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.

How Narrow Is the Gas Phase Mobility Distribution of Enveloped Viruses? The Case of the Φ6 Bacteriophage.

We use the Φ6 bacteriophage previously exploited as a BSL-1 surrogate of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS) coronavirus to obtain the first high-resolution gas phase mobility spectra of an enveloped virus. The relative full width at half-maximum found for the viral mobility distribution (FWHMZ < 3.7%) is substantially narrower than that reported by prior mobility or microscopy studies with other enveloped viruses. It is nevertheless not as narrow as that recently found for several non-enveloped viruses (FWHMZ ≈ 2%), presumably due to particle to particle variability of enveloped viruses. This 3.7% is an upper bound to the actual width. Nevertheless, the well-defined mobility peaks obtained indicate that gas phase mobility analysis is a more discriminating methodology than that previously demonstrated for physically based non-genetic viral diagnostic of enveloped viruses. These results are obtained by analysis of the original cell culture medium containing the virus, purified only by passage through a 0.22 µm filter and by dialysis into a 10 mM aqueous ammonium acetate buffer. We confirmed that this buffer exchange preserves infectivity. Therefore, the 63.7 nm mobility diameter found, although smaller than the 75 nm previously inferred by microscopy, corresponds to the full particle including the envelope.

COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission.

The recent coronavirus disease (COVID-19), caused by SARS-CoV-2, is inarguably the most challenging coronavirus outbreak relative to the previous outbreaks involving SARS-CoV and MERS-CoV. With the number of COVID-19 cases now exceeding 2 million worldwide, it is apparent that (i) transmission of SARS-CoV-2 is very high and (ii) there are large variations in disease severity, one component of which may be genetic variability in the response to the virus. Controlling current rates of infection and combating future waves require a better understanding of the routes of exposure to SARS-CoV-2 and the underlying genomic susceptibility to this disease. In this mini-review, we highlight possible genetic determinants of COVID-19 and the contribution of aerosol exposure as a potentially important transmission route of SARS-CoV-2.

Evaluating Indoor Air Chemical Diversity, Indoor-to-Outdoor Emissions, and Surface Reservoirs Using High-Resolution Mass Spectrometry.

Detailed offline speciation of gas- and particle-phase organic compounds was conducted using gas/liquid chromatography with traditional and high-resolution mass spectrometers in a hybrid targeted/nontargeted analysis. Observations were focused on an unoccupied home and were compared to two other indoor sites. Observed gas-phase organic compounds span the volatile to semivolatile range, while functionalized organic aerosols extend from intermediate volatility to ultra-low volatility, including a mix of oxygen, nitrogen, and sulfur-containing species. Total gas-phase abundances of hydrocarbon and oxygenated gas-phase complex mixtures were elevated indoors and strongly correlated in the unoccupied home. While gas-phase concentrations of individual compounds generally decreased slightly with greater ventilation, their elevated ratios relative to controlled emissions of tracer species suggest that the dilution of gas-phase concentrations increases off-gassing from surfaces and other indoor reservoirs, with volatility-dependent responses to dynamically changing environmental factors. Indoor-outdoor emissions of gas-phase intermediate-volatility/semivolatile organic hydrocarbons from the unoccupied home averaged 6-11 mg h-1, doubling with ventilation. While the largest single-compound emissions observed were furfural (61-275 mg h-1) and acetic acid, observations spanned a wide range of individual volatile chemical products (e.g., terpenoids, glycol ethers, phthalates, other oxygenates), highlighting the abundance of long-lived reservoirs resulting from prior indoor use or materials, and their gradual transport outdoors.

Aligning SARS-CoV-2 indicators via an epidemic model: application to hospital admissions and RNA detection in sewage sludge.

Ascertaining the state of coronavirus outbreaks is crucial for public health decision-making. Absent repeated representative viral test samples in the population, public health officials and researchers alike have relied on lagging indicators of infection to make inferences about the direction of the outbreak and attendant policy decisions. Recently researchers have shown that SARS-CoV-2 RNA can be detected in municipal sewage sludge with measured RNA concentrations rising and falling suggestively in the shape of an epidemic curve while providing an earlier signal of infection than hospital admissions data. The present paper presents a SARS-CoV-2 epidemic model to serve as a basis for estimating the incidence of infection, and shows mathematically how modeled transmission dynamics translate into infection indicators by incorporating probability distributions for indicator-specific time lags from infection. Hospital admissions and SARS-CoV-2 RNA in municipal sewage sludge are simultaneously modeled via maximum likelihood scaling to the underlying transmission model. The results demonstrate that both data series plausibly follow from the transmission model specified and provide a 95% confidence interval estimate of the reproductive number R0 ≈ 2.4 ± 0.2. Sensitivity analysis accounting for alternative lag distributions from infection until hospitalization and sludge RNA concentration respectively suggests that the detection of viral RNA in sewage sludge leads hospital admissions by 3 to 5 days on average. The analysis suggests that stay-at-home restrictions plausibly removed 89% of the population from the risk of infection with the remaining 11% exposed to an unmitigated outbreak that infected 9.3% of the total population.

DNA Sequence-Based Approach for Classifying the Mold Status of Buildings.

Dampness or water damage in buildings and human exposure to the resultant mold growth is an ever-present public health concern. This study provides quantitative evidence that the airborne fungal ecology of homes with known mold growth ("moldy") differs from the normal airborne fungal ecology of homes with no history of dampness, water damage, or visible mold ("no mold"). Settled dust from indoor air and outdoor air and direct samples from building materials with mold growth were examined in homes from 11 cities across dry, temperate, and continental climate regions within the United States. Community analysis based on the sequence of the internal transcribed spacer region of fungal ribosomal RNA encoding genes demonstrated consistent and quantifiable differences between the fungal ecology of settled dust in homes with inspector-verified water damage and visible mold versus the settled dust of homes with no history of dampness, water damage, or visible mold. These differences include lower community richness (padj = 0.01) in the settled dust of moldy homes versus no mold homes, as well as distinct community taxonomic structures between moldy and no mold homes (ANOSIM, R = 0.15, p = 0.001). We identified 11 Ascomycota taxa that were more highly enriched in moldy homes and 14 taxa from Ascomycota, Basidiomycota, and Zygomycota that were more highly enriched in no mold homes. The indoor air differences between moldy versus no mold homes were significant for all three climate regions considered. These distinct but complex differences between settled dust samples from moldy and no homes were used to train a machine learning-based model to classify the mold status of a home. The model was able to accurately classify 100% of moldy homes and 90% of no mold homes. The integration of DNA-based fungal ecology with advanced computational approaches can be used to accurately classify the presence of mold growth in homes, assist with inspection and remediation decisions, and potentially lead to reduced exposure to hazardous microbes indoors.

Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors.

The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.

Global Survey of Antibiotic Resistance Genes in Air.

Despite its emerging significant public health concern, the presence of antibiotic resistance genes (ARGs) in urban air has not received significant attention. Here, we profiled relative abundances (as a fraction, normalized by 16S rRNA gene) of 30 ARG subtypes resistant to seven common classes of antibiotics, which are quinolones, ß-lactams, macrolides, tetracyclines, sulfonamides, aminoglycosides, and vancomycins, in ambient total particulate matter (PM) using a novel protocol across 19 world cities. In addition, their longitudinal changes in PM2.5 samples in Xi'an, China as an example were also studied. Geographically, the ARGs were detected to vary by nearly 100-fold in their abundances, for example, from 0.07 (Bandung, Indonesia) to 5.6 (San Francisco, USA). The ß-lactam resistance gene blaTEM was found to be most abundant, seconded by quinolone resistance gene qepA; and their corresponding relative abundances have increased by 178% and 26%, respectively, from 2004 to 2014 in Xi'an. Independent of cities, gene network analysis indicates that airborne ARGs were differentially contributed by bacterial taxa. Results here reveal that urban air is being polluted by ARGs, and different cities are challenged with varying health risks associated with airborne ARG exposure. This work highlights the threat of urban airborne transmission of ARGs and the need of redefining our current air quality standards in terms with public health.

Indoor/Outdoor Relationships and Anthropogenic Elemental Signatures in Airborne PM2.5 at a High School: Impacts of Petroleum Refining Emissions on Lanthanoid Enrichment.

Outdoor emissions of primary fine particles and their contributions to indoor air quality deterioration were examined by collecting PM2.5 inside and outside a mechanically ventilated high school in the ultraindustrialized ship channel region of Houston, TX over a 2-month period. By characterizing 47 elements including lanthanoids (rare earth elements), using inductively coupled plasma-mass spectrometry, we captured indoor signatures of outdoor episodic emissions arising from nonroutine operations of petroleum refinery fluidized-bed catalytic cracking units. Average indoor-to-outdoor (I/O) abundance ratios for the majority of elements were close to unity providing evidence that indoor metal-bearing PM2.5 had predominantly outdoor origins. Only Co had an I/O abundance ratio >1 but its indoor sources could not be explicitly identified. La and 17 other elements (Na, K, V, Ni, Co, Cu, Zn, Ga, As, Se, Mo, Cd, Sn, Sb, Ba, W, and Pb), including air toxics were enriched relative to the local soil both in indoor and outdoor PM2.5 demonstrating their noncrustal origins. Several lines of evidence including receptor modeling, lanthanoid ratios, and La-Ce-Sm ternary diagrams pointed to petroleum refineries as being largely responsible for enhanced La and total lanthanoid concentrations in the majority of paired indoor and outdoor PM2.5.

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children.

BACKGROUND: Allergic and nonallergic asthma severity in children can be affected by microbial exposures. OBJECTIVE: We sought to examine associations between exposures to household microbes and childhood asthma severity stratified by atopic status. METHODS: Participants (n = 196) were selected from a cohort of asthmatic children in Connecticut and Massachusetts. Children were grouped according to asthma severity (mild with no or minimal symptoms and medication or moderate to severe persistent) and atopic status (determined by serum IgE levels). Microbial community structure and concentrations in house dust were determined by using next-generation DNA sequencing and quantitative PCR. Logistic regression was used to explore associations between asthma severity and exposure metrics, including richness, taxa identification and quantification, community composition, and concentration of total fungi and bacteria. RESULTS: Among all children, increased asthma severity was significantly associated with an increased concentration of summed allergenic fungal species, high total fungal concentrations, and high bacterial richness by using logistic regression in addition to microbial community composition by using the distance comparison t test. Asthma severity in atopic children was associated with fungal community composition (P = .001). By using logistic regression, asthma severity in nonatopic children was associated with total fungal concentration (odds ratio, 2.40; 95% CI, 1.06-5.44). The fungal genus Volutella was associated with increased asthma severity in atopic children (P = .0001, q = 0.04). The yeast genera Kondoa might be protective; Cryptococcus species might also affect asthma severity. CONCLUSION: Asthma severity among this cohort of children was associated with microbial exposure, and associations differed based on atopic status.

We Should Expect More out of Our Sewage Sludge.

Sewage sludge and biosolids production and management are a central component of water and sanitation engineering. The culmination of previous incremental technologies and regulations aimed at solving a current treatment problem, rather than developing the practice for the higher goals of sustainability have resulted in sludge becoming an economic and social liability. Sludge management practice must shift from treatment of a liability toward recovery of the embedded energy and chemical assets, while continuing to protect the environment and human health. This shift will require new research, treatment technologies and infrastructure and must be guided by the application of green engineering principles to ensure economic, social, and environmental sustainability.

Indoor emissions as a primary source of airborne allergenic fungal particles in classrooms.

This study quantifies the influence of ventilation and indoor emissions on concentrations and particle sizes of airborne indoor allergenic fungal taxa and further examines geographical variability, each of which may affect personal exposures to allergenic fungi. Quantitative PCR and multiplexed DNA sequencing were employed to count and identify allergenic fungal aerosol particles indoors and outdoors in seven school classrooms in four different countries. Quantitative diversity analysis was combined with building characterization and mass balance modeling to apportion source contributions of indoor allergenic airborne fungal particles. Mass balance calculations indicate that 70% of indoor fungal aerosol particles and 80% of airborne allergenic fungal taxa were associated with indoor emissions; on average, 81% of allergenic fungi from indoor sources originated from occupant-generated emissions. Principal coordinate analysis revealed geographical variations in fungal communities among sites in China, Europe, and North America (p < 0.05, analysis of similarity), demonstrating that geography may also affect personal exposures to allergenic fungi. Indoor emissions including those released with occupancy contribute more substantially to allergenic fungal exposures in classrooms sampled than do outdoor contributions from ventilation. The results suggest that design and maintenance of buildings to control indoor emissions may enable reduced indoor inhalation exposures to fungal allergens.

Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation.

This study investigated analytical parameters that are inherently relevant to identifying and quantifying fungal communities based on polymerase chain reaction amplicons. Specifically, we evaluated the accuracy of the BLASTn-based identification for internal transcribed spacer (ITS) sequences generated from pure cultures, and quantified the reproducibility of relative abundances as well as α and ß diversity measurements using duplicated environmental samples. The BLASTn-based method produced accurate fungal identification for the pure culture sequences at the genus rank. Percentages of the sequences assigned to correct genera were 99.8%, 99.8% and 99.9% for Alternaria alternata, Cladosporium cladosporioides and Epicoccum nigrum respectively. These fractions were smaller for Aspergillus fumigatus and Penicillium chrysogenum, which have dual nomenclatures or sibling species that are indistinguishable by ITS sequences. Our duplicate environmental analyses demonstrated that α diversity and relative abundance levels were reproducible (r(2) > 0.9), that variability decreases with increased sequence quantity, and that the differences in distinct environmental samples were larger than differences in replicate samples (ß diversity). These results serve to better characterize the identification and quantification limits of ITS-based fungal taxonomic studies, and demonstrate that while diversity quantification is reproducible, limitations in ITS-based taxonomic identification and dual nomenclature conventions are current barriers to identification accuracy.

Hand bacterial communities vary across two different human populations.

This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of US women. Bacterial population profiles and phylogenetically based ordinate analysis demonstrated that the bacterial communities on hands were more similar for selected populations within a country than between the two countries considered. Organisms that have commonly been identified in prior human skin microbiome studies, including members of the Propionibacteriaceae, Staphylococcaceae and Streptococceacea families, were highly abundant on US hands and drove the clustering of US hand microbial communities into a distinct group. The most abundant bacterial taxa on Tanzanian hands were the soil-associated Rhodobacteraceae and Nocardioidaceae. These results help to expand human microbiome results beyond US and European populations, and the identification and abundance of soil-associated bacteria on Tanzanian hands demonstrated the important role of the environment in shaping the microbial communities on human hands.

Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS).

Improvements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program "FHiTINGS" that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and parse internal transcribed spacer (ITS) DNA sequences produced in fungal ecology studies that utilize next-generation DNA sequencing. This tool was designed for use with 454 pyrosequencing and is also appropriate for use with any sequencing platform that allows for BLAST searches against the indicated ITS database. For each sequence, FHiTINGS uses the lowest common ancestor method (LCA) to produce a single identification from BLAST output results, and then assigns taxonomic ranks from species through kingdom when possible for each sequence based on the Index Fungorum database. The program then sums and sorts this data into tabular form to enable rapid analysis of the sample, including α-diversity measures or richness. In silico testing demonstrates the time required to analyze and classify 1000 sequences is reduced from over 2 h by manual sorting to <1 min of computational time when using FHiTINGS, and that the classification output from the software is consistent with that derived from manual sorting of the data.

Mandating indoor air quality for public buildings.

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

Identification of viral pathogen diversity in sewage sludge by metagenome analysis.

The large diversity of viruses that exist in human populations are potentially excreted into sewage collection systems and concentrated in sewage sludge. In the U.S., the primary fate of processed sewage sludge (class B biosolids) is application to agricultural land as a soil amendment. To characterize and understand infectious risks associated with land application, and to describe the diversity of viruses in human populations, shotgun viral metagenomics was applied to 10 sewage sludge samples from 5 wastewater treatment plants throughout the continental U.S, each serving between 100,000 and 1,000,000 people. Nearly 330 million DNA sequences were produced and assembled, and annotation resulted in identifying 43 (26 DNA, 17 RNA) different types of human viruses in sewage sludge. Novel insights include the high abundance of newly emerging viruses (e.g., Coronavirus HKU1, Klassevirus, and Cosavirus) the strong representation of respiratory viruses, and the relatively minor abundance and occurrence of Enteroviruses. Viral metagenome sequence annotations were reproducible and independent PCR-based identification of selected viruses suggests that viral metagenomes were a conservative estimate of the true viral occurrence and diversity. These results represent the most complete description of human virus diversity in any wastewater sample to date, provide engineers and environmental scientists with critical information on important viral agents and routes of infection from exposure to wastewater and sewage sludge, and represent a significant leap forward in understanding the pathogen content of class B biosolids.

Predicting contaminant adsorption in black carbon (biochar)-amended soil for the veterinary antimicrobial sulfamethazine.

Commercial hardwood biochars ranging in N2 specific surface area of 0.1-427 m(2) · g(-1) were added to an agricultural soil at 0, 1, or 2% levels to determine whether they would predictably reduce the pore water concentration of sulfamethazine (SMT). The soil and biochar-soil mixtures were preweathered under mild (2 d, 20 °C) or more severe (28 d, 40 °C) conditions before spiking. The carbon-normalized biochar-water distribution coefficient (KBC) of the biochars varied by a factor of up to 10(4), depending on biochar properties and SMT concentration. Except for the fast-pyrolysis biochar, KBC greatly exceeded the soil organic carbon-water distribution coefficient KOC. Sorption in the mixtures increased as expected with biochar and dose. However, sorption was dramatically overpredicted (by up to 10(2.5)) by the sum of sorption to the individual components, indicating a strong weathering effect even under the mild conditions. The soil-subtracted weathered biochar-water isotherms were more linear, and the KBC values approached or lay within the range of KOC values reported for SMT in 19 soils. Biochars both in intimate contact with soil and placed in a membrane bag suspended in the solution showed reduced N2-B.E.T. surface area after weathering, implicating fouling of the biochar surface by humic substances transferred through water. The results indicate that only highly surfaceous, carbonaceous biochars would be useful for stabilizing soil contaminated with compounds such as SMT. They also suggest that weathering may attenuate the contribution of native (environmental) black carbon to sorption of such compounds in soils and sediments.