SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness

SARS-CoV-2 Disease Severity and Cycle Threshold Values in Children Infected during Pre-Delta, Delta, and Omicron Periods, Colorado, USA, 2021-2022

In adults, viral load and disease severity can differ by SARS-CoV-2 variant, patterns less understood in children. We evaluated symptomatology, cycle threshold (Ct) values, and SARS-CoV-2 variants among 2,299 pediatric SARS-CoV-2 patients (0-21 years of age) in Colorado, USA, to determine whether children infected with Delta or Omicron had different symptom severity or Ct values than during earlier variants. Children infected during the Delta and Omicron periods had lower Ct values than those infected during pre-Delta, and children <1 year of age had lower Ct values than older children. Hospitalized symptomatic children had lower Ct values than asymptomatic patients. Compared with pre-Delta, more children infected during Delta and Omicron were symptomatic (75.4% pre-Delta, 95.3% Delta, 99.5% Omicron), admitted to intensive care (18.8% pre-Delta, 39.5% Delta, 22.9% Omicron), or received oxygen support (42.0% pre-Delta, 66.3% Delta, 62.3% Omicron). Our data reinforce the need to include children, especially younger children, in pathogen surveillance efforts.

Correlates of COVID-19 vaccine uptake among the forcibly displaced: evidence from Libya

BACKGROUND

Vaccine hesitancy and refusal can hinder the control of infectious diseases such as coronavirus disease 2019 (COVID-19). Although forcibly displaced individuals are at high risk of contracting COVID-19, evidence shows that they are less likely to accept the COVID-19 vaccine. Given their predicament, the factors influencing vaccine uptake in the general population might differ vastly from those in displaced populations. Given the limited evidence on vaccine uptake from humanitarian settings, the current study examined the determinants of COVID-19 vaccine uptake among the forcibly displaced in Libya.

METHODS

Data were extracted from the World Bank/United Nations High Commissioner for Refugees (UNHCR) microdata repository. Data were collected between April and July 2021 after the rollout of the first dose of the COVID-19 vaccine in Libya. Percentages, means, and standard deviations were used to quantify the distribution of the sample population. Logistic regression models were employed to identify factors influencing COVID-19 vaccine uptake.

RESULTS

Odds ratios (ORs) with p values are used to present the regression analysis results. The study revealed that people unaffected by COVID-19 were less likely (OR = .71, 95%CI = 0.67-0.89) to accept the vaccine. Similarly, individuals with access to free COVID-19 vaccines were more likely to be vaccinated than those without free vaccines (OR = 38, 95%CI = 0.19-0.28). Finally, the results indicated that individuals were six times more likely to be vaccinated at mass vaccination sites ((OR = 6.31, 95%CI = 5.46- 7.94) and 1.92 times more likely to be vaccinated at local health centers (OR = 1.92, 95%CI = 0.1.72-3.11) than they were at hospitals and distant health facilities.

CONCLUSION

Implementing comprehensive mass vaccination venues, public education initiatives, and awareness campaigns regarding the importance of vaccination can decrease vaccine hesitancy among the forcibly displaced.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

An unprecedented global challenge, emerging trends and innovations in the fight against COVID-19: A comprehensive review

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious and dangerous virus that caused the global COVID-19 pandemic in early 2020. It primarily affects the respiratory system, leading to severe illness and high rates of mortality worldwide. The virus enters the body by binding to a receptor called ACE2, which is present in specific cells of the lungs known as type 2 alveolar epithelial cells. Numerous studies have investigated the consequences of SARS-CoV-2 infection, revealing various impacts on the body. This review provides an overview of SARS-CoV-2, including its structure and how it infects cells. It also examines the different variants of concern, such as Alpha, Beta, Gamma, Delta, and the more recent Omicron variant, discussing their characteristics and the level of damage they cause. The usage of drugs to treat COVID-19 is another aspect that has been covered and compares the effectiveness and use of antiviral drugs in the treatment and its potential benefits in COVID-19 treatment. Furthermore, this review explores the consequences and abnormalities associated with SARS-CoV-2 infection, including its impact on various organs and systems in the body. And also discussing the different COVID-19 vaccines available and their effectiveness in preventing infection and reducing the severity of illness. The current review ensures the recent update of the COVID research with expert's knowledge, collection of numerous data from reliable sources and methodologies as well as update of findings based on reviews. This review also provided clear contextual explanations to aid the interpretation and application of the results. The main motto and limitation of this manuscript are to address the computational methods of drug discovery against the rapidly evolving SARS-CoV-2 virus, which has been discussed. Additionally, current computational approaches which are cost effective and can able to predict the therapeutic agents for the treatment against the virus have also been discussed.

Disparities and Outcomes in the First and Second Year of the Pandemic on Events of Acute Myocardial Infarction in Coronavirus Disease 2019 Patients

Background and Objectives: Coronavirus disease 2019 (COVID-19) caused several cardiovascular complications, including acute myocardial infarction (AMI), in infected patients. This study aims to understand the overall trends of AMI among COVID-19 patients during the first two years of the pandemic and the disparities and outcomes between the first and second years. Materials and Methods: The retrospective analysis was conducted via the 2020 and 2021 National Inpatient Sample (NIS) database for hospitalizations between April 2020 and December 2021 being analyzed for adults with a primary diagnosis of COVID-19 who experienced events of AMI. A comparison of month-to-month events of AMI and mortality of AMI patients with concomitant COVID-19 was made alongside their respective patient characteristics. Results: Out of 2,541,992 COVID-19 hospitalized patients, 3.55% experienced AMI. The highest rate of AMI was in December 2021 (4.35%). No statistical differences in trends of AMI mortality were noted over the 21 months. AMI cases in 2021 had higher odds of undergoing PCI (aOR 1.627, p < 0.01). They experienced higher risks of acute kidney injury (aOR 1.078, p < 0.01), acute ischemic stroke (aOR 1.215, p < 0.01), cardiac arrest (aOR 1.106, p < 0.01), need for mechanical ventilation (aOR 1.133, p < 0.01), and all-cause mortality (aOR 1.032, 95% CI 1.001-1.064, p = 0.043). Conclusions: The incidence of AMI among COVID-19 patients fluctuated over the 21 months of this study, with a peak in December 2021. COVID-19 patients reporting AMI in 2021 experienced higher overall odds of multiple complications, which could relate to the exhaustive burden of the pandemic in 2021 on healthcare, the changing impact of the virus variants, and the hesitancy of infected patients to seek care.

What makes SARS-CoV-2 unique? Focusing on the spike protein

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.

A Longitudinal Evaluation of Coronavirus Disease 2019 and Its Effects on Spinal Decompressions With or Without Fusion

STUDY DESIGN

Retrospective cohort.

OBJECTIVE

The objectives were to (1) compare the safety of spine surgery before and after the emergence of coronavirus disease 2019 (COVID-19) and (2) determine whether patients with a history of COVID-19 were at increased risk of adverse events.

SUMMARY AND BACKGROUND DATA

The COVID-19 pandemic had a tremendous impact on several health care services. In spine surgery, elective cases were canceled and patients received delayed care due to the uncertainty of disease transmission and surgical outcomes. As new coronavirus variants arise, health care systems require guidance on how to provide optimal patient care to all those in need of our services.

PATIENTS AND METHODS

A retrospective review of patients undergoing spine surgery between January 1, 2019 and June 30, 2021 was performed. Patients were split into pre-COVID or post-COVID cohorts based on local government guidelines. Inpatient complications, 90-day readmission, and 90-day mortality were compared between groups. Secondary analysis included multiple logistic regression to determine independent predictors of each outcome.

RESULTS

A total of 2976 patients were included for analysis with 1701 patients designated as pre-COVID and 1275 as post-COVID. The pre-COVID cohort had fewer patients undergoing revision surgery (16.8% vs 21.9%, P < 0.001) and a lower home discharge rate (84.5% vs 88.2%, P = 0.008). Inpatient complication (9.9% vs 9.2%, P = 0.562), inpatient mortality (0.1% vs 0.2%, P = 0.193), 90-day readmission (3.4% vs 3.2%, P = 0.828), and 90-day mortality rates (0.8% vs 0.8%, P = 0.902) were similar between groups. Patients with positive COVID-19 tests before surgery had similar complication rates (7.7% vs 6.1%, P = 1.000) as those without a positive test documented.

CONCLUSIONS

After the emergence of COVID-19, patients undergoing spine surgery had a greater number of medical comorbidities, but similar rates of inpatient complications, readmission, and mortality. Prior COVID-19 infection was not associated with an increased risk of postsurgical complications or mortality.

LEVEL OF EVIDENCE

Level III.

Comparative severity of COVID-19 cases caused by Alpha, Delta or Omicron SARS-CoV-2 variants and its association with vaccination

BACKGROUND

This study compares the severity of SARS-CoV-2 infections caused by Alpha, Delta or Omicron variants in periods of co-circulation in Spain, and estimates the variant-specific association of vaccination with severe disease.

METHODS

SARS-CoV-2 infections notified to the national epidemiological surveillance network with information on genetic variant and vaccination status were considered cases if they required hospitalisation or controls otherwise. Alpha and Delta were compared during June-July 2021; and Delta and Omicron during December 2021-January 2022. Adjusted odds ratios (aOR) were estimated using logistic regression, comparing variant and vaccination status between cases and controls.

RESULTS

We included 5,345 Alpha and 11,974 Delta infections in June-July and 5,272 Delta and 10,578 Omicron in December-January. Unvaccinated cases of Alpha (aOR: 0.57; 95% CI: 0.46-0.69) or Omicron (0.28; 0.21-0.36) had lower probability of hospitalisation vs. Delta. Complete vaccination reduced hospitalisation, similarly for Alpha (0.16; 0.13-0.21) and Delta (June-July: 0.16; 0.14-0.19; December-January: 0.36; 0.30-0.44) but lower from Omicron (0.63; 0.53-0.75) and individuals aged 65+ years.

CONCLUSION

Results indicate higher intrinsic severity of the Delta variant, compared with Alpha or Omicron, with smaller differences among vaccinated individuals. Nevertheless, vaccination was associated to reduced hospitalisation in all groups.

SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants

The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.

Delta Variant in the COVID-19 Pandemic: A Comparative Study on Clinical Outcomes Based on Vaccination Status

BACKGROUND

As the global battle against the COVID-19 pandemic endures, the spread of the Delta variant has introduced nuanced challenges, prompting a nuanced examination.

MATERIALS AND METHODS

We performed a multilevel logistic regression analysis encompassing 197 patients, comprising 44 vaccinated individuals (V group) and 153 unvaccinated counterparts (UV). These patients, afflicted with the Delta variant of SARS-CoV-2, were hospitalized between October 2021 and February 2022 at the COVID-19 department of a University Centre in Cluj-Napoca, Romania. We compared patient characteristics, CT lung involvement, Padua score, oxygen saturation (O2 saturation), ventilation requirements, dynamics of arterial blood gas (ABG) parameters, ICU admission rates, and mortality rates between the two groups.

RESULTS

The UV group exhibited a statistically significant (p < 0.05) proclivity toward developing a more severe form of infection, marked by elevated rates of lung involvement, oxygen requirement, ICU admission, and mortality.

CONCLUSION

Our findings underscore the substantial efficacy of the vaccine in diminishing the incidence of severe disease, lowering the rates of ICU admissions, and mitigating mortality among hospitalized patients.

Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond

Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.

Risk factors for critical COVID-19 illness during Delta- and Omicron-predominant period in Korea; using K-COV-N cohort in the National health insurance service

BACKGROUND

This study evaluated the clinical characteristics of patients with COVID-19 in Korea, and examined the relationship between severe COVID-19 cases and underlying health conditions during the Delta (September 20, 2021 to December 4, 2021) and the Omicron (February 20, 2022 to March 31, 2022) predominant period.

METHODS

This study assessed the association between critical COVID-19 illness and various risk factors, including a variety of underlying health conditions, using multiple logistic regression models based on the K-COV-N cohort, a nationwide data of confirmed COVID-19 cases linked with COVID-19 vaccination status and the National Health Insurance claim information.

RESULTS

We analyzed 137,532 and 8,294,249 cases of COVID-19 infection during the Delta and the Omicron variant dominant periods, respectively. During the Delta as well as the Omicron period, old age (≥80 years) showed the largest effect size among risk factors for critical COVID-19 illness (aOR = 18.08; 95% confidence interval [CI] = 14.71-22.23 for the Delta; aOR = 24.07; 95% CI = 19.03-30.44 for the Omicron period). We found that patients with solid organ transplant (SOT) recipients, unvaccinated, and interstitial lung disease had more than a two-fold increased risk of critical COVID-19 outcomes between the Delta and Omicron periods. However, risk factors such as urban residence, underweight, and underlying medical conditions, including chronic cardiac diseases, immunodeficiency, and mental disorders, had different effects on the development of critical COVID-19 illness between the Delta and Omicron periods.

CONCLUSION

We found that the severity of COVID-19 infection was much higher for the Delta variant than for the Omicron. Although the Delta and the Omicron variant shared many risk factors for critical illness, several risk factors were found to have different effects on the development of critical COVID-19 illness between those two variants. Close monitoring of a wide range of risk factors for critical illness is warranted as new variants continue to emerge during the pandemic.

Difference in mortality risk predicted by leukocyte and lymphocyte levels in COVID-19 patients infected with the Wild-type, Delta, and Omicron strains

This study aimed to investigate the changing trends, level differences, and prognostic performance of the leukocyte and lymphocyte levels of patients infected with the Wild strains, Delta strains and Omicron strains to provide a reference for prognostic assessment. In the current study, we conducted a retrospective cross-sectional study to evaluate the changing trends, level differences, and prognostic performance of leukocyte and lymphocyte of different strains at admission and discharge may already exist in patients with coronavirus disease-2019 (COVID-19) infected with the Wild type, Delta, and Omicron strains. A retrospective cross-sectional study was conducted. We recruited and screened the 243 cases infected with the Wild-type strains in Wuhan, the 629 cases infected with the Delta and 116 cases infected strains with the Omicron strains in Xi'an. The leukocyte and lymphocyte levels were compared the cohort of Wild-type infection with the cohort of Delta and the Omicron. The changes in the levels of leukocytes and lymphocytes exhibit a completely opposite trend in patients with COVID-19 infected with the different strains. The lymphocyte level at admission and discharge in patients with COVID-19 infected with Omicron strains (area under curve [AUC] receiver operating characteristic curve [ROC] 72.8-90.2%, 82.8-97.2%) presented better performance compared patients with COVID-19 infected with Wild type strains (AUC ROC 60.9-80.7%, 82.3-97.2%) and Delta strains (AUC ROC 56.1-84.7%, 40.3-93.3%). Kaplan-Meier curves showed that the leukocyte levels above newly established cutoff values and the lymphocyte levels below newly established cutoff values had a significantly higher risk of in-hospital mortality in COVID-19 patients with Wild-type and Omicron strains (P < .01). The levels of leukocyte and lymphocyte at admission and discharge in patients with COVID-19 infected with the Wild type, Delta, and Omicron strains may be differences among strains, which indicates different death risks. Our research may help clinicians identify patients with a poor prognosis for severe acute respiratory syndrome coronavirus 2 infection.

Vaccines reduced hospital length of stay and fraction of inspired oxygen of COVID-19 patients: A retrospective cohort study

Few studies have focused on the evaluation of vaccine effectiveness (VE) in mainland China. This study was to characterize the VE including the frequent symptoms, laboratory indices, along with endotracheal intubation, hospital length of stay (LoS), and survival status. This retrospective cohort study included patients with COVID-19 admitted to our hospital. Statistical comparisons of continuous variables were carried out with an independent Student's t-test or Mann-Whitney U test. For categorical variables, the Chi-square test and Fisher exact test were used. Multivariable regression analysis was performed to adjust the confounding factors such as age, gender, body mass index (BMI), residential area, smoking status, the Charlson comorbidity index (CCI) score, followed by investigating the effects of vaccination on critical ill prevention, reduced mortality and endotracheal intubation, LoS and inspired oxygen. This study included 549 hospitalized patients with COVID-19, including 222 (40.43 %) vaccinated participants and 327 (59.57 %) unvaccinated counterparts. There was no obvious difference between the two groups in typical clinical symptoms of COVID-19, clinical laboratory results and mortality. Multivariable analysis showed that COVID-19 vaccine obviously reduced LoS by 1.2 days (lnLoS = -0.14, 95 %CI[-0.24,-0.04]; P = 0.005) and decreased fraction of inspired oxygen by 40 % (OR: 0.60; 95 %CI[0.40,0.90]; P = 0.013) after adjusting age, gender, BMI, residential area, smoking status and CCI score. In contrast, vaccination induced reduction in the critically ill, mortality, and endotracheal intubation compared with the unvaccinated counterparts, but with no statistical differences. Vaccinated patients hospitalized with COVID-19 have a reduced LoS and fraction of inspired oxygen compared to unvaccinated cases in China.

Immune Dysregulation in SARS-CoV-2 patients coinfected with Mycobacterium tuberculosis (Mtb) or HIV in China

BACKGROUND

SARS-CoV-2 infections usually cause immune dysregulation in the human body. Studies of immunological changes resulting from coinfections with Mycobacterium tuberculosis (Mtb) or HIV are limited.

METHODS

We conducted a retrospective study focusing on patients with COVID-19. A total of 550 patients infected with SARS-CoV-2 were enrolled in our study and categorized into four groups based on the presence of coinfections; 166 Delta-infected patients, among whom 103 patients had no coinfections, 52 who were coinfected with Mtb, 11 who were coinfected with HIV, and 384 Omicron-infected patients. By collecting data on epidemiologic information, laboratory findings, treatments, and clinical outcomes, we analyzed and compared clinical and immunological characteristics.

RESULTS

Compared with those in the Delta group, the median white blood cell, CD4 + T-cell and B-cell counts were lower in the Mtb group and the HIV group. Except for those in the Omicron group, more than half of the patients in the three groups had abnormal chest CT findings. Among the three groups, there were no significant differences in any of the cytokines. Compared with those in the Delta group, the disease duration and LOS were longer in the Mtb group and the HIV group. For unvaccinated Delta-infected patients, in the Mtb and HIV groups, the number of B cells and CD4 + T cells was lower than that in the Delta group, with no significant difference in the LOS or disease duration. In the Mtb group, three (6%) patients presented with a disease duration greater than four months and had decreased lymphocyte and IL17A counts, possibly due to double infections in the lungs caused by SARS-CoV-2 and M. tuberculosis.

CONCLUSIONS

We found that SARS-CoV-2 patients coinfected with Mtb or HIV exhibited a longer disease duration and longer LOS, with a decrease in B cells and CD4 + T cells, suggesting that these cells are related to immune function. Changes in cytokine levels suggest that coinfection with Mtb or HIV does not result in dysregulation of the immune response. Importantly, we discovered a chronic course of coinfection involving more than four months of Mtb and SARS-CoV-2 infection.

Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study

OBJECTIVES

We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.

DESIGN

A population-based retrospective cohort analysis.

SETTING

Scotland.

PARTICIPANTS

The study involved 5.4 million residents in Scotland.

MAIN OUTCOME MEASURES

Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.

RESULTS

Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR = 4.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged ≥80 years (aHR = 7.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR = 1.64; 95% CI: 1.57-1.72), with existing health conditions (≥5 vs. 0 health conditions, aHR = 4.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (≥6 vs. 0 previous emergency admissions, aHR = 7.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.

CONCLUSIONS

Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.

Frequency of SARS-CoV-2 variants identified by real-time PCR in the AUNA healthcare network, Peru

Introduction

In Peru, on 11 February 2023, the Ministry of Health registered 4 million patients infected with COVID-19 and around 219,260 deaths. In 2020, the SARS-CoV-2 virus was acquiring mutations that impacted the properties of transmissibility, infectivity, and immune evasion, leading to new lineages. In the present study, the frequency of COVID-19 variants was determined during 2021 and 2022 in patients treated in the AUNA healthcare network.

Methods

The methodology used to detect mutations and identify variants was the Allplex™ SARS-CoV-2 Variants Assay I, II, and VII kit RT-PCR. The frequency of variants was presented by epidemiological weeks.

Results

In total, 544 positive samples were evaluated, where the Delta, Omicron, and Gamma variants were identified. The Delta variant was found in 242 (44.5%) patients between epidemiological weeks 39 and 52 in 2021. In the case of Gamma, it was observed in 8 (1.5%) patients at weeks 39, 41, 43, 45, and 46 of 2021. The Omicron variant was the most frequent with 289 (53.1%) patients during weeks 49 to 52 of 2021 and 1 to 22 of 2022. During weeks 1 through 22 of 2022, it was possible to discriminate between BA. 1 (n = 32) and BA.2 (n = 82).

Conclusion

The rapid identification of COVID-19 variants through the RT-PCR methodology contributes to timely epidemiological surveillance, as well as appropriate patient management.

Vaccination and its impact on healthcare utilization in two groups of vaccinated and unvaccinated patients with COVID-19: A cross-sectional study in Iran between 2021 and 2022

Background and Aims

One of the main responsibilities of health systems impacted by the global Coronavirus disease 2019 (COVID-19) pandemic, where the first case was discovered in Wuhan, China, in December 2019, is the provision of medical services. The current study looked into the impact of vaccination on the utilization of services provided to COVID-19 patients.

Methods

This study was conducted in Iran between 2021 and 2022, utilizing a cross-sectional research design. The research team collected data on the utilization of provided services and the number of COVID-19 vaccines administered to 1000 patients in Iran through a random sampling approach. The data were analyzed with statistical methods, including the mean difference test, and multiple linear regression.

Results

Regression estimates show that after controlling for confounding variables like age, type of admission, and comorbidities, vaccination reduces the utilization of healthcare services in the general majority of services. The study's results reveal a fall in COVID-19 patients' utilization of services, specifically in patients administered two or three doses of the vaccine. However, the reduction is not statistically significant. Regression models are in contrast to univariate analysis findings that vaccination increases the mean utilization of healthcare services for COVID-19 patients in general. Comorbidities are a crucial factor in determining the utilization of diagnostic and treatment services for COVID-19 patients.

Conclusion

Full COVID-19 vaccination and other implementations, including investing in public health, cooperating globally, and vaccinating high-risk groups for future pandemics, are essential as a critical response to this pandemic as they reduce healthcare service utilization to alleviate the burden on healthcare systems and allocate resources more efficiently.

Comparative outcomes of hemodialysis patients facing pre-Omicron and Omicron COVID-19 epidemics

INTRODUCTION

This study elucidates factors affecting the severity and mortality in pre-Omicron and Omicron strains of SARS-CoV-2 and vaccination impact.

METHODS

This single-center retrospective observational study included 1598 hospitalized COVID-19 patients. Patients were grouped into "pre-Omicron" and "Omicron" periods. The endpoint was severe COVID-19 (oxygen saturation [SpO2 ] < 94%). Logistic regression examined associations between clinical factors, including hemodialysis (HD), and the endpoint.

RESULTS

The HD patient mortality rate dropped from 16% pre-Omicron to 4% during the Omicron epidemic. HD was significantly associated with the study endpoint in both epidemics. Unvaccinated patients had a greater risk of reaching the study endpoint among patients receiving HD.

CONCLUSION

These findings suggest that the Omicron variant, alongside vaccination and healthcare innovations, led to improved prognoses for HD patients with COVID-19. However, HD patients remain at a greater risk for severe COVID-19. Increased vaccination rates and optimized healthcare resources can improve this vulnerable population's prognoses.

Vaccination against COVID-19 reduced the mortality risk of COVID-positive hip fracture patients to baseline levels: the nationwide data-linked IMPACT Protect study

This nationwide study used data-linked records to assess the effect of COVID-19 vaccination among hip fracture patients. Vaccination was associated with a lower risk of contracting COVID-19 and, among COVID-positive patients, it reduced the mortality risk to that of COVID-negative patients. This provides essential data for future communicable disease outbreaks.

PURPOSE

COVID-19 confers a three-fold increased mortality risk among hip fracture patients. The aims were to investigate whether vaccination was associated with: i) lower mortality risk, and ii) lower likelihood of contracting COVID-19 within 30 days of fracture.

METHODS

This nationwide cohort study included all patients aged > 50 years that sustained a hip fracture in Scotland between 01/03/20-31/12/21. Data from the Scottish Hip Fracture Audit were collected and included: demographics, injury and management variables, discharge destination, and 30-day mortality status. These variables were linked to government-managed population level records of COVID-19 vaccination and laboratory testing.

RESULTS

There were 13,345 patients with a median age of 82.0 years (IQR 74.0-88.0), and 9329/13345 (69.9%) were female. Of 3022/13345 (22.6%) patients diagnosed with COVID-19, 606/13345 (4.5%) were COVID-positive within 30 days of fracture. Multivariable logistic regression demonstrated that vaccinated patients were less likely to be COVID-positive (odds ratio (OR) 0.41, 95% confidence interval (CI) 0.34-0.48, p < 0.001) than unvaccinated patients. 30-day mortality rate was higher for COVID-positive than COVID-negative patients (15.8% vs 7.9%, p < 0.001). Controlling for confounders (age, sex, comorbidity, deprivation, pre-fracture residence), unvaccinated patients with COVID-19 had a greater mortality risk than COVID-negative patients (OR 2.77, CI 2.12-3.62, p < 0.001), but vaccinated COVID19-positive patients were not at increased risk of death (OR 0.93, CI 0.53-1.60, p = 0.783).

CONCLUSION

Vaccination was associated with lower COVID-19 infection risk. Vaccinated COVID-positive patients had a similar mortality risk to COVID-negative patients, suggesting a reduced severity of infection. This study demonstrates the efficacy of vaccination in this vulnerable patient group, and presents data that will be valid in the management of future outbreaks.

Challenges in Emerging Vaccines and Future Promising Candidates against SARS-CoV-2 Variants

Since the COVID-19 outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) virus has evolved into variants with varied infectivity. Vaccines developed against COVID-19 infection have boosted immunity, but there is still uncertainty on how long the immunity from natural infection or vaccination will last. The present study attempts to outline the present level of information about the contagiousness and spread of SARS-CoV-2 variants of interest and variants of concern (VOCs). The keywords like COVID-19 vaccine types, VOCs, universal vaccines, bivalent, and other relevant terms were searched in NCBI, Science Direct, and WHO databases to review the published literature. The review provides an integrative discussion on the current state of knowledge on the type of vaccines developed against SARS-CoV-2, the safety and efficacy of COVID-19 vaccines concerning the VOCs, and prospects of novel universal, chimeric, and bivalent mRNA vaccines efficacy to fend off existing variants and other emerging coronaviruses. Genomic variation can be quite significant, as seen by the notable differences in impact, transmission rate, morbidity, and death during several human coronavirus outbreaks. Therefore, understanding the amount and characteristics of coronavirus genetic diversity in historical and contemporary strains can help researchers get an edge over upcoming variants.

Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) utilizes angiotensin-converting enzyme 2 (ACE2) as its main receptor for cell entry. We bioengineered a soluble ACE2 protein termed ACE2 618-DDC-ABD that has increased binding to SARS-CoV-2 and prolonged duration of action. Here, we investigated the protective effect of this protein when administered intranasally to k18-hACE2 mice infected with the aggressive SARS-CoV-2 Delta variant. k18-hACE2 mice were infected with the SARS-CoV-2 Delta variant by inoculation of a lethal dose (2 × 104 PFU). ACE2 618-DDC-ABD (10 mg/kg) or PBS was administered intranasally six hours prior and 24 and 48 h post-viral inoculation. All animals in the PBS control group succumbed to the disease on day seven post-infection (0% survival), whereas, in contrast, there was only one casualty in the group that received ACE2 618-DDC-ABD (90% survival). Mice in the ACE2 618-DDC-ABD group had minimal disease as assessed using a clinical score and stable weight, and both brain and lung viral titers were markedly reduced. These findings demonstrate the efficacy of a bioengineered soluble ACE2 decoy with an extended duration of action in protecting against the aggressive Delta SARS-CoV-2 variant. Together with previous work, these findings underline the universal protective potential against current and future emerging SARS-CoV-2 variants.

Vaccine-Boosted CCP Decreases Virus Replication and Hastens Resolution of Infection Despite Transiently Enhancing Disease in SARS-CoV-2-Infected Hamsters

Definitive data demonstrating the utility of coronavirus disease 2019 (COVID-19) convalescent plasma (CCP) for treating immunocompromised patients remains elusive. To better understand the mechanism of action of CCP, we studied viral replication and disease progression in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected hamsters treated with CCP obtained from recovered COVID-19 patients that were also vaccinated with an mRNA vaccine, hereafter referred to as Vaxplas. Vaxplas transiently enhanced disease severity and lung pathology in hamsters treated near peak viral replication due to immune complex and activated complement deposition in pulmonary endothelium, and recruitment of M1 proinflammatory macrophages into the lung parenchyma. However, aside from one report, transient enhanced disease has not been reported in CCP recipient patients, and the transient enhanced disease in Vaxplas hamsters may have been due to mismatched species IgG-FcR interactions, infusion timing, or other experimental factors. Despite transient disease enhancement, Vaxplas dramatically reduced virus replication in lungs and improved infection outcome in SARS-CoV-2-infected hamsters.

The Immunogenicity of CpG, MF59-like, and Alum Adjuvant Delta Strain Inactivated SARS-CoV-2 Vaccines in Mice

The continuous evolution and mutation of SARS-CoV-2 have highlighted the need for more effective vaccines. In this study, CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines were prepared, and the immunogenicity of these vaccines in mice was evaluated. The Delta + MF59-like vaccine group produced the highest levels of S- and RBD-binding antibodies and live Delta virus neutralization levels after one shot of immunization, while mice in the Delta + Alum vaccine group had the highest levels of these antibodies after two doses, and the Delta + MF59-like and Delta + Alum vaccine groups produced high levels of cross-neutralization antibodies against prototype, Beta, and Gamma strain SARS-CoV-2 viruses. There was no significant decrease in neutralizing antibody levels in any vaccine group during the observation period. CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines excited different antibody subtypes compared with unadjuvanted vaccines; the Delta + CpG vaccine group had a higher proportion of IgG2b antibodies, indicating bias towards Th1 immunity. The proportions of IgG1 and IgG2b in the Delta + MF59-like vaccine group were similar to those of the unadjuvanted vaccine. However, the Delta + Alum vaccine group had a higher proportion of IgG1 antibodies, indicating bias towards Th2 immunity. Antigen-specific cytokine secretion CD4/8+ T cells were analyzed. In conclusion, the results of this study show differences in the immune efficacy of CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines in mice, which have significant implications for the selection strategy for vaccine adjuvants.

Changes in the intrinsic severity of severe acute respiratory syndrome coronavirus 2 according to the emerging variant: a nationwide study from February 2020 to June 2022, including comparison with vaccinated populations

BACKGROUND

As the population acquires immunity through vaccination and natural infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the intrinsic severity of coronavirus disease (COVID-19) is becoming challenging. We aimed to evaluate the intrinsic severity regarding circulating variants of SARS-CoV-2 and to compare this between vaccinated and unvaccinated individuals.

METHODS

With unvaccinated and initially infected confirmed cases of COVID-19, we estimated the case severity rate (CSR); case fatality rate (CFR); and mortality rate (MR), including severe/critical cases and deaths, stratified by age and compared by vaccination status according to the period regarding the variants of COVID-19 and vaccination. The overall rate was directly standardized with age.

RESULTS

The age-standardized CSRs (aCSRs) of the unvaccinated group were 2.12%, 5.51%, and 0.94% in the pre-delta, delta, and omicron period, respectively, and the age-standardized CFRs (aCFRs) were 0.60%, 2.49%, and 0.63% in each period, respectively. The complete vaccination group had lower severity than the unvaccinated group over the entire period showing under 1% for the aCSR and 0.5% for the aCFR. The age-standardized MR of the unvaccinated group was 448 per million people per month people in the omicron period, which was 11 times higher than that of the vaccinated group. In terms of age groups, the CSR and CFR sharply increased with age from the 60 s and showed lower risk reduction in the 80 s when the period changed to the omicron period.

CONCLUSIONS

The intrinsic severity of COVID-19 was the highest in the delta period, with over 5% for the aCSR, whereas the completely vaccinated group maintained below 1%. This implies that when the population is vaccinated, the impact of COVID-19 will be limited, even if a new mutation appears. Moreover, considering the decreasing intrinsic severity, the response to COVID-19 should prioritize older individuals at a higher risk of severe disease.

Thrombo-inflammatory response in hospitalised patients with COVID-19: a single institution experience

BACKGROUND

Severe COVID-19 causes acute inflammation, which is complicated by venous thromboembolism events (VTE). However, it is unclear if VTE risk has evolved over time since the COVID-19 outbreak.

AIMS

To determine markers of thrombo-inflammation and rates of symptomatic VTE in patients hospitalised for COVID-19 in a metropolitan hospital in Sydney, Australia.

METHODS

A retrospective, single-centre, cohort study was performed by reviewing electronic medical records of consecutive patients admitted to Royal Prince Alfred Hospital between March 2020 and September 2021. This period included three waves of COVID-19 outbreaks in Australia with the ancestral, alpha and delta variants. Standard coagulation assays and inflammatory markers were recorded over 4 weeks.

RESULTS

A total of 205 patients were consecutively admitted during the study period. Activated partial thromboplastin time, neutrophil count and C-reactive protein (CRP) were significantly increased in patients hospitalised in the intensive care unit (ICU) compared with non-ICU patients. The use of anti-inflammatory medication increased in 2021 compared with 2020. The mortality rate was 7.3% in our cohort. Ninety-four per cent of patients received anticoagulation with 6.3% of patients developing VTE.

CONCLUSION

We observed lower rates of VTE compared to the internationally reported rate for the same period. We conclude that in the setting of controlled hospital admission rate and standard anticoagulation guidelines, COVID-19 resulted in similar thrombo-inflammatory response and VTE rates over the first 1.5 years of the pandemic.

The Minnesota Medical Operations Coordination Center: A COVID-19 Statewide Response to Ensure Access to Critical Care and Medical-Surgical Beds

BACKGROUND

COVID-19 led to unprecedented inpatient capacity challenges, particularly in ICUs, which spurred development of statewide or regional placement centers for coordinating transfer (load-balancing) of adult patients needing intensive care to hospitals with remaining capacity.

RESEARCH QUESTION

Do Medical Operations Coordination Centers (MOCC) augment patient placement during times of severe capacity challenges?

STUDY DESIGN AND METHODS

The Minnesota MOCC was established with a focus on transfer of adult ICU and medical-surgical patients; trauma, cardiac, stroke, burn, and extracorporeal membrane oxygenation cases were excluded. The center operated within one health care system's bed management center, using a dedicated 24/7 telephone number. Major health care systems statewide and two tertiary centers in a neighboring state participated, sharing information on system status, challenges, and strategies. Patient volumes and transfer data were tracked; client satisfaction was evaluated through an anonymous survey.

RESULTS

From August 1, 2020, through March 31, 2022, a total of 5,307 requests were made, 2,008 beds identified, 1,316 requests canceled, and 1,981 requests were unable to be fulfilled. A total of 1,715 patients had COVID-19 (32.3%), and 2,473 were negative or low risk for COVID-19 (46.6%). COVID-19 status was unknown in 1,119 (21.1%). Overall, 760 were patients on ventilators (49.1% COVID-19 positive). The Minnesota Critical Care Coordination Center placed most patients during the fall 2020 surge with the Minnesota Governor's stay-at-home order during the peak. However, during the fall 2021 surge, only 30% of ICU patients and 39% of medical-surgical patients were placed. Indicators characterizing severe surge include the number of Critical Care Coordination Center requests, decreasing placements, longer placement times, and time series analysis showing significant request-acceptance differences.

INTERPRETATION

Implementation of a large-scale Minnesota MOCC program was effective at placing patients during the first COVID-19 pandemic fall 2020 surge and was well regarded by hospitals and health systems. However, under worsening duress of limited resources during the fall 2021 surge, placement of ICU and medical-surgical patients was greatly decreased.

COVID-19 in Pakistan: A national analysis of five pandemic waves

OBJECTIVES

The COVID-19 pandemic showed distinct waves where cases ebbed and flowed. While each country had slight, nuanced differences, lessons from each wave with country-specific details provides important lessons for prevention, understanding medical outcomes and the role of vaccines. This paper compares key characteristics from the five different COVID-19 waves in Pakistan.

METHODS

Data was sourced from daily national situation reports (Sitreps) prepared by the National Emergency Operations Centre (NEOC) in Islamabad. We use specific criteria to define COVID-19 waves. The start of each COVID-19 wave is marked by the day of the lowest number of daily cases preceding a sustained increase, while the end is the day with the lowest number of cases following a 7-days decline, which should be lower than the 7 days following it. Key variables such as COVID-19 tests, cases, and deaths with their rates of change to the peak and then to the trough are used to draw descriptive comparisons. Additionally, a linear regression model estimates daily new COVID-19 deaths in Pakistan.

RESULTS

Pakistan saw five distinct waves, each of which displayed the typical topology of a complete infectious disease epidemic. The time from wave-start to peak became progressively shorter, and from wave-peak to trough, progressively longer. Each wave appears to also be getting shorter, except for wave 4, which lasted longer than wave 3. A one percent increase in vaccinations decreased deaths by 0.38% (95% CI: -0.67, -0.08) in wave 5 and the association is statistically significant.

CONCLUSION

Each wave displayed distinct characteristics that must be interpreted in the context of the level of response and the variant driving the epidemic. Key indicators suggest that COVID-19 preventive measures kept pace with the disease. Waves 1 and 2 were mainly about prevention and learning how to clinically manage patients. Vaccination started late during wave 3 and its impact on hospitalizations and deaths became visible in wave 5. The impact of highly virulent strains Alpha/B.1.1.7 and Delta/B.1.617.2 variants during wave 3 and milder but more infectious Omicron/B.1.1.529 during wave 5 are apparent.

Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53

Coronavirus disease 2019 (COVID-19) remains a significant public health threat due to the ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and Middle East respiratory syndrome (MERS)-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here, we use our recently developed integrative DNA And Protein Tagging methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.

The Impact of Effective Vaccination on Clinical and Radiological Involvement in COVID-19 Patients

Objective

We aimed to analyze clinical, radiological, and laboratory differences between vaccinated and unvaccinated patients admitted to hospital due to coronavirus disease-2019 (COVID-19) pneumonia.

Methods

Patients hospitalized in the COVID-19 clinic between February 2022 and August 2022 were included in the study. Demographic, clinical features, and treatment results. Furthermore, the COVID-19 vaccination status of the cases was recorded. The cases were divided into two groups as those with and without COVID vaccination and compared.

Results

A total of 215 patients were included in our study, and the patients were divided into 2 groups according to their vaccination status: those who were unvaccinated against COVID-19 (n=100) and those who vaccinated COVID-19 (n=115). The presence of comorbid chronic diseases and cancer was lower in the unvaccinated group. The duration of hospitalization was longer in the unvaccinated group than in the vaccinated group (9.6 and 7.1 days, respectively) (p<0.001). While there was no difference between the two groups in terms of the radiological involvement pattern, the number of involved segments was significantly higher in the unvaccinated group (p<0.05). The number of patients who received high-dose glucocorticoid therapy in the unvaccinated group was higher (28 cases vs. 11 cases; p<0.001). There was no statistically significant difference between the two groups in terms of transfer of patients to the intensive care unit (p>0.05). 11.3% (13/115) of the patients in the vaccinated group died, whereas 14% (14/100) died in the unvaccinated group.

Conclusions

The vaccinated cases who were infected with COVID-19 had a shorter duration of hospitalization and lower severity of radiological involvement. The requirement for pulse steroids was also less compared with unvaccinated individuals. Despite having chronic diseases and cancer, which is considered to have a significant effect on mortality in COVID-19 patients. In addition, although the vaccinated group was older, they had mortality rates similar to those of unvaccinated subjects.

COVID-19 vaccination effectiveness in the population of Friuli Venezia Giulia, North-East Italy. Control of bias associated with divergent compliance to policies in a test-negative case-control study

BACKGROUND

Vaccine effectiveness (VE) studies consolidate knowledge of real-world effectiveness in different contexts. However, methodological issues may undermine their conclusions: to assess the VE against COVID-19 within the Italian population, a specific threat to validity is related to the consequences of divergent compliance to the Green Pass policy.

METHODS

To address this challenge we conducted a test negative case-control (TNCC) study and multiple sensitivity analysis among residents aged ≥ 12 in Friuli Venezia Giulia Region (FVG), North-east Italy, from February 1, 2021 to March 31, 2022. Information regarding 211,437 cases of COVID-19 infection and 845,748 matched controls was obtained from the regional computerized health database. The investigation considered: COVID-19 infection, hospitalization, and death. Multiple conditional logistic regressions adjusted for covariates were performed and VE was estimated as (1-OR COVID-19vaccinated vs. unvaccinated)x100. Mediation analyses were carried out to offset potential collider variables, particularly, the number of swabs performed after the introduction of pandemic restrictions.

RESULTS

Full-cycle VE against infection decreased from 96% (95% CI: 96, 97) in the Alpha period to 43% (95% CI: 42, 45) in the Omicron period. Booster dose raised the protection in Omicron period to 67% (95% CI: 66, 67). Against the evasive Omicron variant, the protection of the booster dose was 87% (95% CI: 83, 90) for hospitalization and 90% (95% CI: 82, 95) for death. The number of swabs performed was included as a covariate in the adjustments, and the mediation analysis confirmed that it was a strong mediator between vaccination and COVID-19-related outcomes.

CONCLUSIONS

The study suggests that, under similar TNCC settings, mediation analysis and adjustment for number of diagnostic tests should be included, as an effective approach to the challenge of differential testing behavior that may determine substantial selection bias. This correction allowed us to align with results from other studies that show how full-cycle VE against infection was initially high but decreased over time by variant circulation, counterbalanced by booster dose that raised protection across variants and outcome severity.

Safety and efficacy of the intranasal spray SARS-CoV-2 vaccine dNS1-RBD: a multicentre, randomised, double-blind, placebo-controlled, phase 3 trial

BACKGROUND

The live-attenuated influenza virus vector-based intranasal SARS-CoV-2 vaccine (dNS1-RBD, Pneucolin; Beijing Wantai Biological Pharmacy Enterprise, Beijing, China) confers long-lasting and broad protection in animal models and is, to our knowledge, the first COVID-19 mucosal vaccine to enter into human trials, but its efficacy is still unknown. We aimed to assess the safety and efficacy (but not the immunogenicity) of dNS1-RBD against COVID-19.

METHODS

We did a multicentre, randomised, double-blind, placebo-controlled, adaptive design, phase 3 trial at 33 centres (private or public hospitals, clinical research centres, or Centre for Disease Control and Prevention) in four countries (Colombia, Philippines, South Africa, and Viet Nam). Men and non-pregnant women (aged ≥18 years) were eligible if they had never been infected with SARS-CoV-2, and if they did not have a SARS-CoV-2 vaccination history at screening or if they had received at least one dose of other SARS-CoV-2 vaccines 6 months or longer before enrolment. Eligible adults were randomly assigned (1:1) to receive two intranasal doses of dNS1-RBD or placebo administered 14 days apart (0·2 mL per dose; 0·1 mL per nasal cavity), with block randomisation via an interactive web-response system, stratified by centre, age group (18-59 years or ≥60 years), and SARS-CoV-2 vaccination history. All participants, investigators, and laboratory staff were masked to treatment allocation. The primary outcomes were safety of dNS1-RBD in the safety population (ie, those who had received at least one dose of dNS1-RBD or placebo) and efficacy against symptomatic SARS-CoV-2 infection confirmed by RT-PCR occurring 15 days or longer after the second dose in the per-protocol population (ie, those who received two doses, were followed up for 15 days or longer after the second dose, and had no major protocol deviations). The success criterion was predefined as vaccine efficacy of more than 30%. This trial is registered with the Chinese Clinical Trial Registry (ChiCTR2100051391) and is completed.

FINDINGS

Between Dec 16, 2021, and May 31, 2022, 41 620 participants were screened for eligibility and 31 038 participants were enrolled and randomly assigned (15 517 in the vaccine group and 15 521 in the placebo group). 30 990 participants who received at least one dose (15 496 vaccine and 15 494 placebo) were included in the safety analysis. The results showed a favourable safety profile, with the most common local adverse reaction being rhinorrhoea (578 [3·7%] of 15 500 vaccine recipients and 546 [3·5%] of 15 490 placebo recipients) and the most common systemic reaction being headache (829 [5·3%] vaccine recipients and 797 [5·1%] placebo recipients). We found no differences in the incidences of adverse reactions between participants in the vaccine and placebo groups. No vaccination-related serious adverse events or deaths were observed. Among 30 290 participants who received two doses, 25 742 were included in the per-protocol efficacy analysis (12 840 vaccine and 12 902 placebo). The incidence of confirmed symptomatic SARS-CoV-2 infection caused by omicron variants regardless of immunisation history was 1·6% in the vaccine group and 2·3% in the placebo group, resulting in an overall vaccine efficacy of 28·2% (95% CI 3·4-46·6), with a median follow-up duration of 161 days.

INTERPRETATION

Although this trial did not meet the predefined efficacy criteria for success, dNS1-RBD was well tolerated and protective against omicron variants, both as a primary immunisation and as a heterologous booster.

FUNDING

Beijing Wantai Biological Pharmacy Enterprise, National Science and Technology Major Project, National Natural Science Foundation of China, Fujian Provincial Science and Technology Plan Project, Natural Science Foundation of Fujian Province, Xiamen Science and Technology Plan Special Project, Bill & Melinda Gates Foundation, the Ministry of Education of China, Xiamen University, and Fieldwork Funds of Xiamen University.

Epidemiological and clinical features of COVID-19 inpatients in Changsha, China: A retrospective study from 2020 to 2022

Objectives

The spread of SARS-Cov-2 remains a global concern along with the emergence of variants. This study aims to characterize the epidemiological and clinical features of hospitalized patients who were dragonized with five different variants of SARS-CoV-2 during the past 3 years.

Methods

This retrospective study recruited 432 COVID-19 patients who were hospitalized in the First Hospital of Changsha from January 2020 to August 2022. Clinical records on clinical symptoms, laboratory profiles, and chest CT images was collected. The epidemiological and clinical features were compared between COVID-19 patients infected with either the wild-type, Omicron variant or pre- Omicron variants (e.g., Alpha, Beta, Delta).

Results

A total of 432 laboratory-confirmed COVID-19 inpatients were dialogized during three waves, including 247 cases during the wild-type transmission period, 65 cases during the transmission period of pre-Omicron variants, and 119 cases during the transmission period of Omicron variants. The proportion of moderately or severely ill inpatients showed a gradual decline from the wild-type transmission period to the Omicron transmission period. The common symptoms of inpatients infected with SARS-CoV-2 wildtype strains included fever (67.61 %), cough (57.89 %), fatigue (33.60 %), and shortness of breath (12.15 %). In contrast, patients infected with other variants mostly showed upper respiratory symptoms. Based on chest CT images, a lower degree of acute pulmonary infection was observed among inpatients infected with the Omicron variants than those infected with the wild-type strain (31.09 % vs 93.12 %, p-value<0.01).

Conclusions

Compared with the wild-type strain, SARS-CoV-2 variants of concern, especially the Omicron variant, mostly caused a lower degree of acute pulmonary infection, indicating the reduced disease severity and mortality among hospitalized COVID-19 patients.

Innovation-driven trend shaping COVID-19 vaccine development in China

Confronted with the Coronavirus disease 2019 (COVID-19) pandemic, China has become an asset in tackling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and mutation, with several innovative platforms, which provides various technical means in this persisting combat. Derived from collaborated researches, vaccines based on the spike protein of SARS-CoV-2 or inactivated whole virus are a cornerstone of the public health response to COVID-19. Herein, we outline representative vaccines in multiple routes, while the merits and plights of the existing vaccine strategies are also summarized. Likewise, new technologies may provide more potent or broader immunity and will contribute to fight against hypermutated SARS-CoV-2 variants. All in all, with the ultimate aim of delivering robust and durable protection that is resilient to emerging infectious disease, alongside the traditional routes, the discovery of innovative approach to developing effective vaccines based on virus properties remains our top priority.

A Population-Based Outcome-Wide Association Study of the Comorbidities and Sequelae Following COVID-19 Infection

BACKGROUND

Immense attention has been given to the outcome of COVID-19 infection. However, comprehensive studies based on large populational cohort with long-term follow-up are still lacking. This study aimed to investigate the risk of various short-term comorbidities (within one month) and long-term sequelae (above one month) after COVID-19 infection.

METHODS

In this large prospective cohort study with 14 months follow-up information based on UK biobank, we included 16,776 COVID-19-positive participants and 58,281 COVID-19-negative participants matched for comparison. The risk of each comorbidity and sequela was evaluated by multivariable logistic regression analysis and presented as hazard ratio (HR) and 95% confidence interval (95% CI).

RESULTS

COVID-19-positive individuals had a higher risk of 47 types of comorbidities within one month following COVID-19 infection, especially those who were older, male, overweight/obese, ever-smoked, with more pre-existing comorbidities and hospitalized. About 70.37% of COVID-19 patients with comorbidities had more than one co-occurring comorbidities. Additionally, only 6 high-risk sequelae were observed after one month of COVID-19 infection, and the incidence was relatively low (< 1%).

CONCLUSION

In addition to long-term sequelae following COVID-19 infection, plenty of comorbidities were observed, especially in patients with older age, male gender, overweight/obese, more pre-existing comorbidities and severe COVID-19, indicating that more attention should be given to these susceptible persons within this period.

Vaccination reduces viral load and accelerates viral clearance in SARS-CoV-2 Delta variant-infected patients

OBJECTIVE

The purpose of this study was to investigate vaccine effectiveness in relieving symptoms in patients with the SARS-CoV-2 delta (B.1.617.2) variant.

METHODS

In this retrospective study, 31 patients did not receive any vaccine (non-vaccination, NV), 21 patients received 1-dose of inactivated vaccine (one-dose vaccination, OV), and 60 patients received at least 2-dose inactivated vaccine (two-dose vaccination, TV). The baseline data, clinical outcomes and vaccination information were collected and analyzed.

RESULTS

Patients in the OV group were younger than those in the other two groups (p = 0.001), but there was no significant difference in any of the other baseline data among the three groups. The TV group showed higher IgG antibody levels and cycle threshold values of SARS-CoV-2 than the NV and OV groups (p < 0.01), and time to peak viral load was shorter in the TV group (3.5 ± 2.3 d) than in the NV (4.8 ± 2.8 d) and OV groups (4.8 ± 2.9 d, p = 0.03). The patients in the TV group (18%) showed a higher recovery rate without drug therapy (p < 0.001). Viral clearance time and hospital stay were significantly shorter in the TV group than in the NV and OV groups (p < 0.01), and there were no significant differences in these parameters between the OV and NV groups, but IgG values were higher in the OV group (p = 0.025). No severe complications occurred in this study.

CONCLUSIONS

Our results suggest that 2-dose vaccination can reduce viral load and accelerate viral clearance in patients with the delta variant and enhance the protection afforded by IgG antibodies in vivo.Key MessagesIn this study, our results shows that two-dose vaccination can reduce viral loads and accelerate viral clearance, and two-dose vaccination enhance the protection of IgG antibodies in vivo; however, one-dose vaccination did not confer protective effectiveness.

Low level of tonic interferon signalling is associated with enhanced susceptibility to SARS-CoV-2 variants of concern in human lung organoids

There is tremendous heterogeneity in the severity of COVID-19 disease in the human population, and the mechanisms governing the development of severe disease remain incompletely understood. The emergence of SARS-CoV-2 variants of concern (VOC) Delta (B.1.617.2) and Omicron (B.1.1.529) further compounded this heterogeneity. Virus replication and host cell damage in the distal lung is often associated with severe clinical disease, making this an important site to consider when evaluating pathogenicity of SARS-CoV-2 VOCs. Using distal human lung organoids (hLOs) derived from multiple human donors, we compared the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, along with an ancestral clade B variant D614G, and evaluated donor-dependent differences in susceptibility to infection. We observed substantial attenuation of Omicron in hLOs and demonstrated enhanced susceptibility to Omicron and D614G replication in hLOs from one donor. Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity at baseline. We show that hLOs can be used to model heterogeneity of SARS-CoV-2 pathogenesis in humans, and propose that variability in tonic interferon signaling set point may impact susceptibility to SARS-CoV-2 VOCs and subsequent COVID-19 disease progression.

Epidemiological and laboratory characteristics of Omicron infection in a general hospital in Guangzhou: a retrospective study

The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a major global public health concern. In November 2022, Guangzhou experienced a significant outbreak of Omicron. This study presents detailed epidemiological and laboratory data on Omicron infection in a general hospital in Guangzhou between December 1, 2022, and January 31, 2023. Out of the 55,296 individuals tested, 12,346 were found to be positive for Omicron. The highest prevalence of positive cases was observed in the 20 to 39 age group (24.6%), while the lowest was in children aged 0 to 9 years (1.42%). Females had a higher incidence of infection than males, accounting for 56.6% of cases. The peak time of Omicron infection varied across different populations. The viral load was higher in older adults and children infected with Omicron, indicating age-related differences. Spearman's rank correlation analysis revealed positive correlations between Ct values and laboratory parameters in hospitalized patients with Omicron infection. These parameters included CRP (rs = 0.059, p = 0.009), PT (rs = 0.057, p = 0.009), INR (rs = 0.055, p = 0.013), AST (rs = 0.067, p = 0.002), LDH (rs = 0.078, p = 0.001), and BNP (rs = 0.063, p = 0.014). However, EO (Eosinophil, rs = -0.118, p < 0.001), BASO (basophil, rs = -0.093, p < 0.001), and LY (lymphocyte, rs = -0.069, p = 0.001) counts showed negative correlations with Ct values. Although statistically significant, the correlation coefficients between Ct values and these laboratory indices were very low. These findings provide valuable insights into the epidemiology of Omicron infection, including variations in Ct values across gender and age groups. However, caution should be exercised when utilizing Ct values in clinical settings for evaluating Omicron infection.

Superior immunogenicity of mRNA over adenoviral vectored COVID-19 vaccines reflects B cell dynamics independent of anti-vector immunity: Implications for future pandemic vaccines

Both vector and mRNA vaccines were an important part of the response to the COVID-19 pandemic and may be required in future outbreaks and pandemics. The aim of this study was to validate whether immunogenicity differs for adenoviral vectored (AdV) versus mRNA vaccines against SARS-CoV-2, and to investigate how anti-vector immunity and B cell dynamics modulate immunogenicity. We enrolled SARS-CoV-2 infection-naïve health care workers who had received two doses of either AdV AZD1222 (n = 184) or mRNA BNT162b2 vaccine (n = 274) between April and October 2021. Blood was collected at least once, 10-48 days after vaccine dose 2 for antibody and B cell analyses. Median ages were 42 and 39 years, for AdV and mRNA vaccinees, respectively. Surrogate virus neutralization test (sVNT) and spike binding antibody titres were a median of 4.2 and 2.2 times lower, respectively, for AdV compared to mRNA vaccinees (p < 0.001). Median percentages of memory B cells that recognized fluorescent-tagged spike and RBD were 2.9 and 8.3 times lower, respectively for AdV compared to mRNA vaccinees. Titres of IgG reactive with human adenovirus type 5 hexon protein rose a median of 2.2-fold after AdV vaccination but were not correlated with anti-spike antibody titres. Together the results show that mRNA induced substantially more sVNT antibody than AdV vaccine, which reflected greater B cell expansion and targeting of the RBD rather than an attenuating effect of anti-vector antibodies. ClinicalTrials.gov Identifier: NCT05110911.

Cardiomyopathy Does Not Exacerbate the Severity of Pneumonia Caused by a SARS-CoV-2 Delta Variant in the J2N-k Hamster Model

Cardiovascular disease is one of many risk factors that have been linked to increased severity or mortality in coronavirus disease 2019 (COVID-19) patients; however, the exact role of SARS-CoV-2 in the pathogenesis of cardiac inflammatory injury has not been established. A previous study reported that SARS-CoV-2 causes more severe disease with cardiomyopathy in a J2N-k animal model. Here, we investigated the sensitivity of J2N-k hamsters, as a cardiomyopathy animal model, to a delta strain of SARS-CoV-2 compared to J2N-n control animals. We found that J2N-k hamsters were less susceptible to this delta strain than J2N-n animals, and we found no evidence that cardiomyopathy is a risk factor in this animal model. Since the previous study reported that SARS-CoV-2 causes more severe disease with cardiomyopathy in the same animal model, further analysis of the relationship between cardiomyopathy and SARS-CoV-2 infection is needed.

Relationships between COVID-19 healthcare outcomes and county characteristics in the U.S. for Delta (B.1.617.2) and Omicron (B.1.1.529 and BA.1.1) variants

Background

COVID-19 is constantly evolving, and highly populated communities consist of many different characteristics that may contribute to COVID-19 health outcomes. Therefore, we aimed to (1) quantify the relationships between county characteristics and severe and non-severe county-level health outcomes related to COVID-19. We also aimed to (2) compare these relationships across time periods where the Delta (B.1.617.2) and Omicron (B.1.1.529 and BA.1.1) variants were dominant in the U.S.

Methods

We used multiple regression to measure the strength of relationships between healthcare outcomes and county characteristics in the 50 most populous U.S. counties.

Results

We found many different significant predictors including the proportion of a population vaccinated, median household income, population density, and the proportion of residents aged 65+, but mainly found that socioeconomic factors and the proportion of a population vaccinated play a large role in the dynamics of the spread and severity of COVID-19 in communities with high populations.

Discussion

The present study shines light on the associations between public health outcomes and county characteristics and how these relationships change throughout Delta and Omicron's dominance. It is important to understand factors underlying COVID-19 health outcomes to prepare for future health crises.

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.

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity

Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.

Vaccination Status and In-hospital Mortality Among Adults With COVID-19 in Jakarta, Indonesia: A Retrospective Hospital-based Cohort Study

OBJECTIVES

Prospective studies on vaccination status and mortality related to coronavirus disease 2019 (COVID-19) in low-resource settings are still limited. We assessed the association between vaccination status (full, partial, or none) and in-hospital mortality among COVID-19 patients at most hospitals in Jakarta, Indonesia during the Delta predomination wave.

METHODS

We conducted a retrospective cohort study among hospitalized COVID-19 patients who met the study criteria (>18 years old and admitted for inpatient treatment because of laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection). We linked individual-level data in the hospital admission database with vaccination records. Several socio-demographic and clinical characteristics were also analyzed. A Cox proportional hazards regression model was used to explore the association between vaccination status and in-hospital mortality in this patient group.

RESULTS

In total, 40 827 patients were included in this study. Of these, 70% were unvaccinated (n=28 543) and 19.3% (n=7882) died during hospitalization. The mean age of the patients was 49 years (range, 35-59), 53.2% were female, 22.0% had hypertension, and 14.2% were treated in the intensive care unit, and the median hospital length of stay across the group was 9 days. Our study showed that the risk of in-hospital mortality among fully and partially vaccinated patients was lower than among unvaccinated adults (adjusted hazard ratio [aHR], 0.43; 95% confidence interval [CI], 0.40 to 0.47 and aHR, 0.70; 95% CI, 0.64 to 0.77, respectively).

CONCLUSIONS

Vaccinated patients had fewer severe outcomes among hospitalized adults during the Delta wave in Jakarta. These features should be carefully considered by healthcare professionals in treating adults within this patient group.

The impact of Covid-19 on demographic components in Spain, 2020-31: A scenario approach

While considerable attention has been paid to the impact of Covid-19 on mortality and fertility, few studies have attempted to evaluate the pandemic's effect on international migration. We analyse the impact of Covid-19 on births, deaths, and international migration in Spain during 2020, comparing observed data with estimated values assuming there had been no pandemic. We also assess the consequences of three post-pandemic scenarios on the size and structure of the population to 2031. Results show that in 2020, excess mortality equalled 16.2 per cent and births were 6.5 per cent lower than expected. Immigration was the most affected component, at 36.0 per cent lower than expected, while emigration was reduced by 23.8 per cent. If net migration values recover to pre-pandemic levels in 2022, the size and structure of the population in 2031 will be barely affected. Conversely, if levels do not recover until 2025, there will be important changes to Spain's age structure.

Outcome of COVID-19 in patients with autoimmune bullous diseases

Background Data on outcomes of Coronavirus disease 2019 (COVID-19) infection in autoimmune bullous diseases (AIBDs) patients is scarce. Materials and methods This single-centre survey-based-observational study included patients registered in the AIBD clinic of the Postgraduate Institute of Medical Education and Research, Chandigarh, India. All registered patients were contacted over telephone between June and October 2021. A survey was conducted after obtaining informed consent. Results Among 1389 registered patients, 409 completed the survey. Two hundred and twenty-two (55.3%) patients were females and 187 (45.7%) were males. The mean age was 48.52 ± 14.98 years. Active disease was reported by 34% patients. The frequency of COVID-19 infection in responders was 12.2% (50/409), with a case-fatality ratio of 18% (9/50). Rituximab infusion after the onset of pandemic significantly increased the risk of COVID-19 infection. Active AIBD and concomitant comorbidities were significantly associated with COVID-19 related death. Limitation Relative risk of COVID-19 infection and complications among AIBD patients could not be estimated due to lack of control group. The incidence of COVID-19 in AIBD could not be determined due to lack of denominator (source population) data. Other limitations include telephonic nature of the survey and lack of COVID-19 strain identification. Conclusion Use of rituximab is associated with higher probability of COVID-19 infection, while advanced age, active disease and presence of comorbidities may increase the risk of COVID-19 mortality in AIBD patients.

Environmental Contamination of SARS-CoV-2 Delta VOC by COVID-19 Patients Staying in the Hospital for More Than Two Weeks

Background

Patients infected with SARS-CoV-2 Delta VOC have a longer course of disease. We detected the air, surfaces, and patient's personal items in the wards of the second hospital of Nanjing during the outbreak of the COVID-19 Delta Variant to identify the environmental contamination, which provides a theoretical basis for the prevention and control of COVID-19 variation beads in the future.

Methods

In the cross-sectional study, we collected and analyzed clinical features, demographic and epidemiological data, laboratory and swab test results, and surface and air samples of 144 COVID-19 cases.

Results

The time from symptom onset to surface sampling was 25 days (IQR, 21 to 33 days). Positive throat swabs were detected in 52(36.1%) patients, of which only 8(5.6%) patients had N or ORF1a/b genes Ct value <35 on the surface sampling day. Among the 692 environmental surface and air specimens collected from 144 COVID-19 cases, 3 specimens (3/692, 0.4%) related to 5 cases (3.5%, 5/144) were detected positive on RT-PCR. Overall, bedside tables (2/144, 1.4%) were most likely to be contaminated, followed by toilet seats (1/81, 1.2%).

Conclusion

The environmental contamination by SARS-CoV-2 Delta VOC-infected cases with disease duration of more than two weeks is limited.

Forecasting the effects of vaccination on the COVID-19 pandemic in Malaysia using SEIRV compartmental models

OBJECTIVES

This study aimed to develop susceptible-exposed-infectious-recovered-vaccinated (SEIRV) models to examine the effects of vaccination on coronavirus disease 2019 (COVID-19) case trends in Malaysia during Phase 3 of the National COVID-19 Immunization Program amidst the Delta outbreak.

METHODS

SEIRV models were developed and validated using COVID-19 case and vaccination data from the Ministry of Health, Malaysia, from June 21, 2021 to July 21, 2021 to generate forecasts of COVID-19 cases from July 22, 2021 to December 31, 2021. Three scenarios were examined to measure the effects of vaccination on COVID-19 case trends. Scenarios 1 and 2 represented the trends taking into account the earliest and latest possible times of achieving full vaccination for 80% of the adult population by October 31, 2021 and December 31, 2021, respectively. Scenario 3 described a scenario without vaccination for comparison.

RESULTS

In scenario 1, forecasted cases peaked on August 28, 2021, which was close to the peak of observed cases on August 26, 2021. The observed peak was 20.27% higher than in scenario 1 and 10.37% lower than in scenario 2. The cumulative observed cases from July 22, 2021 to December 31, 2021 were 13.29% higher than in scenario 1 and 55.19% lower than in scenario 2. The daily COVID-19 case trends closely mirrored the forecast of COVID-19 cases in scenario 1 (best-case scenario).

CONCLUSIONS

Our study demonstrated that COVID-19 vaccination reduced COVID-19 case trends during the Delta outbreak. The compartmental models developed assisted in the management and control of the COVID-19 pandemic in Malaysia.

Emergence of SARS-CoV-2 Delta Variant and Effect of Nonpharmaceutical Interventions, British Columbia, Canada

In British Columbia, Canada, initial growth of the SARS-CoV-2 Delta variant was slower than that reported in other jurisdictions. Delta became the dominant variant (>50% prevalence) within ≈7-13 weeks of first detection in regions within the United Kingdom and United States. In British Columbia, it remained at <10% of weekly incident COVID-19 cases for 13 weeks after first detection on March 21, 2021, eventually reaching dominance after 17 weeks. We describe the growth of Delta variant cases in British Columbia during March 1-June 30, 2021, and apply retrospective counterfactual modeling to examine factors for the initially low COVID-19 case rate after Delta introduction, such as vaccination coverage and nonpharmaceutical interventions. Growth of COVID-19 cases in the first 3 months after Delta emergence was likely limited in British Columbia because additional nonpharmaceutical interventions were implemented to reduce levels of contact at the end of March 2021, soon after variant emergence.

Efficacy of a monovalent (D614) SARS-CoV-2 recombinant protein vaccine with AS03 adjuvant in adults: a phase 3, multi-country study

Background

The literature on first generation COVID-19 vaccines show they were less effective against new SARS-CoV-2 variants of concern including Omicron (BA.1, BA.2, BA.4 and BA.5 subvariants). New vaccines developed against variant strains may provide cross-protection against emerging variants when used as boosters and facilitate vaccination across a range of countries, healthcare settings and populations. However, there are no data on such vaccines when used as a primary series.

Methods

A global Phase 3, multi-stage efficacy study (NCT04904549) among adults (≥18 years) was conducted in 53 research centres in eight countries (United States, Honduras, Japan, Colombia, Kenya, India, Ghana, Nepal). Participants were randomized 1:1 to receive two intramuscular injections of a monovalent SARS-CoV-2 recombinant protein vaccine with AS03-adjuvant (10 μg of the spike (S) protein from the ancestral D614 strain) or placebo on Day 1 (D01) and Day 22 (D22). The primary efficacy endpoint was prevention of virologically confirmed SARS-CoV-2 infection with symptoms of COVID-19-like illness (CLI) ≥14 days after the second injection (post-dose 2 [PD2]) in participants who were SARS-CoV-2 naïve on D01 + D22. Safety and reactogenicity were also evaluated.

Findings

Between May 26 and November 7, 2021, 10,114 participants received ≥1 study injection, and 9441 participants received both injections. 2108 (20.8%) participants were SARS-CoV-2 naïve at D01 and D22. The primary endpoint was analysed in a subset of the full analysis set (the modified full analysis set PD2 [mFAS-PD2], excluding participants who did not complete the vaccination schedule or received vaccination despite meeting one of the contraindication criteria, had onset of symptomatic COVID-19 between the first injection and before 14 days after the second injection, or participants who discontinued before 14 days after the second injection [n = 9377; vaccine, n = 4702; placebo, n = 4675]). Data were available for 2051 SARS-CoV-2 naïve and 7159 non-naïve participants. At the cut-off date (January 28, 2022), symptomatic COVID-19 was reported in 169 naïve participants (vaccine, n = 81; placebo, n = 88) ≥14 days PD2, with a vaccine efficacy (VE) of 15.3% (95% CI, -15.8; 38.2). VE regardless of D01/D22 serostatus was 32.9% (95% CI, 15.3; 47.0) and VE in non-naïve participants was 52.7% (95% CI, 31.2; 67.9). Viral genome sequencing was performed up to the data cut-off point and identified the infecting strain in 99/169 adjudicated cases in the PD2 naïve population (Delta [25], Omicron [72], other variants [3], one participant had infection with both Delta and Omicron variants and has been included in the totals for both Delta and Omicron). The vaccine was well-tolerated with an acceptable safety profile.

Interpretation

In the context of changing circulating viral variants, it is challenging to induce protection in naïve individuals with a two-dose priming schedule based on the parental D614 strain. However, while the primary endpoint of this trial was not met, the results show that a monovalent D614 vaccine can still be of value in individuals previously exposed to SARS-CoV-2.

Funding

This study was funded in whole or in part by Sanofi and by federal funds from the Biomedical Advanced Research and Development Authority, part of the office of the Administration for Strategic Preparedness and Response at the U.S. Department of Health and Human Services under contract number HHSO100201600005I, and in collaboration with the U.S. Department of Defense Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense under contract number W15QKN-16-9-1002. The views presented here are those of the authors and do not purport to represent those of the Department of the Army, the Department of Health and Human Services, or the U.S. government.