domingo, 20 de septiembre de 2020

COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB

COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB

Public Health Genomics Knowledge Base



COVID-19 Genomics and Precision Public Health Weekly Update Content



Pathogen and Human Genomics Studies

  • Racial/Ethnic Variation in Nasal Gene Expression of Transmembrane Serine Protease 2 (TMPRSS2)
    S Bunyavanitch et al, JAMA, September 10, 2020
    This study of nasal epithelial gene expression in a racially/ethnically diverse cohort showed significantly higher expression of TMPRSS2 in Black individuals compared with other races/ethnicities. Given the essential role of TMPRSS2 in SARS-CoV-2 entry,higher nasal expression of TMPRSS2 may contribute to the higher burden of COVID-19 among Black individuals
  • The emergence of SARS-CoV-2 in Europe and North America
    Worobey M, et al. Science, Sep 10, 2020.
  • Cryptic transmission of SARS-CoV-2 in Washington state
    Bedford T, et al. Science, Sep 10, 2020.
  • Exploring the coronavirus pandemic with the WashU Virus Genome Browser
    Nature Genetics, September 9, 2020
    This is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.
  • The UCSC SARS-CoV-2 Genome Browser
    JD Fernandes et al, Nature Genetics, September 10, 2020
    The browser is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides.
  • Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource
    S Portelli et al, Nature Genetics, September 10, 2020
    Despite the novelty of the virus, global sequencing efforts have already identified genomic variation across isolates. To enable easy exploration and spatial visualization of the potential implications of SARS-CoV-2 mutations in infection, host immunity and drug development, we have developed COVID-3D.
  • Molecular architecture of the SARS-CoV-2 virus
    Y Yao et al, Cell, September 14, 2020
    Molecular architecture of the authentic SARS-CoV-2 virus is unveiled. Native structures of S in RBD down, one RBD up and postfusion conformations are solved. Compositions of the glycans from the native S are characterized. Structure and assembly of the RNPs are revealed in situ
  • SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2
    TM Clausen et al, Cell, September 14, 2020
    We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Docking studies suggest a heparin/heparan sulfate-binding site adjacent to the ACE2 binding site. Both ACE2 and heparin can bind independently to spike protein in vitro.
  • Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
    L Yurkovetskiy et al, Cell, September 15, 2020
    The SARS-CoV-2 D614G S protein variant supplanted the ancestral virus in people. D614G increases infectivity on human lung cells or cells with bat or pangolin ACE2. D614G is potently neutralized by antibodies targeting the receptor binding domain D614G shifts S protein conformation towards an ACE2-binding fusion-competent state.
  • Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing
    J Joung et al, NEJM, September 16, 2020
    We describe a simple test for detection of SARS-CoV-2. The sensitivity of this test is similar to that of reverse-transcription–quantitative polymerase-chain-reaction (RT-qPCR) assays. STOP (SHERLOCK testing in one pot) is a streamlined assay that combines simplified extraction of viral RNA with isothermal amplification and CRISPR-mediated detection.




Non-Genomics Precision Health Studies



News, Reviews and Commentaries



Disclaimer: Articles listed in COVID-19 Genomics and Precision Public Health Weekly Update are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.

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