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COVID-19 GPH|Home|Public Health Genomics and Precision Health Knowledge Base (PHGKB) Last data update: Feb 23, 2024 . (Total: 47032 Documents since 2020)

Last Posted: Feb-23-2024 05:32:44
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Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study
MA Moso et al, Lancet Microbe, February 2024

From the abstract: " There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community."

Effectiveness of Bivalent mRNA COVID-19 Vaccines in Preventing SARS-CoV-2 Infection in Children and Adolescents Aged 5 to 17 Years
LR Feldstein et al, JAMA, February 6, 2024

From the abstract: " What is the effectiveness of the bivalent COVID-19 vaccines among children and adolescents aged 5 to 17 years? In this prospective cohort study including 2959 participants aged 5 to 17 years, vaccine effectiveness against laboratory-confirmed SARS-CoV-2 infection was 54.0% and vaccine effectiveness against symptomatic COVID-19 was 49.4%. During a period when the Omicron BA.4/5 sublineages were the predominant circulating variants, children and adolescents received protection against SARS-CoV-2 infection and symptomatic COVID-19 from the bivalent COVID-19 vaccines compared with those who were unvaccinated or received only the monovalent COVID-19 vaccine."

SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis
Z Raglov et al, Lancet Microbe, January 26, 2024

From the abstract: "In this cohort, prolonged replication-competent omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting longer than 56 days accumulated spike mutations, which were distinct from those seen globally. Populations at high risk should be targeted for repeated testing and treatment and monitored for the emergence of antiviral resistance. "

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections.
Sheri Harari et al. Nat Commun 2024 1 (1) 648

From the abstract: " We harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings."

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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 Records47032
Genomics Precision Health34402
Non-Genomics Precision Health12630

Publication Categories Brand

Variants 14282
Vaccines 11897
Treatment 11315
Mechanism 10969
Diagnosis 8289
Prevention 5652
Surveillance 4314
Forecasting 3735
Transmission 2272
Health Equity 1204

Publication Types

PubMed Records36397
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.