Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas

Molecular dynamic simulation reveals spider antimicrobial peptide Latarcin-1 and human eosinophil cationic protein as peptide inhibitors of SARS-CoV-2 variants

COVID-19 has rapidly proliferated around 180 countries, and new cases are reported frequently. No peptide medication has been developed that can reliably block SARS-CoV-2 infection. The investigation focuses on the crucial host receptors angiotensin-converting enzyme 2 (ACE2) , which can bind receptor-binding domain (RBD) on the SARS-CoV-2 spike protein (S). To investigate the inhibitory effects of human Eosinophil Cationic Protein (hECP) and Latarcin-1 (L1)on SARS-CoV-2 infection, we have selected them as research subjects. Further, we ran extensive molecular dynamics simulations to bring the docked peptide-ACE2 complex into its equilibrium state. The outcomes were then evaluated with g_MMPBSA and interaction analysis. We have also considered the Delta and Omicron variants to examine these peptides' inhibitory effects. The experimental findings revealed an enhanced capability of L1 and hECP as SARS-CoV-2 inhibitors, occupying hot spots and numerous key residues in ACE2. These include ASP30, ASP38, GLU35 and GLU75, which significantly inhibit the binding of RBD and ACE2 and are effective against two common variants in a similar manner. In addition, this study can serve as a springboard for future research on SARS-CoV-2 inhibitors.Communicated by Ramaswamy H. Sarma.

Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera

Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.

Impact of COVID-19 on patients undergoing scheduled procedures for chronic venous disease

OBJECTIVE

The COVID-19 pandemic has drastically altered the medical landscape. Various strategies have been employed to preserve hospital beds, personal protective equipment, and other resources to accommodate the surges of COVID-19 positive patients, hospital overcapacities, and staffing shortages. This has had a dramatic effect on vascular surgical practice. The objective of this study is to analyze the impact of the COVID-19 pandemic on surgical delays and adverse outcomes for patients with chronic venous disease scheduled to undergo elective operations.

METHODS

The Vascular Surgery COVID-19 Collaborative (VASCC) was founded in March 2020 to evaluate the outcomes of patients with vascular disease whose operations were delayed. Modules were developed by vascular surgeon working groups and tested before implementation. A data analysis of outcomes of patients with chronic venous disease whose surgeries were postponed during the COVID-19 pandemic from March 2020 through February 2021 was performed for this study.

RESULTS

A total of 150 patients from 12 institutions in the United States were included in the study. Indications for venous intervention were: 85.3% varicose veins, 10.7% varicose veins with venous ulceration, and 4.0% lipodermatosclerosis. One hundred two surgeries had successfully been completed at the time of data entry. The average length of the delay was 91 days, with a median of 78 days. Delays for venous ulceration procedures ranged from 38 to 208 days. No patients required an emergent intervention due to their venous disease, and no patients experienced major adverse events following their delayed surgeries.

CONCLUSIONS

Interventions may be safely delayed for patients with venous disease requiring elective surgical intervention during the COVID-19 pandemic. This finding supports the American College of Surgeons' recommendations for the management of elective vascular surgical procedures. Office-based labs may be safe locations for continued treatment when resources are limited. Although the interventions can be safely postponed, the negative impact on quality of life warrants further investigation.

Clinical Outcomes of Children With COVID-19 by SARS-CoV-2 Strain: A Cohort Study

OBJECTIVE

We sought to investigate the disease outcomes and predictors of severe outcomes among children infected with the Delta variant of SARS-CoV-2 compared with pre-Delta strains.

METHODS

Single-center retrospective cohort study in an emergency department located within an urban academic children's hospital. Patients included children (0-18 years) who tested positive for SARS-CoV-2. Main outcomes measured include need for hospital admission or COVID-directed therapies.

RESULTS

There was a trend toward decreased hospital admission and no significant difference in the severity of outcomes in the Delta cohort relative to the pre-Delta cohort. The Delta cohort had lower odds of hospital admission (odds ratio [OR], 0.79; 95% confidence interval [CI], 0.51-1.23), but the result was not statistically significant. Logistic regression analyses showed that overall, age 1 to 4 years (OR, 2.35; 95% CI, 1.23-4.57) and public insurance (OR, 1.80, 95% CI, 1.08-3.01) were predictors of hospital admission. Within the Delta cohort, the presence of any comorbidity increased the odds of admission (OR, 2.52; 95% CI, 1.09-6.04). Black children had lower odds of admission than white children (overall OR, 0.53; 95% CI, 0.31-0.90; pre-Delta OR, 0.50; 95% CI, 0.26-0.95).

CONCLUSIONS

The severity of measured disease outcomes was similar in pediatric patients when comparing children infected with the pre-Delta and Delta variants of SARS-CoV-2, even among children with comorbidities once adjusting for acuity.Ongoing research is essential to determine disease severity and risk for children with comorbidities because SARS-CoV-2 continues to mutate, including with Omicron subvariants.

Comparing COVID-19 severity in patients hospitalized for community-associated Delta, BA.1 and BA.4/5 variant infection

Background

Despite decreasing COVID-19 disease severity during the Omicron waves, a proportion of patients still require hospitalization and intensive care.

Objective

To compare demographic characteristics, comorbidities, vaccination status, and previous infections in patients hospitalized for community-associated COVID-19 (CAC) in predominantly Delta, Omicron BA.1 and BA.4/5 SARS-CoV-2 waves.

Methods

Data were extracted from three national databases-the National COVID-19 Database, National Vaccination Registry and National Registry of Hospitalizations.

Results

Among the hospitalized CAC patients analyzed in this study, 5,512 were infected with Delta, 1,120 with Omicron BA.1, and 1,143 with the Omicron BA.4/5 variant. The age and sex structure changed from Delta to BA.4/5, with the proportion of women (9.5% increase), children and adolescents (10.4% increase), and octa- and nonagenarians increasing significantly (24.5% increase). Significantly more patients had comorbidities (measured by the Charlson Comorbidity Index), 30.3% in Delta and 43% in BA.4/5 period. The need for non-invasive ventilatory support (NiVS), ICU admission, mechanical ventilation (MV), and in-hospital mortality (IHM) decreased from Delta to Omicron BA.4/5 period for 12.6, 13.5, 11.5, and 6.3%, respectively. Multivariate analysis revealed significantly lower odds for ICU admission (OR 0.68, CI 0.54-0.84, p < 0.001) and IHM (OR 0.74, CI 0.58-0.93, p = 0.011) during the Delta period in patients who had been fully vaccinated or boosted with a COVID-19 vaccine within the previous 6 months. In the BA.1 variant period, patients who had less than 6 months elapsed between the last vaccine dose and SARS-CoV-2 positivity had lower odds for MV (OR 0.38, CI 0.18-0.72, p = 0.005) and IHM (OR 0.56, CI 0.37- 0.83, p = 0.005), but not for NIVS or ICU admission.

Conclusion

The likelihood of developing severe CAC in hospitalized patients was higher in those with the Delta and Omicron BA.1 variant compared to BA.4/5.

Clinical Features and Outcomes of Hospitalized Adult Patients With Breakthrough COVID-19 Infections: A Propensity-Score-Matched Observational Study

In this study, we aimed to evaluate the impact of vaccination on intensive care unit (ICU) admission and in-hospital mortality among breakthrough coronavirus disease 2019 (COVID-19) infections. A total of 3,351 adult patients hospitalized with COVID-19 in the Memorial Healthcare System (Hollywood, Florida) between June 1 and September 20, 2021, were included; 284 (8.5%) were fully vaccinated. A propensity-score-matched analysis was conducted to compare fully vaccinated patients with unvaccinated controls. Propensity scores were calculated on the basis of variables associated with vaccination status. A 1:1 matching ratio was applied using logistic regression models, ensuring balanced characteristics between the two groups. The matched samples were then subjected to multivariate analysis. Among breakthrough infections, vaccinated patients demonstrated lower incidences of ICU admission (10.3% vs. 16.4%; P = 0.042) and death (12.2% vs. 18.7%; P = 0.041) than the matched controls. Risk-adjusted multivariate analysis demonstrated a significant inverse association between vaccination and ICU admission (odds ratio = 0.52, 95% confidence interval: 0.31, 0.89; P = 0.019) as well as in-hospital mortality (odds ratio = 0.57, 95% confidence interval: 0.34, 0.94; P = 0.027). Vaccinated individuals experiencing breakthrough infections had significantly lower risks of ICU admission and in-hospital mortality. These findings highlight the benefits of COVID-19 vaccines in reducing severe outcomes among patients with breakthrough infections.

Comparison of adult hesitancy towards COVID-19 vaccines and vaccines in general in the USA

BACKGROUND

Adults who are hesitant toward routinely recommended vaccines for adults may also be hesitant toward COVID-19 vaccines. However, the distribution and differences in hesitancy between routinely recommended vaccines and COVID-19 vaccines, and the association of hesitancy regarding routinely recommended vaccines and hesitancy with COVID-19 vaccination status and intent, is unknown.

METHODS

Using the Research and Development Survey (RANDS) during COVID-19, Round 3, a probability-sampled, nationally representative, web and phone survey fielded from May 17 - June 30, 2021 (n = 5,434), we examined the distribution and difference in prevalence of hesitancy towards COVID-19 and vaccines in general, beliefs associated with vaccine hesitancy, and factors impacting plans to be vaccinated against COVID-19.

RESULTS

Reported hesitancy towards COVID-19 vaccines (42.2%) was 6-percentage points higher than hesitancy towards vaccines in general (35.7%). Populations who were most hesitant toward COVID-19 vaccines were younger adults, non-Hispanic Black adults, adults with lower education or income, and adults who were associated with a religion. Beliefs in the social benefit and the importance of vaccination, and the belief that COVID-19 vaccines lower risk for infection, were strongly associated with COVID-19 vaccination and intent to be vaccinated.

CONCLUSIONS

Vaccine hesitancy for both COVID-19 vaccines and vaccines in general is common. Health providers and public health officials should utilize strategies to address vaccine hesitancy, including providing strong clear recommendations for needed vaccines, addressing safety and effectiveness concerns, and utilizing trusted messengers such as religious and community leaders to improve vaccine confidence.

COVID-19 in cancer patients: The impact of vaccination on outcomes early in the pandemic

BACKGROUND

With the rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the development of effective and safe vaccines was of utmost importance to protect vulnerable individuals, including cancer patients. Studies comparing the clinical outcomes of cancer patients with or without vaccination against coronavirus disease 2019 (COVID-19) have not demonstrated clear benefit. We aimed to determine the protective effects of COVID-19 vaccination by comparing vaccinated and unvaccinated cancer patients after the initial phase of vaccine roll-out and to identify risk factors associated with hospitalization, severe COVID-19, and 30-day COVID-19 attributable mortality.

METHODS

We performed a retrospective cohort study of cancer patients with COVID-19 diagnosed by polymerase chain reaction on nasal swabs between January 1, 2021 and July 30, 2021. Outcomes of interest included hospitalization, severe COVID-19, and 30-day COVID-19 attributable mortality. Univariate and multivariate analyses were performed to identify factors associated with clinical outcomes, using vaccination status as a variable of interest in all models.

RESULTS

Key risk factors, such as age ≥ 60 years; comorbidities including diabetes mellitus, heart failure, and lung diseases; and specific cancer types (leukemia and lymphoma) were independently associated with hospital admission for COVID-19, severe COVID-19, and 30-day COVID-19 attributable mortality in cancer patients regardless of their vaccination status. Vaccinated patients were protected against severe COVID-19 but with no impact on hospitalization or mortality due to COVID-19.

CONCLUSION

Our study highlights a significant benefit of COVID-19 vaccination for cancer patients-specifically its protection against severe COVID-19.

Community transmission of SARS-CoV-2 during the Delta wave in New York City

BACKGROUND

Understanding community transmission of SARS-CoV-2 variants of concern (VOCs) is critical for disease control in the post pandemic era. The Delta variant (B.1.617.2) emerged in late 2020 and became the dominant VOC globally in the summer of 2021. While the epidemiological features of the Delta variant have been extensively studied, how those characteristics shaped community transmission in urban settings remains poorly understood.

METHODS

Using high-resolution contact tracing data and testing records, we analyze the transmission of SARS-CoV-2 during the Delta wave within New York City (NYC) from May 2021 to October 2021. We reconstruct transmission networks at the individual level and across 177 ZIP code areas, examine network structure and spatial spread patterns, and use statistical analysis to estimate the effects of factors associated with COVID-19 spread.

RESULTS

We find considerable individual variations in reported contacts and secondary infections, consistent with the pre-Delta period. Compared with earlier waves, Delta-period has more frequent long-range transmission events across ZIP codes. Using socioeconomic, mobility and COVID-19 surveillance data at the ZIP code level, we find that a larger number of cumulative cases in a ZIP code area is associated with reduced within- and cross-ZIP code transmission and the number of visitors to each ZIP code is positively associated with the number of non-household infections identified through contact tracing and testing.

CONCLUSIONS

The Delta variant produced greater long-range spatial transmission across NYC ZIP code areas, likely caused by its increased transmissibility and elevated human mobility during the study period. Our findings highlight the potential role of population immunity in reducing transmission of VOCs. Quantifying variability of immunity is critical for identifying subpopulations susceptible to future VOCs. In addition, non-pharmaceutical interventions limiting human mobility likely reduced SARS-CoV-2 spread over successive pandemic waves and should be encouraged for reducing transmission of future VOCs.

HDSNE a new unsupervised multiple image database fusion learning algorithm with flexible and crispy production of one database: a proof case study of lung infection diagnose In chest X-ray images

Continuous release of image databases with fully or partially identical inner categories dramatically deteriorates the production of autonomous Computer-Aided Diagnostics (CAD) systems for true comprehensive medical diagnostics. The first challenge is the frequent massive bulk release of medical image databases, which often suffer from two common drawbacks: image duplication and corruption. The many subsequent releases of the same data with the same classes or categories come with no clear evidence of success in the concatenation of those identical classes among image databases. This issue stands as a stumbling block in the path of hypothesis-based experiments for the production of a single learning model that can successfully classify all of them correctly. Removing redundant data, enhancing performance, and optimizing energy resources are among the most challenging aspects. In this article, we propose a global data aggregation scale model that incorporates six image databases selected from specific global resources. The proposed valid learner is based on training all the unique patterns within any given data release, thereby creating a unique dataset hypothetically. The Hash MD5 algorithm (MD5) generates a unique hash value for each image, making it suitable for duplication removal. The T-Distributed Stochastic Neighbor Embedding (t-SNE), with a tunable perplexity parameter, can represent data dimensions. Both the Hash MD5 and t-SNE algorithms are applied recursively, producing a balanced and uniform database containing equal samples per category: normal, pneumonia, and Coronavirus Disease of 2019 (COVID-19). We evaluated the performance of all proposed data and the new automated version using the Inception V3 pre-trained model with various evaluation metrics. The performance outcome of the proposed scale model showed more respectable results than traditional data aggregation, achieving a high accuracy of 98.48%, along with high precision, recall, and F1-score. The results have been proved through a statistical t-test, yielding t-values and p-values. It's important to emphasize that all t-values are undeniably significant, and the p-values provide irrefutable evidence against the null hypothesis. Furthermore, it's noteworthy that the Final dataset outperformed all other datasets across all metric values when diagnosing various lung infections with the same factors.

SARS-CoV-2 niches in human placenta revealed by spatial transcriptomics

BACKGROUND

Functional placental niches are presumed to spatially separate maternal-fetal antigens and restrict the vertical transmission of pathogens. We hypothesized a high-resolution map of placental transcription could provide direct evidence for niche microenvironments with unique functions and transcription profiles.

METHODS

We utilized Visium Spatial Transcriptomics paired with H&E staining to generate 17,927 spatial transcriptomes. By integrating these spatial transcriptomes with 273,944 placental single-cell and single-nuclei transcriptomes, we generated an atlas composed of at least 22 subpopulations in the maternal decidua, fetal chorionic villi, and chorioamniotic membranes.

FINDINGS

Comparisons of placentae from uninfected healthy controls (n = 4) with COVID-19 asymptomatic (n = 4) and symptomatic (n = 5) infected participants demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in syncytiotrophoblasts occurred in both the presence and the absence of maternal clinical disease. With spatial transcriptomics, we found that the limit of detection for SARS-CoV-2 was 1/7,000 cells, and placental niches without detectable viral transcripts were unperturbed. In contrast, niches with high SARS-CoV-2 transcript levels were associated with significant upregulation in pro-inflammatory cytokines and interferon-stimulated genes, altered metallopeptidase signaling (TIMP1), with coordinated shifts in macrophage polarization, histiocytic intervillositis, and perivillous fibrin deposition. Fetal sex differences in gene expression responses to SARS-CoV-2 were limited, with confirmed mapping limited to the maternal decidua in males.

CONCLUSIONS

High-resolution placental transcriptomics with spatial resolution revealed dynamic responses to SARS-CoV-2 in coordinate microenvironments in the absence and presence of clinically evident disease.

FUNDING

This work was supported by the NIH (R01HD091731 and T32-HD098069), NSF (2208903), the Burroughs Welcome Fund and the March of Dimes Preterm Birth Research Initiatives, and a Career Development Award from the American Society of Gene and Cell Therapy.

COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020-2021

The SARS-CoV-2 Delta variant, first identified in October 2020, quickly became the dominant variant worldwide. We used publicly available data to explore the relationship between illness and death (peak case rates, death rates, case-fatality rates) and selected predictors (percentage vaccinated, percentage of the population >65 years, population density, testing volume, index of mitigation policies) in 45 high-income countries during the Delta wave using rank-order correlation and ordinal regression. During the Delta-dominant period, most countries reported higher peak case rates (57%) and lower peak case-fatality rates (98%). Higher vaccination coverage was protective against peak case rates (odds ratio 0.95, 95% CI 0.91-0.99) and against peak death rates (odds ratio 0.96, 95% CI 0.91-0.99). Vaccination coverage was vital to preventing infection and death from COVID-19 during the Delta wave. As new variants emerge, public health authorities should encourage the uptake of COVID-19 vaccination and boosters.

Staying Ahead of the Game: How SARS-CoV-2 has Accelerated the Application of Machine Learning in Pandemic Management

In recent years, machine learning (ML) techniques have garnered considerable interest for their potential use in accelerating the rate of drug discovery. With the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the utilization of ML has become even more crucial in the search for effective antiviral medications. The pandemic has presented the scientific community with a unique challenge, and the rapid identification of potential treatments has become an urgent priority. Researchers have been able to accelerate the process of identifying drug candidates, repurposing existing drugs, and designing new compounds with desirable properties using machine learning in drug discovery. To train predictive models, ML techniques in drug discovery rely on the analysis of large datasets, including both experimental and clinical data. These models can be used to predict the biological activities, potential side effects, and interactions with specific target proteins of drug candidates. This strategy has proven to be an effective method for identifying potential coronavirus disease 2019 (COVID-19) and other disease treatments. This paper offers a thorough analysis of the various ML techniques implemented to combat COVID-19, including supervised and unsupervised learning, deep learning, and natural language processing. The paper discusses the impact of these techniques on pandemic drug development, including the identification of potential treatments, the understanding of the disease mechanism, and the creation of effective and safe therapeutics. The lessons learned can be applied to future outbreaks and drug discovery initiatives.

Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples

The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.

Upper respiratory tract mucosal immunity for SARS-CoV-2 vaccines

SARS-CoV-2 vaccination significantly reduces morbidity and mortality, but has less impact on viral transmission rates, thus aiding viral evolution, and the longevity of vaccine-induced immunity rapidly declines. Immune responses in respiratory tract mucosal tissues are crucial for early control of infection, and can generate long-term antigen-specific protection with prompt recall responses. However, currently approved SARS-CoV-2 vaccines are not amenable to adequate respiratory mucosal delivery, particularly in the upper airways, which could account for the high vaccine breakthrough infection rates and limited duration of vaccine-mediated protection. In view of these drawbacks, we outline a strategy that has the potential to enhance both the efficacy and durability of existing SARS-CoV-2 vaccines, by inducing robust memory responses in the upper respiratory tract (URT) mucosa.

CRISPR techniques and potential for the detection and discrimination of SARS-CoV-2 variants of concern

The continuing evolution of the SARS-CoV-2 virus has led to the emergence of many variants, including variants of concern (VOCs). CRISPR-Cas systems have been used to develop techniques for the detection of variants. These techniques have focused on the detection of variant-specific mutations in the spike protein gene of SARS-CoV-2. These sequences mostly carry single-nucleotide mutations and are difficult to differentiate using a single CRISPR-based assay. Here we discuss the specificity of the Cas9, Cas12, and Cas13 systems, important considerations of mutation sites, design of guide RNA, and recent progress in CRISPR-based assays for SARS-CoV-2 variants. Strategies for discriminating single-nucleotide mutations include optimizing the position of mismatches, modifying nucleotides in the guide RNA, and using two guide RNAs to recognize the specific mutation sequence and a conservative sequence. Further research is needed to confront challenges in the detection and differentiation of variants and sublineages of SARS-CoV-2 in clinical diagnostic and point-of-care applications.

A bibliometric analysis of inflammatory bowel disease and COVID-19 researches

Background

Patients with inflammatory bowel disease (IBD) often require immunosuppressive therapy and are hence susceptible to various opportunistic viral and bacterial infections. In this regard, many studies on IBD and COVID-19 have been conducted. However, no bibliometric analysis has been performed. This study provides a general overview of IBD and COVID-19.

Methods

Publications about IBD and COVID-19 from 2020 to 2022 were retrieved from the Web of Science Core Collection (WoSCC) database. Bibliometric analysis was performed using VOSviewer, CiteSpace, and HistCite.

Results

A total of 396 publications were retrieved and considered in this study. The maximum number of publications were from the United States, Italy, and England, and the contributions of these countries were significant. Kappelman ranked first in article citations. The Icahn School of Medicine at Mount Sinai and Inflammatory Bowel Diseases were the most prolific affiliation and journal, respectively. The most influential research topics were "management", "impact", "vaccination", and "receptor". The following keywords represented research frontiers: "depression", "the quality of life of IBD patients", "infliximab", "COVID-19 vaccine", and "second vaccination".

Conclusions

Over the past 3 years, most studies on IBD and COVID-19 have focused on clinical research. In particular, topics such as "depression", "the quality of life of IBD patients", "infliximab", "COVID-19 vaccine", and "second vaccination" were noted to have received much attention recently. Future research should focus on our understanding of the immune response to COVID-19 vaccination in biologically treated patients, the psychological impact of COVID-19, IBD management guidelines, and the long-term impact of COVID-19 in IBD patients. This study will provide researchers with a better understanding of research trends on IBD during COVID-19.

Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond

Here we interrogate the factors responsible for SARS-CoV-2 breakthrough infections in a K18-hACE2 transgenic mouse model. We show that Delta and the closely related Kappa variant cause viral pneumonia and severe lung lesions in K18-hACE2 mice. Human COVID-19 mRNA post-vaccination sera after the 2nd dose are significantly less efficient in neutralizing Delta/Kappa than early 614G virus in vitro and in vivo. By 5 months post-vaccination, ≥50% of donors lack detectable neutralizing antibodies against Delta and Kappa and all mice receiving 5-month post-vaccination sera die after the lethal challenges. Although a 3rd vaccine dose can boost antibody neutralization against Delta in vitro and in vivo, the mean log neutralization titers against the latest Omicron subvariants are 1/3-1/2 of those against the original 614D virus. Our results suggest that enhanced virulence, greater immune evasion, and waning of vaccine-elicited protection account for SARS-CoV-2 variants caused breakthrough infections.

Real-world effectiveness of casirivimab and imdevimab among patients diagnosed with COVID-19 in the ambulatory setting: a retrospective cohort study using a large claims database

OBJECTIVE

To assess the real-world effectiveness of casirivimab and imdevimab (CAS+IMD) versus no COVID-19 antibody treatment among patients diagnosed with COVID-19 in the ambulatory setting, including patients diagnosed during the Delta-dominant period prior to Omicron emergence.

DESIGN

Retrospective cohort study.

SETTING

Komodo Health closed claims database.

PARTICIPANTS

13 273 128 patients diagnosed with COVID-19 (December 2020 through September 2021) were treated with CAS+IMD or untreated but treatment eligible under the Emergency Use Authorization (EUA). Each treated patient was exact and propensity score matched without replacement to up to five untreated EUA-eligible patients.

INTERVENTIONS

CAS+IMD.

PRIMARY AND SECONDARY OUTCOME MEASURES

Composite endpoint of 30-day all-cause mortality or COVID-19-related hospitalisation. Kaplan-Meier estimators were used to calculate outcome risks overall and across subgroups: age, COVID-19 vaccination status, immunocompromised status, and timing of diagnosis (December 2020 to June 2021, and July to September 2021). Cox proportional hazards models were used to estimate adjusted HRs (aHRs) and 95% CIs.

RESULTS

Among 75 159 CAS+IMD-treated and 1 670 338 EUA-eligible untreated patients, 73 759 treated patients were matched to 310 688 untreated patients; matched patients were ~50 years, ~60% were women and generally well balanced across risk factors. The 30-day risk of the composite outcome was 2.1% and 5.2% in the CAS+IMD-treated and CAS+IMD-untreated patients, respectively; equivalent to a 60% lower risk (aHR 0.40; 95% CI, 0.38 to 0.42). The effect of CAS+IMD was consistent across subgroups, including those who received a COVID-19 vaccine (aHR 0.48, 95% CI, 0.41 to 0.56), and those diagnosed during the Delta-dominant period (aHR 0.40, 95% CI, 0.38 to 0.42).

CONCLUSIONS

The real-world effectiveness of CAS+IMD is consistent with the efficacy for reducing all-cause mortality or COVID-19-related hospitalisation reported in clinical trials. Effectiveness is maintained across patient subgroups, including those prone to breakthrough infections, and was effective against susceptible variants including Delta. .

SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City

There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.

Risk Factors for COVID-19 Mortality in Malaysia

Background

Understanding the risks of COVID-19 mortality helps in the planning and prevention of the disease. This study aimed to determine the risk factors for COVID-19 mortality in Malaysia.

Methods

Secondary online data provided by the Ministry of Health, Malaysia and Malaysia's national COVID-19 immunisation programme were used: i) COVID-19 deaths data; ii) vaccination coverage data and iii) population estimate data. Quasi-Poisson regression was performed to determine the risk factors for COVID-19 mortality.

Results

Four risk factors were identified: i) vaccination status (partial versus unvaccinated, incidence rate ratio [IRR]: 0.59; 95% CI: 0.54, 0.64; complete versus unvaccinated, IRR: 0.50; 95% CI: 0.45, 0.56; booster versus unvaccinated, IRR: 0.13; 95% CI: 0.05, 0.26); ii) age group (19 years old-59 years old versus above 60 years old, IRR: 0.90; 95% CI: 0.84, 0.97; 13 years old-18 years old versus above 60 years old, IRR: 0.09; 95% CI: 0.04, 0.19; 6 years old-12 years old versus above 60 years old, IRR: 0.09; 95% CI: 0.03, 0.22; below 5 years old versus above 60 years old, IRR: 0.11; 95% CI: 0.04, 0.23); iii) gender (male versus female, IRR: 1.23; 95% CI: 1.14, 1.32) and iv) comorbidity (yes versus no, IRR: 2.13; 95% CI: 1.96, 2.32).

Conclusion

This study highlighted the risk factors for COVID-19 mortality and the benefit of COVID-19 vaccination, especially of booster vaccination, in reducing the risk of COVID-19 mortality in Malaysia.

Moralization and Mismoralization in Public Health

Moralization is a social-psychological process through which morally neutral issues take on moral significance. Often linked to health and disease, moralization may sometimes lead to good outcomes; yet moralization is often detrimental to individuals and to society as a whole. It is therefore important to be able to identify when moralization is inappropriate. In this paper, we offer a systematic normative approach to the evaluation of moralization. We introduce and develop the concept of 'mismoralization', which is when moralization is metaethically unjustified. In order to identify mismoralization, we argue that one must engage in metaethical analysis of moralization processes while paying close attention to the relevant facts. We briefly discuss one historical example (tuberculosis) and two contemporary cases related to COVID-19 (infection and vaccination status) that we contend to have been mismoralized in public health. We propose a remedy of de-moralization that begins by identifying mismoralization and that proceeds by neutralizing inapt moral content. De-moralization calls for epistemic and moral humility. It should lead us to pull away from our tendency to moralize-as individuals and as social groups-whenever and wherever moralization is unjustified.

The Risk of Hospitalization and Mortality After Breakthrough SARS-CoV-2 Infection by Vaccine Type: Observational Study of Medical Claims Data

BACKGROUND

Several risk factors have been identified for severe COVID-19 disease by the scientific community. In this paper, we focus on understanding the risks for severe COVID-19 infections after vaccination (ie, in breakthrough SARS-CoV-2 infections). Studying these risks by vaccine type, age, sex, comorbidities, and any prior SARS-CoV-2 infection is important to policy makers planning further vaccination efforts.

OBJECTIVE

We performed a comparative study of the risks of hospitalization (n=1140) and mortality (n=159) in a SARS-CoV-2 positive cohort of 19,815 patients who were all fully vaccinated with the Pfizer, Moderna, or Janssen vaccines.

METHODS

We performed Cox regression analysis to calculate the risk factors for developing a severe breakthrough SARS-CoV-2 infection in the study cohort by controlling for vaccine type, age, sex, comorbidities, and a prior SARS-CoV-2 infection.

RESULTS

We found lower hazard ratios for those receiving the Moderna vaccine (P<.001) and Pfizer vaccine (P<.001), with the lowest hazard rates being for Moderna, as compared to those who received the Janssen vaccine, independent of age, sex, comorbidities, vaccine type, and prior SARS-CoV-2 infection. Further, individuals who had a SARS-CoV-2 infection prior to vaccination had some increased protection over and above the protection already provided by the vaccines, from hospitalization (P=.001) and death (P=.04), independent of age, sex, comorbidities, and vaccine type. We found that the top statistically significant risk factors for severe breakthrough SARS-CoV-2 infections were age of >50, male gender, moderate and severe renal failure, severe liver disease, leukemia, chronic lung disease, coagulopathy, and alcohol abuse.

CONCLUSIONS

Among individuals who were fully vaccinated, the risk of severe breakthrough SARS-CoV-2 infection was lower for recipients of the Moderna or Pfizer vaccines and higher for recipients of the Janssen vaccine. These results from our analysis at a population level will be helpful to public health policy makers. Our result on the influence of a previous SARS-CoV-2 infection necessitates further research into the impact of multiple exposures on the risk of developing severe COVID-19.

One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021

Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to SARS-CoV-2 genomes belonging to an outbreak of AY.25 identified through ongoing phylogenomic analyses. Continued phylogenetic analyses were conducted to further describe the AY.25 outbreak. Wastewater collected twice weekly from sites across campus was tested for SARS-CoV-2 by RT-qPCR, and subsequently sequenced to identify variants. The AY.25 outbreak was defined by a single mutation (C18804T) and comprised 379 genomes from SARS-CoV-2 positive cases associated with the university and community. Several undergraduate student gatherings and congregate living settings on campus likely contributed to the rapid spread of COVID-19 across the university with secondary transmission into the community. The clade defining mutation was also found in wastewater samples collected from around student dormitories a week before the semester began, and 9 days before cases were identified. Genomic, epidemiologic, and wastewater surveillance provided evidence that an AY.25 clone was likely imported into the university setting just prior to the onset of the Fall 2021 semester, rapidly spread through a subset of the student population, and then subsequent spillover occurred in the surrounding community. The university and local public health department worked closely together to facilitate timely reporting of cases, identification of close contacts, and other necessary response and mitigation strategies. The emergence of new SARS-CoV-2 variants and potential threat of other infectious disease outbreaks on university campuses presents an opportunity for future comprehensive One Health genomic data driven, targeted interventions.

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

A good amount of research has evolved just in three years in COVID-19 transmission, mortality, vaccination, and some socioeconomic studies. A few bibliometric reviews have already been performed in the literature, especially on the broad theme of COVID-19, without any particular area such as transmission, mortality, or vaccination. This paper fills this gap by conducting a bibliometric review on COVID-19 transmission as the first of its kind. The main aim of this study is to conduct a bibliometric review of the literature in the area of COVID-19 transmission dynamics. We have conducted bibliometric analysis using descriptive and network analysis methods to review the literature in this area using RStudio, Openrefine, VOSviewer, and Tableau. We reviewed 1103 articles published in 2020-2022. The result identified the top authors, top disciplines, research patterns, and hotspots and gave us clear directions for classifying research topics in this area. New research areas are rapidly emerging in this area, which needs constant observation by researchers to combat this global epidemic.

Broad Antiviral Effects of Echinacea purpurea against SARS-CoV-2 Variants of Concern and Potential Mechanism of Action

SARS-CoV-2 variants of concern (VOCs) represent an alarming threat as they show altered biological behavior and may escape vaccination effectiveness. Broad-spectrum antivirals could play an important role to control infections. The activity of Echinacea purpurea (Echinaforce® extract, EF) against (i) VOCs B1.1.7 (alpha), B.1.351.1 (beta), P.1 (gamma), B1.617.2 (delta), AV.1 (Scottish), B1.525 (eta), and B.1.1.529.BA1 (omicron); (ii) SARS-CoV-2 spike (S) protein-pseudotyped viral particles and reference strain OC43 as well as (iii) wild type SARS-CoV-2 (Hu-1) was analyzed. Molecular dynamics (MD) were applied to study the interaction of Echinacea's phytochemical markers with known pharmacological viral and host cell targets. EF extract broadly inhibited the propagation of all investigated SARS-CoV-2 VOCs as well as the entry of SARS-CoV-2 pseudoparticles at EC50's ranging from 3.62 to 12.03 µg/mL. The preventive addition of 25 µg/mL EF to epithelial cells significantly reduced sequential infection with SARS-CoV-2 (Hu-1) and OC43. MD analyses showed constant binding affinities to VOC-typical S protein variants for alkylamides, caftaric acid, and feruloyl-tartaric acid in EF extract and interactions with serine protease TMPRSS-2. EF extract demonstrated stable virucidal activity across seven tested VOCs, likely due to the constant affinity of the contained phytochemical substances to all spike variants. A possible interaction of EF with TMPRSS-2 partially would explain the cell protective benefits of the extract by the inhibition of membrane fusion and cell entry. EF may therefore offer a supportive addition to vaccination endeavors in the control of existing and future SARS-CoV-2 virus mutations.

Time Series Analysis of SARS-CoV-2 Genomes and Correlations among Highly Prevalent Mutations

The efforts of the scientific community to tame the recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seem to have been diluted by the emergence of new viral strains. Therefore, it is imperative to understand the effect of mutations on viral evolution. We performed a time series analysis on 59,541 SARS-CoV-2 genomic sequences from around the world to gain insights into the kinetics of the mutations arising in the viral genomes. These 59,541 genomes were grouped according to month (January 2020 to March 2021) based on the collection date. Meta-analysis of these data led us to identify significant mutations in viral genomes. Pearson correlation of these mutations led us to the identification of 16 comutations. Among these comutations, some of the individual mutations have been shown to contribute to viral replication and fitness, suggesting a possible role of other unexplored mutations in viral evolution. We observed that the mutations 241C>T in the 5' untranslated region (UTR), 3037C>T in nsp3, 14408C>T in the RNA-dependent RNA polymerase (RdRp), and 23403A>G in spike are correlated with each other and were grouped in a single cluster by hierarchical clustering. These mutations have replaced the wild-type nucleotides in SARS-CoV-2 sequences. Additionally, we employed a suite of computational tools to investigate the effects of T85I (1059C>T), P323L (14408C>T), and Q57H (25563G>T) mutations in nsp2, RdRp, and the ORF3a protein of SARS-CoV-2, respectively. We observed that the mutations T85I and Q57H tend to be deleterious and destabilize the respective wild-type protein, whereas P323L in RdRp tends to be neutral and has a stabilizing effect. IMPORTANCE We performed a meta-analysis on SARS-CoV-2 genomes categorized by collection month and identified several significant mutations. Pearson correlation analysis of these significant mutations identified 16 comutations having absolute correlation coefficients of >0.4 and a frequency of >30% in the genomes used in this study. The correlation results were further validated by another statistical tool called hierarchical clustering, where mutations were grouped in clusters on the basis of their similarity. We identified several positive and negative correlations among comutations in SARS-CoV-2 isolates from around the world which might contribute to viral pathogenesis. The negative correlations among some of the mutations in SARS-CoV-2 identified in this study warrant further investigations. Further analysis of mutations such as T85I in nsp2 and Q57H in ORF3a protein revealed that these mutations tend to destabilize the protein relative to the wild type, whereas P323L in RdRp is neutral and has a stabilizing effect. Thus, we have identified several comutations which can be further characterized to gain insights into SARS-CoV-2 evolution.

Vaccine breakthrough infection leads to distinct profiles of neutralizing antibody responses by SARS-CoV-2 variant

Protective immunity against SARS-CoV-2 infection after COVID-19 vaccination may differ by variant. We enrolled vaccinated (n = 39) and unvaccinated (n = 11) individuals with acute, symptomatic SARS-CoV-2 Delta or Omicron infection and performed SARS-CoV-2 viral load quantification, whole-genome sequencing, and variant-specific antibody characterization at the time of acute illness and convalescence. Viral load at the time of infection was inversely correlated with antibody binding and neutralizing antibody responses. Across all variants tested, convalescent neutralization titers in unvaccinated individuals were markedly lower than in vaccinated individuals. Increases in antibody titers and neutralizing activity occurred at convalescence in a variant-specific manner. For example, among individuals infected with the Delta variant, neutralizing antibody responses were weakest against BA.2, whereas infection with Omicron BA.1 variant generated a broader response against all tested variants, including BA.2.

Detecting and mitigating simultaneous waves of COVID-19 infections

The sudden spread of COVID-19 infections in a region can catch its healthcare system by surprise. Can one anticipate such a spread and allow healthcare administrators to prepare for a surge a priori? We posit that the answer lies in distinguishing between two types of waves in epidemic dynamics. The first kind resembles a spatio-temporal diffusion pattern. Its gradual spread allows administrators to marshal resources to combat the epidemic. The second kind is caused by super-spreader events, which provide shocks to the disease propagation dynamics. Such shocks simultaneously affect a large geographical region and leave little time for the healthcare system to respond. We use time-series analysis and epidemiological model estimation to detect and react to such simultaneous waves using COVID-19 data from the time when the B.1.617.2 (Delta) variant of the SARS-CoV-2 virus dominated the spread. We first analyze India's second wave from April to May 2021 that overwhelmed the Indian healthcare system. Then, we analyze data of COVID-19 infections in the United States (US) and countries with a high and low Indian diaspora. We identify the Kumbh Mela festival as the likely super-spreader event, the exogenous shock, behind India's second wave. We show that a multi-area compartmental epidemiological model does not fit such shock-induced disease dynamics well, in contrast to its performance with diffusion-type spread. The insufficient fit to infection data can be detected in the early stages of a shock-wave propagation and can be used as an early warning sign, providing valuable time for a planned healthcare response. Our analysis of COVID-19 infections in the US reveals that simultaneous waves due to super-spreader events in one country (India) can lead to simultaneous waves in other places. The US wave in the summer of 2021 does not fit a diffusion pattern either. We postulate that international travels from India may have caused this wave. To support that hypothesis, we demonstrate that countries with a high Indian diaspora exhibit infection growth soon after India's second wave, compared to countries with a low Indian diaspora. Based on our data analysis, we provide concrete policy recommendations at various stages of a simultaneous wave, including how to avoid it, how to detect it quickly after a potential super-spreader event occurs, and how to proactively contain its spread.

Transmission of SARS-CoV-2 in a primary school setting with and without public health measures using real-world contact data: A modelling study

Background

Stringent public health measures have been shown to influence the transmission of SARS-CoV-2 within school environments. We investigated the potential transmission of SARS-CoV-2 in a primary school setting with and without public health measures, using fine-grained physical positioning traces captured before the COVID-19 pandemic.

Methods

Approximately 172.63 million position data from 98 students and six teachers from an open-plan primary school were used to predict a potential transmission of SARS-CoV-2 in primary school settings. We first estimated the daily average number of contacts of students and teachers with an infected individual during the incubation period. We then used the Reed-Frost model to estimate the probability of transmission per contact for the SARS-CoV-2 Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron variant (B.1.1.529). Finally, we built a binomial distribution model to estimate the probability of onward transmission in schools with and without public health measures, including face masks and physical distancing.

Results

An infectious student would have 49.1 (95% confidence interval (CI) = 46.1-52.1) contacts with their peers and 2.00 (95% CI = 1.82-2.18) contacts with teachers per day. An infectious teacher would have 47.6 (95% CI = 45.1-50.0) contacts with students and 1.70 (95% CI = 1.48-1.92) contacts with their colleague teachers per day. While the probability of onward SARS-CoV-2 transmission was relatively low for the Alpha and Delta variants, the risk increased for the Omicron variant, especially in the absence of public health measures. Onward teacher-to-student transmission (88.9%, 95% CI = 88.6%-89.1%) and teacher-to-teacher SARS-CoV-2 transmission (98.4%, 95% CI = 98.5%-98.6%) were significantly higher for the Omicron variant without public health measures in place.

Conclusions

Our findings illustrate that, despite a lower frequency of close contacts, teacher-to-teacher close contacts demonstrated a higher risk of transmission per contact of SARS-CoV-2 compared to student-to-student close contacts. This was especially significant with the Omicron variant, with onward transmission more likely occurring from teacher index cases than student index cases. Public health measures (eg, face masks and physical distance) seem essential in reducing the risk of onward transmission within school environments.

Monobiotinylated Proteins Tethered to Microspheres for Detection of Antigen-Specific Serum Antibodies

Surface modified microspheres have been leveraged as a useful way to immobilize antigen for serological studies. The use of carboxyl modified microspheres for this purpose is well-established, but commonly associated with technical challenges. Streptavidin modified microspheres require little technical expertise and thus address some of the shortcomings of carboxyl microspheres. An additional feature of streptavidin microspheres is the use of mono-biotinylated proteins, which contain a single biotinylation motif at the C-terminus. However, the relative performance of streptavidin and carboxyl microspheres is unknown. Here, we performed a head-to-head comparison of streptavidin and carboxyl microspheres. We compared antigen binding, orientation, and staining quality and found that both microspheres perform similarly based on these defined parameters. We also evaluated the utility of streptavidin microspheres bound to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD), to reliably detect RBD-specific IgG1, IgG3, and IgA1 produced in individuals recently immunized with Pfizer/BioNTech mRNA coronavirus disease (COVID) vaccine as 'proof-of-concept'. We provide evidence that each of the antibody targets are detectable in serum using RBD-coated microspheres, Ig-specific 'detector' monoclonal antibodies (mAbs), and flow cytometry. We found that cross-reactivity of the detector mAbs can be minimized by antibody titration to improve differentiation between IgG1 and IgG3. We also coated streptavidin microspheres with SARS-CoV-2 delta variant RBD to determine if the streptavidin microsphere approach revealed any differences in binding of immune serum antibodies to wild-type (Wuhan) versus variant RBD (Delta). Overall, our results show that streptavidin microspheres loaded with mono-biotinylated antigen is a robust alternative to chemically cross-linking antigen to carboxyl microspheres for use in serological assays.

Travel-associated SARS-CoV-2 transmission documented with whole genome sequencing following a long-haul international flight

BACKGROUND

Multiple instances of flight-associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during long-haul flights have been reported during the COVID-19 pandemic. However, comprehensive investigations of passenger risk behaviours, before, during and after the flight, are scarce.

METHODS

To investigate suspected SARS-CoV-2 transmission during a flight from United Arab Emirates to Australia in July 2020, systematic, repeated polymerase chain reaction (PCR) testing of passengers in hotel quarantine was linked to whole genome sequencing. Epidemiological analyses of in-depth interviews covering behaviours during the flight and activities pre- and post-boarding were used to identify risk factors for infection.

RESULTS

Seventeen of the 95 passengers from four different travel origins had PCR-confirmed infection yielding indistinguishable genomic sequences. Two of the 17 passengers were symptomatic within 2 days of the flight, and classified as co-primary cases. Seven secondary cases were seated within two rows of the co-primary cases, but five economy passengers seated further away and three business class passengers were also infected (attack rate = 16% [15/93]). In multivariable analysis, being seated within two rows of a primary case [odds ratio (OR) 7.16; 95% confidence interval (CI) 1.66-30.85] and spending more than an hour in the arrival airport (OR 4.96; 95% CI 1.04-23.60) were independent predictors of secondary infection, suggesting travel-associated SARS-CoV-2 transmission likely occurred both during and after the flight. Self-reported increased hand hygiene, frequent aisle walking and using the bathroom on the plane did not independently affect the risk of SARS-CoV-2 acquisition.

CONCLUSIONS

This investigation identified substantial in-flight transmission among passengers seated both within and beyond two rows of the primary cases. Infection of passengers in separate cabin classes also suggests transmission occurred outside the cabin environment, likely at the arrival airport. Recognizing that transmission may occur pre- and post-boarding may inform contact tracing advice and improve efforts to prevent future travel-associated outbreaks.

SARS-CoV-2 infection in pediatric population before and during the Delta (B.1.617.2) and Omicron (B.1.1.529) variants era

BACKGROUND

COVID-19, the coronavirus disease that emerged in December 2019, caused drastic damage worldwide. At the beginning of the pandemic, available data suggested that the infection occurs more frequently in adults than in infants. In this review, we aim to provide an overview of SARS-CoV-2 infection in children before and after B.1.617.2 Delta and B.1.1.529 Omicron variants emergence in terms of prevalence, transmission dynamics, clinical manifestations, complications and risk factors.

METHODS

Our method is based on the literature search on PubMed, Science Direct and Google Scholar. From January 2020 to July 2022, a total of 229 references, relevant for the purpose of this review, were considered.

RESULTS

The incidence of SARS-CoV-2 infection in infants was underestimated. Up to the first half of May, most of the infected children presented asymptomatic or mild manifestations. The prevalence of COVID-19 varied from country to another: the highest was reported in the United States (22.5%). COVID-19 can progress and become more severe, especially with the presence of underlying health conditions. It can also progress into Kawasaki or Multisystem Inflammatory Syndrome (MIS) manifestations, as a consequence of exacerbating immune response. With the emergence of the B.1.617.2 Delta and B.1.1.529 Omicron variants, it seems that these variants affect a large proportion of the younger population with the appearance of clinical manifestations similar to those presented by adults with important hospitalization rates.

CONCLUSION

The pediatric population constitutes a vulnerable group that requires particular attention, especially with the emergence of more virulent variants. The increase of symptomatic SARS-CoV-2 infection and hospitalization rate among children highlights the need to extend vaccination to the pediatric population.

Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study

The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0-9.0) in unvaccinated participants to 6 days (IQR: 5.0-8.0) in those vaccinated (P = 0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19-0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset.

The fourth wave: vaccination status and intensive care unit mortality at a large hospital system in New York City

Background

We aim to describe the demographics and outcomes of patients with severe disease with the Omicron variant. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to mutate, and the availability of vaccines and boosters continue to rise, it is important to understand the health care burden of new variants. We analyze patients admitted to intensive care units (ICUs) in a large Academic Health System during New York City’s fourth surge beginning on November 27, 2021.

Methods

All patients admitted to an ICU were included in the primary analysis. Key demographics and outcomes were retrospectively compared between patients stratified by vaccination status. Univariate and multivariate logistic regression was used to identify risk factors for in-hospital mortality.

Results

In-hospital mortality for all admitted patients during the fourth wave was significantly lower than in previous waves. However, among patients requiring intensive care, in-hospital mortality was high across all levels of vaccination status. In a multivariate model older age was associated with increased in-hospital mortality, vaccination status of overdue for booster was associated with decreased in hospital mortality, and vaccination status of up-to-date with vaccination showed a trend to reduced mortality.

Conclusions

In-hospital mortality of patients with severe respiratory failure from coronavirus disease 2019 (COVID-19) remains high despite decreasing overall mortality. Vaccination against SARS-CoV-2 was protective against mortality. Vaccination remains the best and safest way to protect against serious illness and death from COVID-19. It remains unclear that any other treatment will have success in changing the natural history of the disease.

SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice

The COVID-19 pandemic has been fueled by SARS-CoV-2 novel variants of concern (VOC) that have increased transmissibility, receptor binding affinity, and other properties that enhance disease. The goal of this study is to characterize unique pathogenesis of the Delta VOC strain in the K18-hACE2-mouse challenge model. Challenge studies suggested that the lethal dose of Delta was higher than Alpha or Beta strains. To characterize the differences in the Delta strain's pathogenesis, a time-course experiment was performed to evaluate the overall host response to Alpha or Delta variant challenge. qRT-PCR analysis of Alpha- or Delta-challenged mice revealed no significant difference between viral RNA burden in the lung, nasal wash or brain. However, histopathological analysis revealed high lung tissue inflammation and cell infiltration following Delta- but not Alpha-challenge at day 6. Additionally, pro-inflammatory cytokines were highest at day 6 in Delta-challenged mice suggesting enhanced pneumonia. Total RNA-sequencing analysis of lungs comparing challenged to no challenge mice revealed that Alpha-challenged mice have more total genes differentially activated. Conversely, Delta-challenged mice have a higher magnitude of differential gene expression. Delta-challenged mice have increased interferon-dependent gene expression and IFN-γ production compared to Alpha. Analysis of TCR clonotypes suggested that Delta challenged mice have increased T-cell infiltration compared to Alpha challenged. Our data suggest that Delta has evolved to engage interferon responses in a manner that may enhance pathogenesis. The in vivo and in silico observations of this study underscore the need to conduct experiments with VOC strains to best model COVID-19 when evaluating therapeutics and vaccines.

Infection With the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant Is Associated With Higher Recovery of Infectious Virus Compared to the Alpha Variant in Both Unvaccinated and Vaccinated Individuals

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) B.1.617.2 (Delta) displaced B.1.1.7 (Alpha) and is associated with increases in coronavirus disease 2019 (COVID-19) cases, greater transmissibility, and higher viral RNA loads, but data are lacking regarding the infectious virus load and antiviral antibody levels in the nasal tract.

METHODS

Whole genome sequencing, cycle threshold (Ct) values, infectious virus, anti-SARS-CoV-2 immunoglobulin G (IgG) levels, and clinical chart reviews were combined to characterize SARS-CoV-2 lineages circulating in the National Capital Region between January and September 2021 and differentiate infections in vaccinated and unvaccinated individuals by the Delta, Alpha, and B.1.2 (the predominant lineage prior to Alpha) variants.

RESULTS

The Delta variant displaced the Alpha variant to constitute 99% of the circulating lineages in the National Capital Region by August 2021. In Delta infections, 28.5% were breakthrough cases in fully vaccinated individuals compared to 4% in the Alpha infected cohort. Breakthrough infections in both cohorts were associated with comorbidities, but only Delta infections were associated with a significant increase in the median days after vaccination. More than 74% of Delta samples had infectious virus compared to <30% from the Alpha cohort. The recovery of infectious virus with both variants was associated with low levels of local SARS-CoV-2 IgG.

CONCLUSIONS

Infection with the Delta variant was associated with more frequent recovery of infectious virus in vaccinated and unvaccinated individuals compared to the Alpha variant but was not associated with an increase in disease severity in fully vaccinated individuals. Infectious virus was correlated with the presence of low amounts of antiviral IgG in the nasal specimens.

Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants

The recent emergence of multiple SARS-CoV-2 variants has caused considerable concern due to both reduced vaccine efficacy and escape from neutralizing antibody therapeutics. It is, therefore, paramount to develop therapeutic strategies that inhibit all known and future SARS-CoV-2 variants. Here, we report that all SARS-CoV-2 variants analyzed, including variants of concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron, exhibit enhanced binding affinity to clinical grade and phase 2 tested recombinant human soluble ACE2 (APN01). Importantly, soluble ACE2 neutralized infection of VeroE6 cells and human lung epithelial cells by all current VOC strains with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. Effective inhibition of infections with SARS-CoV-2 variants was validated and confirmed in two independent laboratories. These data show that SARS-CoV-2 variants that have emerged around the world, including current VOC and several variants of interest, can be inhibited by soluble ACE2, providing proof of principle of a pan-SARS-CoV-2 therapeutic.

COVID-19 cases, hospitalizations and deaths after vaccination: a cohort event monitoring study, Islamic Republic of Iran

Objective

To investigate the incidence of coronavirus disease 2019 (COVID-19) cases, hospitalizations and deaths in Iranians vaccinated with either AZD1222 Vaxzevria, CovIran® vaccine, SARS-CoV-2 Vaccine (Vero Cell), Inactivated (lnCoV) or Sputnik V.

Methods

We enrolled individuals 18 years or older receiving their first COVID-19 vaccine dose between April 2021 and January 2022 in seven Iranian cities. Participants completed weekly follow-up surveys for 17 weeks (25 weeks for AZD1222) to report their COVID-19 status and hospitalization. We used Cox regression models to assess risk factors for contracting COVID-19, hospitalization and death.

Findings

Of 89 783 participants enrolled, incidence rates per 1 000 000 person-days were: 528.2 (95% confidence interval, CI: 514.0-542.7) for contracting COVID-19; 55.8 (95% CI: 51.4-60.5) for hospitalization; and 4.1 (95% CI: 3.0-5.5) for death. Compared with SARS-CoV-2 Vaccine (Vero Cell), hazard ratios (HR) for contracting COVID-19 were: 0.70 (95% CI: 0.61-0.80) with AZD1222; 0.73 (95% CI: 0.62-0.86) with Sputnik V; and 0.73 (95% CI: 0.63-0.86) with CovIran®. For hospitalization and death, all vaccines provided similar protection 14 days after the second dose. History of COVID-19 protected against contracting COVID-19 again (HR: 0.76; 95% CI: 0.69-0.84). Diabetes and respiratory, cardiac and renal disease were associated with higher risks of contracting COVID-19 after vaccination.

Conclusion

The rates of contracting COVID-19 after vaccination were relatively high. SARS-CoV-2 Vaccine (Vero Cell) provided lower protection against COVID-19 than other vaccines. People with comorbidities had higher risks of contracting COVID-19 and hospitalization and should be prioritized for preventive interventions.

Spatial Syndromic Surveillance and COVID-19 in the U.S.: Local Cluster Mapping for Pandemic Preparedness

Maps have become the de facto primary mode of visualizing the COVID-19 pandemic, from identifying local disease and vaccination patterns to understanding global trends. In addition to their widespread utilization for public communication, there have been a variety of advances in spatial methods created for localized operational needs. While broader dissemination of this more granular work is not commonplace due to the protections under Health Insurance Portability and Accountability Act (HIPAA), its role has been foundational to pandemic response for health systems, hospitals, and government agencies. In contrast to the retrospective views provided by the aggregated geographies found in the public domain, or those often utilized for academic research, operational response requires near real-time mapping based on continuously flowing address level data. This paper describes the opportunities and challenges presented in emergent disease mapping using dynamic patient data in the response to COVID-19 for northeast Ohio for the period 2020 to 2022. More specifically it shows how a new clustering tool developed by geographers in the initial phases of the pandemic to handle operational mapping continues to evolve with shifting pandemic needs, including new variant surges, vaccine targeting, and most recently, testing data shortfalls. This paper also demonstrates how the geographic approach applied provides the framework needed for future pandemic preparedness.

Diagnostics of messenger ribonucleic acid (mRNA) severe acute respiratory syndrome-corona virus‑2 (SARS-CoV‑2) vaccination-associated myocarditis—A systematic review

Background

Objective

Methods

Results

Conclusion

Supplementary Information

Clinical Characteristics and Outcomes of Critically Ill Patients with 1, 2 and 3 doses of Vaccination against COVID-19 in Australia

Background

Vaccination has been shown to be highly effective in preventing death and severe disease from severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. Currently few studies have directly compared vaccinated and unvaccinated patients with severe COVID‐19 in the intensive care unit (ICU).

Aims

Our aim was to compare the clinical characteristics and outcomes of vaccine recipients and unvaccinated patients with SARS‐CoV‐2 infection admitted to the ICU in a nationwide setting.

Materials and Methods

Data were extracted from the Short PeRiod IncideNce sTudy of Severe Acute Respiratory Infection Australia, in 57 ICUs during Delta and Omicron predominant periods of the COVID‐19 pandemic. The primary outcome was in‐hospital mortality. Secondary outcomes included duration of mechanical ventilation, ICU length of stay, hospital length of stay, and ICU mortality.

Results

2,970 patients were admitted to ICU across participating sites from 26 June 2021 to 8 February 2022. 1,134 (38.2%) patients were vaccine recipients, and 1,836 (61.8%) patients were unvaccinated. Vaccine recipients were older, more comorbid, and less likely to require organ support. Unadjusted in‐hospital mortality was greater in the vaccinated cohort. After adjusting for age, gender and comorbid status, no statistically significant association between in‐hospital or ICU mortality, and vaccination status, was apparent.

Conclusion

We found COVID‐19 infection can cause severe disease and death in vaccine recipients, though comorbid status and older age were significant contributors to mortality. Organ support requirements and the number of deaths were highest in the unvaccinated cohort.

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Surveillance of Post-Vaccination Side Effects of COVID-19 Vaccines among Saudi Population: A Real-World Estimation of Safety Profile

Vaccines are considered to be the most beneficial means for combating the COVID-19 pandemic. Although vaccines against SARS-CoV-2 have demonstrated excellent safety profiles in clinical trials, real-world surveillance of post-vaccination side effects is an impetus. The study investigates the short-term side effects following the administration of the Pfizer-BioNTech and Oxford-AstraZeneca vaccines in Saudi Arabia. A cross-sectional quantitative study was conducted among the general population with age ≥ 18 years, from five regions (Central, Northern, Eastern, Southern, and Western Regions) of Saudi Arabia for a period of 6 months (July to December 2021). A self-administered study instrument was used to record the side effects among the COVID-19 vaccine recipients. Of the total 398 participants (males: 59%), 56.3% received Pfizer and 43.7% were vaccinated with AstraZeneca. Only 22.6% of respondents received the second dose of the COVID-19 vaccines. The most commonly reported side effects were pain at the injection site (85.2%), fatigue (61.8%), bone or joint pain (54.0%), and fever (42.5%). The average side effects score was 3.4 ± 2.2. Females, young people, and Oxford-AstraZeneca recipients had a higher proportion of side effects. The Oxford-AstraZeneca vaccine recipients complained more about fever (p < 0.001), bone and joint pain (p < 0.001), fatigue (p < 0.001), loss of appetite (p = 0.001), headache (p = 0.008), and drowsiness (p = 0.003). The Pfizer-BioNTech vaccinees had more pain and swelling at the injection site (p = 0.001), and sexual disturbance (p = 0.019). The study participants also reported some rare symptoms (<10%) including heaviness, sleep disturbance, fainting, blurred vision, palpitations, osteomalacia, and inability to concentrate. This study revealed that both Pfizer-BioNTech and Oxford-AstraZeneca administration was associated with mild to moderate, transient, short-lived side effects. These symptoms corroborate the results of phase 3 clinical trials of these vaccines. The results could be used to inform people about the likelihood of side effects based on their demographics and the type of vaccine administered. The study reported some rare symptoms that require further validation through more pharmacovigilance or qualitative studies.

Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis

BACKGROUND

COVID-19 messenger RNA (mRNA) vaccines have demonstrated efficacy and effectiveness in preventing symptomatic COVID-19, while being relatively safe in trial studies. However, vaccine breakthrough infections have been reported.

OBJECTIVE

This study aims to identify risk factors associated with COVID-19 breakthrough infections among fully mRNA-vaccinated individuals.

METHODS

We conducted a series of observational retrospective analyses using the electronic health records (EHRs) of the Columbia University Irving Medical Center/New York Presbyterian (CUIMC/NYP) up to September 21, 2021. New York City (NYC) adult residences with at least 1 polymerase chain reaction (PCR) record were included in this analysis. Poisson regression was performed to assess the association between the breakthrough infection rate in vaccinated individuals and multiple risk factors-including vaccine brand, demographics, and underlying conditions-while adjusting for calendar month, prior number of visits, and observational days in the EHR.

RESULTS

The overall estimated breakthrough infection rate was 0.16 (95% CI 0.14-0.18). Individuals who were vaccinated with Pfizer/BNT162b2 (incidence rate ratio [IRR] against Moderna/mRNA-1273=1.66, 95% CI 1.17-2.35) were male (IRR against female=1.47, 95% CI 1.11-1.94) and had compromised immune systems (IRR=1.48, 95% CI 1.09-2.00) were at the highest risk for breakthrough infections. Among all underlying conditions, those with primary immunodeficiency, a history of organ transplant, an active tumor, use of immunosuppressant medications, or Alzheimer disease were at the highest risk.

CONCLUSIONS

Although we found both mRNA vaccines were effective, Moderna/mRNA-1273 had a lower incidence rate of breakthrough infections. Immunocompromised and male individuals were among the highest risk groups experiencing breakthrough infections. Given the rapidly changing nature of the SARS-CoV-2 pandemic, continued monitoring and a generalizable analysis pipeline are warranted to inform quick updates on vaccine effectiveness in real time.

Comparative Analysis of Age, Sex, and Viral Load in Outpatients during the Four Waves of SARS-CoV-2 in A Mexican Medium-Sized City

Governments have implemented measures to minimize SARS-CoV-2 spread. However, these measures were relaxed, and the appearance of new variants has prompted periods of high contagion known as waves. In Mexico, four waves distributed between July and August 2020, January and February 2021, August and September 2021, and January and February 2022 have appeared. Current health policies discourage mass sampling, preferring to focus on the corrective treatment of severe cases. Outpatients are only advised to undergo brief voluntary confinement and symptomatic treatment, with no follow-up. Therefore, the present study aimed to analyze sex, age, and viral load in outpatients during the four waves in a medium-sized city in Mexico. For each wave, the date of peak contagion was identified, and data were collected within ±15 days. In this regard, data from 916 patients (434 men and 482 women) were analyzed. The age range of positive patients (37-45 years) presented a higher frequency during the first and third waves, while 28-36 years was the most frequent age range during the second and fourth waves, while the viral load values were significantly higher, for both sexes, during the fourth wave. Obtained data of COVID-19 prevalence in population segments can be used for decision-making in the design of effective public health policies.

Interaction of surface glycoprotein of SARS-CoV-2 variants of concern with potential drug candidates: A molecular docking study

Background: COVID-19 has become a global threat. Since its first outbreak from Wuhan, China in December 2019, the SARS-CoV-2 virus has gone through structural changes arising due to mutations in its surface glycoprotein. These mutations have led to the emergence of different genetic variants threatening public health due to increased transmission and virulence. As new drug development is a long process, repurposing existing antiviral drugs with potential activity against SARS-CoV-2 might be a possible solution to mitigate the current situation. Methods: This study focused on utilizing molecular docking to determine the effect of potential drugs on several variants of concern (VOCs). The effect of various drugs such as baricitinib, favipiravir, lopinavir, remdesivir and dexamethasone, which might have the potential to treat SARS-CoV-2 infections as evident from previous studies, was investigated for different VOCs. Results: Remdesivir showed promising results for B.1.351 variant (binding energy: -7.3 kcal/mol) with residues Gln319 and Val503 facilitating strong binding. Favipiravir showed favorable results against B.1.1.7 (binding energy: -5.6 kcal/mol), B.1.351 (binding energy: -5.1 kcal/mol) and B.1.617.2 (binding energy: -5 kcal/mol). Molecular dynamics simulation for favipiravir/B.1.1.7 was conducted and showed significant results in agreement with our findings. Conclusions: From structural modeling and molecular docking experiments, it is evident that mutations outside the receptor binding domain of surface glycoprotein do not have a sharp impact on drug binding affinity. Thus, the potential use of these drugs should be explored further for their antiviral effect against SARS-CoV-2 VOCs.

Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II

Variants of the SARS-CoV-2 virus continue to remain a threat 2 years from the beginning of the pandemic. As more variants arise, and the B.1.1.529 (Omicron) variant threatens to create another wave of infections, a method is needed to predict the binding affinity of the spike protein quickly and accurately with human angiotensin-converting enzyme II (ACE2). We present an accurate and convenient energy minimization/molecular mechanics Poisson-Boltzmann surface area methodology previously used with engineered ACE2 therapeutics to predict the binding affinity of the Omicron variant. Without any additional data from the variants discovered after the publication of our first model, the methodology can accurately predict the binding of the spike/ACE2 variant complexes. From this methodology, we predicted that the Omicron variant spike has a Kd of ∼22.69 nM (which is very close to the experimental Kd of 20.63 nM published during the review process of the current report) and that spike protein of the new "Stealth" Omicron variant (BA.2) will display a Kd of ∼12.9 nM with the wild-type ACE2 protein. This methodology can be used with as-yet discovered variants, allowing for quick determinations regarding the variant's infectivity versus either the wild-type virus or its variants.