Age-specific mortality and immunity patterns of SARS-CoV-2

A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves

The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.

On optimal control at the onset of a new viral outbreak

We propose a versatile model with a flexible choice of control for an early-pandemic outbreak prevention when vaccine/drug is not yet available. At that stage, control is often limited to non-medical interventions like social distancing and other behavioral changes. For the SIR optimal control problem, we show that the running cost of control satisfying mild, practically justified conditions generates an optimal strategy, u(t), t ∈ [0, T], that is sustainable up until some moment τ ∈ [0, T). However, for any t ∈ [τ, T], the function u(t) will decline as t approaches T, which may cause the number of newly infected people to increase. So, the window from 0 to τ is the time for public health officials to prepare alternative mitigation measures, such as vaccines, testing, antiviral medications, and others. In addition to theoretical study, we develop a fast and stable computational method for solving the proposed optimal control problem. The efficiency of the new method is illustrated with numerical examples of optimal control trajectories for various cost functions and weights. Simulation results provide a comprehensive demonstration of the effects of control on the epidemic spread and mitigation expenses, which can serve as invaluable references for public health officials.

Proteomic analysis of lung responses to SARS-CoV-2 infection in aged non-human primates: clinical and research relevance

With devastating health and socioeconomic impact worldwide, much work is left to understand the Coronavirus Disease 2019 (COVID-19), with emphasis in the severely affected elderly population. Here, we present a proteomics study of lung tissue obtained from aged vs. young rhesus macaques (Macaca mulatta) and olive baboons (Papio Anubis) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using age as a variable, we identified common proteomic profiles in the lungs of aged infected non-human primates (NHPs), including key regulators of immune function, as well as cell and tissue remodeling, and discuss the potential clinical relevance of such parameters. Further, we identified key differences in proteomic profiles between both NHP species, and compared those to what is known about SARS-CoV-2 in humans. Finally, we explored the translatability of these animal models in the context of aging and the human presentation of the COVID-19.

The post-Cartesian dilemma: Reuniting the mind and body through psychoneuroimmunology

While today, it might seem absurd to hear anyone claim that stress does not alter all aspects of the human experience, including behavioral, cognitive, affective, and physiological processes. Dr. Janice Kiecolt-Glaser started her career at a time when stress was primarily considered a neuroendocrine response with cardiovascular repercussions. She was part of a small group of innovative scientists who began to push the boundaries of stress research - many contemporary immunologists and virologist disputed their early results in 1980s and 90s - and, yet, they persevered by connecting psychological stress to altered immune function via stress-related neuroendocrine changes. As a clinical psychologist, she focused mainly on human research studies to advance the field of psychoneuroimmunology throughout her career. Her research demonstrates how adversity and psychosocial aspects of human experience alter physiological functioning, primarily immune, and health or, in other words, the embodiment of our lived experiences. This short review is a contextualized synthesis of Dr. Kiecolt-Glaser's key contributions to the fields of psychoneuroimmunology and health psychology and her influence on my present day thinking and research approaches, as well as potential steps forward in our post-pandemic world.

A guide to adaptive immune memory

Immune memory - comprising T cells, B cells and plasma cells and their secreted antibodies - is crucial for human survival. It enables the rapid and effective clearance of a pathogen after re-exposure, to minimize damage to the host. When antigen-experienced, memory T cells become activated, they proliferate and produce effector molecules at faster rates and in greater magnitudes than antigen-inexperienced, naive cells. Similarly, memory B cells become activated and differentiate into antibody-secreting cells more rapidly than naive B cells, and they undergo processes that increase their affinity for antigen. The ability of T cells and B cells to form memory cells after antigen exposure is the rationale behind vaccination. Understanding immune memory not only is crucial for the design of more-efficacious vaccines but also has important implications for immunotherapies in infectious disease and cancer. This 'guide to' article provides an overview of the current understanding of the phenotype, function, location, and pathways for the generation, maintenance and protective capacity of memory T cells and memory B cells.

Investigation of Long-Term CD4+ T Cell Receptor Repertoire Changes Following SARS-CoV-2 Infection in Patients with Different Severities of Disease

BACKGROUND

The difference in the immune response to severe acute respiratory syndrome coro-navirus 2 (SARS-CoV-2) in patients with mild versus severe disease remains poorly understood. Recent scientific advances have recognised the vital role of both B cells and T cells; however, many questions remain unanswered, particularly for T cell responses. T cells are essential for helping the generation of SARS-CoV-2 antibody responses but have also been recognised in their own right as a major factor influencing COVID-19 disease outcomes. The examination of T cell receptor (TCR) family differences over a 12-month period in patients with varying COVID-19 disease severity is crucial for understanding T cell responses to SARS-CoV-2.

METHODS

We applied a machine learning approach to analyse TCR vb family responses in COVID-19 patients (n = 151) across multiple timepoints and disease severities alongside SARS-CoV-2 infection-naïve (healthy control) individ-uals (n = 62).

RESULTS

Blood samples from hospital in-patients with moderate, severe, or critical disease could be classified with an accuracy of 94%. Furthermore, we identified significant variances in TCR vb family specificities between disease and control subgroups.

CONCLUSIONS

Our findings suggest advantageous and disadvantageous TCR repertoire patterns in relation to disease severity. Following validation in larger cohorts, our methodology may be useful in detecting protective immunity and the assessment of long-term outcomes, particularly as we begin to unravel the immunological mechanisms leading to post-COVID complications.

Case-control study on risk factors for in-hospital mortality in patients with severe COVID-19

Objective

The purpose of this study was to identify independent risk factors affecting patient survival and explore predictors of severe cases of coronavirus disease 2019 (COVID-19).

Methods

We conducted a retrospective, observational, case-control study on adult patients with severe COVID-19 who were admitted to affiliated hospitals in Tianjin between December 18, 2022, and January 31, 2023. We used univariate and multifactorial logistic regression analyses to analyze demographic indicators, comorbidity profiles, and laboratory parameters in two groups of patients (deceased and surviving) to identify independent risk factors for death in patients with severe COVID-19.

Results

Patients in the deceased group were older than those in the survival group (p = 0.018), and there were more cases of coexisting respiratory insufficiency in the deceased group (p = 0.002). Additionally, laboratory test results for white blood cell count (WBC) and creatine kinase (CK) showed significantly higher values in the deceased group (p = 0.047 and p = 0.029, respectively), while arterial oxygen partial pressure (PAO2) showed significantly lower values compared to the survival group (p = 0.021). Age, respiratory insufficiency, WBCH (highest WBC value), CKH (highest CK value), and PAO2F (first PAO2 value) had area under curve (AUC) values of 0.698, 0.838, 0.721, 0.744, and 0.633, respectively.

Conclusion

The main risk factors for mortality in patients with severe COVID-19 that we identified in this study were the advanced age of patients, coexisting respiratory insufficiency, elevated levels of WBC and CK, and decreased levels of PAO2. Elevated WBC and CK laboratory parameters, in particular, demonstrated good predictive value for in-hospital mortality risk.

Hesitation towards COVID-19 booster vaccination among dialysis patients: a cross-sectional study in Taizhou, China

PURPOSE

This research aimed to explore hesitation towards the COVID-19 booster vaccine among dialysis patients and study the association between COVID-19 pandemic-induced health behavior and vaccination hesitancy.

METHODS

A self-administered online questionnaire evaluating dialysis patients' hesitation to take COVID-19 booster vaccination was conducted between March 24 and 22 April 2022 in Taizhou, China. The logistic regression method was applied to identify factors associated with vaccination hesitancy, and all data were analyzed using R software.

RESULTS

Of the 365 study participants, 272 (74.5%) individuals hesitated to take the booster dose. Health behavior was found to be a significant factor for hesitation to take COVID-19 vaccines, with OR (95% CI) of 1.09 (1.02-1.17). Influenza vaccination history was also significantly associated with the hesitation (OR (95% CI) = 0.39 (0.21-0.74)). In addition, participants with higher education levels exhibited lower vaccine hesitancy compared to those with junior secondary or below, with ORs (95% CIs) of 0.49 (0.27-0.91) for senior secondary and 0.35 (0.14-0.89) for junior college or above, respectively.

CONCLUSION

The proportion of hesitancy for taking the booster vaccination of the COVID-19 vaccine was high among dialysis patients. Health behaviors, influenza vaccination history, and education levels were risk factors in their vaccination hesitancy. These findings may aid efforts to help vaccinate people with underlying diseases against future pandemics.

Platelet dysfunction caused by differentially expressed genes as key pathogenic mechanisms in COVID-19

At the end of 2019, the novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became prevalent worldwide, which brought a heavy medical burden and tremendous economic losses to the world population. In addition to the common clinical respiratory symptoms such as fever, cough and headache, patients with COVID-19 often have hematological diseases, especially platelet dysfunction. Platelet dysfunction usually leads to multiple organ dysfunction, which is closely related to patient severity or mortality. In addition, studies have confirmed significant changes in the gene expression profile of circulating platelets under SARS-CoV-2 infection, which will further lead to changes in platelet function. At the same time, studies have shown that platelets may absorb SARS-COV-2 mRNA independently of ACE2, which further emphasizes the importance of the stability of platelet function in defense against SARS-CoV-2 infection. This study reviewed the relationship between COVID-19 and platelet and SARS-CoV-2 damage to the circulatory system, and further analyzed the significantly differentially expressed mRNA in platelets after infection with SARS-CoV-2 on the basis of previous studies. The top eight hub genes were identified as NLRP3, MT-CO1, CD86, ICAM1, MT-CYB, CASP8, CXCL8 and CXCR4. Subsequently, the effects of SARS-CoV-2 infection on platelet transcript abnormalities and platelet dysfunction were further explored on the basis of 8 hub genes. Finally, the treatment measures of complications caused by platelet dysfunction in patients with COVID-19 were discussed in detail, so as to provide reference for the prevention, diagnosis and treatment of COVID-19.

Support for Nursing Home Caregivers During the COVID-19 Pandemic: A Review

PURPOSE

To review support systems for nursing home caregivers (NHCGs) that were implemented during the first year of the coronavirus disease 2019 (COVID-19) pandemic.

METHOD

Database searches in PubMed, ScienceDirect, and CINAHL resulted in five publications.

RESULTS

Studies differed in design, interventions, and outcomes. An urgent eye movement desensitization and reprocessing protocol was feasible and effective among nurses in services highly mobilized during the acute phase of the pandemic. The "self-help plus" psychological intervention was not associated with significant reductions in anxiety or posttraumatic symptoms but prompted exploration of non-specific factors influencing its effectiveness. The Extension for Community Healthcare Outcomes in Long-Term Care of the Elderly virtual program increased confidence among NHCGs. Self-compassion training was associated with positive changes for certified nursing assistants. Weekly debriefing sessions implemented at one hospital highlighted pathogenic and salutogenic factors.

CONCLUSION

The COVID-19 pandemic had a marked psychosocial impact on NHCGs and necessitated targeted interventions. Despite their limitations, these promising studies provided insights into potential support avenues. Policy considerations should stress the pivotal role of advanced practice nurses in shaping supportive work environments. Future research should focus on robust assessments of the efficacy of psychosocial interventions for NHCGs facing ongoing challenges posed by the pandemic, and even recurrent viral epidemics. [Journal of Gerontological Nursing, 50(10), 24-33.].

Science-based exit from stringent countermeasures against COVID-19: Mortality prediction using immune landscape between 2021 and 2022 in Japan

Background

Stringent public health and social measures against COVID-19 infection were implemented to avoid an overwhelming hospital caseload and excessive number of deaths, especially among elderly people. We analyzed population-level immunity and predicted mortality, calculated as the potential number of deaths on a given calendar date in Japan, to develop a science-based exit strategy from stringent control measures.

Methods

Immune proportions were inferred by age group using vaccination coverage data and the estimated number of naturally infected individuals. Immunity against symptomatic illness and death were estimated separately, allowing for inference of the immune fraction that was protected against either COVID-19-related symptomatic infection or death. By multiplying the infection fatality risk by age group for the immune fraction, the potential number of deaths was obtained.

Results

Accounting for a second and third dose of messenger RNA vaccine in the present-day population, approximately 155,000 potential deaths would be expected among people aged ≥ 60 years if all individuals were infected at the very end of 2022. A fourth dose (i.e., second booster) with a coverage identical to that of the third dose could reduce mortality by 60%. In all examined settings, the largest number of deaths occurred among people aged 80 years and older.

Conclusions

Our estimates can help policymakers understand the mortality impact of the COVID-19 epidemic in a quantitative manner and the critical importance of timely immunization so as to assist in decision making.

Clinical characteristics and outcomes of neonatal SARS-CoV-2 infection after the release of the epidemic situation of COVID-19

BACKGROUND

With the release of the coronavirus disease 2019 (COVID-19) pandemic in late 2022 in China, the number of people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) roared, including neonatal cases. However, there were few studies on neonatal COVID-19, especially multi-center case reports. This study aimed to explore clinical characteristics and short-term outcomes of neonatal COVID-19 in China.

METHODS

We reviewed 187 cases of neonatal COVID-19 between December 11, 2022, and January 12, 2023. The diagnosis was assessed by symptoms, laboratory tests, X-ray manifestations, and diagnosis code. Clinical characteristics and outcomes were evaluated.

RESULTS

In 187 neonatal cases with COVID-19, 84 (44.9%) had severe SARS-CoV-2 infection. Most patients had confirmed exposure to SARS-CoV-2. Fever and respiratory symptoms were common (75.4% and 71.7%, respectively). Severe patients were more likely to have high alanine transaminase (ALT) (> 40U/L) (11.9% vs. 3.9%) and high N-terminal pro-brain natriuretic peptide (NT-proBNP) (> 2000pg/mL) (38.0% vs. 19.6%), compared with nonsevere ones (P < 0.05). None of the patients received COVID-19-specific medical interventions. A few severe patients received corticosteroids (1.1%), and immunoglobulin (0.5%), respectively. All patients were discharged home after the medical care with a median length of stay (LOS) of four days and none of them met the criteria of multisystem inflammatory syndrome in neonates (MIS-N).

CONCLUSIONS

After the release of the epidemic situation of COVID-19 in late 2022 in China, more neonatal cases with severe COVID-19 had high ALT and NT-proBNP level. Few specific medical interventions were given, and the outcome was satisfying.

A novel viral RNA detection method based on the combined use of trans-acting ribozymes and HCR-FRET analyses

The diagnoses of retroviruses are essential for controlling the rapid spread of pandemics. However, the real-time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR), which has been the gold standard for identifying viruses such as SARS-CoV-2 in the early stages of infection, is associated with high costs and logistical challenges. To innovate in viral RNA detection a novel molecular approach for detecting SARS-CoV-2 viral RNA, as a proof of concept, was developed. This method combines specific viral gene analysis, trans-acting ribozymes, and Fluorescence Resonance Energy Transfer (FRET)-based hybridization of fluorescent DNA hairpins. In this molecular mechanism, SARS-CoV-2 RNA is specifically recognized and cleaved by ribozymes, releasing an initiator fragment that triggers a hybridization chain reaction (HCR) with DNA hairpins containing fluorophores, leading to a FRET process. A consensus SARS-CoV-2 RNA target sequence was identified, and specific ribozymes were designed and transcribed in vitro to cleave the viral RNA into fragments. DNA hairpins labeled with Cy3/Cy5 fluorophores were then designed and synthesized for HCR-FRET assays targeting the RNA fragment sequences resulting from ribozyme cleavage. The results demonstrated that two of the three designed ribozymes effectively cleaved the target RNA within 10 minutes. Additionally, DNA hairpins labeled with Cy3/Cy5 pairs efficiently detected target RNA specifically and triggered detectable HCR-FRET reactions. This method is versatile and can be adapted for use with other viruses. Furthermore, the design and construction of a DIY photo-fluorometer prototype enabled us to explore the development of a simple and cost-effective point-of-care detection method based on digital image analysis.

Recurrent stroke admissions with vs without COVID-19 and associated in-hospital mortality: A United States nationwide analysis, 2020

BACKGROUND

Coronavirus disease 2019 (COVID-19) has been shown to increase the risk of stroke. However, the prevalence and risk of recurrent stroke in COVID-19 patients with prior stroke/transient ischemic attack (TIA), as well as its impact on mortality, are not established.

AIM

To evaluate the impact of COVID-19 on in-hospital mortality, length of stay, and healthcare costs in patients with recurrent strokes.

METHODS

We identified admissions of recurrent stroke (current acute ischemic stroke admissions with at least one prior TIA or stroke) in patients with and without COVID-19 using ICD-10-CM codes using the National Inpatient Sample (2020). We analyzed the impact of COVID-19 on mortality following recurrent stroke admissions by subgroups.

RESULTS

Of 97455 admissions with recurrent stroke, 2140 (2.2%) belonged to the COVID-19-positive group. The COVID-19-positive group had a higher prevalence of diabetes and chronic kidney disease vs the COVID-19 negative group (P < 0.001). Among the subgroups, patients aged > 65 years, patients aged 45-64 years, Asians, Hispanics, whites, and blacks in the COVID-19 positive group had higher rates of all-cause mortality than the COVID-19 negative group (P < 0.01). Higher odds of in-hospital mortality were seen in the group aged 45-64 (OR: 8.40, 95%CI: 4.18-16.91) vs the group aged > 65 (OR: 7.04, 95%CI: 5.24-9.44), males (OR: 7.82, 95%CI: 5.38-11.35) compared to females (OR: 6.15, 95%CI: 4.12-9.18), and in Hispanics (OR: 15.47, 95%CI: 7.61-31.44) and Asians/Pacific Islanders (OR: 14.93, 95%CI: 7.22-30.87) compared to blacks (OR: 5.73, 95%CI: 3.08-10.68), and whites (OR: 5.54, 95%CI: 3.79-8.09).

CONCLUSION

The study highlights the increased risk of all-cause in-hospital mortality in recurrent stroke patients with COVID-19, with a more pronounced increase in middle-aged patients, males, Hispanics, or Asians.

Dynamic changes in the circulation of respiratory pathogens in children during and after the containment of the 2019 coronavirus disease pandemic in Kunming, China

PURPOSE

We aimed to determine the changes in the frequency of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during containment of the 2019 coronavirus disease pandemic and elucidate the epidemiological interference that may have occurred after lifting pandemic measures.

METHODS

A total of 4,770 Nasopharyngeal swab samples were collected from children with ARTIs from the First People's Hospital of Yunnan Province between January 2022 and December 2023 and subjected to nucleic acid testing for 13 types of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

The frequency of pathogens among children from 2020 to 2022 was in the following order: HRV > Mp > HADV > H3N2 > HMPV and HRV > HRSV > HPIV > H1N1 > H3N2. In weeks 1 to 3 of 2023, the frequency of pathogens significantly declined, and then H1N1 rebounded significantly in 2023. HRV, HRSV, and H3N2 showed a shift in the season of high frequency. Patterns of multi-pathogen infections were more complex in 2023 than in 2022, with HRV having a higher frequency and co-infection rate than other pathogens. These changes may have been associated with interference caused by the resurgence of SARS-CoV-2 prevalence, in addition to being influenced by changes in pandemic containment and lifting measures.

CONCLUSIONS

The frequency rate of common respiratory pathogens among children was not significantly different and remained high. The study findings help elucidate the aforementioned unique historical period and effectively control respiratory tract infections to reduce the harm to pediatric health caused by respiratory pathogens.

Preschool-age children maintain a distinct memory CD4+ T cell and memory B cell response after SARS-CoV-2 infection

The development of the human immune system lasts for several years after birth. The impact of this maturation phase on the quality of adaptive immunity and the acquisition of immunological memory after infection at a young age remains incompletely defined. Here, using an antigen-reactive T cell (ARTE) assay and multidimensional flow cytometry, we profiled circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-reactive CD3+CD4+CD154+ T cells in children and adults before infection, during infection, and 11 months after infection, stratifying children into separate age groups and adults according to disease severity. During SARS-CoV-2 infection, children younger than 5 years old displayed a lower antiviral CD4+ T cell response, whereas children older than 5 years and adults with mild disease had, quantitatively and phenotypically, comparable virus-reactive CD4+ T cell responses. Adults with severe disease mounted a response characterized by higher frequencies of virus-reactive proinflammatory and cytotoxic T cells. After SARS-CoV-2 infection, preschool-age children not only maintained neutralizing SARS-CoV-2-reactive antibodies postinfection comparable to adults but also had phenotypically distinct memory T cells displaying high inflammatory features and properties associated with migration toward inflamed sites. Moreover, preschool-age children had markedly fewer circulating virus-reactive memory B cells compared with the other cohorts. Collectively, our results reveal unique facets of antiviral immunity in humans at a young age and indicate that the maturation of adaptive responses against SARS-CoV-2 toward an adult-like profile occurs in a progressive manner.

Innate immune response in acute critical illness: a narrative review

BACKGROUND

Activation of innate immunity is a first line of host defense during acute critical illness (ACI) that aims to contain injury and avoid tissue damages. Aberrant activation of innate immunity may also participate in the occurrence of organ failures during critical illness. This review aims to provide a narrative overview of recent advances in the field of innate immunity in critical illness, and to consider future potential therapeutic strategies.

MAIN TEXT

Understanding the underlying biological concepts supporting therapeutic strategies modulating immune response is essential in decision-making. We will develop the multiple facets of innate immune response, especially its cellular aspects, and its interaction with other defense mechanisms. We will first describe the pathophysiological mechanisms of initiation of innate immune response and its implication during ACI. We will then develop the amplification of innate immunity mediated by multiple effectors. Our review will mainly focus on myeloid and lymphoid cellular effectors, the major actors involved in innate immune-mediated organ failure. We will third discuss the interaction and integration of innate immune response in a global view of host defense, thus considering interaction with non-immune cells through immunothrombosis, immunometabolism and long-term reprogramming via trained immunity. The last part of this review will focus on the specificities of the immune response in children and the older population.

CONCLUSIONS

Recent understanding of the innate immune response integrates immunity in a highly dynamic global vision of host response. A better knowledge of the implicated mechanisms and their tissue-compartmentalization allows to characterize the individual immune profile, and one day eventually, to develop individualized bench-to-bedside immunomodulation approaches as an adjuvant resuscitation strategy.

Aberrant innate immune profile associated with COVID-19 mortality in Pretoria, South Africa

The African continent reported the least number of COVID-19 cases and deaths of all the continents, although the exact reasons for this are still unclear. In addition, little is known about the immunological profiles associated with COVID-19 mortality in Africa. The present study compared clinical and immunological parameters, as well as treatment outcomes in patients admitted with COVID-19 in Pretoria, South Africa, to determine if these parameters correlated with mortality in this population. The in-hospital mortality rate for the cohort was 15.79%. The mortality rate in people living with HIV (PLWH) was 10.81% and 17.16% in people without HIV (p = 0.395). No differences in age (p = 0.099), gender (p = 0.127) or comorbidities were found between deceased patients and those who survived. All four of the PLWH who died had a CD4+ T-cell count <200 cells/mm3, a significantly higher HIV viral load than those who survived (p = 0.009), and none were receiving antiretroviral therapy. Seven of 174 (4%) patients had evidence of auto-antibodies neutralizing Type 1 interferons (IFNs). Two of the them died, and their presence was significantly associated with mortality (p = 0.042). In the adjusted model, the only clinical parameters associated with mortality were: higher fraction of inspired oxygen (FiO2) (OR: 3.308, p = 0.011) indicating a greater need for oxygen, high creatinine (OR: 4.424, p = 0.001) and lower platelet counts (OR: 0.203, p = 0.009), possibly secondary to immunothrombosis. Overall, expression of the co-receptor CD86 (p = 0.021) on monocytes and percentages of CD8+ effector memory 2 T-cells (OR: 0.45, p = 0.027) was lower in deceased patients. Decreased CD86 expression impairs the development and survival of effector memory T-cells. Deceased patients had higher concentrations of RANTES (p = 0.003), eotaxin (p = 0.003) and interleukin (IL)-8 (p < 0.001), all involved in the activation and recruitment of innate immune cells. They also had lower concentrations of transforming growth factor (TGF)-β1 (p = 0.40), indicating an impaired anti-inflammatory response. The immunological profile associated with COVID-19 mortality in South Africa points to the role of aberrate innate immune responses.

DDE: Deep Dynamic Epidemiological Modeling for Infectious Illness Development Forecasting in Multi-level Geographic Entities

Understanding and addressing the dynamics of infectious diseases, such as coronavirus disease 2019, are essential for effectively managing the current situation and developing intervention strategies. Epidemiologists commonly use mathematical models, known as epidemiological equations (EE), to simulate disease spread. However, accurately estimating the parameters of these models can be challenging due to factors like variations in social distancing policies and intervention strategies. In this study, we propose a novel method called deep dynamic epidemiological modeling (DDE) to address these challenges. The DDE method combines the strengths of EE with the capabilities of deep neural networks to improve the accuracy of fitting real-world data. In DDE, we apply neural ordinary differential equations to solve variant-specific equations, ensuring a more precise fit for disease progression in different geographic regions. In the experiment, we tested the performance of the DDE method and other state-of-the-art methods using real-world data from five diverse geographic entities: the USA, Colombia, South Africa, Wuhan in China, and Piedmont in Italy. Compared to the state-of-the-art method, DDE significantly improved accuracy, with an average fitting Pearson coefficient exceeding 0.97 across the five geographic entities. In summary, the DDE method enhances the accuracy of parameter fitting in epidemiological models and provides a foundation for constructing simpler models adaptable to different geographic areas.

Inference of epidemic dynamics in the COVID-19 era and beyond

The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required - from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.

Premature aging effects on COVID-19 pathogenesis: new insights from mouse models

Aging is identified as a significant risk factor for severe coronavirus disease-2019 (COVID-19), often resulting in profound lung damage and mortality. Yet, the biological relationship between aging, aging-related comorbidities, and COVID-19 remains incompletely understood. This study aimed to elucidate the age-related COVID19 pathogenesis using an Hutchinson-Gilford progeria syndrome (HGPS) mouse model, a premature aging disease model, with humanized ACE2 receptors. Pathological features were compared between young, aged, and HGPS hACE2 mice following SARS-CoV-2 challenge. We demonstrated that young mice display robust interferon response and antiviral activity, whereas this response is attenuated in aged mice. Viral infection in aged mice results in severe respiratory tract hemorrhage, likely contributing a higher mortality rate. In contrast, HGPS hACE2 mice exhibit milder disease manifestations characterized by minor immune cell infiltration and dysregulation of multiple metabolic processes. Comprehensive transcriptome analysis revealed both shared and unique gene expression dynamics among different mouse groups. Collectively, our studies evaluated the impact of SARS-CoV-2 infection on progeroid syndromes using a HGPS hACE2 mouse model, which holds promise as a useful tool for investigating COVID-19 pathogenesis in individuals with premature aging.

Spatial, temporal, and demographic nonstationary dynamics of COVID-19 exposure among older adults in the U.S

This study examines demographic disparities in COVID-19 exposures across older adults age 60-79 and older adults age 80 and over, and explores the factors driving these dynamics in the United States (U.S.) from January 2020 to July 2022. Spatial clusters were identified, and 14 main health determinants were synthesized from 62 pre-existing county-level variables. The study also assessed the correlation between these health determinants and COVID-19 incidence rates for both age groups during the pandemic years. Further examination of incidence rates in relation to health determinants was carried out through statistical and spatial regression models. Results show that individuals aged 80 and over had much higher hospitalization rates, death rates, and case-fatality rates in 2020-2022. Spatial results indicate that the geographical cluster of high incidence rates for both groups shifted from the Midwest at the beginning of the pandemic to the Southwest in 2022. The study revealed marked spatial, temporal, and demographic nonstationary dynamics in COVID-19 exposures, indicating that the health effects of contextual factors vary across age groups. COVID-19 incidence rates in older adults were strongly influenced by race, healthcare access, social capital, environment, household composition, and mobility. Future public health policies and mitigations should further their efforts by considering temporal and demographic nonstationarity as well as local conditions.

Severe COVID-19 infection: An institutional review and literature overview

BACKGROUND

Our study aimed to describe the group of severe COVID-19 patients at an institutional level, and determine factors associated with different outcomes.

METHODS

A retrospective chart review of patients admitted with severe acute hypoxic respiratory failure due to COVID-19 infection. Based on outcomes, we categorized 3 groups of severe COVID-19: (1) Favorable outcome: progressive care unit admission and discharge (2) Intermediate outcome: ICU care (3) Poor outcome: in-hospital mortality.

RESULTS

Eighty-nine patients met our inclusion criteria; 42.7% were female. The average age was 59.7 (standard deviation (SD):13.7). Most of the population were Caucasian (95.5%) and non-Hispanic (91.0%). Age, sex, race, and ethnicity were similar between outcome groups. Medicare and Medicaid patients accounted for 62.9%. The average BMI was 33.5 (SD:8.2). Moderate comorbidity was observed, with an average Charlson Comorbidity index (CCI) of 3.8 (SD:2.6). There were no differences in the average CCI between groups(p = 0.291). Many patients (67.4%) had hypertension, diabetes (42.7%) and chronic lung disease (32.6%). A statistical difference was found when chronic lung disease was evaluated; p = 0.002. The prevalence of chronic lung disease was 19.6%, 27.8%, and 40% in the favorable, intermediate, and poor outcome groups, respectively. Smoking history was associated with poor outcomes (p = 0.04). Only 7.9% were fully vaccinated. Almost half (46.1%) were intubated and mechanically ventilated. Patients spent an average of 12.1 days ventilated (SD:8.5), with an average of 6.0 days from admission to ventilation (SD:5.1). The intermediate group had a shorter average interval from admission to ventilator (77.2 hours, SD:67.6), than the poor group (212.8 hours, SD:126.8); (p = 0.001). The presence of bacterial pneumonia was greatest in the intermediate group (72.2%), compared to the favorable group (17.4%), and the poor group (56%); this was significant (p<0.0001). In-hospital mortality was seen in 28.1%.

CONCLUSION

Most patients were male, obese, had moderate-level comorbidity, a history of tobacco abuse, and government-funded insurance. Nearly 50% required mechanical ventilation, and about 28% died during hospitalization. Bacterial pneumonia was most prevalent in intubated groups. Patients who were intubated with a good outcome were intubated earlier during their hospital course, with an average difference of 135.6 hours. A history of cigarette smoking and chronic lung disease were associated with poor outcomes.

SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia

Though RNAi and RNA-splicing machineries are involved in regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, their precise roles in coronavirus disease 2019 (COVID-19) pathogenesis remain unclear. Herein, we show that decreased RNAi component (Dicer and XPO5) and splicing factor (SRSF3 and hnRNPA3) expression correlate with increased COVID-19 severity. SARS-CoV-2 N protein induces the autophagic degradation of Dicer, XPO5, SRSF3, and hnRNPA3, inhibiting miRNA biogenesis and RNA splicing and triggering DNA damage, proteotoxic stress, and pneumonia. Dicer, XPO5, SRSF3, and hnRNPA3 knockdown increases, while their overexpression decreases, N protein-induced pneumonia's severity. Older mice show lower expression of Dicer, XPO5, SRSF3, and hnRNPA3 in their lung tissues and exhibit more severe N protein-induced pneumonia than younger mice. PJ34, a poly(ADP-ribose) polymerase inhibitor, or anastrozole, an aromatase inhibitor, ameliorates N protein- or SARS-CoV-2-induced pneumonia by restoring Dicer, XPO5, SRSF3, and hnRNPA3 expression. These findings will aid in developing improved treatments for SARS-CoV-2-associated pneumonia.

Mild and moderate COVID-19 during Alpha, Delta and Omicron pandemic waves in urban Maputo, Mozambique, December 2020-March 2022: A population-based surveillance study

In sub-Saharan Africa, reported COVID-19 numbers have been lower than anticipated, even when considering populations' younger age. The extent to which risk factors, established in industrialised countries, impact the risk of infection and of disease in populations in sub-Saharan Africa, remains unclear. We estimated the incidence of mild and moderate COVID-19 in urban Mozambique and analysed factors associated with infection and disease in a population-based surveillance study. During December 2020-March 2022, 1,561 households (6,049 participants, median 21 years, 54.8% female, 7.3% disclosed HIV positive) of Polana Caniço, Maputo, Mozambique, were visited biweekly to report respiratory symptoms, anosmia, or ageusia, and self-administer a nasal swab for SARS-CoV-2 testing. Every three months, dried blood spots of a subset of participants (1,412) were collected for detection of antibodies against SARS-CoV-2 spike glycoprotein and nucleocapsid protein. Per 1000 person-years, 364.5 (95%CI 352.8-376.1) respiratory illness episodes were reported, of which 72.2 (95%CI 60.6-83.9) were COVID-19. SARS-CoV-2 seroprevalence rose from 4.8% (95%CI 1.1-8.6%) in December 2020 to 34.7% (95%CI 20.2-49.3%) in June 2021, when 3.0% were vaccinated. Increasing age, chronic lung disease, hypertension, and overweight increased risk of COVID-19. Older age increased the risk of SARS-CoV-2 seroconversion. We observed no association between socio-economic status, behaviour and COVID-19 or SARS-CoV-2 seroconversion. Active surveillance in an urban population confirmed frequent COVID-19 underreporting, yet indicated that the large majority of cases were mild and non-febrile. In contrast to reports from industrialised countries, social deprivation did not increase the risk of infection nor disease.

Acute and long COVID-19 symptoms and associated factors in the omicron-dominant period: a nationwide survey via the online platform Wenjuanxing in China

BACKGROUNDS

To our knowledge, there is no available nationwide data on omicron symptom patterns in China mainland. We aim to determine the acute and long COVID-19 symptoms in the omicron-dominant period and to evaluate its association with risk factors.

METHODS

We designed a cross-sectional nationwide study and data about self-reported symptoms were collected by an online platform named Wenjuanxing. Eligible participants were aged 25-65 years and were symptomatic. In this study, the ratios of the number of people of different ages and genders were weighted by the data from the Seventh National Census (2020 years), and validated by a published nationwide representative study through comparing smoking rates. Descriptive indicators were calculated for demographic characteristics, diagnosis ways, and duration time, acute symptoms, hospitalization, severity and long COVID-19 symptoms. And, the associations between risk factors and acute and long COVID-19 symptoms were analyzed by multivariable logistic regression models.

RESULTS

A total of 32,528 individuals diagnosed as COVID-19 infection from October 1, 2022 to February 21, 2023 were included. The first three acute symptoms of COVID-19 infection were fever (69.90%), headache (62.63%), and sore throat (54.29%), respectively. The hospitalization rate within 7 days was 3.07% and symptoms disappearance rate within 21 days was 68.84%, respectively. Among 3983 COVID-19 patients with 3 months or more time difference between first infection and participation into the study, the long COVID-19 rate was 19.68% and the primary symptoms were muscle weakness (19.39%), headache (17.98%) and smell/taste disorder (15.18%). Age groups, smoking, marriage status and vaccination were risk factors for numbers of acute phase symptoms and long COVID-19 symptoms. Lastly, female and current smokers also showed more numbers of symptoms during acute infection period.

CONCLUSIONS

In Chinese mainland, our respondent indicated that current smokers and women were associated with acute COVID-19 symptoms, which should be treated with caution due to the lack of representative.

Immunological characterization and comparison of children with COVID-19 from their adult counterparts at single-cell resolution

Introduction

The immunological characteristics that could protect children with coronavirus disease 2019 (COVID-19) from severe or fatal illnesses have not been fully understood yet.

Methods

Here, we performed single-cell RNA sequencing (scRNA-seq) analysis on peripheral blood samples of 15 children (8 with COVID-19) and compared them to 18 adults (13 with COVID-19).

Results

The child-adult integrated single cell data indicated that children with the disease presented a restrained response to type I interferon in most of the major immune cell types, along with suppression of upstream interferon regulatory factor and toll-like receptor expression in monocytes, which was confirmed by in vitro interferon stimulation assays. Unlike adult patients, children with COVID-19 showed lower frequencies of activated proinflammatory CD14+ monocytes, possibly explaining the rareness of cytokine storm in them. Notably, natural killer (NK) cells in pediatric patients displayed potent cytotoxicity with a rich expression of cytotoxic molecules and upregulated cytotoxic pathways, whereas the cellular senescence, along with the Notch signaling pathway, was significantly downregulated in NK cells, all suggesting more robust cytotoxicity in NK cells of children than adult patients that was further confirmed by CD107a degranulation assays. Lastly, a modest adaptive immune response was evident with more naïve T cells but less activated and proliferated T cells while less naïve B cells but more activated B cells in children over adult patients.

Conclusion

Conclusively, this preliminary study revealed distinct cell frequency and activation status of major immune cell types, particularly more robust NK cell cytotoxicity in PBMC that might help protect children from severe COVID-19.

Analyzing the impact of the Coronavirus disease 2019 pandemic on initial oncologic presentation and treatment of non-small cell lung cancer in the United States

BACKGROUND

A significantly lower rate of non-small cell lung cancer (NSCLC) screening, greater health care avoidance, and changes to oncologic recommendations were some consequences of the Coronavirus disease 2019 (COVID-19) pandemic affecting the medical environment. We sought to determine how the health care environment during the COVID-19 pandemic affected the oncologic treatment of patients diagnosed with non-small cell lung cancer (NSCLC).

METHODS

This was a retrospective cohort study evaluating patients with NSCLC in the National Cancer Database (2019-2020). Patients were divided into prepandemic (2019) and pandemic (2020) cohorts, and patient, oncologic, and treatment variables were compared. Multivariable logistic regression was performed to control for the impact of demographic characteristics on oncologic variables and the impact of oncologic variables on treatment variables.

RESULTS

The study population comprised 250,791 patients, including 114,533 patients (45.7%) in the pandemic cohort. There were 15% fewer new NSCLC diagnoses during the pandemic compared with prepandemic. Patients diagnosed during the pandemic had more advanced clinical TNM stage on presentation (P < .0001) and were more likely to have tumors in overlapping lobes or in a main bronchus (P = .0002). They were less likely to receive cancer treatment (P < .0001) and to undergo primary resection (P < .0001) and more likely to receive adjuvant systemic therapy (P = .004) and a combination of palliative treatment regimens (P < .0001). After risk adjustment, all these differences remained statistically significant (P < .05).

CONCLUSIONS

The COVID-19 pandemic was associated with increased clinical stage at presentation for patients with NSCLC, which impacted subsequent treatment strategies. However, treatment differed minimally when controlling for cancer stage. Future studies will examine the impact of these differences on overall survival and cancer-free survival.

Large and unequal life expectancy declines during the COVID-19 pandemic in India in 2020

Global population health during the COVID-19 pandemic is poorly understood because of weak mortality monitoring in low- and middle-income countries. High-quality survey data on 765,180 individuals, representative of one-fourth of India's population, uncover patterns missed by incomplete vital statistics and disease surveillance. Compared to 2019, life expectancy at birth was 2.6 years lower and mortality was 17% higher in 2020, implying 1.19 million excess deaths in 2020. Life expectancy declines in India were larger and had a younger age profile than in high-income countries. Increases in mortality were greater than expected based on observed seroprevalence and international infection fatality rates, most prominently among the youngest and older age groups. In contrast to global patterns, females in India experienced a life expectancy decline that was 1 year larger than losses for males. Marginalized social groups experienced greater declines than the most privileged social group. These findings uncover large and unequal mortality impacts during the pandemic in the world's most populous country.

Cerebral microbleeds in patients with COVID-19: is there an inevitable connection?

The COVID-19 pandemic has underscored the critical interplay between systemic infections and neurological complications, notably cerebral microbleeds. This comprehensive review meticulously aggregates and analyses current evidence on cerebral microbleeds' prevalence, pathophysiological underpinnings and clinical implications within COVID-19 cohorts. Our findings reveal a pronounced correlation between cerebral microbleeds and increased severity of COVID-19, emphasizing the role of direct viral effects, inflammatory responses and coagulation disturbances. The documented association between cerebral microbleeds and elevated risks of morbidity and mortality necessitates enhanced neurological surveillance in managing COVID-19 patients. Although variability in study methodologies presents challenges, the cumulative evidence substantiates cerebral microbleeds as a critical illness manifestation rather than mere coincidence. This review calls for harmonization in research methodologies to refine our understanding and guide targeted interventions. Prioritizing the detection and study of neurological outcomes, such as cerebral microbleeds, is imperative for bolstering pandemic response strategies and mitigating the long-term neurological impact on survivors.

Impact of age and sex on neuroinflammation following SARS-CoV-2 infection in a murine model

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is known to infect people of all ages and both sexes. Senior populations have the greatest risk of severe COVID-19, and sexual dimorphism in clinical outcomes has been reported. Neurological symptoms are widely observed in COVID-19 patients, with many survivors exhibiting persistent neurological and cognitive impairment. The present study aims to investigate the impact of age and sex on the neuroinflammatory response to SARS-CoV-2 infection using a mouse model. Wild-type C57BL/6J mice were intranasally inoculated with SARS-CoV-2 lineage B.1.351, a variant known to infect mice. Older male mice exhibited a significantly greater weight loss and higher viral loads in the lung at 3 days post infection. Notably, no viral RNA was detected in the brains of infected mice. Nevertheless, expression of IL-6, TNF-α, and CCL-2 in the lung and brain increased with viral infection. RNA-seq transcriptomic analysis of brains showed that SARS-CoV-2 infection caused significant changes in gene expression profiles, implicating innate immunity, defense response to virus, and cerebrovascular and neuronal functions. These findings demonstrate that SARS-CoV-2 infection triggers a neuroinflammatory response, despite the lack of detectable virus in the brain. Aberrant activation of innate immune response, disruption of blood-brain barrier and endothelial cell integrity, and suppression of neuronal activity and axonogenesis underlie the impact of SARS-CoV-2 infection on the brain. Understanding the role of these affected pathways in SARS-CoV-2 pathogenesis helps identify appropriate points of therapeutic interventions to alleviate neurological dysfunction observed during COVID-19.

Human determinants of age-dependent patterns of death from infection

Regardless of microbial virulence (i.e., the global infection-fatality ratio), age generally drives the prevalence of death from infection in unvaccinated humans. Four mortality patterns are recognized: the common U- and L-shaped curves of endemic infections and the unique W- and J-shaped curves of pandemic infections. We suggest that these patterns result from different sets of human genetic and immunological determinants. In this model, it is the interplay between (1) monogenic genotypes affecting immunity to primary infection that preferentially manifest early in life and related genotypes or their phenocopies, including auto-antibodies, which manifest later in life and (2) the occurrence and persistence of adaptive, acquired immunity to primary or cross-reactive infections, which shapes the age-dependent pattern of human deaths from infection.

Pulmonary function and chest CT abnormalities 3 months after discharge from COVID-19, 2020-2021: A nation-wide multicenter prospective cohort study from the Japanese respiratory society

BACKGROUND

No comprehensive analysis of the pulmonary sequelae of coronavirus disease 2019 (COVID-19) in Japan based on respiratory function tests and chest computed tomography (CT) has been reported. We evaluated post-COVID-19 conditions, especially focusing on pulmonary sequelae assessed by pulmonary function tests and chest CT.

METHODS

For this prospective cohort study, we enrolled 1069 patients who presented pneumonia at the time of admission in 55 hospitals from February 2020 to September 2021. Disease severity was classified as moderateⅠ, moderate II, and severe, defined primarily according to the degree of respiratory failure. The data on post-COVID-19 conditions over 12 months, pulmonary function, and chest CT findings at 3 months were evaluated in this study. Additionally, the impact of COVID-19 severity on pulmonary sequelae, such as impaired diffusion capacity, restrictive pattern, and CT abnormalities, was also evaluated.

RESULTS

The most frequently reported post-COVID-19 conditions at 3 months after COVID-19 were muscle weakness, dyspnea, and fatigue (48.4%, 29.0%, and 24.7%, respectively). The frequency of symptoms gradually decreased over subsequent months. In pulmonary function tests at 3 months, the incidence of impaired diffusion capacity and restrictive pattern increased depending on disease severity. There also were differences in the presence of chest CT abnormalities at the 3 months, which was markedly correlated with the severity.

CONCLUSION

We reported a comprehensive analysis of post-COVID-19 condition, pulmonary function, and chest CT abnormalities in Japanese patients with COVID-19. The findings of this study will serve as valuable reference data for future post-COVID-19 condition research in Japan.

HLA-DQA1*01:03 and DQB1*06:01 are risk factors for severe COVID-19 pneumonia

The clinical spectrum of COVID-19 includes a wide range of manifestations, from mild symptoms to severe pneumonia. HLA system plays a pivotal role in immune responses to infectious diseases. The purpose of our study was to investigate the association between HLA and COVID-19 severity in a Japanese population. The study included 209 Japanese COVID-19 patients aged ≥20 years. Saliva samples were collected and used to determine the HLA genotype by HLA imputation through genome-wide association analyses. The association between HLA genotype and COVID-19 severity was then evaluated. The allele frequency was compared between patients with respiratory failure (severe group: 91 cases) and those without respiratory failure (non-severe group: 118 cases), categorising the data into three time periods: pre-Omicron epidemic period, Omicron epidemic period, and total period of this study (from January 2021 to May 2023). In comparing the severe and non-severe groups, the frequencies of the HLA-DQA1*01:03 (35.1% vs. 10.5%, odds ratio [OR] = 4.57, corrected p [pc] = 0.041) and -DQB1*06:01 (32.4% vs. 7.9%, OR = 5.54, pc = 0.030) alleles were significantly higher in the severe group during the pre-Omicron epidemic period. During the Omicron epidemic period, HLA-DQB1*06 (32.4% vs. 7.9%, OR = 5.54, pc = 0.030) was significantly higher in the severe group. During total period of this study, HLA-DQA1*01:03 (30.2% vs. 14.4%, OR = 2.57, corrected pc = 0.0013) and -DQB1*06:01 (44.5% vs. 26.7%, OR = 2.20, pc = 0.013) alleles were significantly higher in the severe group. HLA-DQB1*06:01 and -DQA1*01:03 were in strong linkage disequilibrium with each other (r2 = 0.91) during total period of this study, indicating that these two alleles form a haplotype. The frequency of the HLA-DQA1*01:03-DQB1*06:01 in the severe group was significantly higher than in the non-severe group during pre-Omicron epidemic period (32.4% vs. 7.9%, OR = 5.59, pc = 0.00072), and total period of this study (28.6% vs. 13.1%, OR = 2.63, pc = 0.0013). During Omicron epidemic period, the haplotype did not demonstrate statistical significance, although the odds ratio indicated a value greater 1. Frequencies of the HLA-DQA1*01:03 and -DQB1*06:01 alleles were significantly higher in severe COVID-19 patients, suggesting that these alleles are risk factors for severe COVID-19 pneumonia in the Japanese population.

Pandemic Fatigue and Preferences for COVID-19 Public Health and Social Measures in China: Nationwide Discrete Choice Experiment

BACKGROUND

Information on the public's preferences for current public health and social measures (PHSMs) and people's mental health under PHSMs is insufficient.

OBJECTIVE

This study aimed to quantify the public's preferences for varied PHSMs and measure the level of pandemic fatigue in the COVID-19 normalization stage in China.

METHODS

A nationwide cross-sectional study with a discrete choice experiment and psychometric scales was conducted to assess public preferences for and attitudes toward PHSMs, using the quota sampling method. The COVID-19 Pandemic Fatigue Scale (CPFS) was used to screen fatigue levels among respondents. The multinomial logit model, latent class model, and Mann-Whitney test were used for statistical analysis. We also conducted subgroup analysis based on sex, age, monthly income, mental health status, and pandemic fatigue status.

RESULTS

A total of 689 respondents across China completed the survey. The discrete choice experiment revealed that respondents attached the greatest importance to the risk of COVID-19 infection within 3 months (45.53%), followed by loss of income within 3 months (30.69%). Vulnerable populations (low-income populations and elderly people) were more sensitive to the risk of infection, while younger respondents were more sensitive to income loss and preferred nonsuspension of social places and transportation. Migrants and those with pandemic fatigue had less acceptance of the mandatory booster vaccination and suspension of transportation. Additionally, a higher pandemic fatigue level was observed in female respondents, younger respondents, migrants, and relatively lower-income respondents (CPFS correlation with age: r=-0.274, P<.001; correlation with monthly income: r=-0.25, P<.001). Mandatory booster COVID-19 vaccination was also not preferred by respondents with a higher level of pandemic fatigue, while universal COVID-19 booster vaccination was preferred by respondents with a lower level of pandemic fatigue.

CONCLUSIONS

Pandemic fatigue is widely prevalent in respondents across China, and respondents desired the resumption of normal social life while being confronted with the fear of COVID-19 infection in the normalization stage of COVID-19 in China. During future pandemics, the mental burden and adherence of residents should be considered for the proper implementation of PHSMs.

Nirmatrelvir and ritonavir for inpatients with severe or critical COVID-19 beyond five days of symptom onset: a propensity score-matched, multicenter, retrospective cohort study

BACKGROUND

There is an urgent need for therapeutic strategies for inpatients with severe or critical COVID-19. The evaluation of the clinical benefits of nirmatrelvir and ritonavir (Nmr/r) for these patients beyond five days of symptom onset is insufficient.

METHODS

A new propensity score-matched cohort was constructed by using multicenter data from 6695 adult inpatients with COVID-19 from December 2022 to February 2023 in China after the epidemic control measures were lifted across the country. The severity of disease of the inpatients was based on the tenth trial edition of the Guidelines on the Diagnosis and Treatment of COVID-19 in China. The symptom onset of 1870 enrolled severe or critical inpatients was beyond five days, and they received either Nmr/r plus standard treatment or only standard care. The ratio of patients whose SOFA score improved more than 2 points, crucial respiratory endpoints, changes in inflammatory markers, safety on the seventh day following the initiation of Nmr/r treatment, and length of hospital stay were evaluated.

RESULTS

In the Nmr/r group, on Day 7, the number of patients with an improvement in SOFA score ≥ 2 was much greater than that in the standard treatment group (P = 0.024) without a significant decrease in glomerular filtration rate (P = 0.815). Additionally, the rate of new intubation was lower (P = 0.004) and the no intubation days were higher (P = 0.003) in the first 7 days in the Nmr/r group. Other clinical benefits were limited.

CONCLUSIONS

Our study may provide new insight that inpatients with severe or critical COVID-19 beyond five days of symptom onset benefit from Nmr/r. Future studies, particularly randomized controlled trials, are necessary to verify the above findings.

COVID-19 vaccination uptake in children with epilepsy and vaccine hesitancy among their parents: a survey

This study explored the coronavirus disease 2019 (COVID-19) vaccination coverage among children with epilepsy (CwE), factors affecting vaccination coverage, and the effect of COVID-19 vaccines on epilepsy after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A questionnaire was administered to CwE and their parents at the Pediatric Neurology Clinic of the Second Affiliated Hospital of Xi'an Jiaotong University between December 12, 2022, and February 28, 2023. Data were analyzed using the t-tests, chi-square tests, and logistic regression. The analysis included 250 CwE who responded to the survey; of these, 152 (60.8%) had been vaccinated against COVID-19. COVID-19 vaccine hesitancy in parents whose CwE were not vaccinated was mostly due to concerns of vaccine-related exacerbation of seizures and of vaccine-related adverse reactions (44.30% and 41.90% of the respondents, respectively). Univariate analysis showed that vaccination and number of doses of vaccine did not affect seizure incidence within 1 month of SARS-CoV-2 infection. Logistic regression analysis showed that CwE below primary school age, and those taking two or more antiseizure medication (ASMs) were less likely to be vaccinated (p = 0.007).   Conclusion: The primary reasons for vaccine hesitancy among parents of unvaccinated CwE were concerns regarding seizure exacerbation and adverse reactions following COVID-19 vaccination. CwE who were below primary school age and those who took two or more ASMs were less likely to be vaccinated. Addressing parents' concerns is necessary to build their confidence in COVID-19 vaccines and ensure that CwE are vaccinated. What is Known: • People with epilepsy have a higher risk of severe and fatal COVID-19 than those without epilepsy but, despite this, COVID-19 vaccination coverage is considerably lower in people with epilepsy than in people without epilepsy. What is New: • In unvaccinated children with epilepsy, the foremost reasons for COVID-19 vaccine hesitancy among parents were concerns about seizure exacerbation and vaccine-related adverse reactions. • Vaccination and number of doses of vaccine did not exacerbate seizures in children with epilepsy, those below primary school level and those taking two or more antiseizure medications were less likely to be vaccinated.

The impact of the COVID-19 pandemic on non-COVID-associated mortality: A descriptive longitudinal study of UK data

Background

It has been previously reported in the literature that the COVID-19 pandemic resulted in overall excess deaths and an increase in non-COVID deaths during the pandemic period.Specifically, our research elucidates the impact of the COVID-19 pandemic on non-COVID associated mortality.

Study aim

To compare mortality rates in non-COVID conditions before and after the onset of the COVID-19 pandemic in England and Wales.

Study design

Annual mortality data for the years 2011-2019 (pre-pandemic) and 2020 (pandemic) in England and Wales were retrieved from the Office for National Statistics (ONS). These data were filtered by ICD-10 codes for nine conditions with high associated mortality. We calculated mortality numbers - overall and age stratified (20-64 and 65+ years) and rates per 100 000, using annual mid-year population estimates.

Methods

Interrupted time series analyses were conducted using segmented quasi-Poisson regression to identify whether there was a statistically significant change (p < 0.05) in condition-specific death rates following the pandemic onset.

Results

Eight of the nine conditions investigated in this study had significant changes in mortality rate during the pandemic period (2020). All-age mortality rate was significantly increased in: 'Symptoms Signs and Ill-defined conditions', 'Cirrhosis and Other Diseases of the Liver', and 'Malignant Neoplasm of the Breast', whereas 'Chronic Lower Respiratory Disorders' saw a significant decrease. Age-stratified analyses also revealed significant increases in the 20-64 age-group in: 'Cerebrovascular Disorders', 'Dementia and Alzheimer's Disease', and 'Ischaemic Heart Diseases'.

Conclusion

Trends in non-COVID condition-specific mortality rates from 2011 to 2020 revealed that some non-COVID conditions were disproportionately affected during the pandemic. This may be due to the direct impact COVID-19 had on these conditions or the effect the public health response had on non-COVID risk factor development and condition-related management. Further work is required to understand the reasons behind these disproportionate changes.

Estimating geographic variation of infection fatality ratios during epidemics

Objectives

We aim to estimate geographic variability in total numbers of infections and infection fatality ratios (IFR; the number of deaths caused by an infection per 1,000 infected people) when the availability and quality of data on disease burden are limited during an epidemic.

Methods

We develop a noncentral hypergeometric framework that accounts for differential probabilities of positive tests and reflects the fact that symptomatic people are more likely to seek testing. We demonstrate the robustness, accuracy, and precision of this framework, and apply it to the United States (U.S.) COVID-19 pandemic to estimate county-level SARS-CoV-2 IFRs.

Results

The estimators for the numbers of infections and IFRs showed high accuracy and precision; for instance, when applied to simulated validation data sets, across counties, Pearson correlation coefficients between estimator means and true values were 0.996 and 0.928, respectively, and they showed strong robustness to model misspecification. Applying the county-level estimators to the real, unsimulated COVID-19 data spanning April 1, 2020 to September 30, 2020 from across the U.S., we found that IFRs varied from 0 to 44.69, with a standard deviation of 3.55 and a median of 2.14.

Conclusions

The proposed estimation framework can be used to identify geographic variation in IFRs across settings.

In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants

The SARS-CoV-2 Omicron variants have replaced all earlier variants, due to increased infectivity and effective evasion from infection- and vaccination-induced neutralizing antibodies. Compared to earlier variants of concern (VoCs), the Omicron variants show high TMPRSS2-independent replication in the upper airway organs, but lower replication in the lungs and lower mortality rates. The shift in cellular tropism and towards lower pathogenicity of Omicron was hypothesized to correlate with a lower toll-like receptor (TLR) activation, although the underlying molecular mechanisms remained undefined. In silico analyses presented here indicate that the Omicron spike protein has a lower potency to induce dimerization of TLR4/MD-2 compared to wild type virus despite a comparable binding activity to TLR4. A model illustrating the molecular consequences of the different potencies of the Omicron spike protein vs. wild-type spike protein for TLR4 activation is presented. Further analyses indicate a clear tendency for decreasing TLR4 dimerization potential during SARS-CoV-2 evolution via Alpha to Gamma to Delta to Omicron variants.

Harnessing the power of IFN for therapeutic approaches to COVID-19

Interferons (IFNs) are essential for defense against viral infections but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, we explore the complexity of the IFN response in COVID-19, examine the effects of manipulating IFN on SARS-CoV-2 viral replication and pathogenesis, and highlight pre-clinical and clinical studies evaluating the therapeutic efficacy of IFN in limiting COVID-19 severity.

Serum AXL is a potential molecular marker for predicting COVID-19 progression

Background

The severity, symptoms, and outcome of COVID-19 is thought to be closely linked to how the virus enters host cells. This process involves the key roles of angiotensin-converting enzyme 2 (ACE2) and the Tyrosine protein kinase receptor UFO (AXL) receptors. However, there is limited research on the circulating levels of ACE2 and AXL and their implications in COVID-19.

Methods

A control group of 71 uninfected individuals was also included in the study. According to the Guidance for Corona Virus Disease 2019 (10th edition), a cohort of 358 COVID-19 patients were categorized into non-severe and severe cases. Serum ACE2/AXL levels in COVID-19 patients were detected by enzyme-linked immunosorbent assay (ELISA) at different time points post-COVID-19 infection, including days 0-7, 8-15, 31-179 and >180 days. Serum SARS-CoV-2 IgG/IgM antibodies in COVID-19 patients at the same intervals were assessed by using an iFlash 3000 Chemiluminescence Immunoassay Analyzer. The receiver operating characteristic (ROC) curves were used to assess the diagnostic value of the biological markers, and the association between laboratory parameters and illness progression were explored.

Results

Compared with the uninfected group, the levels of ACE2 and AXL in the COVID-19 group were decreased, and the SARS-COV-2 IgG level was increased. AXL (AUC = 0.774) demonstrated a stronger predictive ability for COVID-19 than ACE2. In the first week after infection, only the level of AXL was statistically different between severe group and non-severe group. After first week, the levels of ACE2 and AXL were different in two groups. Moreover, in severe COVID-19 cases, the serum ACE2, AXL, and SARS-COV-2 IgM levels reached a peak during days 8-15 before declining, whereas serum SARS-COV-2 IgG levels continued to rise, reaching a peak at day 31-180 days before decreasing. In addition, the AXL level continued to decrease and the SARS-COV-2 IgG level continued to increase in the infected group after 180 days compared to the uninfected group.

Conclusions

The levels of serum ACE2 and AXL correlate with COVID-19 severity. However, AXL can also provide early warning of clinical deterioration in the first week after infection. AXL appears to be a superior potential molecular marker for predicting COVID-19 progression.

Lactate Levels and Clearance: Key Predictors of Prognosis for COVID-19 and Non-COVID-19 Septic Shock Patients in the Emergency Department

BACKGROUND

This investigation assesses the prognostic value of lactate levels and their clearance in septic shock patients, particularly emphasizing the comparative analysis between COVID-19 and non-COVID-19 patients in the emergency department. This study aims to elucidate the unique prognostic implications of lactate dynamics in these distinct patient groups, thereby enhancing the management of septic shock.

METHODS

An observational prospective study was conducted, enrolling 114 septic shock patients from the Emergency County Hospital Resita, Romania, categorizing them into COVID-19 and non-COVID-19 groups to examine their initial lactate levels, clearance rates, and their correlation with patient outcomes.

RESULTS

This study identified significant differences in the initial lactate levels and clearance rates between the two groups, indicating higher initial lactate levels and slower clearance rates in COVID-19 patients. Survivors demonstrated significantly lower initial lactate levels (1.5 ± 0.4 mmol/L) and higher lactate clearance rates (33 ± 15%) compared to non-survivors (2.5 ± 0.5 mmol/L and 24 ± 9%, respectively; lactate levels p = 0.001, clearance rates p = 0.002).

CONCLUSIONS

Lactate monitoring, particularly clearance rates, is crucial in the prognostic assessment of septic shock patients. These findings highlight the need for targeted interventions in COVID-19 patients to improve outcomes, underscoring lactate dynamics as a vital component of septic shock management in differing patient populations.

The First Two Years of COVID-19 Hospitalization Characteristics and Costs: Results from the National Discharge Registry

BACKGROUND

The COVID-19 pandemic has emerged as the primary global health challenge of the new millennium. Understanding its impact on health systems and learning from these experiences are crucial for improving system resilience against future health crises. This paper examines hospitalizations related to COVID-19 in Italy from 2020 to 2021, with a specific focus on the costs associated with these admissions.

DESIGN AND METHODS

This is a retrospective, population-based study of Italian hospitalizations of patients diagnosed with COVID-19 during the 2020-2021 period, using data extracted from the National Hospital Discharge Registry. The outcome variables considered include hospital admissions, costs, and length of stay.

RESULTS

In Italy, hospitalizations for COVID-19 totaled 357,354 in 2020 and 399,043 in 2021, with the transfer rate being three times higher than that of other patients. Hospitalizations were predominantly concentrated in the northern regions, especially during the first year. Mortality rates increased with age, while hospitalization rates peaked in the youngest and oldest age groups. The financial impact of COVID-19 hospitalizations was approximately €3.1 billion in 2020 and €3.6 billion in 2021. The cost per admission was around €8000 for standard care and €24,000 for intensive therapy in both years.

CONCLUSION

Conducting a cost-benefit analysis of implementing a protective pad around the entire health system, which leverages networks of family doctors and nurses connected in real-time, could be an important step in strengthening health system resilience.

Increased levels of GM-CSF and CXCL10 and low CD8+ memory stem T Cell count are markers of immunosenescence and severe COVID-19 in older people

BACKGROUND

Ageing leads to altered immune responses, resulting in higher susceptibility to certain infections in the elderly. Immune ageing is a heterogeneous process also associated with inflammaging, a low-grade chronic inflammation. Altered cytotoxic T cell responses and cytokine storm have previously been described in severe COVID-19 cases, however the parameters responsible for such immune response failures are not well known. The aim of our study was to characterize CD8+ T cells and cytokines associated with ageing, in a cohort of patients aged over 70 years stratified by COVID-19 severity.

RESULTS

One hundred and four patients were included in the study. We found that, in older people, COVID-19 severity was associated with (i) higher level of GM-CSF, CXCL10 (IP-10), VEGF, IL-1β, CCL2 (MCP-1) and the neutrophil to lymphocyte ratio (NLR), (ii) increased terminally differentiated CD8+T cells, and (ii) decreased early precursors CD8+ T stem cell-like memory cells (TSCM) and CD27+CD28+. The cytokines mentioned above were found at higher concentrations in the COVID-19+ older cohort compared to a younger cohort in which they were not associated with disease severity.

CONCLUSIONS

Our results highlight the particular importance of the myeloid lineage in COVID-19 severity among older people. As GM-CSF and CXCL10 were not associated with COVID-19 severity in younger patients, they may represent disease severity specific markers of ageing and should be considered in older people care.

Demystifying COVID-19 mortality causes with interpretable data mining

While COVID-19 becomes periodical, old individuals remain vulnerable to severe disease with high mortality. Although there have been some studies on revealing different risk factors affecting the death of COVID-19 patients, researchers rarely provide a comprehensive analysis to reveal the relationships and interactive effects of the risk factors of COVID-19 mortality, especially in the elderly. Through retrospectively including 1917 COVID-19 patients (102 were dead) admitted to Xiangya Hospital from December 2022 to March 2023, we used the association rule mining method to identify the risk factors leading causes of death among the elderly. Firstly, we used the Affinity Propagation clustering to extract key features from the dataset. Then, we applied the Apriori Algorithm to obtain 6 groups of abnormal feature combinations with significant increments in mortality rate. The results showed a relationship between the number of abnormal feature combinations and mortality rates within different groups. Patients with "C-reactive protein > 8 mg/L", "neutrophils percentage > 75.0 %", "lymphocytes percentage < 20%", and "albumin < 40 g/L" have a 2 × mortality rate than the basic one. When the characteristics of "D-dimer > 0.5 mg/L" and "WBC > 9.5 × 10 9 /L" are continuously included in this foundation, the mortality rate can be increased to 3 × or 4 × . In addition, we also found that liver and kidney diseases significantly affect patient mortality, and the mortality rate can be as high as 100%. These findings can support auxiliary diagnosis and treatment to facilitate early intervention in patients, thereby reducing patient mortality.

Influence of grandchildren on COVID-19 vaccination uptake among older adults in China: a parallel-group, cluster-randomized controlled trial

The uptake of COVID-19 booster vaccination among older adults in China is suboptimal. Here, we report the results of a parallel-group cluster-randomized controlled trial evaluating the efficacy of promoting COVID-19 booster vaccination among grandparents (≥60 years) through a health education intervention delivered to their grandchildren (aged ≥16 years) in a Chinese cohort (Chinese Clinical Trial Registry: ChiCTR2200063240 ). The primary outcome was the uptake rate of COVID-19 booster dose among grandparents. Secondary outcomes include grandparents' attitude and intention to get a COVID-19 booster dose. A total of 202 college students were randomized 1:1 to either the intervention arm of web-based health education and 14 daily reminders (n = 188 grandparents) or control arm (n = 187 grandparents) and reported their grandparents' COVID-19 booster vaccination status at baseline and 21 days. Grandparents in the intervention arm were more likely to receive COVID-19 booster vaccination compared to control cohort (intervention, 30.6%; control, 16.9%; risk ratio = 2.00 (95% CI, 1.09 to 3.66)). Grandparents in the intervention arm also had greater attitude change (β = 0.28 (95% CI, 0.04 to 0.52)) and intention change (β = 0.32 (95% CI, 0.12 to 0.52)) to receive a COVID-19 booster dose. Our results show that an educational intervention targeting college students increased COVID-19 booster vaccination uptake among grandparents in China.

Predicting consequences of COVID-19 control measure de-escalation on nosocomial transmission and mortality: a modelling study in a French rehabilitation hospital

INTRODUCTION

Infection control measures are effective for nosocomial COVID-19 prevention but bear substantial health-economic costs, motivating their "de-escalation" in settings at low risk of SARS-CoV-2 transmission. Yet consequences of de-escalation are difficult to predict, particularly in light of novel variants and heterogeneous population immunity.

AIM

To estimate how infection control measure de-escalation influences nosocomial COVID-19 risk.

METHODS

An individual-based transmission model was used to simulate SARS-CoV-2 outbreaks and control measure de-escalation in a French long-term care hospital with multi-modal control measures in place (testing and isolation, universal masking, single-occupant rooms). Estimates of COVID-19 case fatality rates (CFRs) from reported outbreaks were used to quantify excess COVID-19 mortality due to de-escalation.

RESULTS

In a population fully susceptible to infection, de-escalating both universal masking and single rooms resulted in hospital-wide outbreaks of 114 (95% CI: 103-125) excess infections, compared with five (three to seven) excess infections when de-escalating only universal masking or 15 (11-18) when de-escalating only single rooms. When de-escalating both measures and applying CFRs from the first wave of COVID-19, excess patient mortality ranged from 1.57 (1.41-1.71) to 9.66 (8.73-10.57) excess deaths/1000 patient-days. By contrast, when applying CFRs from subsequent pandemic waves and assuming susceptibility to infection among 40-60% of individuals, excess mortality ranged from 0 (0-0) to 0.92 (0.77-1.07) excess deaths/1000 patient-days.

CONCLUSIONS

The de-escalation of bundled COVID-19 control measures may facilitate widespread nosocomial SARS-CoV-2 transmission. However, excess mortality is probably limited in populations at least moderately immune to infection and given CFRs resembling those estimated during the 'post-vaccine' era.