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COVID-19 GPH|Home|Public Health Genomics and Precision Health Knowledge Base (PHGKB) Last data update: Mar 04, 2024 . (Total: 47040 Documents since 2020)

Last Posted: Mar-04-2024 05:31:07
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Adverse Events After XBB.1.5-Containing COVID-19 mRNA Vaccines.
Niklas Worm Andersson et al. JAMA 2024 2

From the article: "The monovalent Omicron XBB.1.5–containing COVID-19 mRNA vaccines were authorized in the US and Europe for use in autumn and winter 2023-2024.In Denmark, the XBB.1.5-containing vaccines were recommended as a fifth COVID-19 vaccine dose to individuals aged 65 years and older beginning October 1, 2023. However, data to support safety evaluations are lacking. We investigated the association between the XBB.1.5-containing vaccine administered as a fifth COVID-19 vaccine dose and the risk of 28 adverse events. In this nationwide cohort of more than 1 million adults aged 65 years and older, no increased risk of 28 adverse events was observed following vaccination with a monovalent XBB.1.5-containing vaccine. "

Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
Mahan Ghafari et al. Nature 2024 2

From the abstract: "Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1,2,3,4,5, give rise to highly divergent lineages6,7,8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. "

The next chapter for Africa's genomic initiatives
P Adepoujo, Lancet Id, March 2024

From the article: " The Africa Pathogen Genomics Initiative 2.0, launched at the end of 2023, plans to strengthen laboratory systems and enhance genomic capacity across Africa. With COVID-19 no longer a Public Health Emergency of International Concern, the demand for SARS-CoV-2 genomic sequencing has reduced. In Africa, this has created an opportunity for the rapidly acquired capacity for genomics to serve other purposes. In 2019, only seven countries in Africa had functional next-generation sequencing capacity in public health laboratories according to the Africa Pathogen Genomics Initiative (Africa PGI), but this rapidly grew to 30 in 2023, with nine regarded as centres of excellence. By 2025, Africa PGI aims to increase the number to 50 through Africa PGI 2.0."

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."

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Intra-host genetic diversity of SARS-CoV-2 Omicron variants in children.
Liu Pengcheng, et al. The Journal of infection 2024 0 0. 106132

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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 Records47040
Genomics Precision Health34406
Non-Genomics Precision Health12634

Publication Categories Brand

Variants 14286
Vaccines 11897
Treatment 11325
Mechanism 10981
Diagnosis 8300
Prevention 5658
Surveillance 4319
Forecasting 3738
Transmission 2275
Health Equity 1205

Publication Types

PubMed Records36400
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.