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  1. Book ; Online: Investigating evolution at the catalytic site of the main SARS-CoV-2 protease using over 15,000 genomes

    Nicola De Maio

    2020  

    Abstract: We investigated evolution and genomic variation of SARS-CoV-2 within the current pandemic at the catalytic site of the main SARS-CoV-2 protease (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and https://openlabnotebooks.org/mapping-the-genetic- ... ...

    Abstract We investigated evolution and genomic variation of SARS-CoV-2 within the current pandemic at the catalytic site of the main SARS-CoV-2 protease (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ ). We used more than 15,000 genomic sequences from GISAID (https://www.epicov.org/) available on the 17th of May 2020. We use a new approach based on phylogenetic inference of homoplasy, clustering of mutations, and ambiguous consensus sequence characters, to identify sites that are likely affected by sequencing artefacts. We find that these sites are mostly conserved, and the amino acid variants observed are only M49I, P52S, N142S, and P168S, all of which appear only at extremely low frequencies (maximum of two samples each).
    Keywords SARS-CoV-2 ; CoViD19 ; protease ; genomic ; variation ; covid19
    Publishing date 2020-05-29
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Genetic Variability at An Allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org. ...

    Abstract This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org.
    Keywords covid19
    Publishing date 2020-11-04
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Book ; Online: Genetic Variability at An Allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org. ...

    Abstract This report is about the druggability and genetic variability at an allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase both across coronaviruses and SARS-CoV-2 samples. This report accompanies this post on openlabnotebook.org.
    Keywords covid19
    Publishing date 2020-11-04
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Book ; Online: Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and the predicted effects of mutations on SAM and RNA binding

    Yazdani, Setayesh / Schapira, Matthieu / Nicola De Maio

    2020  

    Abstract: In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on ...

    Abstract In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on https://openlabnotebooks.org/. The Druggability of SARS-CoV-2 NSP16, the SAM-dependent m7GpppA-specific 2’-O-methyltransferase - Post 5 Mapping the genetic variations of Alpha- and Betacoronavirus UniProt entries onto SARS-CoV-2 NSP16 crystal structure – Post 6 Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and predicted effects of mutations on SAM and RNA binding - Post 7 Predicting the effect of all possible mutations at the 39 sidechains of NSP16 catalytic site on SAM and RNA-binding - Post 8 The energy_matrix_NSP16.icb contains the ICM script for the post 8 above.
    Keywords covid19
    Publishing date 2020-07-02
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Book ; Online: Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and the predicted effects of mutations on SAM and RNA binding

    Yazdani, Setayesh / Schapira, Matthieu / Nicola De Maio

    2020  

    Abstract: In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on ...

    Abstract In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on https://openlabnotebooks.org/. The Druggability of SARS-CoV-2 NSP16, the SAM-dependent m7GpppA-specific 2’-O-methyltransferase - Post 5 Mapping the genetic variations of Alpha- and Betacoronavirus UniProt entries onto SARS-CoV-2 NSP16 crystal structure – Post 6 Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and predicted effects of mutations on SAM and RNA binding - Post 7 Predicting the effect of all possible mutations at the 39 sidechains of NSP16 catalytic site on SAM and RNA-binding - Post 8 The energy_matrix_NSP16.icb contains the ICM script for the post 8 above.
    Keywords covid19
    Publishing date 2020-06-17
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Book ; Online: Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https:// ... ...

    Abstract This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Book ; Online: Druggability and Genetic Variability of the ATPase Site and Central Channel of SARS-CoV-2 nsp13 Helicase Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and the genetic variability of the ATPase site and the central channel of SARS-CoV-2 nsp13 helicase across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks ... ...

    Abstract This document is about the druggability and the genetic variability of the ATPase site and the central channel of SARS-CoV-2 nsp13 helicase across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Book ; Online: Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples

    Setayesh Yazdani / Nicola De Maio / Matthieu Schapira

    2020  

    Abstract: This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https:// ... ...

    Abstract This document is about the druggability and genetic variability of the ADP-bound pocket of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) NiRAN domain across coronaviruses and SARS-CoV-2 samples. This report also accompanies this post on https://openlabnotebooks.org/.
    Keywords covid19
    Publishing date 2020-11-12
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: VGsim

    Vladimir Shchur / Vadim Spirin / Dmitry Sirotkin / Evgeni Burovski / Nicola De Maio / Russell Corbett-Detig

    PLoS Computational Biology, Vol 18, Iss 8, p e

    Scalable viral genealogy simulator for global pandemic.

    2022  Volume 1010409

    Abstract: Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been ... ...

    Abstract Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than 5.5 million viral sequences are publicly available as of November 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages. To our knowledge, there is no framework that is both efficient and flexible enough to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses the problem of simulation genealogies under epidemiological models. The simulation process is split into two phases. During the forward run the algorithm generates a chain of population-level events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the population-level events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape.
    Keywords Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and the predicted effects of mutations on SAM and RNA binding

    Yazdani, Setayesh (8427777) / Schapira, Matthieu (4929295) / Nicola De Maio (233448)

    2020  

    Abstract: In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on ...

    Abstract In this document, we explain the methods of predicting the effect of genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 on SAM and RNA binding. The PDF document contains the detailed methods which accompany the following posts on https://openlabnotebooks.org/ . The Druggability of SARS-CoV-2 NSP16, the SAM-dependent m7GpppA-specific 2’-O-methyltransferase - Post 5 Mapping the genetic variations of Alpha- and Betacoronavirus UniProt entries onto SARS-CoV-2 NSP16 crystal structure – Post 6 Genetic variability at the catalytic site of the SARS-CoV-2 RNA MTase NSP16 and predicted effects of mutations on SAM and RNA binding - Post 7 Predicting the effect of all possible mutations at the 39 sidechains of NSP16 catalytic site on SAM and RNA-binding - Post 8 The energy_matrix_NSP16.icb contains the ICM script for the post 8 above.
    Keywords Biophysics ; Biochemistry ; Microbiology ; Genetics ; Molecular Biology ; Pharmacology ; Infectious Diseases ; Plant Biology ; Virology ; Computational Biology ; Betacoronavirus UniProt entries ; RNA binding ; site ; SAM ; mutation ; Post ; variability ; ICM ; PDF ; SARS-CoV -2 RNA MTase NSP 16 ; covid19
    Subject code 630
    Publishing date 2020-06-17T00:00:00Z
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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