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COVID-10 GPH

COVID-19 GPH|Home|PHGKB Last data update: Aug 07, 2022 . (Total: 38302 Documents since 2020)
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Last Posted: Aug-07-2022 08:33:56
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Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices
GE Martin et al, he Lancet Infectious Diseases, August 4, 2022

Genomic sequencing of SARS-CoV-2 has had a major role in the public health response to the COVID-19 pandemic, enabling mapping of viral transmission at global and local levels, informing infection control measures, and, importantly, identifying and tracking the emergence of new SARS-CoV-2 variants. The rapid detection and characterization of new variants is crucial for informing the potential efficacy of vaccines and therapeutics.

COVID-19 rebound after Paxlovid treatment during Omicron BA.5 vs BA.2.12.1 subvariant predominance period
R Xu et al, MEDRXIV, August 6, 2022

Questions remain as to how COVID-19 rebound after Paxlovid treatment differs between the BA.5 and BA.2.12.1 subvariants. This is a retrospective cohort study of 15,913 patients who contracted COVID-19 between 5/8/2022-7/18/2022 and were prescribed Paxlovid within 5 days of their COVID-19 infection. The risks of both COVID-19 rebound infections and symptoms 2-8 days after Paxlovid treatment were higher in the BA.5 cohort than in the propensity-score matched BA.2.12.1 cohort: rebound infections (Hazard Ratio or HR: 1.32, 95% CI: 1.06-1.66), rebound symptoms (HR: 1.32, 95% CI: 1.04-1.68).

Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology
K Kuehfeldt et al, JAMA Network Open, August 5, 2022

In this cohort study of 140?000 class meetings at a large US university, there were over 850 cases of SARS-CoV-2 infection identified through weekly surveillance testing of all students and faculty on campus during the fall 2021 semester. There were 9 instances of potential in-class transmission identified as identical lineages confirmed by SARS-CoV-2 genome sequencing, and none of these instances were confirmed to be in-class transmission. These results suggest that in-class transmission of SAR-CoV-2 in an urban university with masking and vaccine protocols in-place was negligible.

One Health Genomic Surveillance and Response to a University-Based Outbreak of the SARS-CoV-2 Delta AY.25 Lineage, Arizona, 2021
H Yaglom et al, MEDRXIV, August 4, 2022

Large scale outbreaks of the SARS-CoV-2 Delta variant have occurred in numerous settings, including universities. An outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus with multiple transmission events was identified; genomic analyses characterized this outbreak and complemented contract tracing and wastewater surveillance strategies that strengthened overall public health response actions.


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COVID-19 Prediction With Machine Learning Technique From Extracted Features of Photoplethysmogram Morphology.
Nayan Nazrul Anuar, et al. Frontiers in public health 2022 0 0. 920849

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Early prediction of COVID-19 patient survival by targeted plasma multi-omics and machine learning.
Richard Vincent R, et al. Molecular & cellular proteomics : MCP 2022 0 0. 100277

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Deep learning based COVID-19 detection using medical images: Is insufficient data handled well?
Babu Caren, et al. Current medical imaging 2022 0 0.

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Predictors of invasive mechanical ventilation in hospitalized COVID-19 patients: a retrospective study from Jordan.
Kabbaha Suad, et al. Expert review of respiratory medicine 2022 0 0.

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The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection.
Yang Chih-Yun, et al. International journal of medical sciences 2022 0 0. (8) 1340-1356

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Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2.
Pastorio Chiara, et al. Cell host & microbe 2022 0 0.

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Identification of COVID-19-Specific Immune Markers Using a Machine Learning Method.
Li Hao, et al. Frontiers in molecular biosciences 2022 0 0. 952626

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Different Neutralization Profiles After Primary SARS-CoV-2 Omicron BA.1 and BA.2 Infections.
Medits Iris, et al. Frontiers in immunology 2022 0 0. 946318

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Pyroptotic Patterns in Blood Leukocytes Predict Disease Severity and Outcome in COVID-19 Patients.
Tang Yingkui, et al. Frontiers in immunology 2022 0 0. 888661

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Human coronaviruses: Origin, host and receptor.
Tang Guolu, et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2022 0 0. 105246

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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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Summary

All Records38302
Genomics Precision Health27800
Non-Genomics Precision Health10502

Publication Categories Brand

Variants 10035
Vaccines 8875
Mechanism 8404
Treatment 8143
Diagnosis 5938
Prevention 4560
Surveillance 3301
Forecasting 2987
Transmission 1805
Health Equity 969

Publication Types

PubMed Records28443
Preprints9415
Online News/Reports/Publications431

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.

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