Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection

Serpeloni, Juliana Mara; Neto, Quirino Alves Lima; Lúcio, Léia Carolina; Ramão, Anelisa; Oliveira, Jaqueline Carvalho de; Gradia, Daniela Fiori; Malheiros, Danielle; Ferrasa, Adriano; Marchi, Rafael; Figueiredo, David Livingstone Alves; Silva, Wilson A.; Ribeiro, Enilze M.S.F.; Cólus, I.M.S.; Cavalli, Luciane R.

doi:10.1016/j.imbio.2021.152130

Cited by 14 publications

(13 citation statements)

References 110 publications

(108 reference statements)

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“…The symptoms of this infection may vary between inapparent or mild cases of respiratory insufficiency and sepsis, with the major symptoms including fever, dry cough, and difficulty breathing [ 22 – 24 ]. Additionally, host genetics might be key to understanding the high dissimilarity of symptoms between patients [ 25 ]. The disease relates to an aggressive immune response that may damage the airways.…”

Section: Covid-19mentioning

confidence: 99%

“…The RBM-ACE2 connection causes proteolytic activation of the S protein, exposing the fusion peptide and leading to the adoption of a more favorable conformation with epistatic regions, leading to viral entry into the host cell. This cleavage between S1 and S2 is usually performed by the TMPRSS2 protein, another protease that causes protein-dependent proteolysis of S or through the furin cleavage site or polybasic cleavage site (PRRAR) [ 23 , 25 , 49 , 52 , 62 , 63 ]. Both ACE2 and TMPRSS2 have been studied as molecular markers that confer genetic susceptibility or resistance [ 25 ].…”

Section: Sars-cov-2 Biologymentioning

confidence: 99%

“…This cleavage between S1 and S2 is usually performed by the TMPRSS2 protein, another protease that causes protein-dependent proteolysis of S or through the furin cleavage site or polybasic cleavage site (PRRAR) [ 23 , 25 , 49 , 52 , 62 , 63 ]. Both ACE2 and TMPRSS2 have been studied as molecular markers that confer genetic susceptibility or resistance [ 25 ].…”

Section: Sars-cov-2 Biologymentioning

confidence: 99%

“…Most of the sequence variations reported in the new strains are single nucleotide polymorphisms or variants, along with other point mutations. In addition, some reports have suggested that variations in the virus genome might occur following infection, so-called intrahost mutations [ 25 , 77 – 79 ].…”

Section: Sars-cov-2 Biologymentioning

confidence: 99%

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Spike protein of SARS-CoV-2 variants: a brief review and practical implications

et al. 2022

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The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.

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Section: Covid-19mentioning

confidence: 99%

Section: Sars-cov-2 Biologymentioning

confidence: 99%

Section: Sars-cov-2 Biologymentioning

confidence: 99%

Section: Sars-cov-2 Biologymentioning

confidence: 99%

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Spike protein of SARS-CoV-2 variants: a brief review and practical implications

et al. 2022

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“…Since viral RNAs are targeted by host miRNAs or viral miRNAs can target host transcripts, viral RNAs should be incorporated in miRNA:target networks (Serpeloni et al, 2021;Marchi et al, 2021). More interestingly, there are studies showing that viruses sequester host miRNAs and interfere with their repression function.…”

Section: Introductionmentioning

confidence: 99%

Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network

Yuka

Yılmaz

2021

PeerJ

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Competing endogenous RNAs (ceRNA) play a crucial role in cell functions. Computational methods that provide large-scale analysis of the interactions between miRNAs and their competitive targets can contribute to the understanding of ceRNA regulations and critical regulatory functions. Recent reports showed that viral RNAs can compete with host RNAs against host miRNAs. Regarding SARS-CoV-2 RNA, no comprehensive study had been reported about its competition with cellular ceRNAs. In this study, for the first time, we used the ceRNAnetsim package to assess ceRNA network effects per individual cell and competitive behavior of SARS-CoV-2 RNA in the infected cells using single-cell sequencing data. Our computations identified 195 genes and 29 miRNAs which vary in competitive behavior specifically in presence of SARS-CoV-2 RNA. We also investigated 18 genes that are affected by genes that lost perturbation ability in presence of SARS-CoV-2 RNA in the human miRNA:ceRNA network. These transcripts have associations with COVID-19-related symptoms as well as many dysfunctions such as metabolic diseases, carcinomas, heart failure. Our results showed that the effects of the SARS-CoV-2 genome on host ceRNA interactions and consequent dysfunctions can be explained by competition among various miRNA targets. Our perturbation ability perspective has the potential to reveal yet to be discovered SARS-CoV-2 induced effects invisible to conventional approaches.

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