6482 hot topic(s) found with the query "Coronavirus"
Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates
RH Holm et al, Comm Med, April 9, 2024
(Posted: Apr 10, 2024 8AM)
From the abstract: "We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021–August 2021 in Jefferson County, Kentucky (USA). We show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r?=?0.95) at 1 week lag."
Human leukocyte antigen variants associate with BNT162b2 mRNA vaccine response.
Martina Esposito et al. Commun Med (Lond) 2024 4 (1) 63
(Posted: Apr 05, 2024 9AM)
From the abstract: "We carried out a genome-wide association study to investigate the genetic determinants of the antibody response to the Pfizer-BioNTech vaccine in an Italian cohort of 1351 subjects recruited in three centers. Linear regressions between normalized antibody levels and genotypes of more than 7 million variants was performed, using sex, age, centers, days between vaccination boost and serological test, and five principal components as covariates. We also analyzed the association between normalized antibody levels and 204 HLA alleles, with the same covariates as above. Our study confirms the involvement of the HLA locus and shows significant associations with variants in HLA-A, HLA-DQA1, and HLA-DQB1 genes. In particular, the HLA-A*03:01 allele is the most significantly associated with serum levels of anti-SARS-CoV-2 antibodies. "
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. "
Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events.
Elisabeth Esser et al. Sci Rep 2024 3 (1) 5768
(Posted: Mar 11, 2024 8AM)
From the abstract: "The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals. "
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. "
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."
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
(Posted: Jan 26, 2024 10AM)
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
(Posted: Jan 22, 2024 5AM)
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."
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. "
Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.
Timothy G Vaughan et al. Proc Natl Acad Sci U S A 2024 1 (2) e2308125121
(Posted: Jan 05, 2024 8AM)
From the abstract: " We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for 10 (out of 15) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. These estimates provide a view which is complementary to that provided by those based on traditional line listing data. The genomic-based view is arguably less susceptible to biases resulting from differences in testing protocols, testing intensity, and import of cases into the community of interest."
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"
Vaccines reduce the risk of long COVID in children
S Hall, Nature, December 20, 2023
(Posted: Dec 20, 2023 9AM)
From the article: " Vaccinated children are less likely than unvaccinated children to develop long COVID, the myriad of symptoms that can last for months to years following a SARS-CoV-2 infection, according to a forthcoming US study. “This is really important data,” says Jessica Snowden, a paediatric infectious-disease specialist at the University of Arkansas for Medical Sciences in Little Rock. This will demonstrate to families how important it is that we protect our kids, not just from acute COVID, but from the longer-term impacts of COVID as well.”
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. "
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 SARS-CoV-2 Vaccination Before vs During Pregnancy and Omicron Infection Among Infants.
Orlanda Goh et al. JAMA Netw Open 2023 11 (11) e2342475
(Posted: Nov 11, 2023 4PM)
From the abstract: "s maternal vaccination associated with a lower risk of infection with Omicron SARS-CoV-2 variants, including XBB, among infants up to 6 months of age? In this national population-based cohort study of 7292 infants aged 6 months or younger in Singapore, the estimated vaccine effectiveness in infants against Omicron SARS-CoV-2 variants, including XBB, from maternal messenger RNA (mRNA) SARS-COV-2 vaccination was 42%. A lower risk of infection was only found in infants when the vaccine was administered during pregnancy. "
Changes in SARS-CoV-2 Sequence Linked With Antiviral Use.
Emily Harris et al. JAMA 2023 10 (16) 1515
(Posted: Oct 24, 2023 2PM)
From the article: " The antiviral drug molnupiravir was linked with a pattern of genomic changes in SARS-CoV-2, based on an analysis of more than 15 million global sequences. Molnupiravir is converted in the body to a nucleotide that is incorporated into the virus’ genome, introducing errors into the sequence. These errors tend to reduce the number of surviving viral progeny, giving the immune system a better chance of clearing the virus. However, if a person is unable to fully clear the virus, some of the viral progeny with genomic changes can be passed along to other hosts. "
Distinguishing features of Long COVID identified through immune profiling.
Jon Klein et al. Nature 2023 9
(Posted: Sep 27, 2023 8AM)
From the abstract: "Here, 273 individuals with or without LC were enrolled in a cross-sectional study that included multi-dimensional immune phenotyping and unbiased machine learning methods to identify biological features associated with LC. Marked differences were noted in circulating myeloid and lymphocyte populations relative to matched controls, as well as evidence of exaggerated humoral responses directed against SARS-CoV-2 among participants with LC. Further, higher antibody responses directed against non-SARS-CoV-2 viral pathogens were observed among individuals with LC, particularly Epstein-Barr virus. "
A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes.
Theo Sanderson et al. Nature 2023 9
(Posted: Sep 27, 2023 8AM)
From the abstract: "Using a systematic approach, we find that a specific class of long phylogenetic branches, distinguished by a high proportion of G-to-A and C-to-T mutations, appear almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age-groups with widespread usage of the drug. We identify a mutational spectrum, with preferred nucleotide contexts, from viruses in patients known to have been treated with molnupiravir and show that its signature matches that seen in these long branches, in some cases with onwards transmission of molnupiravir-derived lineages. "
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."
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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.
Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Yinkai Duan et al. Nature 2023 9
(Posted: Sep 12, 2023 7AM)
From the abstract: "Nirmatrelvir is a specific antiviral targeting the main protease (Mpro) of SARS-CoV-2, and has been approved to treat COVID-191,2. As an RNA virus characterized by high mutation rates, whether SARS-CoV-2 will develop resistance to nirmatrelvir is a concern. Here we combined biochemical and structural methods to demonstrate that mutations at the substrate binding pocket of the Mpro can allow SARS-CoV-2 to develop resistance to nirmatrelvir in two distinct ways."
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
(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 a highly mutated coronavirus variant has scientists on alert.
Ewen Callaway et al. Nature 2023 8
(Posted: Aug 23, 2023 7AM)
From the paper: "Researchers are racing to determine whether a highly mutated coronavirus variant that has popped up in three continents will be a global concern — or much ado about nothing. Several laboratories detected the variant last week, and it has been named BA.2.86. Although the lineage seems to be exceedingly rare, it is very different from other circulating variants and carries numerous changes to its spike protein, a key focus of the body’s immune attack on the SARS-CoV-2 virus. To many scientists, the emergence of BA.2.86 is reminiscent of the early days of the Omicron variant in late 2021."
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.
What to Know About EG.5, the Latest SARS-CoV-2 “Variant of Interest”
J Abbasi, JAMA, August 18, 2023
(Posted: Aug 18, 2023 5PM)
The Omicron descendant EG.5 is the latest to be labeled a “variant of interest” by the World Health Organization (WHO), joining the current ranks of XBB.1.16 and XBB.1.5. The new designation, made as part of an August 9 initial risk evaluation of the variant, reflects its “notable rise” in global prevalence during recent weeks. The report comes as the US is experiencing an increase in hospitalizations and deaths and as anticipation mounts for updated vaccines, expected to become available this fall. The EG.5 variant could contribute to a surge in cases, the report noted, although there’s no evidence to date that it causes more severe disease.
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.
Deep-learning-enabled protein–protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution
G Wang et al, Nature Medicine, July 31, 2023
(Posted: Aug 01, 2023 9AM)
Host–pathogen interactions and pathogen evolution are underpinned by protein–protein interactions between viral and host proteins. An understanding of how viral variants affect protein–protein binding is important for predicting viral–host interactions, such as the emergence of new pathogenic SARS-CoV-2 variants. Here we propose an artificial intelligence-based framework called UniBind, in which proteins are represented as a graph at the residue and atom levels. UniBind integrates protein three-dimensional structure and binding affinity and is capable of multi-task learning for heterogeneous biological data integration.
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.
Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults
AJS Armstrong et al, Ebiomedicine, July 2023
(Posted: Jul 24, 2023 11AM)
The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease. The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection.
Had COVID but no symptoms? You might have this genetic mutation
M Koslov, Nature, July 19, 2023
(Posted: Jul 19, 2023 11AM)
At least 20% of people who become infected with the SARS-CoV-2 coronavirus never feel sick. Now scientists have identified a genetic mutation that is linked to a higher likelihood of avoiding symptoms during infection. This mutation might give an advantage to the immune cells of people who have previously been exposed to ‘seasonal’ coronaviruses, which cause the common cold. That extra boost means the immune system can quickly track down and destroy SARS-CoV-2 before it goes haywire trying to defend against the pathogen.
Genetic cheat code might explain why some people catch Covid but never get sick
M Molteni, Stat News, July 19, 2023
(Posted: Jul 19, 2023 11AM)
What makes people able to clear SARS-CoV-2 out of their systems before it gains a foothold has been one of the enduring mysteries of the pandemic. Now, a group of scientists from the University of California, San Francisco, believes it has found an answer: It’s in their genes. In a study published Wednesday in Nature, the team identified a mutation that increases a person’s chance of being asymptomatic by nearly tenfold. “It’s just one of these natural lucky breaks,” said immunogeneticist Jill Hollenbach, who led the research.
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.
Swift and extensive Omicron outbreak in China after sudden exit from 'zero-COVID' policy.
Emma E Goldberg et al. Nat Commun 2023 7 (1) 3888
(Posted: Jul 03, 2023 7AM)
By modeling a combination of case count and survey data, we show that Omicron spread extremely rapidly, at a rate of 0.42/day (95% credibility interval: [0.35, 0.51]/day), translating to an epidemic doubling time of 1.6 days ([1.6, 2.0] days) after the full exit from zero-COVID on Dec. 7, 2022. Consequently, we estimate that the vast majority of the population (97% [95%, 99%], sensitivity analysis lower limit of 90%) was infected during December.
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.
Traveler-based Genomic Surveillance for Early Detection of New SARS-CoV-2 Variants
CDC, June 2023
(Posted: Jun 26, 2023 8AM)
The Traveler Genomic Surveillance program (TGS), run by the Travelers’ Health Branch at CDC in partnership with Ginkgo Bioworks and XpresCheck, plays an important role in U.S. national surveillance by testing travelers to detect new variants entering the country and fill gaps in global surveillance. In September 2021, during the Delta wave, the program began collecting samples from travelers arriving at three major U.S. international airports, John F. Kennedy in New York City, Newark Liberty, and San Francisco.
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.
Fitness, growth and transmissibility of SARS-CoV-2 genetic variants.
Erik Volz et al. Nat Rev Genet 2023 6
(Posted: Jun 20, 2023 7AM)
This review discusses a wide range of approaches that have been rapidly developed in response to the public health threat posed by emerging variants, ranging from new applications of classic population genetics models to contemporary synthesis of epidemiological models and phylodynamic analysis. Many of these approaches can be adapted to other pathogens and will have increasing relevance as large-scale pathogen sequencing becomes a regular feature of many public health systems.
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).
Waning cellular immune responses and predictive factors in maintaining cellular immunity against SARS-CoV-2 six months after BNT162b2 mRNA vaccination.
Takashi Ishii et al. Sci Rep 2023 6 (1) 9607
(Posted: Jun 16, 2023 6AM)
We analyzed cellular immune responses elicited by BNT162b2 mRNA vaccines in 321 health care workers using whole blood interferon-gamma (IFN-?) release assays. IFN-?, induced by CD4 + and CD8 + T cells stimulated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike epitopes (Ag2), levels were highest at 3 weeks after the second vaccination (6 W) and decreased by 37.4% at 3 months (4 M) and 60.0% at 6 months (7 M), the decline of which seemed slower than that of anti-spike antibody levels.
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.
Epidemic modelling of monitoring public behavior using surveys during pandemic-induced lockdowns.
Andreas Koher et al. Commun Med (Lond) 2023 6 (1) 80
(Posted: Jun 11, 2023 8AM)
Implementing a lockdown for disease mitigation is a balancing act: Non-pharmaceutical interventions can reduce disease transmission significantly, but interventions also have considerable societal costs. Therefore, decision-makers need near real-time information to calibrate the level of restrictions.
Here, we find that, unlike mobility, self-reported contacts decreased significantly in all regions before the nation-wide implementation of non-pharmaceutical interventions and improved predicting future hospitalizations compared to mobility data. A detailed analysis of contact types indicates that contact with friends and strangers outperforms contact with colleagues and family members (outside the household) on the same prediction task.
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.
Why the world needs more transparency on the origins of novel pathogens
M Venter, Nature, May 30, 2023
(Posted: May 30, 2023 6AM)
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.
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.
Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program.
M Daniel Brannock et al. Nat Commun 2023 5 (1) 2914
(Posted: May 24, 2023 9AM)
We used electronic health records available through the National COVID Cohort Collaborative to characterize the association between SARS-CoV-2 vaccination and long COVID diagnosis. We found that vaccination was consistently associated with lower odds and rates of long COVID clinical diagnosis and high-confidence computationally derived diagnosis after adjusting for sex, demographics, and medical history.
De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository.
Emily R Pfaff et al. J Am Med Inform Assoc 2023 5
(Posted: May 24, 2023 9AM)
As part of the NIH Researching COVID to Enhance Recovery (RECOVER) Initiative, researchers with the National COVID Cohort Collaborative (N3C) devised and trained an ML-based phenotype to identify patients highly probable to have Long COVID. Supported by RECOVER, N3C and NIH's All of Us study partnered to reproduce the output of N3C's trained model in the All of Us data enclave, demonstrating model extensibility in multiple environments
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.
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.
3-year anniversary of national viral genomics consortium to better map SARS-CoV-2 transmission
CDC, May 2023
(Posted: May 07, 2023 7AM)
In early 2020, CDCs Office of Advanced Molecular Detection (OAMD) launched the Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium?to coordinate SARS-CoV-2 sequencing and help accelerate the use of pathogen sequence data and molecular epidemiology for the pandemic response. Today, the SPHERES collaboration includes 1,800 scientists from clinical and public health laboratories, academic institutions, and non-profit organizations.
End of the Federal COVID-19 Public Health Emergency (PHE) Declaration
CDC, May 5, 2023
(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.
Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity.
He Zhang et al. Nature 2023 5
(Posted: May 03, 2023 6AM)
A break from Covid waves and a breakthrough for preventing Long Covid
E Topol, Ground Truths, May 1, 2023
(Posted: May 01, 2023 10AM)
All indications from genomic surveillance of the virus, wastewater. and the clinical outcomes that are still being tracked (albeit more limited and less periodicity as time goes on), that we’ve (finally) entered an endemic phase (think smaller “wavelets”). There are no new SARS-CoV-2 variants that have yet cropped up with a growth advantage over XBB.1.5 (the recombinant with 2 significant mutations added on) which is dominant throughout much of the world, or its cousin, XBB.1.9.1.
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)
What contributes to the re-positive nucleic acid test results for the omicron variant of SARS-CoV-2 in the shelter cabin hospital in Shanghai, China?
M Peng et al, Heliyon April 23, 2023
(Posted: Apr 24, 2023 6AM)
A large number of hospitalized patients, large-sized wards, and gender are significant contributing factors to re-positivity. Division of the shelter cabin hospital into small independent wards and requirement of three consecutive results daily as the de-isolation criterion might be more beneficial to the control and prevention of the spread of the Omicron variant.
CDC simplifies COVID-19 vaccine recommendations, allows older adults and immunocompromised adults to get second dose of the updated vaccine
CDC, April 19, 2023
(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.
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.
Durability of Bivalent Boosters against Omicron Subvariants.
Dan-Yu Lin et al. N Engl J Med 2023 4
(Posted: Apr 13, 2023 6AM)
The two types of bivalent boosters were associated with an additional reduction in the incidence of omicron infection among participants who had previously been vaccinated or boosted. Although the two bivalent vaccines were designed to target the BA.4–BA.5 subvariants, they were also associated with a lower risk of infection or severe infection with the BQ.1–BQ.1.1 and XBB–XBB.1.5 subvariants. The effectiveness was higher against hospitalization and death than against infection and waned gradually from its peak over time.
Stroke, Myocardial Infarction, and Pulmonary Embolism after Bivalent Booster.
Marie-Joelle Jabagi et al. N Engl J Med 2023 3 (15) 1431-1432
(Posted: Apr 13, 2023 6AM)
At 21 days after the booster dose, we found no evidence of an increased risk of cardiovascular events among the recipients of the bivalent vaccine as compared with recipients of the monovalent vaccine. The evaluated events included ischemic stroke (hazard ratio, 0.86; 95% confidence interval [CI], 0.58 to 1.27), hemorrhagic stroke (hazard ratio, 0.86; 95% CI, 0.46 to 1.61), myocardial infarction (hazard ratio, 0.92; 95% CI, 0.62 to 1.36), pulmonary embolism (hazard ratio, 0.83; 95% CI, 0.49 to 1.40), and all four events combined (hazard ratio, 0.87; 95% CI, 0.69 to 1.09).
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)
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans.
Wafaa B Alsoussi et al. Nature 2023 4
(Posted: Apr 04, 2023 6AM)
It remains unclear, however, whether the additional doses induce germinal centre (GC) reactions where reengaged B cells can further mature and whether variant-derived vaccines can elicit responses to variant-specific epitopes. Here, we show that boosting with either the original monovalent SARS-CoV-2 or bivalent B.1.351/B.1.617.2 (Beta/Delta) mRNA vaccines induces robust spike-specific GC B cell responses in humans. The GC response persisted for at least eight weeks.
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.
Design and Implementation of a National SARS-CoV-2 Monitoring Program in England: REACT-1 Study.
Paul Elliott et al. American journal of public health 2023 3 e1-e10
(Posted: Mar 30, 2023 8AM)
The REal-time Assessment of Community Transmission-1 (REACT-1) Study was funded by the Department of Health and Social Care in England to provide reliable and timely estimates of prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection over time, by person and place.
The study provided inter alia real-time data on SARS-CoV-2 prevalence over time, by area, and by sociodemographic variables; estimates of vaccine effectiveness; and symptom profiles, and detected emergence of new variants based on viral genome sequencing.
COVID-origins report sparks debate over major genome hub GISAID
S Mallapaty, Nature, March 29, 2023
(Posted: Mar 29, 2023 9AM)
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
(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.
SARS-CoV-2 Variants and Multisystem Inflammatory Syndrome in Children.
Brian W McCrindle et al. The New England journal of medicine 2023 3
(Posted: Mar 23, 2023 6AM)
The features of MIS-C at presentation were more often similar to the features of Kawasaki’s disease among patients hospitalized with SARS-CoV-2 infection during the more recent variant periods than among those during the earlier periods; however, without a definitive diagnostic test for either condition, it remains to be determined whether this represents a true change in phenotype or an increase in the number of patients with Kawasaki’s disease who meet the criteria for MIS-C through concurrent but unrelated SARS-CoV-2 infection.
