Transmissibility and transmission of respiratory viruses

SARS-CoV-2 surrogate bacteriophage φ6 cross-contamination between fruits and gloves, survival on discarded gloves and inactivation by photodynamic treatment

This study assessed the SARS-CoV-2 surrogate bacteriophage φ6 cross-contamination between high-density polyethylene or polyvinyl chloride gloves and fruits (tomato and cucumber) using different inoculum levels (6.0 and 4.0 log PFU/sample). Bacteriophage φ6 survival on contaminated gloves was assessed over 9 days at 25 °C. The effectiveness of photodynamic treatment using curcumin as a photosensitizer to inactivate φ6 on fruits was determined. The fruit type and the glove material influenced the φ6 transfer. Longer contact times resulted in greater φ6 transfer. The highest φ6 transfer occurred from tomato to HDPE glove (0.8% or -1.1 log % transfer) after 30 s of contact at the higher inoculum level. Bacteriophage φ6 was detected on cross-contaminated HDPE gloves for up to 6 days. Bacteriophage φ6 survived better on vinyl gloves cross-contaminated by cucumber vs. tomato (detected up to 6 vs 3 days). Photodynamic inactivation of φ6 was time-dependent and varied with the tested fruit but was not influenced by viral starting concentration. Photodynamic treatment decreased the φ6 titer by 3.0 and 2.2 log PFU/sample in tomato and cucumber, respectively. Transmission electronic microscopy showed that photodynamic treatment changed the structure of the φ6 capsid. These findings may help in the management of SARS-CoV-2 contamination risks in fruit handling. They may also help in the establishment of effective measures to manage cross-contamination risk.

Implementation of facemask sampling for the detection of infectious individuals with SARS-CoV-2 in high stakes clinical examinations - a feasibility study

Introduction

SARS-CoV-2 may transmit across vaccinated cohorts during practical clinical examinations. We sought to assess the feasibility of facemask sampling (FMS) to identify individuals emitting SARS-CoV-2 during a mock PACES exam.

Methods

In May 2022 we recruited participants from a mock PACES examination in Leicester, UK. Following a negative lateral flow test assay, all participants wore modified facemasks able to capture exhaled virus during the assessment (FMS). A concomitant upper respiratory tract sample (URTS) was provided prior to FMS. Exposed facemasks were processed by removal and dissolution of sampling matrices fixed within the mask and cycle thresholds values quantified by RT-qPCR. Participants were asked to grade statements regarding the comfort, effort, ethics and communication when providing FMS; laboratory technicians were asked to grade key statements surrounding suitability of samples for processing.

Results

34 participants provided concomitant URTS and FMS during the examination. One participant was positive for SARS-CoV-2, with a cycle threshold value of 22.5 on URTS, but negative (no viral RNA detected) on FMS; no transmission to others was identified from this individual. Participants responded positively to statements regarding FMS describing all four domains; however, 69% of participants felt that a positive result from FMS alone was insufficient for diagnosis and that further tests were required. All but one FMS sample was suitable for processing.

Discussion

FMS during PACES exams are acceptable among participants and samples provided are suitable for processing. Our results demonstrate feasibility of FMS within practical examination settings and support the further assessment of FMS as a scalable tool that can be compared with URTS to identify those who are infectious.

Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review

Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.

Seasonality of common respiratory viruses: Analysis of nationwide time-series data

BACKGROUND AND OBJECTIVE

Understanding the seasonal behaviours of respiratory viruses is crucial for preventing infections. We evaluated the seasonality of respiratory viruses using time-series analyses.

METHODS

This study analysed prospectively collected nationwide surveillance data on eight respiratory viruses, gathered from the Korean Influenza and Respiratory Surveillance System. The data were collected on a weekly basis by 52 nationwide primary healthcare institutions between 2015 and 2019. We performed Spearman correlation analyses, similarity analyses via dynamic time warping (DTW) and seasonality analyses using seasonal autoregressive integrated moving average (SARIMA).

RESULTS

The prevalence of rhinovirus (RV, 23.6%-31.4%), adenovirus (AdV, 9.2%-16.6%), human coronavirus (HCoV, 3.0%-6.6%), respiratory syncytial virus (RSV, 11.7%-20.1%), influenza virus (IFV, 11.7%-21.5%), parainfluenza virus (PIV, 9.2%-12.6%), human metapneumovirus (HMPV, 5.6%-6.9%) and human bocavirus (HBoV, 5.0%-6.4%) were derived. Most of them exhibited a high positive correlation in Spearman analyses. In DTW analyses, all virus data from 2015 to 2019, except AdV, exhibited good alignments. In SARIMA, AdV and RV did not show seasonality. Other viruses showed 12-month seasonality. We describe the viruses as winter viruses (HCoV, RSV and IFV), spring/summer viruses (PIV, HBoV), a spring virus (HMPV) and all-year viruses with peak incidences during school periods (RV and AdV).

CONCLUSION

This is the first study to comprehensively analyse the seasonal behaviours of the eight most common respiratory viruses using nationwide, prospectively collected, sentinel surveillance data.

Identification of JC polyomavirus in upper respiratory samples from Portuguese children

Background

JC polyomavirus (JCPyV) is ubiquitous in the human population and the causative agent of a rare, fatal and demyelinating disease of the central nervous system named Progressive Multifocal Leukoencephalopathy (PML). The route of JCPyV transmission remains unclear, but high values of seroprevalence suggest an easy and frequent mode, such as respiratory route.

Objectives

The present study aims to investigate the presence of JCPyV in upper respiratory samples and contribute to the elucidation of the JCPyV transmission pathway.

Study design

Nasopharyngeal swabs from 587 Portuguese individuals, including 380 children (≤18 years) and 207 adults (>18 years), collected for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis between September and November 2021 were evaluated for the presence of JCPyV DNA.

Results

JCPyV DNA was detected in 3.1 % of the nasopharyngeal swabs analysed, with higher frequency of detection in samples from children (4.5 %) than from adults (0.5 %) (p = 0.005). Infection with SARS-CoV-2 does not potentiate the presence of JCPyV in upper respiratory tract, once only one adult of 28 years with confirmed SARS-CoV-2 infection showed detectable JCPyV DNA. JCPyV DNA was more frequently detected in respiratory samples from children without SARS-CoV-2 infection (6.4 %). As for this group, children under six years of age presents the highest frequency of detection (10.3 %).

Conclusions

The present study demonstrates that upper respiratory secretions of children, particularly under the age of six, may be implicated in JCPyV transmission, regardless of SARS-CoV-2 infection.

The circulating characteristics of common respiratory pathogens in Ningbo, China, both before and following the cessation of COVID-19 containment measures

To assess the circulating characteristics of common respiratory pathogens following the complete relaxation of non-pharmaceutical interventions (NPIs) and the cessation of the dynamic zero-COVID policy. The retrospective analysis was conducted from 14,412 patients with acute respiratory infections (ARIs) from January 24, 2020, to December 31, 2023, including Influenza A virus (IFV-A), Influenza B virus (IFV-B), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), Human Parainfluenza Virus (HPIV), Human Metapneumovirus (HMPV), Human Coronavirus (HCoV), Human Bocavirus (HBoV), Human Adenovirus (HAdV), and Mycoplasma pneumoniae (MP). Compared with 2020-2022, Joinpoint analysis indicated a monthly increase in overall pathogen activity in 2023, rising from an average of 43.05% to an average of 68.46%. The positive rates of IFV-A, IFV-B, HMPV, HPIV, HCoV, and MP increased, while those of HRV and RSV decreased, and no differences in HAdV and HBoV. The outbreak of IFV-A and MP was observed, the positive rate of MP has surpassed pre-COVID-19 pandemic levels and the spread of RSV was interrupted by IFV-A. Infants and toddlers were primarily infected by HRV and RSV, Children and adolescents exhibited a higher prevalence of infections with MP, IFV-A, and HRV, whereas Adults and the elderly were primarily infected by IFV-A. The incidence of co-infections rose from 4.25 to 13.73%. Restricted cubic spline models showed that the susceptible age ranges for multiple pathogens expanded. These changes serve as a reminder to stay alert in the future and offer clinicians a useful guide for diagnosing and treating.

Shape-dependent aerosol dynamics in indoor environments: Penetration, deposition, and dispersion

Particle shape exerts a significant influence on their dynamic behavior, and it is imperative to elucidate these effects given the potential for severe environmental toxicity associated with shaped particles. Despite extensive research on the dynamical processes of spherical particles, the behaviors of non-spherical particles have been insufficiently investigated. In this study, we have developed a suite of computation-based models that account for particle shape and have reported on the typical dynamical behaviors of non-spherical particles within indoor environments. We have explored three typical scenarios, i.e., particle penetration into indoor spaces through building cracks, indoor particle deposition, and indoor particle dispersion. The shape-induced deviations are associated with dynamical processes, showing a decrease trend among penetration, deposition, and dispersion of the non-spherical particles. The maximum discrepancy due to particle shape during the penetration process exceeds 1000 %, observed with particles of approximately 0.02 μm in diameter interacting with straight cracks 4.5 cm in length and 0.25 mm in height. Moreover, there is a discrepancy of more than 70 % in the deposition of particles with a diameter of approximately 10 μm on side walls when using side air supply ventilation. Similarly, a discrepancy of nearly 11 % is noted for particles around 0.02 μm in diameter during dispersion under displacement ventilation within indoor settings. The interaction between shape-related particle dynamics, particularly their diffusion characteristics, and the properties of the flow field leads to these shape-dependent dynamical discrepancies. These findings offer a comprehensive understanding of how the shape of particles affects their indoor dynamic behavior, thereby supporting the control of hazardous particles in indoor environments.

Features that matter: Evolutionary signatures can predict viral transmission routes

Routes of virus transmission between hosts are key to understanding viral epidemiology. Different routes have large effects on viral ecology, and likelihood and rate of transmission; for example, respiratory and vector-borne viruses together encompass the majority of rapid outbreaks and high-consequence animal and plant epidemics. However, determining the specific transmission route(s) can take months to years, delaying mitigation efforts. Here, we identify the viral features and evolutionary signatures which are predictive of viral transmission routes and use them to predict potential routes for fully-sequenced viruses in silico and rapidly, for both viruses with no observed routes, as well as viruses with missing routes. This was achieved by compiling a dataset of 24,953 virus-host associations with 81 defined transmission routes, constructing a hierarchy of virus transmission encompassing those routes and 42 higher-order modes, and engineering 446 predictive features from three complementary perspectives. We integrated those data and features to train 98 independent ensembles of LightGBM classifiers. We found that all features contributed to the prediction for at least one of the routes and/or modes of transmission, demonstrating the utility of our broad multi-perspective approach. Our framework achieved ROC-AUC = 0.991, and F1-score = 0.855 across all included transmission routes and modes, and was able to achieve high levels of predictive performance for high-consequence respiratory (ROC-AUC = 0.990, and F1-score = 0.864) and vector-borne transmission (ROC-AUC = 0.997, and F1-score = 0.921). Our framework ranks the viral features in order of their contribution to prediction, per transmission route, and hence identifies the genomic evolutionary signatures associated with each route. Together with the more matured field of viral host-range prediction, our predictive framework could: provide early insights into the potential for, and pattern of viral spread; facilitate rapid response with appropriate measures; and significantly triage the time-consuming investigations to confirm the likely routes of transmission.

Artificial intelligence-based prediction of pathogen emergence and evolution in the world of synthetic biology

The emergence of new techniques in both microbial biotechnology and artificial intelligence (AI) is opening up a completely new field for monitoring and sometimes even controlling the evolution of pathogens. However, the now famous generative AI extracts and reorganizes prior knowledge from large datasets, making it poorly suited to making predictions in an unreliable future. In contrast, an unfamiliar perspective can help us identify key issues related to the emergence of new technologies, such as those arising from synthetic biology, whilst revisiting old views of AI or including generative AI as a generator of abduction as a resource. This could enable us to identify dangerous situations that are bound to emerge in the not-too-distant future, and prepare ourselves to anticipate when and where they will occur. Here, we emphasize the fact that amongst the many causes of pathogen outbreaks, often driven by the explosion of the human population, laboratory accidents are a major cause of epidemics. This review, limited to animal pathogens, concludes with a discussion of potential epidemic origins based on unusual organisms or associations of organisms that have rarely been highlighted or studied.

Air quality in a small city: criteria pollutants, volatile organic compounds, metals, and microbes

This work presents a year-long integral study of air quality parameters in Ciudad Real, a small city in the center of Spain, and its influence on the nearby national park, Las Tablas de Daimiel. The study covers meteorological parameters and criteria pollutants such as O3, NO, NO2, SO2, and PM10. Additionally, for each month, a 1-week campaign was performed sampling air in sorbent tubes with 8-h time resolution to analyze anthropogenic volatile organic compounds and the effects of seasons, daytime, and working-weekend days. During these campaigns, 24-h PM2.5 samples were also collected to measure the load of bacteria and fungi, as well as the trace concentrations of elements.The city and the national park NOx profiles showed that emissions from the town had a non-perceivable effect on the protected area. PM10 levels in Ciudad Real were influenced by Saharan intrusions, as was the national park; however, Ciudad Real had a higher contribution from anthropogenic sources. Ozone levels were lower in the city during the cold season due to the higher concentration of NOx and have not changed significantly in the last decade.The VOCs with higher average concentrations were toluene, m,p-xylene, benzene, methylene chloride, and o-xylene, with traffic being the main source of these pollutants in the city. For benzene and carbon tetrachloride levels, weak carcinogenic risks were estimated. In PM2.5, the most abundant metals were Na, Zn, Mg, Ca, Al, Fe, and K. The carcinogenic and non-carcinogenic risks estimated from the levels of the studied metals were negligible. Bacterial and fungal counts positively correlated with the concentration of PM2.5. Microbial community composition showed seasonal variability, with the dominance of human pathogenic bacteria which correlated with certain pollutants such as SO2. Bacillus and Cutibacterium were the most abundant genera.

Severe respiratory syncytial virus infection in children: burden, management, and emerging therapies

The global burden of respiratory syncytial virus (RSV) lower respiratory tract infection (LRTI) in young children is high. The RSV prevention strategies approved in 2023 will be essential to lowering the global disease burden. In this Series paper, we describe clinical presentation, burden of disease, hospital management, emerging therapies, and targeted prevention focusing on developments and groundbreaking publications for RSV. We conducted a systematic search for literature published in the past 15 years and used a non-systematic approach to analyse the results, prioritising important papers and the most recent reviews per subtopic. Annually, 33 million episodes of RSV LRTI occur in children younger than 5 years, resulting in 3·6 million hospitalisations and 118 200 deaths. RSV LRTI is a clinical diagnosis but a clinical case definition and universal clinical tool to predict severe disease are non-existent. The advent of molecular point-of-care testing allows rapid and accurate confirmation of RSV infection and could reduce antibiotic use. There is no evidence-based treatment of RSV, only supportive care. Despite widespread use, evidence for high-flow nasal cannula (HFNC) therapy is insufficient and increased paediatric intensive care admissions and intubation indicate the need to remove HFNC therapy from standard care. RSV is now a vaccine-preventable disease in young children with a market-approved long-acting monoclonal antibody and a maternal vaccine targeting the RSV prefusion protein. To have a high impact on life-threatening RSV infection, infants at high risk, especially in low-income and middle-income countries, should be prioritised as an interim strategy towards universal immunisation. The implementation of RSV preventive strategies will clarify the full burden of RSV infection. Vaccine probe studies can address existing knowledge gaps including the effect of RSV prevention on transmission dynamics, antibiotic misuse, the respiratory microbiome composition, and long-term sequalae.

Yeast Surface-Displayed Quenchbody as a Novel Whole-Cell Biosensor for One-Step Detection of Influenza A (H1N1) Virus

Timely surveillance of airborne pathogens is essential to preventing the spread of infectious diseases and safeguard human health. Methods for sensitive, efficient, and cost-effective detection of airborne viruses are needed. With advances in synthetic biology, whole-cell biosensors have emerged as promising platforms for environmental monitoring and medical diagnostics. However, the current design paradigm of whole-cell biosensors is mostly based on intracellular detection of analytes that can transport across the cell membrane, which presents a critical challenge for viral pathogens and large biomolecules. To address this challenge, we developed a new type of whole-cell biosensor by expressing and displaying VHH-based quenchbody (Q-body) on the surface of the yeast Saccharomyces cerevisiae for simple one-step detection of influenza A (H1N1) virus. Seventeen VHH antibody fragments targeting the hemagglutinin protein H1N1-HA were displayed on the yeast cells and screened for the H1N1-HA binding affinity. The functionally displayed VHHs were selected to create surface-displayed Q-body biosensors. The surface-displayed Q-body exhibiting the highest quenching and dequenching efficiency was identified. The biosensor quantitatively detected H1N1-HA in a range from 0.5 to 16 μg/mL, with a half-maximal concentration of 2.60 μg/mL. The biosensor exhibited high specificity for H1N1-HA over other hemagglutinin proteins from various influenza A virus subtypes. Moreover, the biosensor succeeded in detecting the H1N1 virus at concentrations from 2.4 × 104 to 1.5 × 107 PFU/mL. The results from this study demonstrated a new whole-cell biosensor design that circumvents the need for transport of analytes into biosensor cells, enabling efficient detection of the target virus particles.

AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs

Aerosol-transmitted viruses possess strong infectivity and can spread over long distances, earning the difficult-to-control title. They cause various human diseases and pose serious threats to human health. Mutations can increase the transmissibility and virulence of the strains, reducing the protection provided by vaccines and weakening the efficacy of antiviral drugs. In this study, we established a manually curated database (termed AVM) to store information on aerosol-transmitted viral mutations (VMs). The current version of the AVM contains 42,041 VMs (including 2613 immune escape mutations), 45 clinical information datasets, and 407 drugs/antibodies/vaccines. Additionally, we recorded 88 human diseases associated with viruses and found that the same virus can target multiple organs in the body, leading to diverse diseases. Furthermore, the AVM database offers a straightforward user interface for browsing, retrieving, and downloading information. This database is a comprehensive resource that can provide timely and valuable information on the transmission, treatment, and diseases caused by aerosol-transmitted viruses (http://www.bio-bigdata.center/AVM).

Risk of SARS-CoV-2 infection in professional settings, shops, shared transport, and leisure activities in France, 2020-2022

PURPOSE

The aim of the study was to identify settings associated with SARS-CoV-2 transmission throughout the COVID-19 pandemic in France.

METHODS

Cases with recent SARS-CoV-2 infection were matched with controls (4:1 ratio) on age, sex, region, population size, and calendar week. Odds ratios for SARS-CoV-2 infection were estimated for nine periods in models adjusting for socio-demographic characteristics, health status, COVID-19 vaccine, and past infection.

RESULTS

Between October 27, 2020 and October 2, 2022, 175,688 cases were matched with 43,922 controls. An increased risk of infection was documented throughout the study for open-space offices compared to offices without open space (OR range across the nine periods: 1.12 to 1.57) and long-distance trains (1.25 to 1.88), and during most of the study for convenience stores (OR range in the periods with increased risk: 1.15 to 1.44), take-away delivery (1.07 to 1.28), car-pooling with relatives (1.09 to 1.68), taxis (1.08 to 1.89), airplanes (1.20 to 1.78), concerts (1.31 to 2.09) and night-clubs (1.45 to 2.95). No increase in transmission was associated with short-distance shared transport, car-pooling booked over platforms, markets, supermarkets and malls, hairdressers, museums, movie theatres, outdoor sports, and swimming pools. The increased risk of infection in bars and restaurants was no longer present in restaurants after reopening in June 2021. It persisted in bars only among those aged under 40 years.

CONCLUSION

Closed settings in which people are less likely to wear masks were most affected by SARS-CoV-2 transmission and should be the focus of air quality improvement.

CLINICALTRIALS

GOV (03/09/2022): NCT04607941.

Aerosolization ocular surface microorganisms accumulation effect during non-contact tonometer measurements

PURPOSE

This study aimed to verify that aerosolization ocular surface microorganisms (AOSMs) accumulated during non-contact tonometry (NCT) measurements.

METHODS

A total of 508 participants (740 eyes) were enrolled in the study. In Experiment 1, before NCT was performed on each eye, the air was disinfected, and environment air control samples were collected via Air ideal® 3P (Bio Merieux). During NCT measurements, microbial aerosol samples were collected once from each eye. In Experiment 2, we collected initial blank control samples and then repeated Experiment 1. Finally, in Experiment 3, after the background microbial aerosol investigation, we cumulatively sampled AOSMs from each 10 participants then culture once, without any interventions to interrupt the accumulation. The collected samples were incubated and identified using matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF-MS).

RESULTS

Pathogenic Aerococcus viridans and other microorganisms from human eyes can spread and accumulate in the air during NCT measurements. The species and quantity of AOSMs produced by NCT measurements can demonstrate an accumulation effect.

CONCLUSION

AOSMs generated during NCT measurements are highly likely to spread and accumulate in the air, thereby may increase the risk of exposure to and transmission of bio-aerosols.

Pathogen shape: Implication on pathogenicity via respiratory deposition

The shape of environmental aerosols contributes to the discrepancy in their dynamic behavior compared to spherical particles, which have received inadequate consideration. We reported deposition patterns of aerosols and aerosol-transmissible pathogens in real human respiratory systems, taking into account their actual shape, using a validated computational-based model. We found that the shape of the aerosols significantly influenced its deposits and accessibility within the respiratory system, significantly in the tracheobronchial region. As an example, we estimated that over 180 % of differences in deposits in the trachea and bronchi were attributable to pathogens shape, inferring the underlying pathogenicity difference of these regions. These findings, capturing the spatial heterogeneity of pathogens and aerosols deposition in human respiratory system, have major implication for understanding the evolution of aerosol-related disease.

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.

3-chymotrypsin-like protease in SARS-CoV-2

Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.

OLAH connects fatty acid metabolism to the severity of respiratory viral disease

Respiratory virus infections may cause profound respiratory illness, yet the factors that underlie disease severity are not well understood. In this issue of Cell, Jia, Crawford, et al.1 identify the role of oleoyl-ACP-hydrolase (OLAH) in mediating life-threatening inflammation associated with viral respiratory disease severity.

Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020-2021

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic resulted in widespread morbidity and mortality, but generally, the diagnosis of other respiratory viruses was limited. This study aimed to assess the prevalence of other respiratory viruses during the 2020/2021 pandemic among patients of all ages who accessed care at public healthcare facilities in Gauteng Province, South Africa. Laboratory diagnosis for respiratory viruses, with or without SARS-CoV-2, was conducted via multiplex real-time polymerase chain reactions using respiratory specimens. A total of 1776 patients were included from 1 April 2020 to 31 March 2021, of which 766 (43.1%) were positive for respiratory viruses other than SARS-CoV-2. RV (368/1776; 20.7%) was the most prevalent, followed by RSV (304/1776; 17.1%), AdV (112/1776; 6.3%) and EV (105/1776; 5.9%). hCoV-OC43 (39/1776; 2.2%) was the most prevalent common coronavirus. SARS-CoV-2 co-infections were detected in 4.8% (24/500) of patients. Only 27.1% (482/1776) of patients were admitted to high-care or intensive care units. A decrease in respiratory virus detections was observed, except for RSV, EV and hCoV-OC43. RSV prevalence increased in 2021, while influenza A/B viruses remained undetected.

Early detection of highly transmissible viral variants using phylogenomics

As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a serious threat to global health. Statistical models of genome sequence evolution may provide a critical tool for early detection of these strains. Using a novel stochastic model that links transmission rates to the entire viral genome sequence, we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count-based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations. We find that phylogenies in particular can detect novel transmission-enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance.

Multi-component liquid-infused systems: a new approach to functional coatings

Antifouling liquid-infused surfaces have generated interest in multiple fields due to their diverse applications in industry and medicine. In nearly all reports to date, the liquid component consists of only one chemical species. However, unlike traditional solid surfaces, the unique nature of liquid surfaces holds the potential for synergistic and even adaptive functionality simply by including additional elements in the liquid coating. In this work, we explore the concept of multi-component liquid-infused systems, in which the coating liquid consists of a primary liquid and a secondary component or components that provide additional functionality. For ease of understanding, we categorize recently reported multi-component liquid-infused surfaces according to the size of the secondary components: molecular scale, in which the secondary components are molecules; nanoscale, in which they are nanoparticles or their equivalent; and microscale, in which the additional components are micrometer size or above. We present examples at each scale, showing how introducing a secondary element into the liquid can result in synergistic effects, such as maintaining a pristine surface while actively modifying the surrounding environment, which are difficult to achieve in other surface treatments. The review highlights the diversity of fabrication methods and provides perspectives on future research directions. Introducing secondary components into the liquid matrix of liquid-infused surfaces is a promising strategy with significant potential to create a new class of multifunctional materials. Keywords: Active surfaces; Antimicrobial; Antifouling; Interfaces; Sensing surfaces.

Assessment of immunopathological responses of a novel non-chemical biocide in C57BL/6 for safe disinfection usage

BACKGROUND

Water electrospray technology has been developed and extensively studied for its physical properties and potential application as a non-chemical biocide against airborne pathogens. However, there are still concerns regarding the safety and potential toxicity of inhaling water electrospray (WE) particles. To address these potential hazards and offer insights into the impact of WE on humans, we analyzed the immunopathological response to WE by employing an intranasal challenge C57BL/6 mouse model. This analysis aimed to compare the effects of WE with those of sodium hypochlorite (SH), a well-known biocidal agent.

RESULTS

The study findings suggest that the WE did not trigger any pathological immune reactions in the intranasal-challenged C57BL/6 mouse model. Mice challenged with WE did not experience body weight loss, and there was no increase in inflammatory cytokine production compared to SH-treated mice. Histopathological analysis revealed that WE did not cause any damage to the lung tissue. In contrast, mice treated with SH exhibited significant lung tissue damage, characterized by the infiltration of neutrophils and eosinophils. Transcriptomic analysis of lung tissue further confirmed the absence of a pathological immune response in mice treated with WE compared to those treated with SH. Upon intranasal challenge with WE, the C57BL/6 mouse model did not show any evidence of immunopathological damage.

CONCLUSIONS

The results of this study suggest that WE is a safe technology for disinfecting airborne pathogens. It demonstrated little to no effect on immune system activation and pathological outcomes in the intranasal challenge C57BL/6 mouse model. These findings not only support the potential use of WE as an effective and safe method for air disinfection but also highlight the value of the intranasal challenge of the C57BL/6 mouse model in providing significant immunopathological insights for assessing the inhalation of novel materials for potential use.

Ventilation does not affect close-range transmission of influenza virus in a ferret playpen setup

Sustained community spread of influenza viruses relies on efficient person-to-person transmission. Current experimental transmission systems do not mimic environmental conditions (e.g., air exchange rates, flow patterns), host behaviors, or exposure durations relevant to real-world settings. Therefore, results from these traditional systems may not be representative of influenza virus transmission in humans. To address this pitfall, we developed a close-range transmission setup that implements a play-based scenario and used it to investigate the impact of ventilation rates on transmission. In this setup, four immunologically naive recipient ferrets were exposed to a donor ferret infected with a genetically barcoded 2009 H1N1 virus (H1N1pdm09) for 4 h. The ferrets interacted in a shared space that included toys, similar to a childcare setting. Transmission efficiency was assessed under low and high ventilation, with air exchange rates of ~1.3 h-1 and 23 h-1, respectively. Transmission efficiencies observed in three independent replicate studies were similar between ventilation conditions. The presence of infectious virus or viral RNA on surfaces and in air throughout the exposure area was also not impacted by the ventilation rate. While high viral genetic diversity in donor ferret nasal washes was maintained during infection, recipient ferret nasal washes displayed low diversity, revealing a narrow transmission bottleneck regardless of ventilation rate. Examining the frequency and duration of ferret physical touches revealed no link between these interactions and a successful transmission event. Our findings indicate that exposures characterized by frequent, close-range interactions and the presence of fomites can overcome the benefits of increased ventilation.

Unveiling the intersection: ferroptosis in influenza virus infection

The influenza virus (IFV) imposes a considerable health and economic burden globally, requiring a comprehensive understanding of its pathogenic mechanisms. Ferroptosis, an iron-dependent lipid peroxidation cell death pathway, holds unique implications for the antioxidant defense system, with possible contributions to inflammation. This exploration focuses on the dynamic interplay between ferroptosis and the host defense against viruses, emphasizing the influence of IFV infections on the activation of the ferroptosis pathway. IFV causes different types of cell death, including apoptosis, necrosis, and ferroptosis. IFV-induced ferroptotic cell death is mediated by alterations in iron homeostasis, intensifying the accumulation of reactive oxygen species and promoting lipid peroxidation. A comprehensive investigation into the mechanism of ferroptosis in viral infections, specifically IFV, has great potential to identify therapeutic strategies. This understanding may pave the way for the development of drugs using ferroptosis inhibitors, presenting an effective approach to suppress viral infections.

Factors influencing long-term care facility performance during the COVID-19 pandemic: a scoping review

BACKGROUND

The COVID-19 pandemic wreaked havoc on long-term care facilities (LTCFs). Some LTCFs performed better than others at slowing COVID-19 transmission. Emerging literature has mostly described infection prevention and control strategies implemented by LTCFs during the pandemic. However, there is a need for a comprehensive review of factors that influenced the performance of LTCFs in containing COVID-19 spread to inform public health policy.

OBJECTIVE

To build on the existing literature, we conducted a scoping review of factors that influenced LTCF performance during the COVID-19 pandemic using a multidimensional conceptual framework of performance.

METHODS

We followed the Joanna Briggs Institute's methodology for scoping reviews. We queried CINAHL, MEDLINE (Ovid), CAIRN, Science Direct, Scopus, and Web of Science for peer-reviewed literature in English or French published between January 1st, 2020 and December 31st, 2021. Retrieved records were screened for context (COVID-19 pandemic), population (LTCFs), interest (internal and external factors that influenced LTCF performance), and outcomes (dimensions of performance: equity, accessibility, reactivity, safety, continuity, efficacy, viability, efficiency). Descriptive characteristics of included articles were summarized. Dimensions of performance as well as internal (e.g., facility characteristics) and external (e.g., visitors) factors identified to have influenced LTCF performance were presented.

RESULTS

We retained 140 articles of which 68% were classified as research articles, 47% originated in North America, and most covered a period between March and July 2020. The most frequent dimensions of performance were "efficacy" (75.7%) and "safety" (75.7%). The most common internal factors were "organizational context" (72.9%) and "human resources" (62.1%), and the most common external factors were "visitors" (27.1%) and "public health guidelines" (25.7%).

CONCLUSIONS

Our review contributes to a global interest in understanding the impact of the COVID-19 pandemic on vulnerable populations residing and working in LTCFs. Though a myriad of factors were reported, a lack of randomized controlled trials makes it impossible to establish causality between the identified factors and LTCF performance. The use of a multidimensional framework can be recommended to evaluate healthcare system performance not merely in terms of efficacy and safety, but alongside other critical dimensions such as efficiency and equity.

TRIAL REGISTRATION

Research Registry ID: researchregistry7026.

An intranasal nanoparticle STING agonist protects against respiratory viruses in animal models

Respiratory viral infections cause morbidity and mortality worldwide. Despite the success of vaccines, vaccination efficacy is weakened by the rapid emergence of viral variants with immunoevasive properties. The development of an off-the-shelf, effective, and safe therapy against respiratory viral infections is thus desirable. Here, we develop NanoSTING, a nanoparticle formulation of the endogenous STING agonist, 2'-3' cGAMP, to function as an immune activator and demonstrate its safety in mice and rats. A single intranasal dose of NanoSTING protects against pathogenic strains of SARS-CoV-2 (alpha and delta VOC) in hamsters. In transmission experiments, NanoSTING reduces the transmission of SARS-CoV-2 Omicron VOC to naïve hamsters. NanoSTING also protects against oseltamivir-sensitive and oseltamivir-resistant strains of influenza in mice. Mechanistically, NanoSTING upregulates locoregional interferon-dependent and interferon-independent pathways in mice, hamsters, as well as non-human primates. Our results thus implicate NanoSTING as a broad-spectrum immune activator for controlling respiratory virus infection.

Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology

Wastewater-based epidemiology (WBE) can help mitigate the spread of respiratory infections through the early detection of viruses, pathogens, and other biomarkers in human waste. The need for sample collection, shipping, and testing facilities drives up the cost of WBE and hinders its use for rapid detection and isolation in environments with small populations and in low-resource settings. Given the ubiquitousness and regular outbreaks of respiratory syncytial virus, SARS-CoV-2, and various influenza strains, there is a rising need for a low-cost and easy-to-use biosensing platform to detect these viruses locally before outbreaks can occur and monitor their progression. To this end, we have developed an easy-to-use, cost-effective, multiplexed platform able to detect viral loads in wastewater with several orders of magnitude lower limit of detection than that of mass spectrometry. This is enabled by wafer-scale production and aptamers preattached with linker molecules, producing 44 chips at once. Each chip can simultaneously detect four target analytes using 20 transistors segregated into four sets of five for each analyte to allow for immediate statistical analysis. We show our platform's ability to rapidly detect three virus proteins (SARS-CoV-2, RSV, and Influenza A) and a population normalization molecule (caffeine) in wastewater. Going forward, turning these devices into hand-held systems would enable wastewater epidemiology in low-resource settings and be instrumental for rapid, local outbreak prevention.

Potential effects of aerosol generation and transmission during bedside endoscope cleaning

Airborne transmission is among the most frequent types of nosocomial infection. Recent years have witnessed frequent outbreaks of airborne diseases, such as severe acute respiratory syndrome (SARS) in 2002, Middle East respiratory syndrome (MERS) in 2012, and coronavirus disease 2019 (COVID-19), with the latter being on the rampage since the end of 2019 and bringing the effect of aerosols on health back to the fore (Gralton et al., 2011; Wang et al., 2021). An increasing number of studies have shown that certain highly transmissible pathogens can maintain long-term stability and efficiently spread through aerosols (Leung, 2021; Lv et al., 2021). As reported previously, influenza viruses that can spread efficiently through aerosols remain stable for a longer period compared to those that cannot. The World Health Organization (WHO) has stated that aerosol-generating procedures (AGPs) play an important role in aerosol transmission in hospitals (Calderwood et al., 2021). AGPs, referring to medical procedures that produce aerosols, including dental procedures, endotracheal intubation, sputum aspiration, and laparoscopic surgeries, have been reported to be significantly associated with an increased risk of nosocomial infection among medical personnel (Hamilton, 2021).

Short-term effects of PM2.5 components on the respiratory infectious disease: a global perspective

Although previous research has reached agreement on the significant impact of particulate matter (PM2.5) on respiratory infectious diseases, PM2.5 acts as an aggregation of miscellaneous pollutants and the individual effect of each component has not been examined. Here, we investigate the effects of PM2.5 components, including black carbon (BC), organic carbon (OC), sulfate ion (SO4), dust, and sea salt (SS), on the morbidity and mortality of the recent respiratory disease, i.e. COVID-19. The daily data of 236 countries and provinces/states (e.g., in the United States and China) worldwide during 2020-2022 are utilized. To derive the pollutant-specific causal effects, optimal instrumental variables for each pollutant are selected from a large set of atmospheric variables. We find that one µg/m3 increase in OC increases the number of cases and death by about 3% to 6% from the mean worldwide during a lag of one day up to three days. Our findings remain consistent and robust when we change control variables such as the flight index and weather proxies, and also when applying a sine transformation to the positivity and death rate. When analyzing health effects among different areas, we find stronger impact in China, for its higher local OC concentration, as opposed to the impact in the United States. Health benefits from PM2.5 pollution reduction are comparatively high for developed regions, yet decreases in cases and deaths number are rather overt in less developing regions. Our research provides inspiration and reference for dealing with other respiratory diseases in the post-pandemic era.

Association between ambient temperature and influenza prevalence: A nationwide time-series analysis in 201 Chinese cities from 2013 to 2018

BACKGROUND

Temperature affects influenza transmission; however, currently, limited evidence exists about its effect in China at the national and city levels as well as how temperature can be integrated into influenza interventions.

METHODS

Meteorological, pollutant, and influenza data from 201 cities in mainland China between 2013 and 2018 were analyzed at both the city and national levels to investigate the relationship between temperature and influenza prevalence. We examined the impact of temperature on the time-varying reproduction number (Rt) using generalized additive quasi-Poisson regression models combined with the distributed lag nonlinear model. Threshold temperatures were determined for seven regions based on the early warning threshold of serious influenza outbreaks, set at Rt = 1.2. A multivariate random-effects meta-analysis was employed to assess region-specific associations. The excess risk (ER) index was defined to investigate the correlation between Rt and temperature, modified based on seasonal and regional characteristics.

RESULTS

At the national level and in the central, northern, northwestern, and southern regions, temperature was found to be negatively correlated with relative risk, whereas the shapes of the data curves for the eastern, southwestern, and northeastern regions were not well defined. Low temperatures had an observable effect on influenza prevalence; however, the effects of high temperatures were not obvious. At an Rt of 1.2, the threshold temperatures for reaching a warning for serious influenza outbreaks were - 24.3 °C in the northeastern region, 16.6 °C in the northwestern region, and between 1℃ and 10 °C in other regions.

CONCLUSION

The study findings revealed that temperature had a varying effect on influenza transmission trends (Rt) across different regions in China. By identifying region-specific temperature thresholds at Rt = 1.2, more effective early warning systems for influenza outbreaks could be tailored. These findings emphasize the significance of the region-specific adaptation of influenza prevention and control measures.

Self-Promoted Hydroxyl Radical Releasing Magnetic Zn@Fe Particles

Semiconductor photocatalysts, such as TiO2 and ZnO, have garnered significant attention for their ability to generate hydroxyl radicals, offering various practical applications. However, the reliance on UV light to facilitate electron-hole separation for hydroxyl radical production poses limitations. In this study, a novel approach is presented utilizing Zn@Fe core/shell particles capable of generating hydroxyl radicals without external energy input. The generation process involves electron donation from Zn to O2, resulting in the formation of radical species .O2 -/H2O2, followed by Fe-catalyzed conversion of H2O2 into hydroxyl radicals through the Fenton reaction. The release of .OH imparts good antimicrobial and antiviral properties to the Zn@Fe particles. Furthermore, the inclusion of Fe confers magnetic properties to the material. This dual functionality holds promise for diverse potential applications for the Zn@Fe particles.

Emerging contaminants: A One Health perspective

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

Repurposing Anticancer Drugs Targeting the MAPK/ERK Signaling Pathway for the Treatment of Respiratory Virus Infections

Respiratory virus infections remain a significant challenge to human health and the social economy. The symptoms range from mild rhinitis and nasal congestion to severe lower respiratory tract dysfunction and even mortality. The efficacy of therapeutic drugs targeting respiratory viruses varies, depending upon infection time and the drug resistance engendered by a high frequency of viral genome mutations, necessitating the development of new strategies. The MAPK/ERK pathway that was well delineated in the 1980s represents a classical signaling cascade, essential for cell proliferation, survival, and differentiation. Since this pathway is constitutively activated in many cancers by oncogenes, several drugs inhibiting Raf/MEK/ERK have been developed and currently used in anticancer treatment. Two decades ago, it was reported that viruses such as HIV and influenza viruses could exploit the host cellular MAPK/ERK pathway for their replication. Thus, it would be feasible to repurpose this category of the pathway inhibitors for the treatment of respiratory viral infections. The advantage is that the host genes are not easy to mutate such that the drug resistance rarely occurs during short-period treatment of viruses. Therefore, in this review we will summarize the research progress on the role of the MAPK/ERK pathway in respiratory virus amplification and discuss the potential of the pathway inhibitors (MEK inhibitors) in the treatment of respiratory viral infections.

Identifying the panorama of potential pandemic pathogens and their key characteristics: a systematic scoping review

The globe has recently seen several terrifying pandemics and outbreaks, underlining the ongoing danger presented by infectious microorganisms. This literature review aims to explore the wide range of infections that have the potential to lead to pandemics in the present and the future and pave the way to the conception of epidemic early warning systems. A systematic review was carried out to identify and compile data on infectious agents known to cause pandemics and those that pose future concerns. One hundred and fifteen articles were included in the review. They provided insights on 25 pathogens that could start or contribute to creating pandemic situations. Diagnostic procedures, clinical symptoms, and infection transmission routes were analyzed for each of these pathogens. Each infectious agent's potential is discussed, shedding light on the crucial aspects that render them potential threats to the future. This literature review provides insights for policymakers, healthcare professionals, and researchers in their quest to identify potential pandemic pathogens, and in their efforts to enhance pandemic preparedness through building early warning systems for continuous epidemiological monitoring.

Masks and respirators for prevention of respiratory infections: a state of the science review

SUMMARYThis narrative review and meta-analysis summarizes a broad evidence base on the benefits-and also the practicalities, disbenefits, harms and personal, sociocultural and environmental impacts-of masks and masking. Our synthesis of evidence from over 100 published reviews and selected primary studies, including re-analyzing contested meta-analyses of key clinical trials, produced seven key findings. First, there is strong and consistent evidence for airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens. Second, masks are, if correctly and consistently worn, effective in reducing transmission of respiratory diseases and show a dose-response effect. Third, respirators are significantly more effective than medical or cloth masks. Fourth, mask mandates are, overall, effective in reducing community transmission of respiratory pathogens. Fifth, masks are important sociocultural symbols; non-adherence to masking is sometimes linked to political and ideological beliefs and to widely circulated mis- or disinformation. Sixth, while there is much evidence that masks are not generally harmful to the general population, masking may be relatively contraindicated in individuals with certain medical conditions, who may require exemption. Furthermore, certain groups (notably D/deaf people) are disadvantaged when others are masked. Finally, there are risks to the environment from single-use masks and respirators. We propose an agenda for future research, including improved characterization of the situations in which masking should be recommended or mandated; attention to comfort and acceptability; generalized and disability-focused communication support in settings where masks are worn; and development and testing of novel materials and designs for improved filtration, breathability, and environmental impact.

Severe Human Parainfluenza Virus Community- and Healthcare-Acquired Pneumonia in Adults at Tertiary Hospital, Seoul, South Korea, 2010-2019

The characteristics of severe human parainfluenza virus (HPIV)-associated pneumonia in adults have not been well evaluated. We investigated epidemiologic and clinical characteristics of 143 patients with severe HPIV-associated pneumonia during 2010-2019. HPIV was the most common cause (25.2%) of severe virus-associated hospital-acquired pneumonia and the third most common cause (15.7%) of severe virus-associated community-acquired pneumonia. Hematologic malignancy (35.0%), diabetes mellitus (23.8%), and structural lung disease (21.0%) were common underlying conditions. Co-infections occurred in 54.5% of patients admitted to an intensive care unit. The 90-day mortality rate for HPIV-associated pneumonia was comparable to that for severe influenza virus-associated pneumonia (55.2% vs. 48.4%; p = 0.22). Ribavirin treatment was not associated with lower mortality rates. Fungal co-infections were associated with 82.4% of deaths. Clinicians should consider the possibility of pathogenic co-infections in patients with HPIV-associated pneumonia. Contact precautions and environmental cleaning are crucial to prevent HPIV transmission in hospital settings.

Social contacts in Switzerland during the COVID-19 pandemic: Insights from the CoMix study

To mitigate the spread of SARS-CoV-2, the Swiss government enacted restrictions on social contacts from 2020 to 2022. In addition, individuals changed their social contact behavior to limit the risk of COVID-19. In this study, we aimed to investigate the changes in social contact patterns of the Swiss population. As part of the CoMix study, we conducted a survey consisting of 24 survey waves from January 2021 to May 2022. We collected data on social contacts and constructed contact matrices for the age groups 0-4, 5-14, 15-29, 30-64, and 65 years and older. We estimated the change in contact numbers during the COVID-19 pandemic to a synthetic pre-pandemic contact matrix. We also investigated the association of the largest eigenvalue of the social contact and transmission matrices with the stringency of pandemic measures, the effective reproduction number (Re), and vaccination uptake. During the pandemic period, 7084 responders reported an average number of 4.5 contacts (95% confidence interval, CI: 4.5-4.6) per day overall, which varied by age and survey wave. Children aged 5-14 years had the highest number of contacts with 8.5 (95% CI: 8.1-8.9) contacts on average per day and participants that were 65 years and older reported the fewest (3.4, 95% CI: 3.2-3.5) per day. Compared with the pre-pandemic baseline, we found that the 15-29 and 30-64 year olds had the largest reduction in contacts. We did not find statistically significant associations between the largest eigenvalue of the social contact and transmission matrices and the stringency of measures, Re, or vaccination uptake. The number of social contacts in Switzerland fell during the COVID-19 pandemic and remained below pre-pandemic levels after contact restrictions were lifted. The collected social contact data will be critical in informing modeling studies on the transmission of respiratory infections in Switzerland and to guide pandemic preparedness efforts.

Cutting Edge: First Lung Infection Permanently Enlarges Lymph Nodes and Enhances New T Cell Responses

Humans experience frequent respiratory infections. Immunology and vaccinology studies in mice are typically performed in naive specific pathogen-free animals responding to their very first respiratory challenge. We found that the first respiratory infection induces lifelong enlargement of the lung-draining mediastinal lymph nodes (medLNs). Furthermore, infection-experienced medLNs supported better naive T cell surveillance and effector responses to new unrelated infections that exhibited more biased accumulation and memory establishment within the lung. Moreover, we observed that weight loss induced by influenza infection was substantially reduced in mice that had recovered from a previous unrelated respiratory viral challenge. These data show that the lack of infectious history and corresponding medLN hypoplasia in specific pathogen-free mice alter their immune response to lung infections. Preclinical vaccination and immunology studies should consider the previous infectious experience of the model organism.

Rapid and accurate SERS assay of disease-related nucleic acids based on isothermal cascade signal amplifications of CRISPR/Cas13a system and catalytic hairpin assembly

Developing rapid, accurate and convenient nucleic acid diagnostic techniques is essential for the prevention and control of contagious diseases that are prone to gene mutations and may have homologous sequences, especially emerging infectious diseases such as the SARS-CoV-2 pandemic. Herein, a one-pot SERS assay integrating isothermal cascade signal amplification strategy (i.e., CRISPR/Cas13a system (Cas13a) and catalytic hairpin assembly (CHA), Cas13a-CHA) and SERS-active silver nanorods (AgNRs) sensing chips was proposed for rapid and accurate detection of disease-related nucleic acids. Taking SARS-CoV-2 RNA assay as a model, the Cas13a-CHA based SERS sensing strategy can achieve ultra-high sensitivity low to 5.18 × 102 copies·mL-1 within 60 min, and excellent specificity, i.e., not only the ability to identify SARS-CoV-2 RNA from gene mutations, but also incompatibility with coronaviruses such as severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and other respiratory viruses. The proposed Cas13a-CHA based SERS assay for SARS-CoV-2 RNA has satisfactory sensitivity, specificity, uniformity, and repeatability, and can be easily expanded and universalized for screening different viruses, which is expected to promise as a crucial role for diagnosis of disease-related nucleic acids in various medical application scenarios.

A COVID-19 cluster analysis in an office: Assessing the long-range aerosol and fomite transmissions with infection control measures

Simulated exposure to severe acute respiratory syndrome coronavirus 2 in the environment was demonstrated based on the actual coronavirus disease 2019 cluster occurrence in an office, with a projected risk considering the likely transmission pathways via aerosols and fomites. A total of 35/85 occupants were infected, with the attack rate in the first stage as 0.30. It was inferred that the aerosol transmission at long-range produced the cluster at virus concentration in the saliva of the infected cases on the basis of the simulation, more than 108 PFU mL-1. Additionally, all wearing masks effectiveness was estimated to be 61%-81% and 88%-95% reduction in risk for long-range aerosol transmission in the normal and fit state of the masks, respectively, and a 99.8% or above decline in risk of fomite transmission. The ventilation effectiveness for long-range aerosol transmission was also calculated to be 12%-29% and 36%-66% reductions with increases from one air change per hour (ACH) to two ACH and six ACH, respectively. Furthermore, the virus concentration reduction in the saliva to 1/3 corresponded to the risk reduction for long-range aerosol transmission by 60%-64% and 40%-51% with and without masks, respectively.

How Does the Burden of Respiratory Syncytial Virus Compare to Influenza in Spanish Adults?

BACKGROUND

Respiratory syncytial virus (RSV) and influenza infections cause significant annual morbidity and mortality worldwide in at-risk populations. This study is aimed at assessing hospital burden and healthcare resource utilization (HRU) of RSV and influenza in adults in Spain.

METHODS

Data were obtained from the Projected Hospitalisation Database of inpatient episodes (ages: younger adults 18-50 and 51-64 years; older adults 65-74, 75-84, and ≥ 85 years) during 2015, 2017, and 2018 in Spanish public hospitals. Incidence, mean hospitalization, and HRU assessments, including length of stay (LOS), intensive care unit (ICU) usage, and age-standardized mortality rates, were collected and stratified by age group, with analyses focusing on the adult population (≥ 18 years old).

RESULTS

Mean hospitalization rate in the population across all years was lower in individuals with RSV versus influenza (7.2/100,000 vs. 49.7/100,000 individuals). ICU admissions and median LOS were similar by age group for both viruses. Age-standardized mortality was 6.3/100,000 individuals and 6.1/100,000 individuals in patients with RSV and influenza, respectively, and mortality rates were similar in older adults (≥ 65 years) for both viruses.

CONCLUSIONS

RSV and influenza infection were associated with considerable HRU. There is a substantial disease burden for RSV infection in older adults ≥ 65 years. While RSV hospitalization rates in adults reported here appeared lower than influenza, RSV is still underdiagnosed in the hospital setting and its incidence might be similar to, or higher than, influenza.

SARS-CoV-2 genome incidence on the inanimate surface of the material used in the flow of biological samples from the collection point to the testing unit

Despite the undeniable effect of vaccination against COVID-19 in reducing disease severity, there is still a need to monitor and limit SARS-CoV-2 circulation and transmission. Thus, this study evaluated the presence of the SARS-CoV-2 genome on the surfaces of highly touched objects manipulated in the biological sample collection point and at the reception unit of the diagnostic laboratory. Surfaces were sampled once a week, for 6 weeks, between September 18th and October 23rd, 2020. RT-qPCR was used for SARS-CoV-2 detection. The coolers for biological sample transportation and the envelope containing the patient form were the objects with the highest occurrence of viral genome detection, although it was detected in each object in only two of the 6 evaluations. And the SARS-CoV-2 genome was detected just once on the vehicle steering wheel, computer keyboard, bathroom door handle and disinfection bench. The virus genome was not detected in any object on three of the six evaluations. And eight was the largest number of surfaces contaminated by the virus genome on one occasion. The reduced incidence of object contamination by the SARS-CoV-2 genome can be explained by the exposure of the objects to environmental conditions and the adoption of virus-spread containment measures. It can also reflect the low incidence of SARS-CoV-2 during the study's development period. Despite the low frequency of SARS-CoV-2 genome detection, our findings show that the virus was present in the environment at some point. This highlights the importance of adopting personal preventive measures to reduce respiratory virus spread, especially during epidemics and outbreaks.

Utilizing Rapid Hydrogen Peroxide Generation from 6-Hydroxycatechol to Design Moisture-Activated, Self-Disinfecting Coating

A coating that can be activated by moisture found in respiratory droplets could be a convenient and effective way to control the spread of airborne pathogens and reduce fomite transmission. Here, the ability of a novel 6-hydroxycatechol-containing polymer to function as a self-disinfecting coating on the surface of polypropylene (PP) fabric was explored. Catechol is the main adhesive molecule found in mussel adhesive proteins. Molecular oxygen found in an aqueous solution can oxidize catechol and generate a known disinfectant, hydrogen peroxide (H2O2), as a byproduct. However, given the limited amount of moisture found in respiratory droplets, there is a need to enhance the rate of catechol autoxidation to generate antipathogenic levels of H2O2. 6-Hydroxycatechol contains an electron donating hydroxyl group on the 6-position of the benzene ring, which makes catechol more susceptible to autoxidation. 6-Hydroxycatechol-coated PP generated over 3000 μM of H2O2 within 1 h when hydrated with a small amount of aqueous solution (100 μL of PBS). The generated H2O2 was three orders of magnitude higher when compared to the amount generated by unmodified catechol. 6-Hydroxycatechol-containing coating demonstrated a more effective antimicrobial effect against both Gram-positive (Staphylococcus aureus and Staphylococcus epidermidis) and Gram-negative (Pseudomonas aeruginosa and Escherichia coli) bacteria when compared to unmodified catechol. Similarly, the self-disinfecting coating reduced the infectivity of both bovine viral diarrhea virus and human coronavirus 229E by as much as a 2.5 log reduction value (a 99.7% reduction in viral load). Coatings containing unmodified catechol did not generate sufficient H2O2 to demonstrate significant virucidal effects. 6-Hydroxycatechol-containing coating can potentially function as a self-disinfecting coating that can be activated by the moisture present in respiratory droplets to generate H2O2 for disinfecting a broad range of pathogens.

Contraction of Respiratory Viral Infection During air Travel: An Under-Recognized Health Risk for Athletes

Air travel has an important role in the spread of viral acute respiratory infections (ARIs). Aircraft offer an ideal setting for the transmission of ARI because of a closed environment, crowded conditions, and close-contact setting. Numerous studies have shown that influenza and COVID-19 spread readily in an aircraft with one virus-positive symptomatic or asymptomatic index case. The numbers of secondary cases differ markedly in different studies most probably because of the wide variation of the infectiousness of the infector as well as the susceptibility of the infectees. The primary risk factor is sitting within two rows of an infectious passenger. Elite athletes travel frequently and are thus prone to contracting an ARI during travel. It is anecdotally known in the sport and exercise medicine community that athletes often contract ARI during air travel. The degree to which athletes are infected in an aircraft by respiratory viruses is unclear. Two recent studies suggest that 8% of Team Finland members traveling to major winter sports events contracted the common cold most probably during air travel. Further prospective clinical studies with viral diagnostics are needed to understand the transmission dynamics and to develop effective and socially acceptable preventive measures during air travel.

Outbreak of influenza and SARS-CoV-2 at the Armed Forces of the Philippines Health Service Education and Training Center, September 25-October 10, 2023

In the last week of September 2023, a surge of influenza-like illness was observed among students of the Armed Forces of the Philippines (AFP) Health Service Education and Training Center, where 48 (27 males and 21 females; age in years: mean 33, range 27-41) of 247 military students at the Center presented with respiratory symptoms. Between September 25 and October 10, 2023, all 48 symptomatic students were evaluated with real-time reverse transcription polymerase chain reaction and sequencing for both influenza and SARS-CoV-2. Thirteen (27%) students were found positive for influenza A/H3 only, 6 (13%) for SARS-CoV-2 only, and 4 (8%) were co-infected with influenza A/H3 and SARS-CoV-2. Seventeen influenza A/ H3N2 viruses belonged to the same clade, 3C.2a1b.2a.2a.3a, and 4 SARSCoV-2 sequences belonged to the JE1.1 lineage, indicating a common source outbreak for both. The influenza A/H3N2 circulating virus belonged to a different clade than the vaccine strain for 2023 (3C.2a1b.2a.2a). Only 4 students had received the influenza vaccine for 2023. In response, the AFP Surgeon General issued a memorandum to all military health institutions on October 19, 2023 that mandated influenza vaccination as a prerequisite for enrollment of students at all education and training centers, along with implementation of non-pharmaceutical interventions and early notification and testing of students exhibiting influenza-like-illness.

Epidemiology of Respiratory Viruses in Korean Children Before and After the COVID-19 Pandemic: A Prospective Study From National Surveillance System

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic led to a decrease in the seasonal incidence of many respiratory viruses worldwide due to the impact of nonpharmaceutical interventions (NPIs). However, as NPI measures were relaxed, respiratory viral infections re-emerged. We aimed to characterize the epidemiology of respiratory viruses in Korean children during post-COVID-19 pandemic years compared to that before the pandemic.

METHODS

A nationwide prospective ongoing surveillance study has been conducted for detection of respiratory viruses between January 2017 and June 2023. We included data on adenovirus (AdV), human bocavirus (HBoV), human coronavirus (HCoV), human metapneumovirus (HMPV), human rhinovirus (HRV), influenza virus (IFV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV), which were detected in children and adolescents younger than 20 years. We analyzed the weekly detection frequency of individual viruses and the age distribution of the affected children. The study period was divided into prepandemic (2017-2019) and postpandemic (2021-2023) periods.

RESULTS

A total of 19,589 and 14,068 samples were collected in the pre- and postpandemic periods, respectively. The overall detection rate of any virus throughout the study period was 63.1%, with the lowest occurring in the 2nd half of 2020 (50.6%) and the highest occurring in the 2nd half of 2021 (72.3%). Enveloped viruses (HCoV, HMPV, IFV, PIV, and RSV) almost disappeared, but nonenveloped viruses (AdV, HBoV, and HRV) were detected even during the peak of the COVID-19 pandemic. The codetection rate increased from 15.0% prepandemic to 19.1% postpandemic (P < 0.001). During the postpandemic period, a large out-of-season PIV and HMPV epidemic occurred, but the usual seasonality began to be restored in 2023. The mean age of children with each virus detected in 2023 was significantly greater than that in prepandemic years (P = 0.003 and 0.007 for AdV and HCoV, respectively; P < 0.001 for others). The mean age of children with IFV increased in 2022 (11.1 ± 5.2 years) from prepandemic years (7.9 ± 4.6 years) but decreased to 8.7 ± 4.1 years in 2023.

CONCLUSION

With the relaxation of NPI measures, several seasonal respiratory viruses cocirculated with unusual seasonal epidemic patterns and were associated with increasing age of infected children.

A propensity score matched analysis of COVID-19 ongoing symptoms in primary medical staff members with different levels of stress in Jiangsu Province, China

Objective

Ongoing symptoms which originated from coronavirus disease 2019 (COVID-19) infections threaten the health of a broad population of patients. With recent changes in COVID-19 control measures in China, medical staff members are currently experiencing a high level of stress. This study aimed to investigate the prevalence of ongoing symptomatic COVID-19 and explore the potential association between stress and ongoing COVID symptoms.

Methods

From January 17th to February 2, 2023, primary medical staff members in Jiangsu Province were surveyed using a self-designed questionnaire. Univariate multinomial logistic analysis was used to illustrate the relationship between stress and ongoing symptoms after matching the low- and high-stress groups in a 1:1 ratio based on propensity scores.

Results

Analysis revealed that 14.83 % (3785/25,516) of primary medical staff members infected with COVID-19 experienced ongoing symptoms, the most common of which included cough (9.51 %), dyspnea (9.51 %), sleep problems (4.40 %), anxiety (2.29 %), and reproductive system symptoms (1.89 %). In matched patients, higher stress levels were associated with a greater risk of ongoing symptoms than in patients without ongoing symptoms for 14 of the 15 reported symptoms in this study (odds ratios [ORs] > 1 and P < 0.05). Moreover, higher levels of stress were associated with a greater risk of more ongoing symptoms, and the overall ORs increased with the number of symptoms (ORs >1 and P < 0.05).

Conclusion

To mitigate the possibility of experiencing ongoing symptoms, healthcare organizations and local authority agencies should institute helpful measures to decrease stress levels such as medical staff augmentation and enabling all staff to have a reasonable work-life balance.

Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control

Introduction

Residents of long-term care facilities (LTCFs) are at high risk of morbidity and mortality due to COVID-19, especially when new variants of concern (VOC) emerge. To provide intradisciplinary data in order to tailor public health interventions during future epidemics, available epidemiologic and genomic data from Slovenian LTCFs during the initial phases of the COVID-19 pandemic was analyzed.

Methods

The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission.

Results

370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population.

Discussion

Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.