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COVID-19 GPH|Home|PHGKB Last data update: Sep 21, 2021 . (Total: 25781 Documents since 2020)

Last Posted: Sep-21-2021 08:49:33
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The biological and clinical significance of emerging SARS-CoV-2 variants.
Tao Kaiming et al. Nature reviews. Genetics 2021 9

The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.

High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape
F Schmidt et al, Nature, September 20, 2021

By aggregating VOC-associated and antibody-selected spike substitutions into a single polymutant spike protein, we show that 20 naturally occurring mutations in SARS-CoV-2 spike are sufficient to generate pseudotypes with near-complete resistance to the polyclonal neutralizing antibodies generated by convalescents or mRNA vaccine recipients. Strikingly, however, plasma from individuals who had been infected and subsequently received mRNA vaccination, neutralized pseudotypes bearing this highly resistant SARS-CoV-2 polymutant spike, or diverse sarbecovirus spike proteins. Thus, optimally elicited human polyclonal antibodies against SARS-CoV-2 should be resilient to substantial future SARS-CoV-2 variation and may confer protection against potential future sarbecovirus pandemics.

Widening Disparities in Online Information Access during the COVID-19 Pandemic
J Suh et al, MEDRXIV, September 17, 2021

We observe a widening of digital inequalities through a population-scale study of 55 billion everyday web search interactions during the COVID-19 pandemic across 25,150 US ZIP codes. We observe that ZIP codes with low socioeconomic status (SES) and high racial/ethnic diversity did not leverage health information and pandemic-relevant online resources (e.g., online learning, online food delivery) as much as regions with higher SES and lower levels of diversity. We also show increased shifts in online information access to financial or unemployment assistance for ZIP codes with low SES and high racial/ethnic diversity.

The Unequal Burden of the Covid-19 Pandemic: Racial/Ethnic Disparities in US Cause-Specific Mortality
AN Luck et al, MEDRXIV, September 17, 2021

Using 2019 and 2020 provisional death counts from the National Center for Health Statistics and population estimates from the US Census Bureau, we estimate age-standardized death rates by race/ethnicity and attribute changes in mortality to various causes of death. We also examine how patterns of change across racial/ethnic groups vary by age and sex. Covid-19 death rates in 2020 were highest in the Hispanic community whereas Black individuals had the largest increase in all-cause mortality between 2019 and 2020. Increases in mortality from heart disease, diabetes, and external causes of death accounted for the adverse trend in all-cause mortality within the Black population.

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[Current state of the obesity research: genetic aspects, the role of microbiome, and susceptibility to COVID-19].
Timasheva Ya R, et al. Problemy endokrinologii 2021 0 0. (4) 20-35

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Detection of SARS-CoV-2 in the community by nucleic acid amplification testing of saliva
F Fronza et al, MEDRXIV, September 21, 2021

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Self-reported and physiological reactions to the third BNT162b2 mRNA COVID-19 (booster) vaccine dose
M Mofaz et al, MEDRXIV, September 21, 2021

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Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interest
A Russell et al, MEDRXIV, September 20, 2021

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Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients
VV Babenko et al, BIORXIV, September 20, 2021

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Environmental factors and mobility predict COVID-19 seasonality
MJ Hoogeveen et al, MEDRXIV, September 20, 2021

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SARS-CoV-2 variants in Paraguay: Detection and surveillance with a readily modifiable, multiplex real-time RT-PCR
M Martinez et al, MEDRXIV, September 20, 2021

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Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants.
HW Despres et al, MEDRXIV, September 20,2021

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
Martin Darren P, et al. Cell 2021 0 0.

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Clinical features of COVID-19 by SARS-CoV-2 Gamma variant: a prospective cohort study of vaccinated and unvaccinated healthcare workers.
Luna-Muschi Alessandra, et al. The Journal of infection 2021 0 0.

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About COVID-19 GPH

COVID-19 GPH is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other materials that captures emerging discoveries and applications of genomics, molecular and other precision medicine and precision public health tools in the investigation and control of COVID-19. Contents include PubMed records via an automated pubmed search algorithm, preprint records from NIH iCite, the relevant information from many media sources picked by experts, and linkages to contents from our curated PHGKB databases.
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All Records25781
Genomics Precision Health18433
Non-Genomics Precision Health7348

Publication Categories Brand

Mechanism 4835
Treatment 4453
Vaccines 4445
Variants 4020
Diagnosis 3214
Prevention 3053
Forecasting 2042
Surveillance 1931
Transmission 1018
Health Equity 667
Case Report 488

Publication Types

PubMed Records18750
Online News/Reports/Publications474

Genomics Precision Health (GPH): The use of pathogen and human genomics and advanced molecular detection methods in discovery, clinical and public health investigations and response to COVID-19.
Non Genomics Precision Health (non-GPH): The use of big data, data science, digital health, machine learning and predictive analytic methods (not involving genomics) in discovery, clinical and public health investigations and response to COVID-19

Following categories are annotated by LitCovid from NCBI NIH.
MechanismUnderlying cause(s) of covid-19 infections and transmission & possible drug mechanism of action
Transmission Characteristics and modes of covid-19 transmissions, such as human-to-human
DiagnosisDisease assessment through symptoms, test results, and radiological features
PreventionPrevention, control, response and management strategies
Case ReportDescriptions of specific patient cases
ForecastingModelling and estimating the trend of covid-19 spread

Following categories are annotated by the text mining tool from CDC PHGKB
Health EquityRelevant to health equity. Search terms are derived from a list provided by the Association for Territorial Health Officials which include terms such as diversity, health disparities, and others.
VaccineRelevant to vaccine development, evaluation, implementation and impact. For additional information on vaccines and COVID-19. Check out general CDC Information pages
VariantRelevant to SARS-CoV-2 variants and their impact on public health. For additional information on variants COVID-19. Check out CDC New Variants of the Virus that Causes COVID-19 page
SurveillanceRelevant to SARS-CoV-2 public health surveillance and tracking. For additional information on COVID-19 surveillance, check out CDC COVID-19 Data Tracker

Disclaimer: Articles listed in the Public Health Genomics and Precision Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the 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 update, 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.