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How COVID-19 affected academic publishing: a 3-year study of 17 million research papers.
BackgroundThe COVID-19 pandemic induced an unprecedented response from the scientific research community. Previous studies have described disruption of the norms of academic publishing during this time. This study uses an epidemiological statistical toolkit alongside machine-learning methods to investigate the functioning of the scientific information-generation and -consumption ecosystem throughout the pandemic.MethodsA dataset of 17 million scientific research papers that were published between January 2019 and December 2022 was analysed. Data on citations and Altmetrics were harvested, and topic modelling was applied to abstracts. COVID-19-related articles were identified from title text. We investigated publication dynamics, correlations between citation metrics and Altmetrics, rates of publication in preprints, and temporal trends in topics, and compared these metrics in COVID-19 papers vs non-COVID-19 papers.ResultsThroughout 2020-2, 3.7% of English-language research output was on the topic of COVID-19. Journal articles on COVID-19 were published at a consistent rate during this period, while preprints peaked in early 2020 and decreased thereafter. COVID-19 preprints had lower publication rates in the peer-reviewed literature than other preprints, particularly those that were preprinted during early 2020. COVID-19 research received significantly more media and social media attention than non-COVID-19 research, and preprints received more attention, on average, than journal articles, with attention peaking during the initial wave and subsequent peaks corresponding to the emergence of novel variants. COVID-19 articles exhibited a higher correlation between Altmetrics and citation metrics compared with non-COVID-19 publications, suggesting a strong alignment between scientific and public attention.ConclusionThis study provides a comprehensive description of the rapid expansion of COVID-19 research, revealing evolving research areas and waxing and waning public interest across different topics. Preprints played an important role in disseminating scientific findings, but the level of coverage of preprinted findings emphasizes the need for guidelines in handling preprint research in media, particularly during a pandemic.
Epidemiological profiles and outcomes of healthcare workers hospitalized for COVID-19 in five Sub-Saharan African countries: a cohort study.
BackgroundThe COVID-19 pandemic placed immense strain on global health systems and healthcare workers (HCWs). This study aimed to analyze the epidemiological profiles and outcomes of HCWs hospitalized for COVID-19 across five sub-Saharan African countries.MethodsThis was a cohort study using secondary data collected between January 30, 2020, and December 31, 2022, as part of the International Severe Acute Respiratory and emerging Infection Consortium study. The study population consisted of HCWs who were hospitalized due to clinically suspected or laboratory-confirmed SARS-CoV-2 infection. Demographic and clinical characteristics and case management were summarized using proportions or medians and interquartile ranges. Factors associated with risk of mortality among HCWs were assessed using a Cox proportional hazards model, adjusted for age and sex.ResultsFindings showed that South Africa recorded a lower percentage (2.4%) of patients who were HCWs compared to Gambia, Ghana, Guinea, and Malawi. Overall, many HCWs were aged ≥50 years and the majority were females (66.8%). In three of the five countries, however, the majority of the HCWs were <39 years old and were males. Antibiotics were the most commonly used medical treatments across three countries (Ghana, 67.8%; Guinea, 97.3%; Malawi, 80%), while antimalarials were commonly used in Guinea (87.8%) and Ghana (30.4%). Guinea and South Africa reported deaths with case-fatality rates varying from 22% in March 2020 to 1.4% in February 2022. Risk factors for mortality included age over 50 years, hypertension, diabetes mellitus, and chronic kidney disease.ConclusionsOur study underscores the critical need for continuous protection and enhanced readiness for HCWs, particularly during epidemics and pandemics. Strengthening infection prevention and control measures and focusing on vulnerable groups such as older and female HCWs are essential for mitigating the impact of future health crises. Further research is required to fully comprehend the implications of these findings.
Association of cancer and outcomes of patients hospitalized for COVID-19 between 2020 and 2023.
BackgroundThe coronavirus disease 2019 (COVID-19) has caused substantial morbidity and mortality on a global scale. A strong correlation has been found between COVID-19 treatment outcomes and noncommunicable diseases such as cancers. However, there is limited information on the outcomes of cancer patients who were hospitalised for COVID-19.MethodsWe conducted an analysis on data collected in a large prospective cohort study set-up by the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC). All patients with laboratory-confirmed or clinically-diagnosed SARS-CoV-2 infection were included. Cancer was defined as having a current solid organ or haematological malignancy. The following outcomes were assessed; 30-day in-hospital mortality, intensive care unit (ICU) admission, length of hospitalization and receipt of higher-level care.ResultsOf the 560,547 hospitalised individuals who were analysed, 27,243 (4.9%) had cancer. Overall, cancer patients were older and had more comorbidities than non-cancer patients. Patients with cancer had higher 30-day in-hospital mortality than non-cancer patients (29.1.3% vs 18.0%) and longer hospital stays (median of 12 days vs 8 days). However, patients with cancer were admitted less often to intensive care units than non-cancer patients (12.6% vs 17.1%) and received less invasive mechanical ventilation than non-cancer patients (4.5% vs 7.6%). The hazard ratio of dying from cancer, adjusted for age, sex and country income level was 1.18 (95%CI: 1.15-1.2).ConclusionsThis study's findings underscore the heightened vulnerability of hospitalized COVID-19 patients with cancer, revealing a higher mortality rate, longer hospital stays, and an unstructured pattern of care that reflects the complexity of managing severely ill patients during a public health crisis like the COVID-19 pandemic.
Research prioritisation in preparedness for and response to outbreaks of high-consequence pathogens: a scoping review
Abstract Background Priority setting for research on epidemic/pandemic-prone pathogens is essential for the allocation of limited resources to optimise impact. It involves the identification of gaps in knowledge crucial to effective preparedness and response to outbreaks. This review maps priority-setting exercises, reviews their approaches to research prioritisation and describes associated monitoring and evaluation processes for research priorities on high-consequence pathogens. Methods Using search terms associated with high-consequence pathogens, as defined by the WHO (2020), EMERGE (2019), European CDC (2022) and the Association of Southeast Asian Nations (2021), and research prioritisation, we searched WHO Global Index Medicus; Ovid Medline; Ovid Embase; Ovid Global Health; and Scopus. Grey literature sources were Google Scholar and the WHO websites, complemented by recommendations from stakeholder consultation. Two independent reviewers screened abstracts and full-texts including documents describing research prioritisation activities. Results were analysed using descriptive statistics and narrative synthesis. Results We identified 125 publications presenting priority setting activities on 17 high-consequence pathogens published between 1975 and 2022. Most (62%) were related to SARS-CoV-2, 5.6% to Ebola virus and 5% to Zika virus. Three different broad approaches to setting priorities were identified, most (53%) involved external consultations with experts. Few (6%) indicated plans to monitor progress against set priorities. Conclusions Our results highlight the diversity in research prioritisation practice in the context of high-consequence pathogens and a limited application of the existing standards in health research prioritisation. An increased uptake of these standards and harmonisation of practice may improve quality and confidence and ultimately improve alignment of funded research with the resulting priorities.
Strengthening respectful communication with patients and colleagues in neonatal units — developing and evaluating a communication and emotional competence training for nurse managers in Kenya
Introduction: Effective communication is essential to delivering compassionate, high-quality nursing care. The intensive, stressful and technical environment of a new-born unit (NBU) in a low-resource setting presents communication-related challenges for nurses, with negative implications for nurse well-being, team relationships and patient care. We adapted a pre-existing communication and emotional competence course with NBU nurse managers working in Kenya, explored its’ value to participants and developed a theory of change to evaluate its’ potential impact. Methods 18 neonatal nurse managers from 14 county referral hospitals helped adapt and participated in a nine-month participatory training process. Training involved guided ‘on the job’ self-observation and reflection to build self-awareness, and two face-to-face skills-building workshops. The course and potential for future scale up was assessed using written responses from participant nurses (baseline questionnaires, reflective assignments, pre and post workshop questionnaires), workshop observation notes, two group discussions and nine individual in-depth interviews. Results Participants were extremely positive about the course, with many emphasizing its direct relevance and applicability to their daily work. Increased self-awareness and ability to recognize their own, colleagues’ and patients’ emotional triggers, together with new knowledge and practical skills, reportedly inspired nurses to change; in turn influencing their ability to provide respectful care, improving their confidence and relationships and giving them a stronger sense of professional identity. Conclusion Providing respectful care is a major challenge in low-resource, high-pressure clinical settings but there are few strategies to address this problem. The participatory training process examined addresses this challenge and has potential for positive impacts for families, individual workers and teams, including worker well-being. We present an initial theory of change to support future evaluations aimed at exploring if and how positive gains can be sustained and spread within the wider system.
Prediction and characterisation of the human B cell response to a heterologous two-dose Ebola vaccine.
Ebola virus disease (EVD) outbreaks are increasing, posing significant threats to affected communities. Effective outbreak management depends on protecting frontline health workers, a key focus of EVD vaccination strategies. IgG specific to the viral glycoprotein serves as the correlate of protection for recent vaccine licensures. Using advanced cellular and transcriptomic analyses, we examined B cell responses to the Ad26.ZEBOV, MVA-BN-Filo EVD vaccine. Our findings reveal robust plasma cell and lasting B cell memory responses post-vaccination. Machine-learning models trained on blood gene expression predicted antibody response magnitude. Notably, we identified a unique B cell receptor CDRH3 sequence post-vaccination resembling known Orthoebolavirus zairense (EBOV) glycoprotein-binding antibodies. Single-cell analyses further detailed changes in plasma cell frequency, subclass usage, and CDRH3 properties. These results highlight the predictive power of early immune responses, captured through systems immunology, in shaping vaccine-induced B cell immunity.
Antibiotic use attributable to RSV infections during infancy-an international prospective birth cohort study.
BackgroundEarly-life antibiotic use impacts microbiome composition and contributes to the emergence of antimicrobial resistance. Despite respiratory syncytial virus (RSV) being a leading cause of acute respiratory infections (ARI), accurate estimates of antibiotic use attributable to RSV are lacking.ObjectivesTo assess RSV-associated antibiotic use during the first year of life.Patients and methodsThe RESCEU birth cohort study followed healthy term infants, born (n = 9154) between 1 July 2017 and 31 July 2020 from five European countries, to identify RSV-ARI hospitalizations during infancy. In a nested cohort (n = 993), we performed active RSV surveillance by collecting nasal swabs in case of ARI symptoms during RSV seasons (October-April). Antibiotic use during hospitalization was identified through chart review, while outpatient data were collected via parental questionnaires.ResultsIn the total cohort, antibiotics were used in 22.8% of RSV hospitalizations (33/145) and 62.5% of RSV intensive care admissions (5/8). In the nested cohort, antibiotics were used in 5.2% of any-severity RSV-ARI (13/250) and 9.9% of medically attended RSV-ARI (13/131). This results in an estimated incidence of 1.3% (95%CI: 0.8-2.0) of healthy term infants receiving ≥1 course of antibiotics associated with RSV infection in their first year, with an incidence rate of 1.1 RSV-associated antibiotic prescriptions per 1000 infant-months (95%CI: 0.6-1.9). As such, RSV accounts for 22.9% of antibiotic prescriptions for ARI during RSV seasons.ConclusionsOne in 77 healthy term infants receives antibiotics during RSV infection before their first birthday. Real-world evidence is needed to establish the impact of RSV immunization on antibiotic use during infancy.Clinical trials registrationNCT03627572.
Developing the next-generation of adenoviral vector vaccines.
The COVID-19 pandemic saw the first extensive use of adenoviral vector vaccines, with over 3 billion doses produced during the first year of the pandemic alone and an estimated 6 million lives saved. These vaccines were safe and effective, and could be produced at low cost in several continents allowing widespread use in low- and middle-income countries (LMICs). Despite their successful deployment against SARS-CoV-2, their impact has been overshadowed by relatively lower immunogenicity in contrast to mRNA vaccine technologies and very rare but serious adverse events such as vaccine-induced thrombotic thrombocytopaenia (VITT). The next-generation of adenoviral vector vaccines must address these challenges: here, we explore strategies to improve immunogenicity and safety by novel serotype selection, vector engineering, capsid modification and new delivery technologies, and discuss opportunities for next-generation adenoviral vectors against infectious disease and cancer.
Air and surface sampling for clade Ib monkeypox virus in United Kingdom hospitals, 2024 to 2025
Air and surface sampling was performed in isolation rooms of seven patients with clade Ib mpox admitted to high consequence infectious disease centres in the United Kingdom. We detected monkeypox virus (MPXV) DNA in 66/90 surfaces samples and 1/14 air samples; replication competent MPXV was identified in 4/21 surface samples selected for viral isolation. These findings demonstrate that viable clade Ib MPXV contamination can occur during treatment of clade Ib mpox patients reinforcing the importance of infection prevention and control measures.
Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine.
Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6-14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.