Aging shapes infection profiles of influenza A virus and SARS-CoV-2 in human lung slices (preprint)

The recent coronavirus disease 2019 (COVID-19) outbreak revealed the susceptibility of elderly patients to respiratory virus infections, showing cell senescence or subclinical persistent inflammatory profiles and favouring the development of severe pneumonia. In our study, we evaluated the potential influence of lung aging on the efficiency of replication of influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2), as well as determined the pro-inflammatory and antiviral responses of the distal lung tissue. Using precision-cut lung slices (PCLS) from donors of different ages, we found that pandemic H1N1 and avian H5N1 IAV replicated in the lung parenchyma with high efficacy. In contrast to these IAV strains, SARS-CoV-2 early isolate and Delta variant of concern (VOC) replicated less efficiently in PCLS. Interestingly, both viruses showed reduced replication in PCLS from older compared to younger donors, suggesting that aged lung tissue represents a sub optimal environment for viral replication. Regardless of the age-dependent viral loads, PCLS responded to infection with both viruses by an induction of IL-6 and IP-10/CXCL10 mRNAs, being highest for H5N1. Finally, while SARS-CoV-2 infection was not causing detectable cell death, IAV infection caused significant cytotoxicity and induced significant early interferon responses. In summary, our findings suggest that aged lung tissue might not favour viral dissemination, pointing to a determinant role of dysregulated immune mechanisms in the development of severe disease.

Timing and Depth Selection for Sedated Gastroscopy After SARS-CoV-2 Infection—A Retrospective Cohort Study (preprint)

Background Sedated gastroscopy is a crucial procedure for patients with upper respiratory infections. SARS-CoV-2-infected patients are more susceptible to anesthesia-related complications, such as edema, pharyngeal mucosa congestion, laryngospasm, and pulmonary infections.Methods We retrospectively analyzed a total of 386 patients who underwent sedated gastroscopy at the Affiliated Hospital of Qingdao University during the SARS-CoV-2 infection period. The patients were divided into three groups based on SARS-CoV-2 status: Negative (N), Two-week post-SARS-CoV-2 infection (T), and Three-week post-SARS-CoV-2 infection (Th) groups. Based on the anesthesia method, patients were divided into mild/moderate sedation and deep sedation/general anesthesia groups. Additionally, patients were categorized into groups based on COVID-19 severity and vaccination status. We recorded the laryngeal mucosal conditions, the occurrence rates of adverse reactions such as coughing, laryngospasm, and transient oxygen desaturation during the examination, as well as the satisfaction of patients and endoscopists were recorded.Results The T group displayed a significantly higher occurrence rate of adverse reactions when compared to the N and Th group, with decreased satisfaction levels of patients and endoscopists. In the T group, the occurrence rate of adverse reactions was higher in mild to moderate sedation than in deep sedation/general anesthesia methods, while patient and endoscopist satisfaction was lower. In the Th group, there was no statistically significant difference in the examination success rate or patient satisfaction between the mild/moderate sedation and deep sedation/general anesthesia methods; however, endoscopist satisfaction was lower with mild/moderate sedation method than deep sedation/general anesthesia method. There was a significant difference in the gastroscopy success rates of patients with different COVID-19 classifications. A significant difference was observed in the gastroscopy success rates among patients with different vaccination statuses.Conclusions Sedated gastroscopy post-three weeks of SARS-CoV-2 infection is safe. Moreover, using a deep sedation/general anesthesia method for sedated gastroscopy in SARS-CoV-2-infected patients within three weeks is significantly safer.

Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs (preprint)

Breast cancer is the second most common cancer globally. Most deaths from breast cancer are due to metastatic disease which often follows long periods of clinical dormancy1. Understanding the mechanisms that disrupt the quiescence of dormant disseminated cancer cells (DCC) is crucial for addressing metastatic progression. Infection with respiratory viruses (e.g. influenza or SARS-CoV-2) is common and triggers an inflammatory response locally and systemically2,3. Here we show that influenza virus infection leads to loss of the pro-dormancy mesenchymal phenotype in breast DCC in the lung, causing DCC proliferation within days of infection, and a greater than 100-fold expansion of carcinoma cells into metastatic lesions within two weeks. Such DCC phenotypic change and expansion is interleukin-6 (IL-6)-dependent. We further show that CD4 T cells are required for the maintenance of pulmonary metastatic burden post-influenza virus infection, in part through attenuation of CD8 cell responses in the lungs. Single-cell RNA-seq analyses reveal DCC-dependent impairment of T-cell activation in the lungs of infected mice. SARS-CoV-2 infected mice also showed increased breast DCC expansion in lungs post-infection. Expanding our findings to human observational data, we observed that cancer survivors contracting a SARS-CoV-2 infection have substantially increased risks of lung metastatic progression and cancer-related death compared to cancer survivors who did not. These discoveries underscore the significant impact of respiratory viral infections on the resurgence of metastatic cancer, offering novel insights into the interconnection between infectious diseases and cancer metastasis.

Human long noncoding RNA,VILMIR, is induced by major respiratory viral infections and modulates the host interferon response (preprint)

Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response ( VILMIR ), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro . We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to IFN-β treatment in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.

Short-term exposure to ambient air pollution and mortality and hospital admission in the Netherlands (preprint)

This study aimed to examine acute effects of exposure to ambient air pollution on COVID-19 hospital admissions and mortality in the Netherlands. We hypothesized that exposure to increased air pollution in the preceding week might trigger an exacerbation of health of infected individuals. Associations between daily concentrations of particulate matter with an aerodynamic diameter ≤2.5 µm (PM2.5) and ≤10 µm (PM10), nitrogen dioxide (NO2), ozone (O3) and risk of hospital admissions and mortality due to COVID-19 from February to December 2020 was analyzed across all 352 Dutch municipalities grouped into 12 provinces. Time-series models were used to fit province-specific estimates, followed by meta-analyses to produce national estimates. Analyses were based on daily averages of PM2.5, PM10, NO2, and maximum 8-hour running average of O3 on a 1x1 km grid and averaged on municipality level by population weight. Models were adjusted for spatiotemporal confounders, including government policies in response to the number of COVID-19 infections. Since there were only few COVID-19 cases during the summertime when O3 levels were highest, associations between O3 and COVID-19 health outcomes were not further explored. We found associations between exposure to air pollution in the preceding week (average of lag 0-7 days) and COVID-19 hospital admissions and mortality. On a national level, an interquartile range increase in PM2.5, PM10 and NO2 exposure was associated with 11-12% increased mortality risk; the risk for hospital admissions was higher: 19-25%. Observed associations were more robust for PM than NO2 in two-pollutant models. Our results suggest that short-term exposure to PM2.5 and PM10 may increase the risk of COVID-19 mortality and hospital admission. This indicates that, consistent with previous studies on air pollution and respiratory infections, the population at risk of being hospitalized or dying of COVID-19 is extra vulnerable to the adverse effects of short-term air pollution exposure.

The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication (preprint)

SARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections with S. aureus or influenza, ongoing pulmonary M. tuberculosis infection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNF and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.

Polarised human alveolar epithelia enable identification of dichloroacetate as an effective drug against respiratory viruses (preprint)

Respiratory viral infections are a significant cause of morbidity and mortality worldwide. The COVID-19 pandemic has highlighted the lack of chemotherapeutic tools available for fighting emerging viruses and the need to focus on preclinical models that better recapitulate human disease. We performed a comparative analysis of inhibitors of the PI3K/AKT/mTOR pathway, which is involved in virus-induced metabolic reprogramming, since strategies aimed at identifying cellular targets could serve to combat diverse viruses and hamper the development of resistance. Tests were performed in two human cell lines, MRC5 lung fibroblasts and Huh7 hepatoma cells, and the results showed that the inhibitors had markedly different effects on energy metabolism and antiviral activity. Thus, dichloroacetate (DCA) has potent antiviral activity against HCoV-229E in MRC5 cells but not in Huh7 cells, suggesting that the screening model is more critical than previously assumed. DCA was then tested in polarized human alveolar epithelia in air-liquid interface, a 3D model used to study respiratory infections. DCA reduced the viral progeny of HCoV-229E, SARS-CoV-2 and respiratory syncytial virus by 2-3 orders of magnitude, and it was effective even when applied once infection had been established. Although DCA has previously been shown to be effective against other viruses, suggesting that it could be a broad-spectrum antiviral, our experiments reinforce the need to use physiologically appropriate disease models to screen antiviral compound. 

Etiological analysis of acute respiratory infections in hospitalized children after the relaxation of COVID-19 non-pharmacological interventions in Quzhou, China (preprint)

Background: Acute respiratory infections (ARIs) can cause morbidity and mortality in children. This study was to determine the characteristics of pathogens in hospitalized children with ARIs after the relaxation of COVID-19 non-pharmacological interventions (NPIs) in Quzhou, China. Methods: Hospitalized children with ARIs were enrolled between May and October 2023, and thirteen common respiratory pathogens were tested by fluorescent quantitative polymerase chain reaction. Mono- and co-infections were assessed, and the association between pathogens and age was explored using restricted cubic spline analysis. Results: A total of 1225 children were included, 820 of them detected one pathogen and 238 of them detected two or more pathogens. Children aged 1-3 years had the highest positive detection rates. The dominant pathogen varied monthly. Mycoplasma pneumoniae (Mp) was the most common pathogen in monoinfection, followed by respiratory syncytial virus (RSV) and human rhinovirus (HRV), while influenza virus was detected at a lower rate. Mp+HRV was the most common combination of coinfections. The detection rates of Mp and HRV were higher in coinfections than in monoinfection, but there was no difference in the detection rate of RSV. In the restricted cubic spline models, a J-shaped association was consistently observed between age and Mp infection, the risk of HRV first increased and then decreased, the risk of RSV was relatively flat until 1.5 years and then decreased raplidly. Conclusion: Our study revealed the epidemiological characteristics of ARIs pathogens after the relaxation of NPIs. There is still a need to enhanced pathogen surveillance, especially for Mp.

Accurate Diagnosis of SARS-CoV-2 JN.1 by Sanger Sequencing of Receptor-Binding Domain Is Needed for Clinical Evaluation of Its Immune Evasion (preprint)

Background: SARS-CoV-2 Omicron JN.1 has the highest number of amino acid mutations in its receptor binding domain (RBD) and has acquired a hallmark L455S mutation. The immune evasion capability of JN.1 is a subject of scientific investigation. The US CDC used RT-qPCR SGTF as the proxy indicator of JN.1 infections for evaluation of the effectiveness of updated monovalent XBB.1.5 COVID-19 vaccines against JN.1 and recommended that all persons aged ≥6 months should receive an updated COVID-19 vaccine dose. Objective: Recommend Sanger sequencing for diagnosis of JN.1 infections to generate the data based on which guidelines are made to direct vaccination policies. Methods: The RNA in nasopharyngeal swab specimens from patients with clinical respiratory infection was subjected to nested RT-PCR, targeting a 398-base segment of the N-gene and a 445-base segment of the RBD of SARS-CoV-2 for amplification. The DNA sequences were analyzed for amino acid mutations. Results: The N-gene sequence showed Q229K, usually associated with Omicron BA.2.86 (+JN.1). The RBD sequence showed 24 amino acid mutations, including the hallmark L455S mutation for JN.1 and the V483del for BA.2.86 lineage. Conclusions: The CDC should consider Sanger sequencing of the RBD to diagnose JN.1 infections for statistical analysis in making vaccination policies.

Estimating the impact of public health interventions on COVID mortality in the United States using reductions in influenza mortality as an indicator of non-pharmaceutical infection control (preprint)

Background: Non-pharmaceutical interventions (NPIs) for control of COVID include a range of methods from masks to closures of schools and businesses with the efficacy of any individual strategy contingent on which other NPIs are employed and the extent of compliance with those strategies. In the case of a public health intervention, one typically looks at historical data for comparison, but, because COVID is a new disease, we have no such data. However, we do have extensive historical data for influenza, a respiratory disease with similar modes of transmission. Influenza incidence and mortality dropped dramatically during the COVID pandemic, almost certainly because of these NPIs. The extent of that drop provides an indirect measure of the efficacy of COVID NPIs in stopping the transmission of respiratory infections. This study evaluates the association of influenza mortality reduction (IMR) during the pandemic with age-adjusted COVID mortality among US states, adjusting for mortality prior to the introduction of NPIs and vaccination rates, while taking into account the impact of population density on NPI effectiveness. Results A simple linear model with pre-intervention COVID mortality, IMR, vaccination rate, and population density explained 70% of the state-to-state variability in age adjusted COVID mortality. The resulting model suggests that NPIs prevented 831,000 COVID related deaths in the United States over the course of the pandemic. Conclusions These results provide strong evidence that IMR is an accurate indicator of the efficacy of NPIs in controlling transmission of respiratory infections, including COVID. This analysis suggests that NPIs together with vaccination prevented an estimated 2.15 million COVID related deaths and full intervention could have prevented over 700,000 more.  

Healthcare-associated infections and antimicrobial use in acute care hospitals: a point prevalence survey in Lombardy, Italy, in 2022 (preprint)

Background: Healthcare-Associated Infections (HAIs) are a global public health issue, representing a significant burden of disease that leads to prolonged hospital stays, inappropriate use of antimicrobial drugs, intricately linked to the development of resistant microorganisms, and higher costs for healthcare systems. The study aimed to measure the prevalence of HAIs, the use of antimicrobials, and assess healthcare- and patient-related risk factors, to help identify key intervention points for effectively reducing the burden of HAIs.Methods: A total of 28 acute care hospitals in the Lombardy region, Northern Italy, participated in the third European Point Prevalence Survey (PPS-3) coordinated by ECDC for the surveillance of HAIs in acute care hospitals (Protocol 6.0).Results: HAIs were detected in 1,259 (10.1%, 95% CI 9.6–10.7%) out of 12,412 enrolled patients. 1,385 HAIs were reported (1.1 HAIs per patient on average). The most common types of HAIs were bloodstream infections (262 cases, 18.9%), urinary tract infections (237, 17.1%), SARS-CoV-2 infections (236, 17.0%), pneumonia and lower respiratory tract infections (231, 16.7%), and surgical site infections (152, 11.0%). Excluding SARS-CoV-2 infections, the overall prevalence of HAIs was 8.4% (95% CI 7.9–8.9%).

Prospective Clinical Surveillance for Severe Acute Respiratory Illness in Kenyan Hospitals during the COVID-19 pandemic (preprint)

There are limited data from sub-Saharan Africa describing the pattern of admissions to public hospitals with severe acute respiratory infections during the COVID-19 pandemic. We conducted a prospective longitudinal hospital-based sentinel surveillance between May 2020 and December 2022 at 16 public hospitals in Kenya. All patients aged above 18 years admitted to adult medical wards in the participating hospitals were included. Demographic and clinical characteristics, COVID-19 infection and vaccination status and outcome data were collected. Of the 52,714 patients included in the study, 18,001 (35%) were admitted with severe acute respiratory illness (SARI). The mean age was 51 years. Patients were equally distributed across sexes. Pneumonia was the most common diagnosis at discharge. Hypertension, HIV and diabetes mellitus were the most common comorbidities. COVID-19 test results were positive in 2,370 (28%) of the 8,517 (47%) patients that underwent testing. Overall inpatient case fatality for SARI was 21% (n=3,828). After adjusting for age, sex and presence of a comorbidity, SARI patients had higher inpatient mortality compared to non-SARI patients regardless of their COVID-19 status (aHR 1.31, 95% CI 1.19 - 1.46). COVID-19 positive SARI patients had a higher inpatient mortality rate compared to their negative counterparts (aHR 1.31, 95% CI 1.12 - 1.54, p value < 0.0001). COVID-19 vaccine effectiveness against mortality due to SARI after adjusting for age, sex and presence of a comorbidity was 34% (95% CI 11% - 51%). We have provided a comprehensive description of the pattern of admissions with respiratory illnesses in Kenyan hospitals during the COVID-19 pandemic period. We have demonstrated the utility of routine surveillance activities within public hospitals in low-income settings which if strengthened can enhance the response to emerging health threats.

A Comprehensive Machine Learning Approach for COVID-19 Target Discovery in the Small-Molecule Metabolome (preprint)

Respiratory viruses, including influenza, RSV, and COVID-19, cause various respiratory infections. Distinguishing these viruses relies on diagnostic methods such as PCR testing. Challenges stem from overlapping symptoms and the emergence of new strains. Advanced diagnostics are crucial for accurate detection and effective management. This study leveraged nasopharyngeal metabolome data to predict respiratory virus scenarios including control vs RSV, control vs influenza A, control vs COVID-19, control vs all respiratory viruses, and COVID-19 vs influenza A/RSV. Our advanced machine learning models, including linear discriminant analysis, support vector machine, random forest, and logistic regression, exhibited superior accuracy, sensitivity, and specificity to previous supervised machine learning approaches. Key techniques such as feature ranking, standard scaling, and SMOTE were used to address class imbalances, thus enhancing model robustness. SHAP analysis identified crucial metabolites influencing positive predictions, thereby providing valuable insights into diagnostic markers. Our approach not only outperformed existing methods but also revealed top dominant features for predicting COVID-19, including Lysophosphatidylcholine acyl C18:2, Kynurenine, Phenylalanine, Valine, tyrosine, and aspartic Acid (Asp). These compounds play critical roles in metabolic pathways and have been identified as top contributors to predictive models in COVID-19 respiratory virus scenarios.

Kidney Outcomes and Trajectories of Tubular Injury and Function in Critically Ill Persons with and without Coronavirus-2019 (preprint)

Background Coronavirus disease-2019 (COVID-19) may injure the kidney tubules via activation of inflammatory host responses and/or direct viral infiltration. Most studies of kidney injury in COVID-19 lacked contemporaneous controls or measured kidney biomarkers at a single time point. To better understand mechanisms of AKI in COVID-19, we compared kidney outcomes and trajectories of tubular injury, viability, and function in prospectively enrolled critically ill adults with and without COVID-19.Methods The COVID-19 Host Response and Outcomes (CHROME) study prospectively enrolled patients admitted to intensive care units in Washington state with symptoms of lower respiratory tract infection, determining COVID-19 status by nucleic acid amplification on arrival. We evaluated major adverse kidney events (MAKE) defined as a doubling of serum creatinine, kidney replacement therapy, or death, in 330 patients after inverse probability weighting. In the 181 patients with available biosamples, we determined trajectories of urine kidney injury molecule-1 (KIM-1) and epithelial growth factor (EGF), and urine:plasma ratios of endogenous markers of tubular secretory clearance.Results At ICU admission, mean age was 55\(\pm\)16 years; 45% required mechanical ventilation; and mean serum creatinine concentration was 1.1 mg/dL. COVID-19 was associated with a 70% greater incidence of MAKE (95% CI 1.05, 2.74) and a 741% greater incidence of KRT (95% CI 1.69, 32.41). The biomarker cohort had a median of three follow-up measurements. Urine EGF, secretory clearance ratios, and eGFR increased over time in the COVID-19 negative group but remained unchanged in the COVID-19 positive group. In contrast, urine KIM-1 concentrations did not significantly change over the course of the study in either group.Conclusions Among critically ill adults, COVID-19 is associated with a more protracted course of proximal tubular dysfunction.

Delayed Fatal Pulmonary Hemorrhage Following COVID-19 Vaccination: Case Report, Batch Analysis, And Proposed Autopsy Checklist (preprint)

We present a case of a 47-year-old male who died unexpectedly from acute pulmonary hemorrhage 555 days after completing the BNT162b2 (Pfizer) COVID-19 vaccination primary series. Before death, he exhibited symptoms of a mild respiratory infection. Despite a healthy medical history and no medication use, the patient’s condition rapidly deteriorated and he experienced severe respiratory distress, followed by cardiopulmonary arrest with evidence of profuse pulmonary bleeding. Autopsy findings revealed massive lung congestion without embolism, normal heart size, moderate coronary atherosclerosis without myocardial infarction, and no evidence of other hemorrhagic events. The patient tested negative for COVID-19 and other respiratory pathogens at autopsy. Despite these findings, the medical examiner determined the cause of death was attributed to atherosclerotic and hypertensive cardiovascular disease, without considering the recent pulmonary hemorrhage and unremarkable medical history. Investigation into the vaccine batch indicated a higher-than-average number of serious adverse events, including fatalities. The patient's BNT162b2 batch was among the top 2.8% for reported deaths. Moreover, the autopsy failed to investigate potential contributions from the vaccine, such as the presence of the Spike protein or related antibodies. The evidence suggests that the pulmonary hemorrhage, exacerbated by a viral infection, was the immediate cause of death, with the COVID-19 vaccine potentially playing a role in the development of cardiopulmonary pathology and hemorrhage. We propose autopsy protocols for COVID-19 vaccine recipients to better investigate vaccine-related pathologies among those with one or more prior injections.

Changes of respiratory pathogen and clinical features of in acute exacerbation of chronic obstructive pulmonary disease after COVID-19 pandemic (preprint)

Respiratory infections are common causes of acute exacerbation of chronic obstructive lung disease (AECOPD). We explored whether the pathogens causing AECOPD and clinical features changed from before to after the coronavirus disease 2019 (COVID-19) outbreak. We reviewed the medical records of patients hospitalized with AECOPD at four university hospitals between January 2017 and December 2018 and between January 2021 and December. We evaluated 1,180 patients with AECOPD for whom medication histories were available. After the outbreak, the number of patients hospitalized with AECOPD was almost 44% lower compared with before the outbreak. Patients hospitalized with AECOPD after the outbreak were younger (75 vs. 77 years, p = 0.003) and more often stayed at home (96.6% vs. 88.6%, p < 0.001) than patients of AECOPD before the outbreak. Hospital stay was longer after the outbreak than before the outbreak (10 vs. 8 days. p < 0.001). After the COVID-19 outbreak, the identification rates of S. pneumoniae (15.3 vs. 6.2%, p < 0.001) and Hemophilus influenzae (6.4 vs. 2.4%, p = 0.002) decreased, whereas the identification rates of P. aeruginosa (9.4 vs. 13.7%, p = 0.023), Klebsiella pneumoniae (5.3 vs. 9.8%, p = 0.004), and methicillin-resistant Staphylococcus aureus (1.0 vs. 2.8%, p = 0.023) increased. After the outbreak, the identification rate of influenza A decreased (10.4 vs. 1.0%, p = 0.023). After the outbreak, the number of patients hospitalized with AECOPD was lower and the identification rates of community-transmitted pathogens tended to decrease, whereas the rates of pathogens capable of chronic colonization tended to increase. During the period of large-scale viral outbreaks that require quarantine, patients with AECOPD should consider treatment against strains that can colonize chronic respiratory disease rather than community acquired pathogens.

Sufficient reproduction numbers to prevent recurrent epidemics (preprint)

Current practice in the design and evaluation of epidemic control measures, including vaccination, is largely based on reproduction numbers (RNs), which represent prognostic indexes of long-term disease transmission, both in naive populations (basic RN) and in the presence of prior exposure or interventions (effective RN). A standard control objective is to establish herd immunity, e.g., by immunizing enough susceptible individuals to achieve RN<1. However, attaining this goal is not sufficient to avoid transient outbreaks that, in the short term, might revamp epidemics by coalescence of subthreshold flare-ups. Using reactivity analysis applied to a discrete SIR model with age-of-infection structure, we determine sufficient conditions to prevent transient epidemic dynamics and recurrent, non-periodic outbreaks due to imported cases. These conditions are based on fundamental infection characteristics, namely the average infectiousness clearance rate, the generation time distribution, and the RN. We show that preventing subthreshold epidemicity requires stricter RN thresholds than simply maintaining RN<1. Taking into account a wide spectrum of respiratory viral infections, epidemicity-curbing RN thresholds vary between 0.10 (rubella) and 0.51 (MERS), with a median of 0.26 close to the estimate of 0.24 for the ancestral SARS-CoV-2 virus. The portion of the population that needs to be included in containment efforts to avoid short-term outbreaks is considerably higher than herd immunity thresholds (HITs) based solely on the basic RN (e.g., 93% vs. 72% for ancestral SARS-CoV-2). We also find that subthreshold epidemicity is harder to prevent for pathogens with a longer mean generation time, smaller standard deviation of the generation time distribution, longer duration of infection, and higher RN. Determining sufficient RN thresholds to prevent transient outbreaks is a key challenge in disease ecology, with practical consequences for the design of control measures, as the weaker RN reductions and HITs associated with customary control targets may prove ineffective in preventing potentially recurrent flare-ups. Due to its modest data requirements, our modeling framework may also have important implications for human and non-human diseases caused by emerging pathogens.

Human coronavirus 229E infection inactivates pyroptosis executioner gasdermin D but ultimately leads to lytic cell death partly mediated by gasdermin E (preprint)

Human coronavirus 229E (HCoV-229E) is associated with upper respiratory tract infections and causes local respiratory symptoms. It has been reported that HCoV-229E can cause cell death in a variety of cells in vitro. However, the molecular pathways that lead to virus-induced cell death remain poorly characterized. Here, we show that the main protease (Mpro) of HCoV-229E can cleave the pyroptosis executioner gasdermin D (GSDMD) within its active N-terminal domain at two different sites (Q29 and Q193) to generate fragments unable to cause pyroptosis. Despite GSDMD cleavage by HCoV-229E Mpro, we show that HCoV-229E infection leads to lytic cell death. We further demonstrate that virus-induced lytic cell death is partially dependent on the activation of caspases-3 and -8. Interestingly, inhibition of caspases does not only reduce lytic cell death upon infection, but also sustains the release of virus particles over time, which suggests that caspase-mediated cell death is a mechanism to limit virus replication and spread. Finally, we show that pyroptosis is partially dependent on another gasdermin family member, gasdermin E (GSDME). During HCoV-229E infection, GSDME is cleaved to yield its N-terminal pore-forming domain (p30). Accordingly, GSDME knockout cells show a significant decrease in lytic cell death upon virus, whereas this is not the case for GSDMD knockout cells, which aligns with the observation that GSDMD is also inactivated by caspase-3 during infection. These results suggest that GSDMD is inactivated during HCoV-229E infection, and point to GSDME as an important player in the execution of virus-induced cell death.

SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity (preprint)

Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to a limited understanding of how pregnancy shapes immune responses. To gain insight into the role of pregnancy in modulating immune responses at steady state and upon perturbation, we collected peripheral blood mononuclear cells (PBMC), plasma, and stool from 226 women, including 152 pregnant individuals (n = 96 with SARS-CoV-2 infection and n = 56 healthy controls) and 74 non-pregnant women (n = 55 with SARS-CoV-2 and n = 19 healthy controls). We found that SARS-CoV-2 infection was associated with altered T cell responses in pregnant compared to non-pregnant women. Differences included a lower percentage of memory T cells, a distinct clonal expansion of CD4-expressing CD8+ T cells, and the enhanced expression of T cell exhaustion markers, such as programmed cell death-1 (PD-1) and T cell immunoglobulin and mucin domain-3 (Tim-3), in pregnant women. We identified additional evidence of immune dysfunction in severely and critically ill pregnant women, including a lack of expected elevation in regulatory T cell (Treg) levels, diminished interferon responses, and profound suppression of monocyte function. Consistent with earlier data, we found maternal obesity was also associated with altered immune responses to SARS-CoV-2 infection, including enhanced production of inflammatory cytokines by T cells. Certain gut bacterial species were altered in pregnancy and upon SARS-CoV-2 infection in pregnant individuals compared to non-pregnant women. Shifts in cytokine and chemokine levels were also identified in the sera of pregnant individuals, most notably a robust increase of interleukin-27 (IL-27), a cytokine known to drive T cell exhaustion, in the pregnant uninfected control group compared to all non-pregnant groups. IL-27 levels were also significantly higher in uninfected pregnant controls compared to pregnant SARS-CoV-2-infected individuals. Using two different preclinical mouse models of inflammation-induced fetal demise and respiratory influenza viral infection, we found that enhanced IL-27 protects developing fetuses from maternal inflammation but renders adult female mice vulnerable to viral infection. These combined findings from human and murine studies reveal nuanced pregnancy-associated immune responses, suggesting mechanisms underlying the increased susceptibility of pregnant individuals to viral respiratory infections.

Syndromic case definitions for Lower Respiratory Tract Infection (LRTI) are less sensitive in older age: an analysis of symptoms among hospitalised adults (preprint)

Background Lower Respiratory Tract Infections (LRTI) pose a serious threat to older adults but may be underdiagnosed due to atypical presentations. Here we assess LRTI symptom profiles and syndromic (symptom-based) case ascertainment in older (≥65y) as compared to younger adults (<65y). Methods We included adults (≥18y) with confirmed LRTI admitted to two acute care Trusts in Bristol, UK from 1st August 2020- 31st July 2022.  Logistic regression was used to assess whether age ≥65y reduced the probability of meeting syndromic LRTI case definitions, using patients’ symptoms at admission. We also calculated relative symptom frequencies (log-odds ratios) and evaluated how symptoms were clustered across different age groups. Results Of 17,620 clinically confirmed LRTI cases, 8,487 (48.1%) had symptoms meeting the case definition. Compared to those not meeting the definition these cases were younger, had less severe illness and were less likely to have received a SARS-CoV-2 vaccination or to have active SARS-CoV-2 infection. Prevalence of dementia/cognitive impairment and levels of comorbidity were lower in this group. After controlling for sex, dementia and comorbidities, age ≥65y significantly reduced the probability of meeting the case definition (aOR=0.67, 95% CI:0.63-0.71). Cases aged ≥65y were less likely to present with fever and LRTI-specific symptoms (e.g., pleurisy, sputum) than younger cases, and those aged ≥85y were characterised by lack of cough but frequent confusion and falls. Conclusions LRTI symptom profiles changed considerably with age in this hospitalised cohort. Standard screening protocols may fail to detect older and frailer cases of LRTI based on their symptoms.