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Last Posted: May 31, 2023
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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.

COVID's future: mini-waves rather than seasonal surges Three years after the start of the pandemic, SARS-CoV-2 shows no signs of settling into a seasonal pattern of spread, like influenza has.
E Callaway, Nature, May 1, 2023

Whether you call it a surge, a spike, a wave or perhaps just a wavelet, there are signs of a rise in SARS-CoV-2 infections — again. A growing proportion of tests in some countries are coming back positive, and new variants, most notably a lineage called XBB.1.16, are pushing aside older strains, fuelling some of the uptick in cases. Welcome to the new normal: the ‘wavelet’ era. Scientists say that explosive, hospital-filling COVID-19 waves are unlikely to return. Instead, countries are starting to see frequent, less deadly waves, characterized by relatively high levels of mostly mild infections and sparked by the relentless churn of new variants.

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19.
Daniela Matuozzo et al. Genome medicine 2023 4 (1) 22

We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P?=?1.1?×?10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR?=?3.70[95%CI 1.3–8.2], P?=?2.1?×?10-4).

Joint COVID-19 and influenza-like illness forecasts in the United States using internet search information.
Simin Ma et al. Communications medicine 2023 3 (1) 39

We combine related internet search and bi-disease time series information for the U.S. national level and state level forecasts. Our proposed ARGOX-Joint-Ensemble adopts a new ensemble framework that integrates ILI and COVID-19 disease forecasting models to pool the information between the two diseases and provide joint multi-resolution and multi-target predictions. Through a winner-takes-all ensemble fashion, our framework is able to adaptively select the most predictive COVID-19 or ILI signals. In the retrospective evaluation, our model steadily outperforms alternative benchmark methods, and remains competitive with other publicly available models in both point estimates and probabilistic predictions (including intervals).

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.