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HGNC Genes

SARS-CoV-2 proteins

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    Host immune response driving SARS-CoV-2 evolution

    Authors: Rui Wang; Yuta Hozumi; Yong-Hui Zheng; Changchuan Yin; Guo-Wei Wei

    id:2008.07488v2 Date: 2020-08-17 Source: arXiv

    The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance to the controlling and combating of coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic. Currently, near 15, 000 SARS-CoV-2 MESHD single mutations have been recorded, having a great ramification to the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is known about SARS-CoV-2 evolutionary characteristics and general trend. In this work, we present a comprehensive genotyping analysis of existing SARS-CoV-2 mutations. We reveal that host immune response via APOBEC and ADAR HGNC gene editing gives rise to near 65\% of recorded mutations. Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 MESHD because of their overreacting to the viral infection MESHD. Moreover, we uncover that populations of Oceania and Africa react significantly more intensively to SARS-CoV-2 infection MESHD than those of Europe and Asia, which may explain why African Americans were shown to be at increased risk of dying from COVID-19 MESHD, in addition to their high risk of getting sick from COVID-19 MESHD caused by systemic health and social inequities. Finally, our study indicates that for two viral genome sequences of the same origin, their evolution order may be determined from the ratio of mutation type C$>$T over T$>$C.

    A-to-I RNA editing in SARS-COV-2: real or artifact?

    Authors: Ernesto Picardi; Luigi Mansi; Graziano Pesole

    doi:10.1101/2020.07.27.223172 Date: 2020-07-27 Source: bioRxiv

    ADAR1 HGNC-mediated deamination of adenosines in long double stranded RNAs plays an important role in modulating the innate immune response. However, recent investigations based on metatranscriptomic samples of COVID-19 MESHD patients and SARS-COV-2 infected MESHD Vero cells have recovered contrasting findings. Using RNAseq data from time course experiments of infected human cell lines and transcriptome data from Vero cells and clinical samples, we prove that A-to-G changes observed in SARS-COV-2 genomes represent genuine RNA editing events, likely mediated by ADAR1 HGNC. While the A-to-I editing rate is generally low, changes are distributed along the entire viral genome, are overrepresented in exonic regions and are, in the majority of cases, nonsynonymous. The impact of RNA editing on virus-host interactions could be relevant to identify potential targets for therapeutic interventions.

    Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection MESHD

    Authors: Rafeed Rahman Turjya; Md. Abdullah-Al-Kamran Khan; Abul B.M.M.K. Islam

    doi:10.1101/2020.06.29.177204 Date: 2020-06-29 Source: bioRxiv

    BackgroundSince December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection MESHD and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 MESHD pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected MESHD lung epithelial cells. ResultsOur analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR HGNC, EDN1 HGNC, KYNU HGNC, MALL HGNC, TLR2 HGNC and YWHAG HGNC; and also AKAP8L HGNC, EXOSC5 HGNC, GDF15 HGNC, HECTD1 HGNC, LARP4B HGNC, LARP7 HGNC, MIPOL1 HGNC, UPF1 HGNC, MOV10 HGNC and PRKAR2A HGNC, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival. ConclusionsOur investigation determines that deregulated lncRNAs in SARS-CoV-2 infection MESHD are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option.

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MeSH Disease
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SARS-CoV-2 Proteins


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