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1.
PLoS Genet ; 18(3): e1010130, 2022 03.
Article in English | MEDLINE | ID: covidwho-1770640

ABSTRACT

SARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomic data from multiple bronchoalveolar lavage fluid samples of COVID-19 patients, revealing an appreciable number of A-to-I RNA editing candidate sites in SARS-CoV-2. We confirm the enrichment of A-to-I RNA editing signals at these candidate sites through evaluating four characteristics specific to RNA editing: the inferred RNA editing sites exhibit (i) stronger ADAR1 binding affinity predicted by a deep-learning model built from ADAR1 CLIP-seq data, (ii) decreased editing levels in ADAR1-inhibited human lung cells, (iii) local clustering patterns, and (iv) higher RNA secondary structure propensity. Our results have critical implications in understanding the evolution of SARS-CoV-2 as well as in COVID-19 research, such as phylogenetic analysis and vaccine development.


Subject(s)
COVID-19 , SARS-CoV-2 , Adenosine Deaminase/metabolism , COVID-19/genetics , Humans , Nucleotides/metabolism , Pandemics , Phylogeny , RNA/metabolism , RNA Editing/genetics , SARS-CoV-2/genetics
2.
J Appl Genet ; 63(2): 423-428, 2022 May.
Article in English | MEDLINE | ID: covidwho-1739445

ABSTRACT

Analysis of the SARS-CoV-2 transcriptome has revealed a background of low-frequency intra-host genetic changes with a strong bias towards transitions. A similar pattern is also observed when inter-host variability is considered. We and others have shown that the cellular RNA editing machinery based on ADAR and APOBEC host-deaminases could be involved in the onset of SARS-CoV-2 genetic variability. Our hypothesis is based both on similarities with other known forms of viral genome editing and on the excess of transition changes, which is difficult to explain with errors during viral replication. Zong et al. criticize our analysis on both conceptual and technical grounds. While ultimate proof of an involvement of host deaminases in viral RNA editing will depend on experimental validation, here, we address the criticism to suggest that viral RNA editing is the most reasonable explanation for the observed intra- and inter-host variability.


Subject(s)
COVID-19 , RNA Editing , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , COVID-19/genetics , Humans , RNA Editing/genetics , SARS-CoV-2/genetics , Transcriptome/genetics
3.
Nucleic Acids Res ; 50(5): 2509-2521, 2022 03 21.
Article in English | MEDLINE | ID: covidwho-1722548

ABSTRACT

Upon SARS-CoV-2 infection, viral intermediates specifically activate the IFN response through MDA5-mediated sensing and accordingly induce ADAR1 p150 expression, which might lead to viral A-to-I RNA editing. Here, we developed an RNA virus-specific editing identification pipeline, surveyed 7622 RNA-seq data from diverse types of samples infected with SARS-CoV-2, and constructed an atlas of A-to-I RNA editing sites in SARS-CoV-2. We found that A-to-I editing was dynamically regulated, varied between tissue and cell types, and was correlated with the intensity of innate immune response. On average, 91 editing events were deposited at viral dsRNA intermediates per sample. Moreover, editing hotspots were observed, including recoding sites in the spike gene that affect viral infectivity and antigenicity. Finally, we provided evidence that RNA editing accelerated SARS-CoV-2 evolution in humans during the epidemic. Our study highlights the ability of SARS-CoV-2 to hijack components of the host antiviral machinery to edit its genome and fuel its evolution, and also provides a framework and resource for studying viral RNA editing.


Subject(s)
COVID-19/immunology , Immunity, Innate/immunology , RNA Editing/immunology , SARS-CoV-2/immunology , Adenosine Deaminase/genetics , Adenosine Deaminase/immunology , Adenosine Deaminase/metabolism , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/immunology , Angiotensin-Converting Enzyme 2/metabolism , Base Sequence , Binding Sites/genetics , COVID-19/genetics , COVID-19/virology , Evolution, Molecular , Gene Expression/immunology , Humans , Immunity, Innate/genetics , Interferon-Induced Helicase, IFIH1/genetics , Interferon-Induced Helicase, IFIH1/immunology , Interferon-Induced Helicase, IFIH1/metabolism , Mutation , Protein Binding , RNA Editing/genetics , RNA-Binding Proteins/genetics , RNA-Binding Proteins/immunology , RNA-Binding Proteins/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Sequence Homology, Nucleic Acid , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism
4.
Proc Natl Acad Sci U S A ; 119(6)2022 02 08.
Article in English | MEDLINE | ID: covidwho-1642083

ABSTRACT

Adenosine deaminases acting on RNA (ADAR) are RNA-editing enzymes that may restrict viral infection. We have utilized deep sequencing to determine adenosine to guanine (A→G) mutations, signifying ADAR activity, in clinical samples retrieved from 93 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients in the early phase of the COVID-19 pandemic. A→G mutations were detected in 0.035% (median) of RNA residues and were predominantly nonsynonymous. These mutations were rarely detected in the major viral population but were abundant in minor viral populations in which A→G was more prevalent than any other mutation (P < 0.001). The A→G substitutions accumulated in the spike protein gene at positions corresponding to amino acids 505 to 510 in the receptor binding motif and at amino acids 650 to 655. The frequency of A→G mutations in minor viral populations was significantly associated with low viral load (P < 0.001). We additionally analyzed A→G mutations in 288,247 SARS-CoV-2 major (consensus) sequences representing the dominant viral population. The A→G mutations observed in minor viral populations in the initial patient cohort were increasingly detected in European consensus sequences between March and June 2020 (P < 0.001) followed by a decline of these mutations in autumn and early winter (P < 0.001). We propose that ADAR-induced deamination of RNA is a significant source of mutated SARS-CoV-2 and hypothesize that the degree of RNA deamination may determine or reflect viral fitness and infectivity.


Subject(s)
Adenosine Deaminase/genetics , COVID-19/epidemiology , Point Mutation , RNA Editing , RNA, Viral/genetics , RNA-Binding Proteins/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Adenosine/metabolism , Adenosine Deaminase/metabolism , Adult , Aged , Aged, 80 and over , Amino Acid Substitution , COVID-19/genetics , COVID-19/transmission , COVID-19/virology , Deamination , Female , Genetic Fitness , Genome, Viral , Guanine/metabolism , Host-Pathogen Interactions/genetics , Humans , Male , Middle Aged , RNA, Viral/metabolism , RNA-Binding Proteins/metabolism , SARS-CoV-2/growth & development , SARS-CoV-2/pathogenicity , Signal Transduction , Spike Glycoprotein, Coronavirus/metabolism , Sweden/epidemiology , Viral Load , Virulence
5.
Genome Biol Evol ; 13(11)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1483441

ABSTRACT

Adenosine Deaminases that Act on RNA (ADARs) are RNA editing enzymes that play a dynamic and nuanced role in regulating transcriptome and proteome diversity. This editing can be highly selective, affecting a specific site within a transcript, or nonselective, resulting in hyperediting. ADAR editing is important for regulating neural functions and autoimmunity, and has a key role in the innate immune response to viral infections, where editing can have a range of pro- or antiviral effects and can contribute to viral evolution. Here we examine the role of ADAR editing across a broad range of viral groups. We propose that the effect of ADAR editing on viral replication, whether pro- or antiviral, is better viewed as an axis rather than a binary, and that the specific position of a given virus on this axis is highly dependent on virus- and host-specific factors, and can change over the course of infection. However, more research needs to be devoted to understanding these dynamic factors and how they affect virus-ADAR interactions and viral evolution. Another area that warrants significant attention is the effect of virus-ADAR interactions on host-ADAR interactions, particularly in light of the crucial role of ADAR in regulating neural functions. Answering these questions will be essential to developing our understanding of the relationship between ADAR editing and viral infection. In turn, this will further our understanding of the effects of viruses such as SARS-CoV-2, as well as many others, and thereby influence our approach to treating these deadly diseases.


Subject(s)
Adenosine Deaminase/metabolism , RNA Editing , RNA Viruses/genetics , Adenosine Deaminase/genetics , Animals , Evolution, Molecular , Host-Pathogen Interactions/immunology , Humans , Immunity , RNA Viruses/classification , RNA Viruses/physiology , RNA, Viral/genetics , RNA, Viral/metabolism , Virus Replication/genetics
6.
Scand J Immunol ; 94(5): e13100, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1388399

ABSTRACT

The SARS-CoV-2 epidemic infections in Australia during 2020 were small in number in epidemiological terms and are well described. The SARS-CoV-2 genomic sequence data of many infected patients have been largely curated in a number of publicly available databases, including the corresponding epidemiological data made available by the Victorian Department of Health and Human Services. We have critically analysed the available SARS-CoV-2 haplotypes and genomic sequences in the context of putative deficits in innate immune APOBEC and ADAR deaminase anti-viral responses. It is now known that immune impaired elderly co-morbid patients display clear deficits in interferon type 1 (α/ß) and III (λ) stimulated innate immune gene cascades, of which APOBEC and ADAR induced expression are part. These deficiencies may help explain some of the clear genetic patterns in SARS-CoV-2 genomes isolated in Victoria, Australia, during the 2nd Wave (June-September, 2020). We tested the hypothesis that predicted lowered innate immune APOBEC and ADAR anti-viral deaminase responses in a significant proportion of elderly patients would be consistent with/reflected in a low level of observed mutagenesis in many isolated SARS-CoV-2 genomes. Our findings are consistent with this expectation. The analysis also supports the conclusions of the Victorian government's Department of Health that essentially one variant or haplotype infected Victorian aged care facilities where the great majority (79%) of all 820 SARS-CoV-2 associated deaths occurred. The implications of our data analysis for other localized epidemics and efficient coronavirus vaccine design and delivery are discussed.


Subject(s)
APOBEC Deaminases/genetics , Adenosine Deaminase/genetics , COVID-19 Vaccines/immunology , COVID-19/immunology , RNA-Binding Proteins/genetics , SARS-CoV-2/physiology , APOBEC Deaminases/metabolism , Adenosine Deaminase/metabolism , Age Factors , Aged, 80 and over , COVID-19/epidemiology , COVID-19/virology , Female , Gene Regulatory Networks , Haplotypes , Humans , Immunity, Innate , Immunologic Deficiency Syndromes , Interferon Type I/genetics , Male , RNA-Binding Proteins/metabolism , Victoria/epidemiology
7.
Clin Chem Lab Med ; 59(9): 1592-1599, 2021 Aug 26.
Article in English | MEDLINE | ID: covidwho-1206211

ABSTRACT

OBJECTIVES: The aim of the present study was to validate a commercially available automated assay for the measurement of total adenosine deaminase (tADA) and its isoenzymes (ADA1 and ADA2) in saliva in a fast and accurate way, and evaluate the possible changes of these analytes in individuals with SARS-CoV-2 infection. METHODS: The validation, in addition to the evaluation of precision and accuracy, included the analysis of the effects of the main procedures that are currently being used for SARS-CoV-2 inactivation in saliva and a pilot study to evaluate the possible changes in salivary tADA and isoenzymes in individuals infected with SARS-CoV-2. RESULTS: The automated assay proved to be accurate and precise, with intra- and inter-assay coefficients of variation below 8.2%, linearity under dilution linear regression with R2 close to 1, and recovery percentage between 80 and 120% in all cases. This assay was affected when the sample is treated with heat or SDS for virus inactivation but tolerated Triton X-100 and NP-40. Individuals with SARS-CoV-2 infection (n=71) and who recovered from infection (n=11) had higher mean values of activity of tADA and its isoenzymes than healthy individuals (n=35). CONCLUSIONS: tADA and its isoenzymes ADA1 and ADA2 can be measured accurately and precisely in saliva samples in a rapid, economical, and reproducible way and can be analyzed after chemical inactivation with Triton X-100 and NP-40. Besides, the changes observed in tADA and isoenzymes in individuals with COVID-19 open the possibility of their potential use as non-invasive biomarkers in this disease.


Subject(s)
Adenosine Deaminase/metabolism , Biological Assay/methods , Biomarkers/metabolism , COVID-19/diagnosis , SARS-CoV-2/enzymology , Saliva/enzymology , Adult , COVID-19/virology , Case-Control Studies , Female , Humans , Isoenzymes , Male , Middle Aged , Pilot Projects , Young Adult
8.
Biochem Biophys Res Commun ; 538: 35-39, 2021 01 29.
Article in English | MEDLINE | ID: covidwho-1139448

ABSTRACT

The extensive sequence data generated from SARS-CoV-2 during the 2020 pandemic has facilitated the study of viral genome evolution over a brief period of time. This has highlighted instances of directional mutation pressures exerted on the SARS-CoV-2 genome from host antiviral defense systems. In this brief review we describe three such human defense mechanisms, the apolipoprotein B mRNA editing catalytic polypeptide-like proteins (APOBEC), adenosine deaminase acting on RNA proteins (ADAR), and reactive oxygen species (ROS), and discuss their potential implications on SARS-CoV-2 evolution.


Subject(s)
APOBEC Deaminases/metabolism , Adenosine Deaminase/metabolism , COVID-19/virology , Gene Editing , Genome, Viral , Host-Pathogen Interactions/genetics , RNA-Binding Proteins/metabolism , SARS-CoV-2/genetics , COVID-19/epidemiology , Humans , Reactive Oxygen Species/metabolism
9.
Clin Immunol ; 226: 108699, 2021 05.
Article in English | MEDLINE | ID: covidwho-1101151

ABSTRACT

RNA editing is a fundamental biological process with 2 major forms, namely adenosine-to-inosine (A-to-I, recognized as A-to-G) and cytosine-to-uracil (C-to-U) deamination, mediated by ADAR and APOBEC enzyme families, respectively. A-to-I RNA editing has been shown to directly affect the genome/transcriptome of RNA viruses with significant repercussions for viral protein synthesis, proliferation and infectivity, while it also affects recognition of double-stranded RNAs by cytosolic receptors controlling the host innate immune response. Recent evidence suggests that RNA editing may be present in SARS-CoV-2 genome/transcriptome. The majority of mapped mutations in SARS-CoV-2 genome are A-to-G/U-to-C(opposite strand) and C-to-U/G-to-A(opposite strand) substitutions comprising potential ADAR-/APOBEC-mediated deamination events. A single nucleotide substitution can have dramatic effects on SARS-CoV-2 infectivity as shown by the D614G(A-to-G) substitution in the spike protein. Future studies utilizing serial sampling from patients with COVID-19 are warranted to delineate whether RNA editing affects viral replication and/or the host immune response to SARS-CoV-2.


Subject(s)
APOBEC Deaminases/metabolism , Adenosine Deaminase/metabolism , COVID-19/immunology , Immunity, Innate , RNA Editing , RNA Viruses/genetics , RNA-Binding Proteins/metabolism , SARS-CoV-2/genetics , APOBEC Deaminases/genetics , Adenosine Deaminase/genetics , COVID-19/enzymology , COVID-19/virology , Humans , Mutation , RNA Viruses/pathogenicity , RNA, Double-Stranded/metabolism , RNA-Binding Proteins/genetics , SARS-CoV-2/metabolism
10.
Sci Rep ; 10(1): 17766, 2020 10 20.
Article in English | MEDLINE | ID: covidwho-882928

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection induces severe pneumonia and is the cause of a worldwide pandemic. Coronaviruses, including SARS-CoV-2, have RNA proofreading enzymes in their genomes, resulting in fewer gene mutations than other RNA viruses. Nevertheless, variants of SARS-CoV-2 exist and may induce different symptoms; however, the factors and the impacts of these mutations are not well understood. We found that there is a bias to the mutations occurring in SARS-CoV-2 variants, with disproportionate mutation to uracil (U). These point mutations to U are mainly derived from cytosine (C), which is consistent with the substrate specificity of host RNA editing enzymes, APOBECs. We also found the point mutations which are consistent with other RNA editing enzymes, ADARs. For the C-to-U mutations, the context of the upstream uracil and downstream guanine from mutated position was found to be most prevalent. Further, the degree of increase of U in SARS-CoV-2 variants correlates with enhanced production of cytokines, such as TNF-α and IL-6, in cell lines when compared with stimulation by the ssRNA sequence of the isolated virus in Wuhan. Therefore, RNA editing is a factor for mutation bias in SARS-CoV-2 variants, which affects host inflammatory cytokines production.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections/pathology , Pneumonia, Viral/pathology , APOBEC Deaminases/metabolism , Adenosine Deaminase/metabolism , Betacoronavirus/classification , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , Cell Line, Tumor , Coronavirus Infections/immunology , Coronavirus Infections/virology , Humans , Interleukin-6/metabolism , Pandemics , Phylogeny , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Point Mutation , RNA Editing , SARS-CoV-2 , Tumor Necrosis Factor-alpha/metabolism , Uracil/metabolism
11.
Sci Adv ; 6(25): eabb5813, 2020 06.
Article in English | MEDLINE | ID: covidwho-619103

ABSTRACT

The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/metabolism , Coronavirus Infections/genetics , Host-Pathogen Interactions/genetics , Pneumonia, Viral/genetics , RNA Editing/genetics , Transcriptome , APOBEC Deaminases/genetics , APOBEC Deaminases/metabolism , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , Base Sequence/genetics , Bronchoalveolar Lavage Fluid/virology , COVID-19 , Coronavirus Infections/virology , Genome, Viral/genetics , Humans , Mutation Rate , Nucleotides/genetics , Nucleotides/metabolism , Pandemics , Pneumonia, Viral/virology , RNA, Viral/genetics , SARS-CoV-2 , Virus Replication/genetics
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