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COVID-10 GPH

COVID-19 GPH|Home|Public Health Genomics and Precision Health Knowledge Base (PHGKB)
Effective August 1, 2024, this database will be discontinued. All content will remain searchable and be preserved online for historical purposes only until 2029.

Last data update: Jul 16, 2024 . (Total: 47596 Documents since 2020)
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Last Posted: Jul-16-2024 10:38:31
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Vaccine effectiveness against emerging COVID-19 variants using digital health data

From the abstract: " Here, we develop a methodology for identifying changes in vaccine effectiveness and COVID-19 symptomatology using the University of Maryland COVID Trends and Impact Survey data from three middle-income countries (Guatemala, Mexico, and South Africa). We implement conditional logistic regression to develop estimates of vaccine effectiveness conditioned on the prevalence of various definitions of self-reported COVID-like illness in lieu of confirmed diagnostic test results. Results: We highlight a reduction in vaccine effectiveness during Omicron-dominated waves of infections when compared to periods dominated by the Delta variant."

Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates
RH Holm et al, Comm Med, April 9, 2024

From the abstract: "We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021–August 2021 in Jefferson County, Kentucky (USA). We show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r?=?0.95) at 1 week lag."

Concerted efforts toward genomic surveillance of viral pathogens in immunocompromised individuals.
Matheus Filgueira Bezerra et al. Lancet Microbe 2024 4

From the article: "A recent study underscores the crucial need to closely monitor immunocompromised individuals with prolonged SARS-CoV-2 infections for emerging variants and investigate their phenotypic implications. Sequencing the genomes of the viruses from these cases would marginally elevate the cost in the whole COVID-19 genomic surveillance effort, and many countries with universal health systems could effectively integrate the tracking of prolonged COVID-19 infections in people living with HIV into their primary care programmes. "

Human leukocyte antigen variants associate with BNT162b2 mRNA vaccine response.
Martina Esposito et al. Commun Med (Lond) 2024 4 (1) 63

From the abstract: "We carried out a genome-wide association study to investigate the genetic determinants of the antibody response to the Pfizer-BioNTech vaccine in an Italian cohort of 1351 subjects recruited in three centers. Linear regressions between normalized antibody levels and genotypes of more than 7 million variants was performed, using sex, age, centers, days between vaccination boost and serological test, and five principal components as covariates. We also analyzed the association between normalized antibody levels and 204 HLA alleles, with the same covariates as above. Our study confirms the involvement of the HLA locus and shows significant associations with variants in HLA-A, HLA-DQA1, and HLA-DQB1 genes. In particular, the HLA-A*03:01 allele is the most significantly associated with serum levels of anti-SARS-CoV-2 antibodies. "


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COVID Lung Proteome Provides Recovery, Convalescence Clues
GenomeWeb, Jul 9, 2024.

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Genomic epidemiology of SARS-CoV-2 in Senegal in 2020-2021.
Adjiratou Aissatou Ba et al. J Infect Dev Ctries 2024 7 (6) 851-861

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Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.
Karolayne S Azevedo et al. BMC Bioinformatics 2024 7 (1) 231

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KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution.
Joana Reis de Andrade et al. Biol Methods Protoc 2024 7 (1) bpae046

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Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis.
Christian Bundschuh et al. Data Brief 2024 7 110607

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Eight-Fold Increased COVID-19 Mortality in Autosomal Dominant Tubulointerstitial Kidney Disease due to MUC1 Mutations: An Observational Study.
Kidd Kendrah O, et al. medRxiv : the preprint server for health sciences 2024 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 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.

update trend

Summary

All Records47596
Genomics Precision Health34835
Non-Genomics Precision Health12761

Publication Categories Brand

Variants 14534
Vaccines 12057
Treatment 11500
Mechanism 11135
Diagnosis 8438
Prevention 5733
Surveillance 4427
Forecasting 3812
Transmission 2306
Health Equity 1222

Publication Types

PubMed Records36904
Preprints10245
Online News/Reports/Publications434

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 Public Health Genomics Branch 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.

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