Exhaled Breath Aerosol Shedding of Highly Transmissible Versus Prior Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

BACKGROUND: Aerosol inhalation is recognized as the dominant mode of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Three highly transmissible lineages evolved during the pandemic. One hypothesis to explain increased transmissibility is that natural selection favors variants with higher rates of viral aerosol shedding. However, the extent of aerosol shedding of successive SARS-CoV-2 variants is unknown. We aimed to measure the infectivity and rate of SARS-CoV-2 shedding into exhaled breath aerosol (EBA) by individuals during the Delta and Omicron waves and compared those rates with those of prior SARS-CoV-2 variants from our previously published work. METHODS: Individuals with coronavirus disease 2019 (COVID-19) (n = 93; 32 vaccinated and 20 boosted) were recruited to give samples, including 30-minute breath samples into a Gesundheit-II EBA sampler. Samples were quantified for viral RNA using reverse-transcription polymerase chain reaction and cultured for virus. RESULTS: Alpha (n = 4), Delta (n = 3), and Omicron (n = 29) cases shed significantly more viral RNA copies into EBAs than cases infected with ancestral strains and variants not associated with increased transmissibility (n = 57). All Delta and Omicron cases were fully vaccinated and most Omicron cases were boosted. We cultured virus from the EBA of 1 boosted and 3 fully vaccinated cases. CONCLUSIONS: Alpha, Delta, and Omicron independently evolved high viral aerosol shedding phenotypes, demonstrating convergent evolution. Vaccinated and boosted cases can shed infectious SARS-CoV-2 via EBA. These findings support a dominant role of infectious aerosols in transmission of SARS-CoV-2. Monitoring aerosol shedding from new variants and emerging pathogens can be an important component of future threat assessments and guide interventions to prevent transmission.

Coronavirus Disease 2019 and Airborne Transmission: Science Rejected, Lives Lost. Can Society Do Better?

This is an account that should be heard of an important struggle: the struggle of a large group of experts who came together at the beginning of the COVID-19 pandemic to warn the world about the risk of airborne transmission and the consequences of ignoring it. We alerted the World Health Organization about the potential significance of the airborne transmission of SARS-CoV-2 and the urgent need to control it, but our concerns were dismissed. Here we describe how this happened and the consequences. We hope that by reporting this story we can raise awareness of the importance of interdisciplinary collaboration and the need to be open to new evidence, and to prevent it from happening again. Acknowledgement of an issue, and the emergence of new evidence related to it, is the first necessary step towards finding effective mitigation solutions.

Viral Load of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Respiratory Aerosols Emitted by Patients With Coronavirus Disease 2019 (COVID-19) While Breathing, Talking, and Singing.

BACKGROUND: Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading events suggest that aerosols play an important role in driving the coronavirus disease 2019 (COVID-19) pandemic. To better understand how airborne SARS-CoV-2 transmission occurs, we sought to determine viral loads within coarse (>5 µm) and fine (≤5 µm) respiratory aerosols produced when breathing, talking, and singing. METHODS: Using a G-II exhaled breath collector, we measured viral RNA in coarse and fine respiratory aerosols emitted by COVID-19 patients during 30 minutes of breathing, 15 minutes of talking, and 15 minutes of singing. RESULTS: Thirteen participants (59%) emitted detectable levels of SARS-CoV-2 RNA in respiratory aerosols, including 3 asymptomatic and 1 presymptomatic patient. Viral loads ranged from 63-5821 N gene copies per expiratory activity per participant, with high person-to-person variation. Patients earlier in illness were more likely to emit detectable RNA. Two participants, sampled on day 3 of illness, accounted for 52% of total viral load. Overall, 94% of SARS-CoV-2 RNA copies were emitted by talking and singing. Interestingly, 7 participants emitted more virus from talking than singing. Overall, fine aerosols constituted 85% of the viral load detected in our study. Virus cultures were negative. CONCLUSIONS: Fine aerosols produced by talking and singing contain more SARS-CoV-2 copies than coarse aerosols and may play a significant role in SARS-CoV-2 transmission. Exposure to fine aerosols, especially indoors, should be mitigated. Isolating viable SARS-CoV-2 from respiratory aerosol samples remains challenging; whether this can be more easily accomplished for emerging SARS-CoV-2 variants is an urgent enquiry necessitating larger-scale studies.

Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks and variants on aerosol shedding are not well understood. METHODS: We recruited coronavirus disease 2019 (COVID-19) cases to give blood, saliva, mid-turbinate and fomite (phone) swabs, and 30-minute breath samples while vocalizing into a Gesundheit-II, with and without masks at up to 2 visits 2 days apart. We quantified and sequenced viral RNA, cultured virus, and assayed serum samples for anti-spike and anti-receptor binding domain antibodies. RESULTS: We enrolled 49 seronegative cases (mean days post onset 3.8 ±â€…2.1), May 2020 through April 2021. We detected SARS-CoV-2 RNA in 36% of fine (≤5 µm), 26% of coarse (>5 µm) aerosols, and 52% of fomite samples overall and in all samples from 4 alpha variant cases. Masks reduced viral RNA by 48% (95% confidence interval [CI], 3 to 72%) in fine and by 77% (95% CI, 51 to 89%) in coarse aerosols; cloth and surgical masks were not significantly different. The alpha variant was associated with a 43-fold (95% CI, 6.6- to 280-fold) increase in fine aerosol viral RNA, compared with earlier viruses, that remained a significant 18-fold (95% CI, 3.4- to 92-fold) increase adjusting for viral RNA in saliva, swabs, and other potential confounders. Two fine aerosol samples, collected while participants wore masks, were culture-positive. CONCLUSIONS: SARS-CoV-2 is evolving toward more efficient aerosol generation and loose-fitting masks provide significant but only modest source control. Therefore, until vaccination rates are very high, continued layered controls and tight-fitting masks and respirators will be necessary.

ICN: Extracting interconnected communities in gene Co-expression networks.

MOTIVATION: The analysis of gene co-expression network (GCN) is critical in examining the gene-gene interactions and learning the underlying complex yet highly organized gene regulatory mechanisms. Numerous clustering methods have been developed to detect communities of co-expressed genes in the large network. The assumed independent community structure, however, can be oversimplified and may not adequately characterize the complex biological processes. RESULTS: We develop a new computational package to extract interconnected communities from gene co-expression network. We consider a pair of communities be interconnected if a subset of genes from one community is correlated with a subset of genes from another community. The interconnected community structure is more flexible and provides a better fit to the empirical co-expression matrix. To overcome the computational challenges, we develop efficient algorithms by leveraging advanced graph norm shrinkage approach. We validate and show the advantage of our method by extensive simulation studies. We then apply our interconnected community detection method to an RNA-seq data from The Cancer Genome Atlas (TCGA) Acute Myeloid Leukemia (AML) study and identify essential interacting biological pathways related to the immune evasion mechanism of tumor cells. AVAILABILITY: The software is available at Github: https://github.com/qwu1221/ICN and Figshare: https://figshare.com/articles/software/ICN-package/13229093. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Minimal transmission in an influenza A (H3N2) human challenge-transmission model within a controlled exposure environment.

Uncertainty about the importance of influenza transmission by airborne droplet nuclei generates controversy for infection control. Human challenge-transmission studies have been supported as the most promising approach to fill this knowledge gap. Healthy, seronegative volunteer 'Donors' (n = 52) were randomly selected for intranasal challenge with influenza A/Wisconsin/67/2005 (H3N2). 'Recipients' randomized to Intervention (IR, n = 40) or Control (CR, n = 35) groups were exposed to Donors for four days. IRs wore face shields and hand sanitized frequently to limit large droplet and contact transmission. One transmitted infection was confirmed by serology in a CR, yielding a secondary attack rate of 2.9% among CR, 0% in IR (p = 0.47 for group difference), and 1.3% overall, significantly less than 16% (p<0.001) expected based on a proof-of-concept study secondary attack rate and considering that there were twice as many Donors and days of exposure. The main difference between these studies was mechanical building ventilation in the follow-on study, suggesting a possible role for aerosols.

Characterization of aerosol plumes from singing and playing wind instruments associated with the risk of airborne virus transmission.

The exhalation of aerosols during musical performances or rehearsals posed a risk of airborne virus transmission in the COVID-19 pandemic. Previous research studied aerosol plumes by only focusing on one risk factor, either the source strength or convective transport capability. Furthermore, the source strength was characterized by the aerosol concentration and ignored the airflow rate needed for risk analysis in actual musical performances. This study characterizes aerosol plumes that account for both the source strength and convective transport capability by conducting experiments with 18 human subjects. The source strength was characterized by the source aerosol emission rate, defined as the source aerosol concentration multiplied by the source airflow rate (brass 383 particle/s, singing 408 particle/s, and woodwind 480 particle/s). The convective transport capability was characterized by the plume influence distance, defined as the sum of the horizontal jet length and horizontal instrument length (brass 0.6 m, singing 0.6 m and woodwind 0.8 m). Results indicate that woodwind instruments produced the highest risk with approximately 20% higher source aerosol emission rates and 30% higher plume influence distances compared with the average of the same risk indicators for singing and brass instruments. Interestingly, the clarinet performance produced moderate source aerosol concentrations at the instrument's bell, but had the highest source aerosol emission rates due to high source airflow rates. Flute performance generated plumes with the lowest source aerosol emission rates but the highest plume influence distances due to the highest source airflow rate. Notably, these comprehensive results show that the source airflow is a critical component of the risk of airborne disease transmission. The effectiveness of masking and bell covering in reducing aerosol transmission is due to the mitigation of both source aerosol concentrations and plume influence distances. This study also found a musician who generated approximately five times more source aerosol concentrations than those of the other musicians who played the same instrument. Despite voice and brass instruments producing measurably lower average risk, it is possible to have an individual musician produce aerosol plumes with high source strength, resulting in enhanced transmission risk; however, our sample size was too small to make generalizable conclusions regarding the broad musician population.

Current Insights Into Respiratory Virus Transmission and Potential Implications for Infection Control Programs : A Narrative Review.

Policies to prevent respiratory virus transmission in health care settings have traditionally divided organisms into Droplet versus Airborne categories. Droplet organisms (for example, influenza) are said to be transmitted via large respiratory secretions that rapidly fall to the ground within 1 to 2 meters and are adequately blocked by surgical masks. Airborne pathogens (for example, measles), by contrast, are transmitted by aerosols that are small enough and light enough to carry beyond 2 meters and to penetrate the gaps between masks and faces; health care workers are advised to wear N95 respirators and to place these patients in negative-pressure rooms. Respirators and negative-pressure rooms are also recommended when caring for patients with influenza or SARS-CoV-2 who are undergoing "aerosol-generating procedures," such as intubation. An increasing body of evidence, however, questions this framework. People routinely emit respiratory particles in a range of sizes, but most are aerosols, and most procedures do not generate meaningfully more aerosols than ordinary breathing, and far fewer than coughing, exercise, or labored breathing. Most transmission nonetheless occurs at close range because virus-laden aerosols are most concentrated at the source; they then diffuse and dilute with distance, making long-distance transmission rare in well-ventilated spaces. The primary risk factors for nosocomial transmission are community incidence rates, viral load, symptoms, proximity, duration of exposure, and poor ventilation. Failure to appreciate these factors may lead to underappreciation of some risks (for example, overestimation of the protection provided by medical masks, insufficient attention to ventilation) or misallocation of limited resources (for example, reserving N95 respirators and negative-pressure rooms only for aerosol-generating procedures or requiring negative-pressure rooms for all patients with SARS-CoV-2 infection regardless of stage of illness). Enhanced understanding of the factors governing respiratory pathogen transmission may inform the development of more effective policies to prevent nosocomial transmission of respiratory pathogens.

Viral RNA and Infectious Influenza Virus on Mobile Phones of Patients With Influenza in Hong Kong and the United States.

Mobile phones are among the most highly touched personal objects. As part of a broader study on the contribution of fomites to influenza transmission, between 2017 and 2019, we swabbed mobile phones from 138 patients with influenza in 2 locations. Influenza viral RNA detection rates were 23% (23 of 99 phones) and 36% (14 of 39) in Hong Kong and Maryland, respectively. In Hong Kong, infectious influenza virus was recovered from 3 of 23 mobile phones which had influenza viral RNA detected. Mobile phone influenza contamination was positively associated with upper respiratory tract viral load and negatively associated with age. Cleaning personal objects of patients with influenza should be recommended, and individuals should avoid sharing objects with these patients.

Link predictions for incomplete network data with outcome misclassification.

Link prediction is a fundamental problem in network analysis. In a complex network, links can be unreported and/or under detection limits due to heterogeneous sources of noise and technical challenges during data collection. The incomplete network data can lead to an inaccurate inference of network based data analysis. We propose a parametric link prediction model and consider latent links as misclassified binary outcomes. We develop new algorithms to optimize model parameters and yield robust predictions of unobserved links. Theoretical properties of the predictive model are also discussed. We apply the new method to a partially observed social network data and incomplete brain network data. The results demonstrate that our method outperforms the existing latent-link prediction methods.

Infectious virus in exhaled breath of symptomatic seasonal influenza cases from a college community.

Little is known about the amount and infectiousness of influenza virus shed into exhaled breath. This contributes to uncertainty about the importance of airborne influenza transmission. We screened 355 symptomatic volunteers with acute respiratory illness and report 142 cases with confirmed influenza infection who provided 218 paired nasopharyngeal (NP) and 30-minute breath samples (coarse >5-µm and fine ≤5-µm fractions) on days 1-3 after symptom onset. We assessed viral RNA copy number for all samples and cultured NP swabs and fine aerosols. We recovered infectious virus from 52 (39%) of the fine aerosols and 150 (89%) of the NP swabs with valid cultures. The geometric mean RNA copy numbers were 3.8 × 104/30-minutes fine-, 1.2 × 104/30-minutes coarse-aerosol sample, and 8.2 × 108 per NP swab. Fine- and coarse-aerosol viral RNA were positively associated with body mass index and number of coughs and negatively associated with increasing days since symptom onset in adjusted models. Fine-aerosol viral RNA was also positively associated with having influenza vaccination for both the current and prior season. NP swab viral RNA was positively associated with upper respiratory symptoms and negatively associated with age but was not significantly associated with fine- or coarse-aerosol viral RNA or their predictors. Sneezing was rare, and sneezing and coughing were not necessary for infectious aerosol generation. Our observations suggest that influenza infection in the upper and lower airways are compartmentalized and independent.

Quantitative aerobiologic analysis of an influenza human challenge-transmission trial.

Despite evidence that airborne transmission contributes to influenza epidemics, limited knowledge of the infectiousness of human influenza cases hinders pandemic preparedness. We used airborne viral source strength and indoor CO2 monitoring from the largest human influenza challenge-transmission trial (EMIT: Evaluating Modes of Influenza Transmission, ClinicalTrials.gov number NCT01710111) to compute an airborne infectious dose generation rate q = 0.11 (95% CI 0.088, 0.12)/h and calculate the quantity of airborne virus per infectious dose σ = 1.4E + 5 RNA copies/quantum (95% CI 9.9E + 4, 1.8E + 5). We then compared these calculated values to available data on influenza airborne infectious dose from several previous studies, and applied the values to dormitory room environments to predict probability of transmission between roommates. Transmission risk from typical, moderately to severely symptomatic influenza cases is dramatically decreased by exposure reduction via increasing indoor air ventilation. The minority of cases who shed the most virus (ie, supershedders) may pose great risk even in well-ventilated spaces. Our modeling method and estimated infectiousness provide a ground work for (a) epidemiologic studies of transmission in non-experimental settings and (b) evaluation of the extent to which airborne exposure control strategies could limit transmission risk.

Pesticide monitoring on soccer fields via shoe wipes and urine samples.

OBJECTIVE: We sought to determine the feasibility of measuring pesticide exposure of children using athletic fields to which pesticides were recently applied. DESIGN AND SAMPLE: This project was a pilot feasibility study designed to measure pre and posttest environmental exposure to Horsepower; a combination herbicide containing (4-Chloro-2-methylphenoxy) acetic acid (MCPA), dicamba and triclopyr. A spot application of Horsepower to a soccer field occurred at 8AM. Six players, ages 5-11 years, provided shoe wipes and urine samples before and after evening soccer practice on the field later the same day. MEASUREMENTS AND RESULTS: We sent samples to commercial labs where shoe wipes were analyzed for a panel of herbicides and urine samples were analyzed for dicamba, triclopyr, and creatinine. All analytes were below level of detection. CONCLUSIONS: We established the feasibility of both the recruitment and sampling procedures. Spot application, in the one instance examined, did not result in measurable exposure to pesticides. A larger study involving both spot and broadcast application and including direct observation of pesticide application is needed to ascertain whether pesticide application on athletic fields results in measurable and potentially hazardous exposure of children.

Influenza virus aerosols in human exhaled breath: particle size, culturability, and effect of surgical masks.

The CDC recommends that healthcare settings provide influenza patients with facemasks as a means of reducing transmission to staff and other patients, and a recent report suggested that surgical masks can capture influenza virus in large droplet spray. However, there is minimal data on influenza virus aerosol shedding, the infectiousness of exhaled aerosols, and none on the impact of facemasks on viral aerosol shedding from patients with seasonal influenza. We collected samples of exhaled particles (one with and one without a facemask) in two size fractions ("coarse">5 µm, "fine"≤5 µm) from 37 volunteers within 5 days of seasonal influenza onset, measured viral copy number using quantitative RT-PCR, and tested the fine-particle fraction for culturable virus. Fine particles contained 8.8 (95% CI 4.1 to 19) fold more viral copies than did coarse particles. Surgical masks reduced viral copy numbers in the fine fraction by 2.8 fold (95% CI 1.5 to 5.2) and in the coarse fraction by 25 fold (95% CI 3.5 to 180). Overall, masks produced a 3.4 fold (95% CI 1.8 to 6.3) reduction in viral aerosol shedding. Correlations between nasopharyngeal swab and the aerosol fraction copy numbers were weak (r = 0.17, coarse; r = 0.29, fine fraction). Copy numbers in exhaled breath declined rapidly with day after onset of illness. Two subjects with the highest copy numbers gave culture positive fine particle samples. Surgical masks worn by patients reduce aerosols shedding of virus. The abundance of viral copies in fine particle aerosols and evidence for their infectiousness suggests an important role in seasonal influenza transmission. Monitoring exhaled virus aerosols will be important for validation of experimental transmission studies in humans.

Log-Linear Modeling of Agreement among Expert Exposure Assessors.

BACKGROUND: Evaluation of expert assessment of exposure depends, in the absence of a validation measurement, upon measures of agreement among the expert raters. Agreement is typically measured using Cohen's Kappa statistic, however, there are some well-known limitations to this approach. We demonstrate an alternate method that uses log-linear models designed to model agreement. These models contain parameters that distinguish between exact agreement (diagonals of agreement matrix) and non-exact associations (off-diagonals). In addition, they can incorporate covariates to examine whether agreement differs across strata. METHODS: We applied these models to evaluate agreement among expert ratings of exposure to sensitizers (none, likely, high) in a study of occupational asthma. RESULTS: Traditional analyses using weighted kappa suggested potential differences in agreement by blue/white collar jobs and office/non-office jobs, but not case/control status. However, the evaluation of the covariates and their interaction terms in log-linear models found no differences in agreement with these covariates and provided evidence that the differences observed using kappa were the result of marginal differences in the distribution of ratings rather than differences in agreement. Differences in agreement were predicted across the exposure scale, with the likely moderately exposed category more difficult for the experts to differentiate from the highly exposed category than from the unexposed category. CONCLUSIONS: The log-linear models provided valuable information about patterns of agreement and the structure of the data that were not revealed in analyses using kappa. The models' lack of dependence on marginal distributions and the ease of evaluating covariates allow reliable detection of observational bias in exposure data.

Relative efficacy of masks and respirators as source control for viral aerosol shedding from people infected with SARS-CoV-2: a controlled human exhaled breath aerosol experimental study.

BACKGROUND: Tight-fitting masks and respirators, in manikin studies, improved aerosol source control compared to loose-fitting masks. Whether this translates to humans is not known. METHODS: We compared efficacy of masks (cloth and surgical) and respirators (KN95 and N95) as source control for SARS-CoV-2 viral load in exhaled breath of volunteers with COVID-19 using a controlled human experimental study. Volunteers (N = 44, 43% female) provided paired unmasked and masked breath samples allowing computation of source-control factors. FINDINGS: All masks and respirators significantly reduced exhaled viral load, without fit tests or training. A duckbill N95 reduced exhaled viral load by 98% (95% CI: 97%-99%), and significantly outperformed a KN95 (p < 0.001) as well as cloth and surgical masks. Cloth masks outperformed a surgical mask (p = 0.027) and the tested KN95 (p = 0.014). INTERPRETATION: These results suggest that N95 respirators could be the standard of care in nursing homes and healthcare settings when respiratory viral infections are prevalent in the community and healthcare-associated transmission risk is elevated. FUNDING: Defense Advanced Research Projects Agency, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, and The Flu Lab.

Mandating indoor air quality for public buildings.

If some countries lead by example, standards may increasingly become normalized.

Determinants of exposure to 2-butoxyethanol from cleaning tasks: a quasi-experimental study.

BACKGROUND: The quantitative assessment of airborne cleaning exposures requires numerous measurement methods, which are costly and difficult to apply in the workplace. Exposure determinants can be used to predict exposures but have yet to be investigated for cleaning activities. We identified determinants of exposure to 2-butoxyethanol (2-BE), a known respiratory irritant and suspected human carcinogen, commonly found in cleaning products. In addition, we investigated whether 2-BE exposures can be predicted from exposure determinants and total volatile organic compounds (TVOCs) measured with direct reading methods, which are easier to apply in field investigations. METHODS: Exposure determinants were studied in a quasi-experimental study design. Cleaning tasks were performed similarly as in the workplace, but potential factors that can impact exposures were controlled. Simultaneously for each task, we measured concentrations of (1) 2-BE according to the National Institute for Occupational Health and Safety 1430 method and (2) TVOC with photoionization detectors (PIDs). Simple and multiple linear regression analyses were performed to identify 2-BE exposure determinants and to develop exposure prediction models. RESULTS: Significant determinants from univariate analyses consisted of product type, tasks performed, room volume, and ventilation. The best-fit multivariable model was the one comprised of product type, tasks performed, 2-BE product concentration, room volume, and ventilation (R(2) = 77%). We found a strong correlation between the 2-BE and the TVOC concentrations recorded by the PID instruments. A multivariable model with TVOC explained a significant portion of the 2-BE concentrations (R(2) = 72%) when product type and room ventilation were included in the model. CONCLUSIONS: Our results suggest that quantitative exposure assessment for an epidemiologic investigation of cleaning health effects may be feasible even without performing integrated sampling and analytic measurements.