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Hot Topics of the Day are picked by experts to capture the latest information and publications on public health genomics and precision health for various diseases and health topics. Sources include published scientific literature, reviews, blogs and popular press articles.

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3536 hot topic(s) found with the query "Covid-19"

Vaccine effectiveness against emerging COVID-19 variants using digital health data
(Posted: May 09, 2024 6PM)

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."

Concerted efforts toward genomic surveillance of viral pathogens in immunocompromised individuals.
Matheus Filgueira Bezerra et al. Lancet Microbe 2024 4 (Posted: Apr 08, 2024 9AM)

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. "

Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections.
Claudia Fredolini et al. Commun Med (Lond) 2024 4 (1) 55 (Posted: Apr 04, 2024 9AM)

From the abstract: "Our three studies display highly consistent variance of protein levels and share associations of proteins with sex (e.g., MMP3) and age (e.g., GDF-15). Studying seropositive (IgG+) and seronegative (IgG-) donors from the first pandemic wave reveals a network of proteins reflecting immunity, inflammation, coagulation, and stress response. Proteome analysis of volumetric self-sampled DBS facilitates precise analysis of clinically relevant proteins, including those secreted into the circulation or found on blood cells, augmenting previous COVID-19 reports with clinical blood collections. Our population surveys support the usefulness of DBS, underscoring the role of timing the sample collection to complement clinical and precision health monitoring initiatives. "

Adverse Events After XBB.1.5-Containing COVID-19 mRNA Vaccines.
Niklas Worm Andersson et al. JAMA 2024 2 (Posted: Feb 27, 2024 9AM)

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 (Posted: Feb 23, 2024 3PM)

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 (Posted: Feb 23, 2024 3PM)

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 (Posted: Feb 13, 2024 9AM)

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 (Posted: Feb 06, 2024 1PM)

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."

Maximizing scarce colonoscopy resources: the crucial role of Stool-Based tests.
Gloria D Coronado et al. J Natl Cancer Inst 2024 2 (Posted: Feb 04, 2024 4PM)

From the abstract: "During the COVID-19 pandemic, health systems, including federally qualified health centers (FQHCs), experienced disruptions in colorectal cancer (CRC) screening. National organizations called for greater use of at-home stool-based testing followed by colonoscopy for those with abnormal test results to limit (in-person) colonoscopy exams to people with acute symptoms, or who were high-risk. This ‘stool-test-first’ strategy may also be useful for adults with low-risk adenomas who are due for surveillance colonoscopy. "

As COVID-19 Cases Surge, Here’s What to Know About JN.1, the Latest SARS-CoV-2 “Variant of Interest”
R Rubin, JAMA, January 12, 2024 (Posted: Jan 12, 2024 0PM)

From the article: "BA.2.86’s spawn, JN.1, has become the dominant SARS-CoV-2 variant in the US, status its parent variant never achieved. Fortunately, although COVID-19 cases have surged, hospitalizations and deaths from the disease are still considerably lower than they were the same time a year earlier. When BA.2.86 joined the SARS-CoV-2 Omicron family last summer, it grabbed pandemic trackers’ attention because it was so different from its progenitor, BA.2. Compared with BA.2, BA.2.86’s spike protein carries more than 30 mutations, suggesting that it might spread more easily than its predecessors. But even armed with those new mutations, BA.2.86 failed to dominate the other subvariants. "

Phylogenomic early warning signals for SARS-CoV-2 epidemic waves
KO Drake et al, EBiomedicine, January 8, 2024 (Posted: Jan 10, 2024 8AM)

From the abstract: "Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often been associated with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Rapid detection of growing genomic variants can therefore serve as a predictor of future waves, enabling timely implementation of countermeasures. Using phylogenomic analysis, we identified leading indicators that would have generated EWS ahead of significant increases in COVID-19 hospitalisations between August 2020 and March 2022. Our results also show that EWS lead time is sensitive to the threshold set for the number of false positive (FP) EWS. "

Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts.
Luca Ferretti et al. Nature 2023 12 (Posted: Jan 02, 2024 10AM)

From the abstract: "Here we analysed 7 million contacts notified by the NHS COVID-19 app6,7 in England and Wales to infer how app measurements translated to actual transmissions. Empirical metrics and statistical modelling showed a strong relation between app-computed risk scores and actual transmission probability. Longer exposures at greater distances had similar risk to shorter exposures at closer distances. The probability of transmission confirmed by a reported positive test increased initially linearly with duration of exposure (1.1% per hour) and continued increasing over several days. "

Unsupervised machine learning to investigate trajectory patterns of COVID-19 symptoms and physical activity measured via the MyHeart Counts App and smart devices.
Varsha Gupta et al. NPJ Digit Med 2023 12 (1) 239 (Posted: Jan 02, 2024 10AM)

From the abstract: " Previous studies have associated COVID-19 symptoms severity with levels of physical activity. We therefore investigated longitudinal trajectories of COVID-19 symptoms in a cohort of healthcare workers (HCWs) with non-hospitalised COVID-19 and their real-world physical activity. 121 HCWs with a history of COVID-19 infection who had symptoms monitored through at least two research clinic visits, and via smartphone were examined. HCWs with a compatible smartphone were provided with an Apple Watch Series 4 and were asked to install the MyHeart Counts Study App to collect COVID-19 symptom data and multiple physical activity parameters"

Machine learning identifies risk factors associated with long-term sick leave following COVID-19 in Danish population
KD Jacobsen et al, Comm Med, December 20, 2023 (Posted: Dec 20, 2023 9AM)

From the abstract: "Here, in a cohort of 88,818 individuals, including 37,482 with a confirmed SARS-CoV-2 infection, the RD of long-term sick-leave is 3.3% (95% CI 3.1% to 3.6%). We observe a high degree of effect heterogeneity, with conditional RDs ranging from -3.4% to 13.7%. Age, high BMI, depression, and sex are the most important variables explaining heterogeneity. "

Self-copying RNA vaccine wins first full approval: what’s next?
E Dolgin, Nature News, December 6, 2023 (Posted: Dec 07, 2023 8AM)

From the article: " Conventional mRNA-based COVID-19 shots consist mainly of the genetic instructions for a viral protein that are surrounded by regulatory sequences. A cell’s machinery produces the protein for as long as these instructions persist, and that protein — known as an antigen — stimulates an immune response. By contrast, saRNA jabs go a step further by integrating the genes needed for the replication and synthesis of the antigen-encoding RNA, effectively establishing a biological printing press for fabricating the vaccine inside cells "

A medical multimodal large language model for future pandemics
Liu et al, NPJ Digital Medicine, December 2, 2023 (Posted: Dec 02, 2023 8AM)

From the paper: "With the goal of quick deployment of tools for rapid response to rare diseases, we present the medical multimodal large language model (Med-MLLM) framework. We evaluate the effectiveness of Med-MLLM using the COVID-19 pandemic “in replay”, showing that Med-MLLM is able to accomplish accurate COVID-19 decision-support tasks with limited labelled data. In contrast, existing efforts usually require thousands, or even more, labelled data to achieve similar performance. "

The Ethics of Using COVID-19 Host Genomic Information for Clinical and Public Health Decision-making: A Survey of US Health Professionals.
Sheethal Jose et al. HGG Adv 2023 11 100255 (Posted: Nov 20, 2023 8AM)

From the abstract: "In 2021, a cross-sectional online survey was fielded to US health professionals. The survey explored how they view the value and ethical acceptability of using COVID-19 host genomic information in three main decision-making settings: (1) clinical, (2) public health, and (3) workforce. The survey also assessed participants' personal and professional experience with genomics and infectious diseases and collected key demographic data. A total of 603 participants completed the survey. A majority (84%) of participants agreed that it is ethically acceptable to use host genomics to make decisions about clinical care and 73% agreed that genetic screening has an important role to play in the public health control of COVID-19. However, more than 90% disagreed that it is ethically acceptable to use host genomics to deny resources or admission to individuals when hospital resources are scarce. "

mRNA COVID vaccines saved lives and won a Nobel - what's next for the technology?
Elie Dolgin et al. Nature 2023 10 (Posted: Oct 05, 2023 9AM)

From the paper: "In just three short years, mRNA vaccines have saved millions of lives, achieved household recognition and, as of this week, become the subject of a Nobel Prize. Yet the field shows no signs of slowing down. Vaccines based on mRNA rose to fame not only for their safety and efficacy, but also for the speed with which they were developed and rolled out during the COVID-19 pandemic. "

Updated COVID-19 Vaccine Now Available in US, Recommended for Everyone Older Than 6 Months
R Rubin, JAMA, September 18, 2023 (Posted: Sep 18, 2023 11AM)

From the article: "The US Centers for Disease Control and Prevention (CDC) on September 12 recommended that everyone 6 months or older get a new COVID-19 monovalent vaccine targeting the Omicron subvariant XBB.1.5. The CDC’s move came the day after the US Food and Drug Administration (FDA) approved Moderna’s and Pfizer-BioNTech’s updated COVID-19 messenger RNA (mRNA) vaccines for people 12 years or older and authorized the shots for emergency use in children 6 months through 11 years of age." "

CDC Recommends Updated COVID-19 Vaccine for Fall/Winter Virus Season
CDC, September 12, 2023 (Posted: Sep 13, 2023 6AM)

CDC recommends everyone 6 months and older get an updated COVID-19 vaccine to protect against the potentially serious outcomes of COVID-19 illness this fall and winter. Updated COVID-19 vaccines from Pfizer-BioNTech and Moderna will be available later this week. Vaccination remains the best protection against COVID-19-related hospitalization and death. Vaccination also reduces your chance of suffering the effects of Long COVID, which can develop during or following acute infection and last for an extended duration.? If you have not received a COVID-19 vaccine in the past 2 months, get an updated COVID-19 vaccine to protect yourself this fall and winter.

CDC Assesses Risk From BA.2.86, Highly Mutated COVID-19 Variant
E Harris, JAMA, August 30, 2023 (Posted: Aug 30, 2023 1PM)

From the paper: "Based on currently available data, updated COVID-19 vaccines targeting the XBB.1.5 variant are expected to be effective against BA.2.86—a highly mutated new SARS-CoV-2 variant—for reducing severe disease and hospitalization, according to an August 23 US Centers for Disease Control and Prevention (CDC) risk assessment."

Risk Assessment Summary for SARS CoV-2 Sublineage BA.2.86
CDC, August 23, 2023 Brand (Posted: Aug 23, 2023 0PM)

Based on what CDC knows now, existing tests used to detect and medications used to treat COVID-19 appear to be effective with this variant. BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines. Scientists are evaluating the effectiveness of the forthcoming, updated COVID-19 vaccine. CDC’s current assessment is that this updated vaccine will be effective at reducing severe disease and hospitalization. At this point, there is no evidence that this variant is causing more severe illness. That assessment may change as additional scientific data are developed. CDC will share more as we know more.

Why Blood Type Seems to Be Linked With COVID-19 Risk.
Rita Rubin et al. JAMA 2023 8 (Posted: Aug 21, 2023 2PM)

Since the early months of the COVID-19 pandemic, scientists have investigated whether ABO blood group is related to the risk of SARS-CoV-2 infection and illness. Most studies of the relationship between SARS-CoV-2 and blood group have found that, all other things being equal, people with type A were more likely to become infected than people with type O. Although some studies have found no relationship between blood type and COVID-19 risk, none has linked type O to a higher risk of SARS-CoV-2 infection. Why would blood group make any difference to SARS-CoV-2? Several new studies offer possible explanations. One from Stowell and colleagues, recently published in Blood, suggests that having type A blood makes SARS-CoV-2 “stickier” to host cells.

How are genetics, lifestyles, and cardiovascular and thromboembolic events associated following COVID-19 diagnosis?
TS Lomte, News Medical, August 2023 (Posted: Aug 11, 2023 11AM)

A recent study published in Nature Communications evaluated the associations between host genetics, lifestyle factors, and cardiovascular and thromboembolic events (CVEs) after coronavirus disease 2019 (COVID-19). Although prophylactic coagulation is recommended for hospitalized COVID-19 patients, mixed evidence exists for milder ambulatory and more critical COVID-19 patients. Polygenic risk scores (PRSs) have been proposed for early risk stratification and precision medicine. Whether genetic susceptibility to chronic CVD predisposes COVID-19 patients to CVE complications is unknown.

The Inflammatory Profile Correlates with COVID-19 Severity and Mortality in Cancer Patients
CE Budin et al, JPM, August 7, 2023 (Posted: Aug 08, 2023 8PM)

The correlation of the inflammatory profile with the severity of the disease in neoplastic patients with SARS-CoV-2 infection was addressed. A database of 1537 patients hospitalized in the pneumology department was analyzed. After applying the inclusion and exclusion criteria, 83 patients (67% males, 33% females) were included. Most of the analyzed patients were hospitalized with a moderate form of disease, explaining the significant percentage of 25% mortality. The frequency of the type of neoplasm was higher for lung cancer, followed by malignant colon tumor. We identified a significant association between the increased value of ferritin (p < 0.0001, OR = 22.31), fibrinogen (p = 0.009, OR = 13.41), and C-reactive protein (p = 0.01, OR = 7.65), respectively, and the level of severity of COVID-19.

A Genetic Explanation for Why Some People Had Asymptomatic COVID-19
J Abbasi, JAMA, August 2, 2023 (Posted: Aug 02, 2023 6PM)

A recent study of COVID-19 infected individuals found that a common variant, or allele, known as HLA-B*15:01 was present in 20% of asymptomatic participants but only 9% of participants who reported symptoms. People with 2 copies of the variant, inherited from both parents, were more than 8 times as likely to not have symptoms than those who carried no copies. The variant also had a strong association with asymptomatic infection in 2 independent cohorts. A meta-analysis of data from the discovery and independent cohorts found that asymptomatic infections were more than twice as common in people who carried the variant. The T cell analysis revealed that before the pandemic even began, participants with the variant had killer T cells that could effectively target SARS-CoV-2.

Text-based predictions of COVID-19 diagnosis from self-reported chemosensory descriptions
H Li et al, Comm Med, July 27, 2023 (Posted: Jul 28, 2023 8AM)

We developed a machine learning method based on Natural Language Processing (NLP) using Large Language Models (LLM) to predict COVID-19 diagnosis solely based on text descriptions of acute changes in chemosensation, i.e., smell, taste and chemesthesis, caused by the disease. The dataset of more than 1500 subjects was obtained from survey responses early in the COVID-19 pandemic, in Spring 2020.

A new era of pathogen surveillance using genomic sequencing
Open Access Government, July 19, 2023 (Posted: Jul 21, 2023 7AM)

Genomic sequencing is a method scientists use to decipher the genetic material found in organisms or viruses. The significance of genomic sequencing tools was truly brought to the fore during the COVID-19 pandemic as researchers were able to observe any sudden changes (or mutations) in a virus’s genetic code which may give it an advantage over other variants of itself, for example, spreading faster or causing more harm to those it infects.

Metagenomic assessment of gut microbial communities and risk of severe COVID-19.
Peggy Lai et al. Res Sq 2022 6 (Posted: Jul 19, 2023 7AM)

We profiled 127 hospitalized patients with COVID-19 (n?=?79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID,” suggesting these microbes may serve as early biomarkers for the eventual development of long COVID.

Tackling covid-19 variants.
Kayoko Shioda et al. BMJ 2023 7 p1603 (Posted: Jul 16, 2023 9AM)

SARS-CoV-2 is probably here to stay. The question is whether countries have the necessary tools and capacity to detect new variants and evaluate their severity so that we can act quickly to protect the most vulnerable populations. Surveillance is the obvious essential tool, but is it robust enough? What is our current situation, and where are we headed? Genomic surveillance has a critical role in detecting new variants, but 32% of countries lacked this capacity in January 2022, despite the scale-up during the covid-19 pandemic.

Gene linked to long COVID found in analysis of thousands of patients
H Ledfor, Nature, July 11, 2023 (Posted: Jul 12, 2023 7AM)

For more than three years, the global COVID-19 Host Genetics Initiative has been searching for DNA sequences that are associated with a risk of developing severe COVID-19. That hunt, which is ongoing, has implicated genes involved in the immune system and in allowing the SARS-CoV-2 virus to enter cells2. The long-COVID study is a spin-off from that effort. The first genome-wide hunt to find genetic risk factors for long COVID has yielded a hit: a DNA sequence near a gene called FOXP4, which is active in the lungs and in some immune cells.

Genome-wide Association Study of Long COVID
V Lammi et al, MEDRXIV, July 2023 (Posted: Jul 12, 2023 7AM)

We leveraged the COVID-19 Host Genetics Initiative to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity, lung function, and cancers.

New COVID jabs are coming — who should get them? Countries rolling out updated vaccines weigh up whether to restrict them to high-risk individuals.
M Koslov, Nature, June 29, 2023 (Posted: Jul 03, 2023 8AM)

Confronted once again with waning immunity against SARS-CoV-2, health officials around the world are planning to roll out booster jabs in the next few months. But these booster campaigns might not have the come-one, come-all approach of previous years. Now that the COVID-19 global emergency is over and infections have dwindled, officials have been rethinking who should receive the jab and when.

Precision Medicine for More Oxygen (P4O2)—Study Design and First Results of the Long COVID-19 Extension
N Baalbaki et al, JPM, June 2023 (Posted: Jun 28, 2023 11AM)

The Precision Medicine for more Oxygen (P4O2) consortium COVID-19 extension aims to identify long COVID patients that are at risk for developing chronic lung disease and furthermore, to identify treatable traits and innovative personalized therapeutic strategies for prevention and treatment. This study aims to describe the study design and first results of the P4O2 COVID-19 cohort.

Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.
Igor M Rouzine et al. Commun Med (Lond) 2023 6 (1) 86 (Posted: Jun 24, 2023 10AM)

Once the first SARS-CoV-2 vaccine became available, mass vaccination was the main pillar of the public health response to the COVID-19 pandemic. It was very effective in reducing hospitalizations and deaths. Here, we discuss the possibility that mass vaccination might accelerate SARS-CoV-2 evolution in antibody-binding regions compared to natural infection at the population level. Using the evidence of strong genetic variation in antibody-binding regions and taking advantage of the similarity between the envelope proteins of SARS-CoV-2 and influenza, we assume that immune selection pressure acting on these regions of the two viruses is similar.

New tool uncovers COVID-19 susceptibility mechanism
Wellcome Trust Sanger Institute, June 2023 (Posted: Jun 23, 2023 10AM)

Researchers have discovered a mechanism for COVID-19 susceptibility using a newly created tool. The tool, GASPACHO, captures dynamic changes in gene expression along the innate immune response, allowing researchers to identify genes and molecular pathways associated with disease risk that have previously been too complex to detect or interpret.

Risk of myocarditis and pericarditis in mRNA COVID-19-vaccinated and unvaccinated populations: a systematic review and meta-analysis.
Abdallah Alami et al. BMJ Open 2023 6 (6) e065687 (Posted: Jun 23, 2023 7AM)

Seven studies met the inclusion criteria, of which six were included in the quantitative synthesis. Our meta-analysis indicates that within 30-day follow-up period, vaccinated individuals were twice as likely to develop myo/pericarditis in the absence of SARS-CoV-2 infection compared to unvaccinated individuals, with a rate ratio of 2.05 (95% CI 1.49-2.82). Although the absolute number of observed myo/pericarditis cases remains quite low, a higher risk was detected in those who received mRNA COVID-19 vaccinations compared with unvaccinated individuals in the absence of SARS-CoV-2 infection.

WHO Introduces Worldwide Pathogen Surveillance Network
E Harris, JAMA, June 20, 2023 (Posted: Jun 21, 2023 7AM)

A global collaboration, known as the International Pathogen Surveillance Network, will harness pathogen genomics to improve disease surveillance and identify and respond to disease-causing agents before they become pandemics or epidemics, the World Health Organization (WHO) announced. The Network will connect members of different countries to improve sample collection and analysis and facilitate public health decision-making, among other goals. Pathogen genomics—which involves analyzing the genomes of viruses, bacteria, and other contagions to understand their infectivity, deadliness, and transmission—has played a key role in the world’s ability to respond to diseases, from COVID-19 to HIV.

BA.1 Bivalent COVID-19 Vaccine Use and Stroke in England.
Nick Andrews et al. JAMA 2023 6 (Posted: Jun 19, 2023 1PM)

This analysis showed no evidence of an increased risk of stroke in the 21 days immediately after vaccination with either of the 2 mRNA COVID-19 bivalent BA.1 vaccines in England, with similar results for ischemic and hemorrhagic stroke and for the subset aged 65 years and older given influenza vaccine on the same day as the bivalent COVID-19 vaccine. For ischemic stroke, the upper bounds of CIs for the RI were all below the point estimate of a relative risk of 1.47.

Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.
Kevin C Ma et al. MMWR Morb Mortal Wkly Rep 2023 6 (24) 651-656 (Posted: Jun 16, 2023 7AM)

CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023. During this period, the Omicron variant remained predominant, with various descendant lineages reaching national predominance (>50% prevalence).

Host genetic determinants of COVID-19 susceptibility and severity: A systematic review and meta-analysis.
Setegn Eshetie et al. Rev Med Virol 2023 6 e2466 (Posted: Jun 13, 2023 8AM)

The meta-analysis showed that a cluster of highly correlated 9 SNPs (R2 > 0.9) at 3p21.31 gene locus covering LZTFL1 and SLC6A20 genes was significantly associated with COVID-19 severity, with a pooled OR of 1.8 [1.5-2.0]. Meanwhile, another 3 SNPs (rs2531743-G, rs2271616-T, and rs73062389-A) within the locus was associated with COVID-19 susceptibility, with pooled estimates of 0.95 [0.93-0.96], 1.23 [1.19-1.27] and 1.15 [1.13-1.17], respectively.

Proteomic characterization of acute kidney injury in patients hospitalized with SARS-CoV2 infection
I Paranjpe et al, Comm Med, June 12, 2023 (Posted: Jun 12, 2023 9AM)

Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

Severity Outcomes among Adult Patients with Primary Immunodeficiency and COVID-19 Seen in Emergency Departments, United States, April 2020–August 2021
CDC Visual Abstracts, June 2023 Brand (Posted: Jun 09, 2023 8AM)

Severe COVID-19 outcomes, including hospitalization, IMV, ICU admission, and death, are more frequent in PI patients than in non-PI patients seen in emergency departments. These results provide real-world evidence that PI is a risk factor for adverse COVID-19 outcomes.

Safety Monitoring of mRNA COVID-19 Vaccine Third Doses Among Children Aged 6 Months-5 Years - United States, June 17, 2022-May 7, 2023.
Anne M Hause et al. MMWR Morb Mortal Wkly Rep 2023 6 (23) 621-626 (Posted: Jun 09, 2023 7AM)

All children aged 6 months–5 years are recommended to receive =1 bivalent mRNA COVID-19 vaccine dose; approximately 550,000 children in these age groups have received a third monovalent or bivalent mRNA vaccine dose. In v-safe, 38% of children had no reported reactions after a third dose; most reported reactions were mild and transient. Vaccination errors accounted for 78% of events reported to the Vaccine Adverse Event Reporting System.

Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy
MR Cronin et al, Nat Comm, June 7, 2023 (Posted: Jun 07, 2023 1PM)

COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively.

China’s rolling COVID waves could hit every six months — infecting millions
Y Ye, Nature, June 7, 2023 (Posted: Jun 07, 2023 1PM)

The latest surge in COVID-19 cases in China is not surprising to researchers, who say that China will see an infection cycle every six months now that all COVID-19 restrictions have been removed and highly infectious variants are dominant. But they caution that rolling waves of infection carry the risk of new variants emerging.

A Review of the Role of Artificial Intelligence in Healthcare
A Al Kuweiti et al, J Per Med, June 5, 2023 (Posted: Jun 05, 2023 8AM)

AI meets several technical, ethical, and social challenges, including privacy, safety, the right to decide and try, costs, information and consent, access, and efficacy, while integrating AI into healthcare. The governance of AI applications is crucial for patient safety and accountability and for raising HCPs’ belief in enhancing acceptance and boosting significant health consequences. Effective governance is a prerequisite to precisely address regulatory, ethical, and trust issues while advancing the acceptance and implementation of AI. Since COVID-19 hit the global health system, the concept of AI has created a revolution in healthcare, and such an uprising could be another step forward to meet future healthcare needs.

Assessing the potential of polygenic scores to strengthen medical risk prediction models of COVID-19.
Aldo Córdova-Palomera et al. PLoS One 2023 5 (5) e0285991 (Posted: May 27, 2023 6AM)

In UK Biobank participants of European ancestry, the model achieved a relatively high performance (area under the receiver operating characteristic curve ~90%). Polygenic scores for COVID-19 computed from summary statistics of the Covid19 Host Genetics Initiative displayed significant associations with COVID-19 in the UK Biobank (p-values as low as 3.96e-9, all with R2 under 1%), but were unable to robustly improve predictive performance of the non-genetic factors.

Use of digital technologies for public health surveillance during the COVID-19 pandemic: A scoping review.
Lorie Donelle et al. Digit Health 2023 5 20552076231173220 (Posted: May 24, 2023 9AM)

The most frequently used technologies included mobile phone devices and applications, location tracking technologies, drones, temperature scanning technologies, and wearable devices. The utility of digital technologies for public health surveillance was impacted by factors including uptake of digital technologies across targeted populations, technological capacity and errors, scope, validity and accuracy of data, guiding legal frameworks, and infrastructure to support technology use.

Why is COVID life-threatening for some people? Genetics study offers clues Immune genes could play a part in the risk of needing intensive care when infected with SARS-CoV-2.
H Ledford, Nature, May 17, 2023 (Posted: May 17, 2023 4PM)

An analysis of DNA from more than 24,000 people who had COVID-19 and required treatment in intensive care has yielded more than a dozen new genetic links to the risk of developing extreme illness from the disease. The study has more than 2,000 authors, highlights the role of the immune system in fuelling the later stages of particularly severe COVID-19. The results could one day contribute to the development of therapies for COVID-19 — and potentially other diseases that cause acute respiratory distress or sepsis.

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19
EP Castineira et al, Nature, May 17, 2023 (Posted: May 17, 2023 0PM)

Here we analyze 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously.

Severity Outcomes among Adult Patients with Primary Immunodeficiency and COVID-19 Seen in Emergency Departments, United States, April 2020–August 2021
E Drzymalla et al, JCM, May 17, 2023 (Posted: May 17, 2023 11AM)

We used Premier Healthcare Database, which contains information on inpatient discharges, to analyze COVID-19 outcomes among 853 adult PI and 1,197,430 non-PI patients who visited the emergency department. Hospitalization, intensive care unit (ICU) admission, invasive mechanical ventilation (IMV), and death had higher odds in PI patients than in non-PI patients (hospitalization aOR: 2.36, 95% CI: 1.87–2.98; ICU admission aOR: 1.53, 95% CI: 1.19–1.96; IMV aOR: 1.41, 95% CI: 1.15–1.72; death aOR: 1.37, 95% CI: 1.08–1.74), and PI patients spent on average 1.91 more days in the hospital than non-PI patients when adjusted for age, sex, race/ethnicity, and chronic conditions associated with severe COVID-19.

Wasting no time: CDC adapts wastewater surveillance to stay vigilant for emerging threats
A Kirby, CDC, May 2023 Brand (Posted: May 10, 2023 6AM)

The COVID-19 pandemic made the value of sewage clear. For epidemiologists, CDC’s National Wastewater Surveillance System (NWSS) provides invaluable insights by helping identify community infection trends before they appear in clinical cases. In 2022, NWSS enhanced detection of SARS-CoV-2 and its variants. But perhaps equally critical were efforts to adapt wastewater surveillance for other emerging infectious disease challenges.

Innate immune cell genetic risk factors are linked to COVID-19 severity.
et al. Nat Genet 2023 5 (Posted: May 09, 2023 10AM)

Single-cell RNA-sequencing analysis combined with host genetic data for a Japanese population reveals the dysfunction of innate immune cells, particularly non-classical monocytes, in individuals with severe COVID-19, as well as enrichment of host genetic risk factors for severe COVID-19 in monocytes and dendritic cells.

End of the Federal COVID-19 Public Health Emergency (PHE) Declaration
CDC, May 5, 2023 Brand (Posted: May 07, 2023 6AM)

May 11, 2023, marks the end of the federal COVID-19 PHE declaration. After this date, CDC’s authorizations to collect certain types of public health data will expire. The United States has mobilized and sustained a historic response to the COVID-19 pandemic. As a nation, we now find ourselves at a different point in the pandemic – with more tools and resources than ever before to better protect ourselves and our communities.

Wuhan market samples fail to shed further light on COVID origins New analysis of genomic data from market swabs highlights their limitations.
D Lewis, Nature, May 4, 2023 (Posted: May 04, 2023 7AM)

Samples collected at the Huanan Seafood Wholesale Market in Wuhan, China, in the early weeks of the COVID-19 pandemic are of limited value for pinpointing which animal species — if any — infected people at the market, according to a new analysis. Two previous analyses of the data described genetic material from various wild animals, suggesting it was possible that these animals could have passed the virus to people at the market. The new analysis attempts to identify the specific animal responsible for the spillover — but comes up empty.

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 (Posted: May 01, 2023 10AM)

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.

Effectiveness of Monovalent mRNA COVID-19 Vaccination in Preventing COVID-19-Associated Invasive Mechanical Ventilation and Death Among Immunocompetent Adults During the Omicron Variant Period - IVY Network, 19 U.S. States, February 1, 2022-January 31, 2023.
Jennifer DeCuir et al. MMWR Morb Mortal Wkly Rep 2023 4 (17) 463-468 (Posted: Apr 28, 2023 7AM)

In this case-control analysis, the effectiveness of 2-4 monovalent mRNA COVID-19 vaccine doses was evaluated against COVID-19-associated invasive mechanical ventilation (IMV) and in-hospital death among immunocompetent adults aged =18 years during February 1, 2022-January 31, 2023. Vaccine effectiveness (VE) against IMV and in-hospital death was 62% among adults aged =18 years and 69% among those aged =65 years. When stratified by time since last dose, VE was 76% at 7-179 days, 54% at 180-364 days, and 56% at =365 days.

Are repeat COVID infections dangerous? What the science says.
Cassandra Willyard et al. Nature 2023 4 (7958) 650-652 (Posted: Apr 27, 2023 9AM)

When the coronavirus pandemic began in early 2020, the SARS-CoV-2 virus was a strange and terrifying adversary that plunged the world into chaos. More than three years later, the infection’s symptoms are all too familiar and COVID-19 is here to stay — part of a long list of common diseases that infect humans. Experts estimate that the majority of the world’s population has been infected at least once; in the United States, some estimates suggest that as many as 65% of people have had multiple infections. And it’s likely that in the decades to come, we’re all destined to get COVID-19 many more times.

Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity.
Ryuya Edahiro et al. Nat Genet (Posted: Apr 25, 2023 7AM)

CDC simplifies COVID-19 vaccine recommendations, allows older adults and immunocompromised adults to get second dose of the updated vaccine
CDC, April 19, 2023 Brand (Posted: Apr 21, 2023 6AM)

CDC’s new recommendations allow an additional updated (bivalent) vaccine dose for adults ages 65 years and older and additional doses for people who are immunocompromised. This allows more flexibility for healthcare providers to administer additional doses to immunocompromised patients as needed. Monovalent (original) mRNA COVID-19 vaccines will no longer be recommended for use in the United States. CDC recommends that everyone ages 6 years and older receive an updated (bivalent) mRNA COVID-19 vaccine, regardless of whether they previously completed their (monovalent) primary series.

The Association of Reported Experiences of Racial and Ethnic Discrimination in Health Care with COVID-19 Vaccination Status and Intent - United States, April 22, 2021-November 26, 2022.
Laurie D Elam-Evans et al. MMWR Morb Mortal Wkly Rep (16) 437-444 (Posted: Apr 21, 2023 6AM)

There is a growing awareness of racism as a cause of health inequities, health disparities, and disease. Adults reporting experiences of racial and ethnic discrimination in health care had a significantly higher prevalence of being unvaccinated against COVID-19 overall and among most racial and ethnic groups.

Mainstreaming Wastewater Surveillance for Infectious Disease.
Michelle M Mello et al. N Engl J Med 2023 4 (16) 1441-1444 (Posted: Apr 20, 2023 11AM)

During the Covid-19 pandemic, valuable intelligence on trends in the infection rates, variants, and distribution of SARS-CoV-2 in the United States was obtained from the humblest of assets: the country’s sewage. Analyzing fragments of viral RNA shed into sewers, organizations including universities and the Centers for Disease Control and Prevention (CDC) used wastewater to understand disease dynamics. This information became especially important as new variants emerged and use of home antigen testing exacerbated the reporting bias present in traditional testing systems.

Newborn Screening in a Pandemic—Lessons Learned
M Mlinaric et al, IJNS, April 11, 2023 (Posted: Apr 14, 2023 7AM)

The COVID-19 pandemic affected many essential aspects of public health, including newborn screening programs (NBS). The pandemic can be regarded as a stress test of the NBS under real-world conditions, highlighting critical aspects of this multidisciplinary system and the need for establishing local, national, and global strategies to improve its robustness and reliability in times of shortage and overloaded national healthcare systems.

High risk of autoimmune diseases after COVID-19.
Chetan Sharma et al. Nat Rev Rheumatol 2023 4 (Posted: Apr 14, 2023 7AM)

The full picture of post-COVID-19 autoimmune diseases and their prevalence is lacking despite numerous case reports and small series. Two studies that use large cohorts now highlight that SARS-CoV-2 infection is linked to a substantially increased risk of developing a diverse spectrum of new-onset autoimmune diseases.

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 (Posted: Apr 09, 2023 7AM)

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).

Pregnancy-specific responses to COVID-19 revealed by high-throughput proteomics of human plasma.
Nardhy Gomez-Lopez et al. Communications medicine 2023 4 (1) 48 (Posted: Apr 07, 2023 8AM)

Herein, we profile the plasma proteome of pregnant and non-pregnant COVID-19 patients and controls and show alterations that display a dose-response relationship with disease severity; yet, such proteomic perturbations are dampened during pregnancy. In both pregnant and non-pregnant state, the proteome response induced by COVID-19 shows enrichment of mediators implicated in cytokine storm, endothelial dysfunction, and angiogenesis.

Effectiveness of BNT162b2 after extending the primary series dosing interval in children and adolescents aged 5-17.
Francisco Tsz Tsun Lai et al. Nature communications 2023 4 (1) 1845 (Posted: Apr 05, 2023 6AM)

For vaccine recipients with extended intervals [=28 days, adjusted odds ratio 0.718, 95% Confidence Interval: 0.619, 0.833] there was a 29.2%-reduced risk of Covid-19 infection compared to those with regular intervals (21-27 days). If the threshold was set at eight weeks, the risk reduction was estimated at 43.5% (aOR 0.565, 95% CI: 0.456, 0.700). In conclusion, longer dosing intervals for children and adolescents should be considered.

Surveillance of SARS-CoV-2 at the Huanan Seafood Market
WJ Liu et al, Nature, April 5, 2023 (Posted: Apr 05, 2023 5AM)

SARS-CoV-2, the causative agent of COVID-19, emerged in December 2019. Its origins remain uncertain. It has been reported that a number of the early human cases had a history of contact with the Huanan Seafood Market. Here we present the results of surveillance for SARS-CoV-2 within the market. From January 1st 2020, after closure of the market, 923 samples were collected from the environment. From 18th January, 457 samples were collected from 18 species of animals, comprising of unsold contents of refrigerators and freezers, swabs from stray animals, and the contents of a fish tank. Using RT-qPCR, SARS-CoV-2 was detected in 73 environmental samples, but none of the animal samples.

Stratification of Pediatric COVID-19 cases by inflammatory biomarker profiling and machine learning
D Subramanian et al, MEDRXIV, April 4, 2023 (Posted: Apr 05, 2023 5AM)

Longitudinal Analysis of Humoral and Cellular Immune Response Following SARS-CoV-2 Vaccination Supports Utilizing Point-Of-Care Tests to Enhance COVID-19 Booster Uptake.
M Mallory et al, MEDRXIV, April 4, 2023 (Posted: Apr 05, 2023 5AM)

Modified SCOPE (mSCOPE) Score as a Tool to Predict Mortality in COVID-19 Critically Ill Patients
S Zanelli et al, J Per Med, April 2, 2023 (Posted: Apr 03, 2023 7AM)

Transmission Characteristics and Inactivated Vaccine Effectiveness Against Transmission of SARS-CoV-2 Omicron BA.5 Variants in Urumqi, China.
Kai Wang et al. JAMA network open 2023 3 (3) e235755 (Posted: Mar 31, 2023 6AM)

What were the transmission characteristics of SARS-CoV-2 Omicron BA.5 variants, and was inactivated vaccine associated with a protective outcome against the transmission of these variants? This cohort study of 1139 individuals with COVID-19 found that despite active contact tracing, high vaccine coverage, and other intensive control measures, Omicron BA.5 variants had high risks of transmission in household settings and among younger and older individuals. Compared with a 2-dose inactivated vaccine, a booster dose was associated with a protective outcome against Omicron BA.5 transmission.

Association of Glucose-6-Phosphate Dehydrogenase Deficiency With Outcomes in US Veterans With COVID-19.
Sarah H Elsea et al. JAMA network open 2023 3 (3) e235626 (Posted: Mar 31, 2023 6AM)

Is G6PD deficiency, the most common enzyme deficiency in the world, associated with COVID-19 severity in US veterans? In this cohort study of 24?700 veterans, G6PD deficiency was present in 9.4% of veterans with SARS-CoV-2 infection and was associated with a 1.5-fold increased likelihood of severe outcomes in male veterans less than 65 years of age who self-identified as Black, and a 3.6-fold greater likelihood of severe outcomes in male veterans 65 years of age and older who self-identified as White.

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 (Posted: Mar 29, 2023 8AM)

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).

Determinants of COVID-19 vaccine fatigue.
Tanja A Stamm et al. Nature medicine 2023 3 (Posted: Mar 28, 2023 6AM)

Our results suggest that vaccination campaigns should be tailored to subgroups based on their vaccination status. Among the unvaccinated, campaign messages conveying community spirit had a positive effect (0.343, confidence interval (CI) 0.019–0.666), whereas offering positive incentives, such as a cash reward (0.722, CI 0.429–1.014) or voucher (0.670, CI 0.373–0.967), was pivotal to the decision-making of those vaccinated once or twice. Among the triple vaccinated, vaccination readiness increased when adapted vaccines were offered (0.279, CI 0.182–0.377), but costs (-0.795, CI -0.935 to -0.654) and medical dissensus (-0.161, CI -0.293 to -0.030) reduced their likelihood to get vaccinated.

Rare Primary Immunodeficiency Diseases and COVID-19: Evolving Insights and Implications for Clinical and Public Health Practice
E Drzymalla et al, CDC Blog Post, March 27, 2023 Brand (Posted: Mar 27, 2023 9AM)

We explore how new research on rare genetic diseases is contributing to our understanding of COVID-19 occurrence and outcomes and discuss potential clinical and public health implications. Understanding the mechanisms involved in these inherited disorders may shed light on biological mechanisms and natural history of COVID-19. Although only a small proportion of patients are ill due to rare, single gene disorders, studying them may improve understanding of underlying biological pathways, eventually leading to new therapies that are relevant across the disease spectrum.

Predicting vaccine effectiveness against severe COVID-19 over time and against variants: a meta-analysis.
Deborah Cromer et al. Nature communications 2023 3 (1) 1633 (Posted: Mar 27, 2023 7AM)

We find that predicted neutralising antibody titres are strongly correlated with observed vaccine effectiveness against symptomatic (Spearman [Formula: see text] = 0.95, p < 0.001) and severe (Spearman [Formula: see text] = 0.72, p < 0.001 for both) COVID-19 and that the loss of neutralising antibodies over time and to new variants are strongly predictive of observed vaccine protection against severe COVID-19.

People who catch Omicron are less likely to get Long Covid Vaccination, virus biology may be driving down risk
J Couzin-Frankel, Science, March 2023 (Posted: Mar 25, 2023 8AM)

After Omicron began spreading in late 2021, COVID-19 deaths became a rarity even among frail and immunocompromised patients, he says. And infections now carry a lower threat of lingering complications. “These patients with Omicron, they’re much less likely to get Long Covid,” says Willan, whose patients are overwhelmingly vaccinated. Earlier this month, he reported in the British Journal of Haematology that his patients’ risk of Long Covid symptoms 3 months after infection had dropped from 46% with the original coronavirus strain and another called Alpha, to 35% with the Delta variant, to 14% with Omicron.

Maternal third dose of BNT162b2 mRNA vaccine and risk of infant COVID-19 hospitalization
M Lipshhuetz et al, Nature Medicine, March 23, 2023 (Posted: Mar 24, 2023 6AM)

Compared to the second dose, the third dose was associated with reduced infant hospitalization with estimated effectiveness of 53% (95% CI: 36–65%). Greater protection was associated with a shorter interval between vaccination and delivery. A third maternal dose during pregnancy reduced the risk of infant hospitalization for COVID-19 during the first 4?months of life, supporting clinical and public health guidance for maternal booster vaccination to prevent infant COVID-19 hospitalization.

Neutralization of BQ.1, BQ.1.1, and XBB with RBD-Dimer Vaccines.
Dedong Li et al. The New England journal of medicine 2023 3 (12) 1142-1145 (Posted: Mar 23, 2023 6AM)

The currently circulating omicron subvariants, especially BQ.1, BQ.1.1, and XBB, showed immune escape to the humoral immunity elicited by prototype strain sequence-based vaccines, such as inactivated vaccine and ZF2001. Our study showed that next-generation and updated Covid-19 vaccines are needed for better protection and pandemic control.

Heterogeneous Treatment Effects of Therapeutic-Dose Heparin in Patients Hospitalized for COVID-19.
Ewan C Goligher et al. JAMA 2023 3 (Posted: Mar 22, 2023 7AM)

In an exploratory analysis of a multiplatform randomized trial of therapeutic-dose heparin for early-pandemic patients with moderate or severe COVID-19, 3 approaches for testing HTE—conventional subgroup analysis, risk-based analysis, and effect-based analysis—were congruent in findings that therapeutic-dose heparin was more likely to be beneficial in patients who were less severely ill at presentation or who had lower body mass index, and more likely to be harmful in sicker patients and those with higher body mass index. Benefits and harms of therapeutic-dose heparin varied by hospitalized COVID-19 patient characteristics, illustrating the importance of considering HTE in the design and analysis of randomized clinical trials.

COVID-19 Forecasting and Mathematical Modeling
CDC, March 2023 Brand (Posted: Mar 20, 2023 2PM)

CDC is working closely with state, tribal, local, and territorial health departments, and other public health partners, to respond to the COVID-19 pandemic. Forecasts of disease burden help inform public health decision making by projecting the likely impact of COVID-19 in the next few weeks. These forecasts are generated using mathematical models by CDC partners in the COVID-19 Forecast Hub. Forecasts are used to inform public health decisions about pandemic planning, resource allocation, implementation of social distancing measures, and other interventions.

School-Based Interventions to Increase Student COVID-19 Vaccination Coverage in Public School Populations with Low Coverage - Seattle, Washington, December 2021-June 2022.
Tarayn Fairlie et al. MMWR. Morbidity and mortality weekly report 2023 3 (11) 283-287 (Posted: Mar 20, 2023 2PM)

Vaccination decreases risk for COVID-19 illness, severe disease, and death. U.S. pediatric COVID-19 vaccination coverage remains low. Seattle Public Schools implemented a COVID-19 vaccination program through multiple community engagements. During December 2021–June 2022, completion of the primary COVID-19 vaccination series among Seattle Public Schools students aged 5–18 years increased from 56.5% to 80.3%.

Comparative effectiveness of BNT162b2 versus mRNA-1273 covid-19 vaccine boosting in England: matched cohort study in OpenSAFELY-TPP.
William J Hulme et al. BMJ (Clinical research ed.) 2023 3 e072808 (Posted: Mar 18, 2023 3PM)

This matched observational study of adults estimated a modest benefit of booster vaccination with mRNA-1273 compared with BNT162b2 in preventing positive SARS-CoV-2 tests and hospital admission with covid-19 20 weeks after vaccination, during a period of delta followed by omicron variant dominance.

Estimation of COVID-19 mRNA Vaccine Effectiveness and COVID-19 Illness and Severity by Vaccination Status During Omicron BA.4 and BA.5 Sublineage Periods
RL Gelles et al, JAMA Network Open, March 15, 2023 (Posted: Mar 15, 2023 4PM)

What is the estimated vaccine effectiveness (VE) associated with first-generation COVID-19 mRNA vaccines against medically attended COVID-19 during Omicron BA.4 and BA.5 sublineage predominance? This case-control study included 82?229 emergency department or urgent care encounters and 21?007 hospitalizations for COVID-19–like illness. Among hospitalized patients, estimated 3-dose VE was 68% for those with the third dose 7 to 119 days prior, but was lower by 120 days or longer after vaccination (VE, 36%). These findings suggest that first-generation COVID-19 mRNA vaccines were associated with protection against COVID-19 during the Omicron BA.4/BA.5 sublineage-predominant periods but protection declined over time.

Host genomics for better infectious disease treatment
H Carr, PHG Foundation, March 6, 2023 (Posted: Mar 10, 2023 3PM)

Individuals can respond very differently to the same infectious disease, even when they have similar characteristics, comorbidities, and environmental exposures. Host genomics is the field that looks for genetic differences that help to explain the variations in response at certain points of an infection. While the COVID-19 pandemic significantly raised the profile of host genomics as a tool to better understand severe COVID-19, before the pandemic, scientists had been exploring host genomics to understand differences in host response to various infectious diseases.

An Explainable Host Genetic Severity Predictor Model for COVID-19 Patients
A Onoja et al, MEDRXIV, March 9, 2023 (Posted: Mar 10, 2023 3PM)

A host genetic severity predictor (HGSP) model was developed by combining several state-of-the-art machine learning algorithms (decision tree-based models: Random Forest and XGBoost classifiers). These models were trained using a genetic Whole Exome Sequencing (WES) dataset and clinical covariates (age and gender) formulated from a 5-fold stratified cross-validation computational strategy to randomly split the dataset to overcome model instability. Our study validated the HGSP model based on the 18 features (i.e., 16 identified candidate genetic variants and 2 covariates.

Comparison of Symptoms Associated With SARS-CoV-2 Variants Among Children in Canada.
Madeleine W Sumner et al. JAMA network open 2023 3 (3) e232328 (Posted: Mar 09, 2023 8PM)

Do the symptom profiles among children with SARS-CoV-2 infection evaluated in tertiary care emergency departments differ by variant type? In this multicenter Canadian cohort study of 1440 children with SARS-CoV-2 infection, those with Alpha variant infection reported the fewest core COVID-19 symptoms, while those with Omicron variant infection reported more fever, lower respiratory tract, and systemic symptoms than those infected by other variants. Hospitalization and intensive care admission rates were comparable across variants.

Forecasting the trajectory of the COVID-19 pandemic into 2023 under plausible variant and intervention scenarios: a global modelling study
R Reiner et al, MEDRXIV, March 9, 2023 (Posted: Mar 09, 2023 1PM)

This paper samples across a range of potential variant-level characteristics to provide global forecasts of infections, hospitalisations, and deaths in the face of ongoing Omicron-related transmission and waning levels of past immunity and evaluates a range of interventions that may diminish the impact of future waves. We created a susceptible-exposed-infectious dynamic model that accounts for vaccine uptake and effectiveness, antiviral administration, the emergence of new variants, and waning protection from both infection- and vaccine-derived immunity.

Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes.
Ramandip Grewal et al. Nature communications 2023 3 (1) 1273 (Posted: Mar 08, 2023 6PM)

We included 11,160 cases and 62,880 tests for test-negative controls. Depending on the age group, compared to unvaccinated adults, VE was 91–98% 7–59 days after a third dose, waned to 76–87% after =240 days, was restored to 92–97% 7–59 days after a fourth dose, and waned to 86–89% after =120 days. VE was lower and declined faster during BA.4/BA.5 versus BA.1/BA.2 predominance, particularly after =120 days. Here we show that booster doses of monovalent mRNA COVID-19 vaccines restored strong protection against severe outcomes for at least 3 months after vaccination.

Phenome-wide association study to explore the long-term symptoms after infection with novel coronavirus in the UK Biobank
K Zhang et al, MEDRXIV, March 5, 2023 (Posted: Mar 06, 2023 6PM)

We leveraged individual-level data from UK Biobank to implement a phenome-wide association study to explore the relationships between COVID-19 and 1061 diseases. Then, the inverse-variance weighted (IVW) method was adopted with summary-level data from global consortiums as sensitivity analyses combined with other MR methods with different model assumptions to identify robust associations. Findings The PheWAS found severe respiratory, hospitalized, and susceptibility COVID-19 had detrimental effects on 36, 37, and 51 kinds of diseases, separately.

Spatially-resolved wastewater-based surveillance enables COVID-19 case localization across a university campus, and confirms lower SARS-CoV-2 RNA burden relative to the surrounding community
J Lee et al, MEDRXIV, March 6, 2023 (Posted: Mar 06, 2023 6PM)

Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this technology has not been well assessed at more granular scales, including large work sites such as University campuses.

A circulating proteome-informed prognostic model of COVID-19 disease activity that relies on routinely available clinical laboratories
W Ma et al, MEDRXIV, March 6, 2023 (Posted: Mar 06, 2023 6PM)

A minority of people infected with SARS-CoV-2 will develop severe COVID-19 disease. To help physicians predict who is more likely to require admission to ICU, we conducted an unsupervised stratification of the circulating proteome that identified six endophenotypes (EPs) among 731 SARS-CoV-2 PCR-positive hospitalized participants in the Biobanque Québécoise de la COVID-19, with varying degrees of disease severity and times to intensive care unit (ICU) admission.

COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1,2,5 and Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history
H Townsley et al, MEDRXIV, March 6, 2023 (Posted: Mar 06, 2023 6PM)

Safety and immunogenicity of the protein-based PHH-1V compared to BNT162b2 as a heterologous SARS-CoV-2 booster vaccine in adults vaccinated against COVID-19: a multicentre, randomised, double-blind, non-inferiority phase IIb trial
J Corominas et al, MEDRXIV, March 2, 2023 (Posted: Mar 04, 2023 8AM)

An AI-enabled research support tool for the classification system of COVID-19
A Tiwari et al, Front Public Health, March 3, 2023 (Posted: Mar 03, 2023 4PM)

The objective of the present study is to build a research support tool that will help the researchers swiftly identify the relevant literature on a specific field or topic regarding COVID-19 through a hierarchical classification system. The three main tasks done during this study are data preparation, data annotation and text data classification through bi-directional long short-term memory (bi-LSTM).

Predicting the efficacy of variant-modified COVID-19 vaccine boosters.
David S Khoury et al. Nature medicine 2023 3 (Posted: Mar 03, 2023 9AM)

Here we aggregate data on neutralization titers from 14 reports (three published papers, eight preprints, two press releases and notes of one advisory committee meeting) comparing booster vaccination with the current ancestral-based vaccines or variant-modified vaccines. Using these data, we compare the immunogenicity of different vaccination regimens and predict the relative protection of booster vaccines under different scenarios. We predict that boosting with ancestral vaccines can markedly enhance protection against both symptomatic and severe disease from SARS-CoV-2 variant viruses.

Financing covid-19 mRNA vaccines.
Victor Roy et al. BMJ (Clinical research ed.) 2023 3 p413 (Posted: Mar 02, 2023 9AM)

US public investment in development of mRNA covid-19 vaccines: retrospective cohort study.
Hussain S Lalani et al. BMJ (Clinical research ed.) 2023 3 e073747 (Posted: Mar 02, 2023 9AM)

The US government invested at least $31.9bn to develop, produce, and purchase mRNA covid-19 vaccines, including sizeable investments in the three decades before the pandemic through March 2022. These public investments translated into millions of lives saved and were crucial in developing the mRNA vaccine technology that also has the potential to tackle future pandemics and to treat diseases beyond covid-19.

Estimated Effectiveness of Postpartum Maternal Messenger RNA COVID-19 Vaccination Against Delta and Omicron SARS-CoV-2 Infection and Hospitalization in Infants Younger Than 6 Months
SCJ Jorgenson et al, JAMA Pediatrics, February 27, 2023 (Posted: Feb 27, 2023 11AM)

Postpartum maternal COVID-19 vaccination was moderately effective against Delta infection in infants younger than 6 months but conferred little protection against Omicron. Indirect comparisons suggest postpartum maternal COVID-19 vaccination may be inferior to maternal vaccination during pregnancy, particularly against Omicron.


Disclaimer: Articles listed in Hot Topics of the Day are selected by Public Health Genomics Branch to provide current awareness of the scientific 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 Clips, 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.