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

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

• Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score
  SR Knight et al, BMJ, September 9, 2020
  An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups.
• Socio-economic disparities and COVID-19 in the USA
  A Paul et al, MEDRXIV, September 11, 2020
  We correlate the COVID-19 prevalence and death rate with data from the US Census Bureau and point out how the spreading patterns of the disease show asymmetries in urban and rural areas separately and is preferentially affecting the counties where a large fraction of the population is non-white.
• Racial disparities in COVID-19 mortality are driven by unequal infection risks.
  J Zelner et al, MEDRXIV, September 11, 2020
  We used individual-level COVID-19 incidence and mortality data from Michigan to estimate age-specific incidence and mortality rates by race/ethnic group. The findings suggest that well-documented racial disparities in mortality in hard-hit settings, are driven primarily by variation in household, community and workplace exposure rather than case-fatality rates.
• The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning
  SW Marvel et al, MEDRXIV, September 13, 2020
  The COVID-19 PVI Dashboard monitors multiple data streams to communicate county-level trends and vulnerabilities and facilitates decision-making and communication among government officials, scientists, community leaders, and the public to enable effective and coordinated action to combat the pandemic.

News, Reviews and Commentaries

• Use of “normal” risk to improve understanding of dangers of covid-19
  D Spiegelhalter, BMJ, September 9, 2020
  Accumulating data on deaths from covid-19 show an association with age that closely matches the “normal” risk we all face. Explaining risk in this way could help people understand and manage their response,
• Why obesity worsens COVID-19
  M Wadman, Science, September 11, 2020
  Since the pandemic began, dozens of studies have reported that many of the sickest COVID-19 patients have been people with obesity. In recent weeks, that link has come into sharper focus as large new population studies have cemented the association and demonstrated that even people who are merely overweight are at higher risk.
• The Coronavirus Is Mutating, and That’s Fine (So Far) SARS-CoV-2 has been slowly changing in small ways, without getting more dangerous.
  E Holmes, NY Times, September 11, 2020
• On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US
  S Kefayati et al, MEDRXIV, September 13, 2020
• Is the Covid-19 pandemic a tipping point for digital health?
  E Cooney, Stat News, September 9, 2020
• Genetics and COVID-19: How to Protect the Susceptible
  CRI Field et al, Trends in Genetics, August 29, 2020
  Until a vaccine or effective treatment is available, those whose genomes make them especially vulnerable might be considered ill-suited for exposure-prone jobs, especially in health care. They might also face resistance in other spheres, such as health-related insurance, apartment leases, nursing home placements, and even bank loans.
• Genome Data Help to Track COVID-19 Superspreading Event
  NIH Director's blog, September 8, 2020
  As SARS-CoV-2 spreads, the virus sometimes picks up a new mutation. Those changes in the viral genome usually have no effect on how the virus causes disease, but they do serve as distinct fingerprints that can be used by researchers can trace the path the virus took through a community and beyond,identifying connections that would be untrackable otherwise.
• Investigating Whether Blood Type Is Linked to COVID-19 Risk
  R Rubin, JAMA, September 16, 2020
  The upshot: “The basic science on this is extremely weak,” Latz said of the relationship between blood type (ABO) and COVID-19. So at least for now, blood type should not be used to identify which people who become sick with COVID-19 are likely to develop severe disease."

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.