 cells, which use the signature GGACU whereas in viral RNAs the signature is GAACU.
 
The study team hypothesizes that the differences of DRACH motif biases, might force the convergent evolution of the viral genome resulting in better adaptation to target sequence preferences of writer, reader and eraser enzymes.
 
This is the first study findings to date that report on m6A epitranscriptome of the SARS-CoV-2 infected Vero cells by direct RNA sequencing, which is the sensu stricto RNA-seq.
 
These study findings are not only worrisome but also foretell the magnitude of long COVID burden as time passes and the variety of health complications we can expect.
 
The study findings were published in the peer reviewed journal: Frontiers in Cellular and Infection Microbiology. https://www.frontiersin.org/articles/10.3389/fcimb.2022.906578/full
 
This is the first time since the COVID-19 pandemic started that a study has demonstrated that infection by SARS-CoV-2, the virus that cause s COVID-19, changes the functioning of host cell RNA.
 
While governments, health authorities, ‘paid’ prominent experts and COVID-19 News outlets are trying to downplay the seriousness of SARS-CoV-2 infections and claiming that infections are mostly mild or symptomatic, and that COVID-19 is now endemic and seasonal like common flu, the facts remain that as far as possible, people should avoid at all costs getting exposed to the SARS-CoV-2 as the kind of long-term damage it can do silently even with the least of symptoms is terrifying!
 
The study team’s analysis of 13 past datasets obtained during four studies of viral, human and animal cell RNA also had clearly shown the effects of the virus on infected host cells.
 
In this most recent study, the research team examined the epitranscriptome of Vero cells (derived from monkeys) and human Calu-3 cells by direct RNA sequencing.
 
Basically, an epitranscriptome is the collection of biochemical modifications of cell RNA, such as methylation.
 
First author, Dr Marcelo Briones, a professor at UNIFESP's Medical School (EPM) and a researcher affiliated with its Center for Medical Bioinformatics told Thailand Medical News, “The most important finding in this study was that infection by SARS-CoV-2 increases the level of m6a [N6-methyladenosine], a type of methylation, in host cells compared with non-infected cells.”
 
The process of methylation is a biochemical modification involving the addition of a methyl group to a substrate. It occurs in cells via the action of enzymes capable of transferring part of one molecule to another. This changes the behavior of proteins, enzymes, hormones and genes.
 
The study team demonstrated changes to infected cell RNA quantitatively by analyzing all the RNAs present in the cells and qualitatively by locating on a map the number of methylations per region in the nucleotides.
 
This research was a continuation of an earlier genomic analysis published in 2021, where the researchers analyzed the methylation pattern in SARS-CoV-2.
https://pubmed.ncbi.nlm.nih.gov/34834915/
 
Professor Briones added, "Methylation has two functions in viruses. It regulates protein expression, and it defends the virus against the action of interferon, a potent antiviral substance produced by the host organism."
 
The research team in both studies analyzed m6a because it is the most common type of RNA nucleotide modification and is involved in several significant processes, such as intracellular location and protein translation. RNA nucleotides contain nitrogenous bases (adenine, guanine, uracil, or cytosine) running along a single strand.
 
The research team also discovered that different strains of the virus displayed variations in the sequences of nitrogenous bases in their nucleotides.
 
Professor Briones said, "Some strains may be much more methylated than others. If so, they can proliferate better inside host cells.”
 
The research team also found that nucleotide sequences known as m6a DRACH motifs were slightly different in SARS-CoV-2 and in cells. In this acronym, which is frequently used in epigenetics, the letter D stands for adenine, guanine or uracil; R for adenine or guanine; A for the methylated residue; C for cytosine; and H for adenine, cytosine or uracil.
 
Viruses typically uses cell enzymes for its own methylation, producing evolutionary pressure for adaptation of viral DRACH sequences so that they become more similar to cell sequences. The viral strains that adapt best are able to escape interferon more successfully.
 
Upon completion of their investigation of how SARS-CoV-2 modifies m6A in host cells, the research team’s next step will be to analyze the stored data in search of a correlation between viral RNA methylation levels and the number of viruses released from each infected cell, known as viral burst size.
 
Professor Briones explained, "The more methylated the viruses, the more they grow in the cell cytoplasm and the larger the burst size.”
 
Typically, under normal conditions, without stimuli, a viral particle replicates a thousand times.
 
These findings might pave the way to novel treatments for COVID-19 and repurposing of known drugs. These findings can also offer elements for a deeper understanding of how viral strains escape the immune system.
 
The Oxford Nanopore Technologies direct RNA sequencing method used in the study has several advantages, according to the researchers. One of these is that it dispenses with the modifications required by the conventional method (reverse transcription polymerase chain reaction, or RT-PCR) to read the RNA strand.

In order to examine a virus using RT–PCR, scientists must first convert its RNA to DNA (reverse transcription). The result is cDNA, where the 'c' stands for complementary. This is because only DNA (which is double-stranded) can be copied. The cDNA is then amplified by being copied hundreds of thousands of times, creating billions of clones so that enough of the target sections of viral DNA are available for analysis, instead of a minuscule amount.
 
According to Professor Briones, researchers may be confused by distortions resulting from the production of viral sequences from cDNA.
 
Professor Briones said, "Some scientists think nucleotides are switched owing to the presence of epigenetically modified bases. This needs to be investigated in a systematic manner.”
 
The detailed increase in cell methylation was mapped by two m6A detection programs. One of these (m6anet) used a machine learning technique called multiple instance learning (MIL). The other (EpiNano) validated the results using a technique called support vector machine (SVM).
 
The study findings have caused a stir among researchers in the COVID-19 and Long COVID community, has the alteration of host RNA has numerous implications about possible damage, dysfunction and alterations in numerous cellular pathways and even gene and critical proteases regulation.
 
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