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COVID-19 GPH|Home|PHGKB Last data update: Jun 07, 2023 . (Total: 45402 Documents since 2020)

Last Posted: Jun-07-2023 06:32:38
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Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.
Emily A Smith et al. Microb Genom 2023 6 (6)

The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet.

Why the world needs more transparency on the origins of novel pathogens
M Venter, Nature, May 30, 2023

Platforms such as GISAID (the Global Initiative on Sharing All Influenza Data) have enabled important sequencing data to be shared by scientists, with the aim of also protecting researchers’ intellectual property. However, users of these data need to work more closely with the data owners to maintain trust and ensure that sharing continues in the future. Most importantly, we urge scientists and governments to make available all data, research and reports that can help in the identification of the origins of novel pathogens for all outbreaks, epidemics and global health emergencies.

Assessing the potential of polygenic scores to strengthen medical risk prediction models of COVID-19.
Aldo Córdova-Palomera et al. PLoS One 2023 5 (5) e0285991

In UK Biobank participants of European ancestry, the model achieved a relatively high performance (area under the receiver operating characteristic curve ~90%). Polygenic scores for COVID-19 computed from summary statistics of the Covid19 Host Genetics Initiative displayed significant associations with COVID-19 in the UK Biobank (p-values as low as 3.96e-9, all with R2 under 1%), but were unable to robustly improve predictive performance of the non-genetic factors.

Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program.
M Daniel Brannock et al. Nat Commun 2023 5 (1) 2914

We used electronic health records available through the National COVID Cohort Collaborative to characterize the association between SARS-CoV-2 vaccination and long COVID diagnosis. We found that vaccination was consistently associated with lower odds and rates of long COVID clinical diagnosis and high-confidence computationally derived diagnosis after adjusting for sex, demographics, and medical history.

news Latest News and Publications
Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature.
Knafou Julien, et al. Systematic reviews 2023 0 0. (1) 94

New Added Today

The Implications of Using Digital Technologies in the Management of COVID-19: Comparative Study of Japan and South Korea.
Yang Sou Hee, et al. Journal of medical Internet research 2023 0 0. e45705

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Effects of the COVID-19 pandemic: new approaches for accelerated delivery of gene to first-in-human CMC data for recombinant proteins.
Broly Hervé, et al. mAbs 2023 0 0. (1) 2220150

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Severe acute respiratory syndrome coronavirus-2 antibody response after Moderna vaccine booster on healthcare providers.
Fachrucha Fanny, et al. Journal of infection in developing countries 2023 0 0. (5) 617-622

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Development and validation of a novel CD4 T cell-related gene signature to detect severe COVID-19.
Zhang Da-Wei, et al. Clinical and translational medicine 2023 0 0. (6) e1294

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Identification and characterization of 7-azaindole derivatives as inhibitors of the SARS-CoV-2 spike-hACE2 protein interaction.
Wang Chaojie, et al. International journal of biological macromolecules 2023 0 0. 125182

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Hamster model for post-COVID-19 alveolar regeneration offers an opportunity to understand post-acute sequelae of SARS-CoV-2.
Heydemann Laura, et al. Nature communications 2023 0 0. (1) 3267

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Has COVID-19 changed the spectrum of arrhythmias and the incidence of sudden cardiac death?
Kuck Karl-Heinz, et al. Herz 2023 0 0. 1-6

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LAPIS is a fast web API for massive open virus sequencing data.
Chen Chaoran, et al. BMC bioinformatics 2023 0 0. (1) 232

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Pre-assessment and management of long COVID patients requiring elective surgery: challenges and guidance.
Boles Sophie, et al. Perioperative medicine (London, England) 2023 0 0. (1) 20

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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 capture 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.

Site Citation:
Wei Yu, et al. COVID-19 GPH: tracking the contribution of genomics and precision health to the COVID-19 pandemic response. BMC Infectious Diseases (2022) 22:402.

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All Records45402
Genomics Precision Health33226
Non-Genomics Precision Health12176

Publication Categories Brand

Variants 13589
Vaccines 11415
Treatment 10726
Mechanism 10493
Diagnosis 7811
Prevention 5435
Surveillance 4046
Forecasting 3555
Transmission 2187
Health Equity 1167

Publication Types

PubMed Records34895
Online News/Reports/Publications433

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 Genomics and Precision Public Health 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.