SARS-CoV-2: a systematic review of indoor air sampling for virus detection

Hunting for a viral proxy in bioaerosols of swine buildings using molecular detection and metagenomics

There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine. The effectiveness of dust mitigation strategies such as oil sprinkling, to decrease risk of airborne virus transmission are unknown. Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents. Air particles were collected from swine buildings using high-volume air samplers. Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by high-throughput sequencing. Porcine astroviruses group 2 were common (from 102 to 105 genomic copies per cubic meter of air or gc/m3, 93% positivity) while no norovirus genogroup II was recovered from air samples. Porcine torque teno sus virus were detected by qPCR in low concentrations (from 101 to 102 gc/m3, 47% positivity). Among the identified viral families by metagenomics analysis, Herelleviridae, Microviridae, Myoviridae, Podoviridae, and Siphoviridae were dominant. The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m3 among the samples taken for the present study (97% positivity) and banked samples from 5- and 15-year old studies (89% positivity). According to the present study, both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.

Filling the knowledge gap: Scoping review regarding sampling methods, assays, and further requirements to assess airborne viruses

Assessment of occupational exposure to viruses is crucial to identify virus reservoirs and sources of dissemination at an early stage and to help prevent spread between employees and to the general population. Measuring workers' exposure can facilitate assessment of the effectiveness of protective and mitigation measures in place. The aim of this scoping review is to give an overview of available methods and those already implemented for airborne virus' exposure assessment in different occupational and indoor environments. The results retrieved from the different studies may contribute to the setting of future standards and guidelines to ensure a reliable risk characterization in the occupational environments crucial for the implementation of effective control measures. The search aimed at selecting studies between January 1st 2010 and June 30th 2023 in the selected databases. Fifty papers on virus exposure assessment fitted the eligibility criteria and were selected for data extraction. Overall, this study identified gaps in knowledge regarding virus assessment and pinpointed the needs for further research. Several discrepancies were found (transport temperatures, elution steps, …), as well as a lack of publication of important data related to the exposure conditions (contextual information). With the available information, it is impossible to compare results between studies employing different methods, and even if the same methods are used, different conclusions/recommendations based on the expert judgment have been reported due to the lack of consensus in the contextual information retrieved and/or data interpretation. Future research on the field targeting sampling methods and in the laboratory regarding the assays to employ should be developed bearing in mind the different goals of the assessment.

Investigation of the Use of Environmental Samples for the Detection of EHV-1 in the Stalls of Subclinical Shedders

In populations of healthy show horses, the subclinical transmission and circulation of respiratory pathogens can lead to disease outbreaks. Due to recent outbreaks of equine herpesvirus-1 myeloencephalopathy (EHM) in the USA and Europe, many show organizers have instituted various biosecurity protocols such as individual horse testing, monitoring for early clinical disease and increasing hygiene and cleanliness protocols. The aim of this study was to determine the accuracy of detecting EHV-1 in the various environmental samples collected from the stalls of subclinical shedders. Four healthy adult horses were vaccinated intranasally with a modified-live EHV-1 vaccine in order to mimic subclinical shedding. Three additional horses served as non-vaccinated controls. All the horses were stabled in the same barn in individual stalls. Each vaccinated horse had nose-to-nose contact with at least one other horse. Prior to the vaccine administration, and daily thereafter for 10 days, various samples were collected, including a 6" rayon-tipped nasal swab, an environmental sponge, a cloth strip placed above the automatic waterer and an air sample. The various samples were processed for nucleic acid purification and analyzed for the presence of EHV-1 via quantitative PCR (qPCR). EHV-1 in nasal secretions was only detected in the vaccinated horses for 1-2 days post-vaccine administration. The environmental sponges tested EHV-1 qPCR-positive for 2-5 days (median 3.5 days) in the vaccinated horses and 1 day for a single control horse. EHV-1 was detected by qPCR in stall strips from three out of four vaccinated horses and from two out of three controls for only one day. EHV-1 qPCR-positive air samples were only detected in three out of four vaccinated horses for one single day. For the vaccinated horses, a total of 25% of the nasal swabs, 35% of the environmental stall sponges, 7.5% of the strips and 7.5% of the air samples tested qPCR positive for EHV-1 during the 10 study days. When monitoring the subclinical EHV-1 shedders, the collection and testing of the environmental sponges were able to detect EHV-1 in the environment with greater frequency as compared to nasal swabs, stationary strips and air samples.

On-The-Spot Sampling and Detection of Viral Particles on Solid Surfaces Using a Sponge Virus Sensor Incorporated with Finger-Press Fluid Release

This paper presents a sponge-based electrochemical sensor for rapid, on-site collection and analysis of infectious viruses on solid surfaces. The device utilizes a conducting porous sponge modified with graphene, graphene oxide, and specific antibodies. The sponge serves as a hydrophilic porous electrode capable of liquid collection and electrochemical measurements. The device operation involves spraying an aqueous solution on a target surface, swiping the misted surface using the sponge, discharging an electrolyte solution with a simple finger press, and performing in situ incubation and electrochemical measurements. By leveraging the water-absorbing ability of the biofunctionalized conducting sponge, the sensor can effectively collect and quantify virus particles from the surface. The portability of the device is enhanced by introducing a push-release feature that dispenses the liquid electrolyte from a miniature reservoir onto the sensor surface. This reservoir has sharp edges to rupture a liquid sealing film with a finger press. The ability of the device to sample and quantify viral particles is demonstrated by using influenza A virus as the model. The sensor provided a calculated limit of detection of 0.4 TCID50/mL for H1N1 virus, along with a practical concentration range from 1-106 TCID50/mL. Additionally, it achieves a 15% collection efficiency from single-run swiping on a tabletop surface. This versatile device allows for convenient on-site virus detection within minutes, eliminating the need for sample pretreatment and simplifying the entire sample collecting and measuring process. This device presents significant potential for rapid virus detection on solid surfaces.

Advancements in Airborne Viral Nucleic Acid Detection with Wearable Devices

Wearable health sensors for an expanding range of physiological parameters have experienced rapid development in recent years and are poised to disrupt the way healthcare is tracked and administered. The monitoring of environmental contaminants with wearable technologies is an additional layer of personal and public healthcare and is also receiving increased focus. Wearable sensors that detect exposure to airborne viruses could alert wearers of viral exposure and prompt proactive testing and minimization of viral spread, benefitting their own health and decreasing community risk. With the high levels of asymptomatic spread of COVID-19 observed during the pandemic, such devices could dramatically enhance our pandemic response capabilities in the future. To facilitate advancements in this area, this review summarizes recent research on airborne viral detection using wearable sensing devices as well as technologies suitable for wearables. Since the low concentration of viral particles in the air poses significant challenges to detection, methods for airborne viral particle collection and viral sensing are discussed in detail. A special focus is placed on nucleic acid-based viral sensing mechanisms due to their enhanced ability to discriminate between viral subtypes. Important considerations for integrating airborne viral collection and sensing on a single wearable device are also discussed.

Evaluation of Real and Perceived Risk to Health Care Workers Caring for Patients With the Omicron Variant of the SARS-CoV-2 Virus in Surgery and Obstetrics

OBJECTIVES

The Omicron variant of the SARS-CoV-2 virus is described as more contagious than previous variants. We sought to assess risk to health care workers (HCWs) caring for patients with COVID-19 in surgical/obstetrical settings, and the perception of risk among this group.

METHODS

From January to April 2022, reverse transcription polymerase chain reaction was used to detect the presence of SARS-CoV-2 viral ribonucleic acid in patient, environmental (floor, equipment, passive air) samples, and HCWs' masks (inside surface) during urgent surgery or obstetrical delivery for patients with SARS-CoV-2 infection. The primary outcome was the proportion of HCWs' masks testing positive. Results were compared with our previous cross-sectional study involving obstetrical/surgical patients with earlier variants (2020-2021). HCWs completed a risk perception electronic questionnaire.

RESULTS

Eleven patients were included: 3 vaginal births and 8 surgeries. In total, 5/108 samples (5%) tested positive (SARS-CoV-2 Omicron) viral ribonucleic acid: 2/5 endotracheal tubes, 1/22 floor samples, 1/4 patient masks, and 1 nasal probe. No samples from the HCWs' masks (0/35), surgical equipment (0/10), and air (0/11) tested positive. No significant differences were found between the Omicron and 2020/21 patient groups' positivity rates (Mann-Whitney U test, P = 0.838) or the level of viral load from the nasopharyngeal swabs (P = 0.405). Nurses had a higher risk perception than physicians (P = 0.038).

CONCLUSION

No significant difference in contamination rates was found between SARS-CoV-2 Omicron BA.1 and previous variants in surgical/obstetrical settings. This is reassuring as no HCW mask was positive and no HCW tested positive for COVID-19 post-exposure.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Research advances in microfluidic collection and detection of virus, bacterial, and fungal bioaerosols

Bioaerosols are airborne suspensions of fine solid or liquid particles containing biological substances such as viruses, bacteria, cellular debris, fungal spores, mycelium, and byproducts of microbial metabolism. The global Coronavirus disease 2019 (COVID-19) pandemic and the previous emergence of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza have increased the need for reliable and effective monitoring tools for bioaerosols. Bioaerosol collection and detection have aroused considerable attention. Current bioaerosol sampling and detection techniques suffer from long response time, low sensitivity, and high costs, and these drawbacks have forced the development of novel monitoring strategies. Microfluidic technique is considered a breakthrough for high performance analysis of bioaerosols. In recent years, several emerging methods based on microfluidics have been developed and reported for collection and detection of bioaerosols. The unique advantages of microfluidic technique have enabled the integration of bioaerosol collection and detection, which has a higher efficiency over conventional methods. This review focused on the research progress of bioaerosol collection and detection methods based on microfluidic techniques, with special attention on virus aerosols and bacterial aerosols. Different from the existing reviews, this work took a unique perspective of the targets to be collected and detected in bioaerosols, which would provide a direct index of bioaerosol categories readers may be interested in. We also discussed integrated microfluidic monitoring system for bioaerosols. Additionally, the application of bioaerosol detection in biomedicine was presented. Finally, the current challenges in the field of bioaerosol monitoring are presented and an outlook given of future developments.

Mycological Methods for Routine Air Sampling and Interpretation of Results in Operating Theaters

Many infectious diseases are transmitted via the air and are, therefore, particularly difficult to combat. These infections include various invasive mycoses caused by molds. The usual route of infection is the inhalation of conidia. In hospitals, infection can also occur through the deposition of conidia in otherwise sterile anatomical sites during surgical and other invasive procedures. Therefore, knowledge of airborne mold concentrations can lead to measures to protect patients from fungal infections. The literature on this topic contains insufficient and sometimes ambiguous information. This is evidenced by the fact that there are no international recommendations or guidelines defining the methodology of air sampling and the interpretation of the results obtained. Surgical departments, intensive care units and medical mycology laboratories are, therefore, left to their own devices, leading to significant differences in the implementation of mycological surveillance in hospitals. The aim of this mini-review is to provide an overview of the current methods of air sampling and interpretation of results used in medical mycology laboratories.

Environmental dissemination of respiratory viruses: dynamic interdependencies of respiratory droplets, aerosols, aerial particulates, environmental surfaces, and contribution of viral re-aerosolization

During the recent pandemic of COVID-19 (SARS-CoV-2), influential public health agencies such as the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention (CDC) have favored the view that SARS CoV-2 spreads predominantly via droplets. Many experts in aerobiology have openly opposed that stance, forcing a vigorous debate on the topic. In this review, we discuss the various proposed modes of viral transmission, stressing the interdependencies between droplet, aerosol, and fomite spread. Relative humidity and temperature prevailing determine the rates at which respiratory aerosols and droplets emitted from an expiratory event (sneezing, coughing, etc.) evaporate to form smaller droplets or aerosols, or experience hygroscopic growth. Gravitational settling of droplets may result in contamination of environmental surfaces (fomites). Depending upon human, animal and mechanical activities in the occupied space indoors, viruses deposited on environmental surfaces may be re-aerosolized (re-suspended) to contribute to aerosols, and can be conveyed on aerial particulate matter such as dust and allergens. The transmission of respiratory viruses may then best be viewed as resulting from dynamic virus spread from infected individuals to susceptible individuals by various physical states of active respiratory emissions, instead of the current paradigm that emphasizes separate dissemination by respiratory droplets, aerosols or by contaminated fomites. To achieve the optimum outcome in terms of risk mitigation and infection prevention and control (IPAC) during seasonal infection peaks, outbreaks, and pandemics, this holistic view emphasizes the importance of dealing with all interdependent transmission modalities, rather than focusing on one modality.

Experimental and in silico evaluations of the possible molecular interaction between airborne particulate matter and SARS-CoV-2

During the early stage of the COVID-19 pandemic (winter 2020), the northern part of Italy has been significantly affected by viral infection compared to the rest of the country leading the scientific community to hypothesize that airborne particulate matter (PM) could act as a carrier for the SARS-CoV-2. To address this controversial issue, we first verified and demonstrated the presence of SARS-CoV-2 RNA genome on PM2.5 samples, collected in the city of Bologna (Northern Italy) in winter 2021. Then, we employed classical molecular dynamics (MD) simulations to investigate the possible recognition mechanism(s) between a newly modelled PM2.5 fragment and the SARS-CoV-2 Spike protein. The potential molecular interaction highlighted by MD simulations suggests that the glycans covering the upper Spike protein regions would mediate the direct contact with the PM2.5 carbon core surface, while a cloud of organic and inorganic PM2.5 components surround the glycoprotein with a network of non-bonded interactions resulting in up to 4769 total contacts. Moreover, a binding free energy of -207.2 ± 3.9 kcal/mol was calculated for the PM-Spike interface through the MM/GBSA method, and structural analyses also suggested that PM attachment does not alter the protein conformational dynamics. Although the association between the PM and SARS-CoV-2 appears plausible, this simulation does not assess whether these established interactions are sufficiently stable to carry the virus in the atmosphere, or whether the virion retains its infectiousness after the transport. While these key aspects should be verified by further experimental analyses, for the first time, this pioneering study gains insights into the molecular interactions between PM and SARS-CoV-2 Spike protein and will support further research aiming at clarifying the possible relationship between PM abundance and the airborne diffusion of viruses.

Microbial communities in aerosol generated from cyanobacterial bloom-affected freshwater bodies: an exploratory study in Nakdong River, South Korea

Toxic blooms of cyanobacteria, which can produce cyanotoxins, are prevalent in freshwater, especially in South Korea. Exposure to cyanotoxins via ingestion, inhalation, and dermal contact may cause severe diseases. Particularly, toxic cyanobacteria and their cyanotoxins can be aerosolized by a bubble-bursting process associated with a wind-driven wave mechanism. A fundamental question remains regarding the aerosolization of toxic cyanobacteria and cyanotoxins emitted from freshwater bodies during bloom seasons. To evaluate the potential health risk of the aerosolization of toxic cyanobacteria and cyanotoxins, the objectives of this study were as follows: 1) to quantify levels of microcystin in the water and air samples, and 2) to monitor microbial communities, including toxic cyanobacteria in the water and air samples. Water samples were collected from five sites in the Nakdong River, South Korea, from August to September 2022. Air samples were collected using an air pump with a mixed cellulose ester membrane filter. Concentrations of total microcystins were measured using enzyme-linked immunosorbent assay. Shotgun metagenomic sequencing was used to investigate microbial communities, including toxic cyanobacteria. Mean concentrations of microcystins were 960 μg/L ranging from 0.73 to 5,337 μg/L in the water samples and 2.48 ng/m³ ranging from 0.1 to 6.8 ng/m³ in the air samples. In addition, in both the water and air samples, predominant bacteria were Microcystis (PCC7914), which has a microcystin-producing gene, and Cyanobium. Particularly, abundance of Microcystis (PCC7914) comprised more than 1.5% of all bacteria in the air samples. This study demonstrates microbial communities with genes related with microcystin synthesis, antibiotic resistance gene, and virulence factors in aerosols generated from cyanobacterial bloom-affected freshwater body. In summary, aerosolization of toxic cyanobacteria and cyanotoxins is a critical concern as an emerging exposure route for potential risk to environmental and human health.

SARS-CoV2 in public spaces in West London, UK during COVID-19 pandemic

BACKGROUND

Spread of SARS-CoV2 by aerosol is considered an important mode of transmission over distances >2 m, particularly indoors.

OBJECTIVES

We determined whether SARS-CoV2 could be detected in the air of enclosed/semi-enclosed public spaces.

METHODS AND ANALYSIS

Between March 2021 and December 2021 during the easing of COVID-19 pandemic restrictions after a period of lockdown, we used total suspended and size-segregated particulate matter (PM) samplers for the detection of SARS-CoV2 in hospitals wards and waiting areas, on public transport, in a university campus and in a primary school in West London.

RESULTS

We collected 207 samples, of which 20 (9.7%) were positive for SARS-CoV2 using quantitative PCR. Positive samples were collected from hospital patient waiting areas, from hospital wards treating patients with COVID-19 using stationary samplers and from train carriages in London underground using personal samplers. Mean virus concentrations varied between 429 500 copies/m³ in the hospital emergency waiting area and the more frequent 164 000 copies/m³ found in other areas. There were more frequent positive samples from PM samplers in the PM2.5 fractions compared with PM10 and PM1. Culture on Vero cells of all collected samples gave negative results.

CONCLUSION

During a period of partial opening during the COVID-19 pandemic in London, we detected SARS-CoV2 RNA in the air of hospital waiting areas and wards and of London Underground train carriage. More research is needed to determine the transmission potential of SARS-CoV2 detected in the air.

Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review

Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.

Research progress of severe acute respiratory syndrome coronavirus 2 on aerosol collection and detection

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 has negatively affected people's lives and productivity. Because the mode of transmission of SARS-CoV-2 is of great concern, this review discusses the sources of virus aerosols and possible transmission routes. First, we discuss virus aerosol collection methods, including natural sedimentation, solid impact, liquid impact, centrifugal, cyclone and electrostatic adsorption methods. Then, we review common virus aerosol detection methods, including virus culture, metabolic detection, nucleic acid-based detection and immunology-based detection methods. Finally, possible solutions for the detection of SARS-CoV-2 aerosols are introduced. Point-of-care testing has long been a focus of attention. In the near future, the development of an instrument that integrates sampling and output results will enable the real-time, automatic monitoring of patients.

Size distribution and relationship of airborne SARS-CoV-2 RNA to indoor aerosol in hospital ward environments

Aerosol particles proved to play a key role in airborne transmission of SARS-CoV-2 viruses. Therefore, their size-fractionated collection and analysis is invaluable. However, aerosol sampling in COVID departments is not straightforward, especially in the sub-500-nm size range. In this study, particle number concentrations were measured with high temporal resolution using an optical particle counter, and several 8 h daytime sample sets were collected simultaneously on gelatin filters with cascade impactors in two different hospital wards during both alpha and delta variants of concern periods. Due to the large number (152) of size-fractionated samples, SARS-CoV-2 RNA copies could be statistically analyzed over a wide range of aerosol particle diameters (70-10 µm). Our results revealed that SARS-CoV-2 RNA is most likely to exist in particles with 0.5-4 µm aerodynamic diameter, but also in ultrafine particles. Correlation analysis of particulate matter (PM) and RNA copies highlighted the importance of indoor medical activity. It was found that the daily maximum increment of PM mass concentration correlated the most with the number concentration of SARS-CoV-2 RNA in the corresponding size fractions. Our results suggest that particle resuspension from surrounding surfaces is an important source of SARS-CoV-2 RNA present in the air of hospital rooms.

Spread of viruses, which measures are the most apt to control COVID-19?

The persistent debate about the modes of transmission of SARS-CoV2 and preventive measures has illustrated the limits of our knowledge regarding the measures to be implemented in the face of viral risk. Past and present (pandemic-related) scientific data underline the complexity of the phenomenon and its variability over time. Several factors contribute to the risk of transmission, starting with incidence in the general population (i.e., colonization pressure) and herd immunity. Other major factors include intensity of symptoms, interactions with the reservoir (proximity and duration of contact), the specific characteristics of the virus(es) involved, and a number of unpredictable elements (humidity, temperature, ventilation…). In this review, we will emphasize the difficulty of "standardizing" the situations that might explain the discrepancies found in the literature. We will show that the airborne route remains the main mode of transmission. Regarding preventive measures of prevention, while vaccination remains the cornerstone of the fight against viral outbreaks, we will remind the reader that wearing a mask is the main barrier measure and that the choice of type of mask depends on the risk situations. Finally, we believe that the recent pandemic should induce us in the future to modify our recommendations by adapting our measures in hospitals, not to the pathogen concerned, which is currently the case, but rather to the type of at-risk situation.

Detection of hospital environmental contamination during SARS-CoV-2 Omicron predominance using a highly sensitive air sampling device

Background and objectives

The high transmissibility of SARS-CoV-2 has exposed weaknesses in our infection control and detection measures, particularly in healthcare settings. Aerial sampling has evolved from passive impact filters to active sampling using negative pressure to expose culture substrate for virus detection. We evaluated the effectiveness of an active air sampling device as a potential surveillance system in detecting hospital pathogens, for augmenting containment measures to prevent nosocomial transmission, using SARS-CoV-2 as a surrogate.

Methods

We conducted air sampling in a hospital environment using the AerosolSense^TM air sampling device and compared it with surface swabs for their capacity to detect SARS-CoV-2.

Results

When combined with RT-qPCR detection, we found the device provided consistent SARS-CoV-2 detection, compared to surface sampling, in as little as 2 h of sampling time. The device also showed that it can identify minute quantities of SARS-CoV-2 in designated "clean areas" and through a N95 mask, indicating good surveillance capacity and sensitivity of the device in hospital settings.

Conclusion

Active air sampling was shown to be a sensitive surveillance system in healthcare settings. Findings from this study can also be applied in an organism agnostic manner for surveillance in the hospital, improving our ability to contain and prevent nosocomial outbreaks.

Monitoring of indoor bioaerosol for the detection of SARS-CoV-2 in different hospital settings

Background

Spore Trap is an environmental detection technology, already used in the field of allergology to monitor the presence and composition of potentially inspirable airborne micronic bioparticulate. This device is potentially suitable for environmental monitoring of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in hospital, as well as in other high-risk closed environments. The aim of the present study is to investigate the accuracy of the Spore Trap system in detecting SARS-CoV-2 in indoor bioaerosol of hospital rooms.

Methods

The Spore Trap was placed in hospital rooms hosting patients with documented SARS-CoV-2 infection (n = 36) or, as a negative control, in rooms where patients with documented negativity to a Real-Time Polymerase Chain Reaction molecular test for SARS-CoV-2 were admitted (n = 10). The monitoring of the bioaerosol was carried on for 24 h. Collected samples were analyzed by real-time polymerase chain reaction.

Results

The estimated sensitivity of the Spore Trap device for detecting SARS-CoV-2 in an indoor environment is 69.4% (95% C.I. 54.3-84.4%), with a specificity of 100%.

Conclusion

The Spore Trap technology is effective in detecting airborne SARS-CoV-2 virus with excellent specificity and high sensitivity, when compared to previous reports. The SARS-CoV-2 pandemic scenario has suggested that indoor air quality control will be a priority in future public health management and will certainly need to include an environmental bio-investigation protocol.

SARS-CoV-2 RNA Is Readily Detectable at Least 8 Months after Shedding in an Isolation Facility

Environmental monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for research and public health purposes has grown exponentially throughout the coronavirus disease 2019 (COVID-19) pandemic. Monitoring wastewater for SARS-CoV-2 provides early warning signals of virus spread and information on trends in infections at a community scale. Indoor environmental monitoring (e.g., swabbing of surfaces and air filters) to identify potential outbreaks is less common, and the evidence for its utility is mixed. A significant challenge with surface and air filter monitoring in this context is the concern of "relic RNA," noninfectious RNA found in the environment that is not from recently deposited virus. Here, we report detection of SARS-CoV-2 RNA on surfaces in an isolation unit (a university dorm room) for up to 8 months after a COVID-19-positive individual vacated the space. Comparison of sequencing results from the same location over two time points indicated the presence of the entire viral genome, and sequence similarity confirmed a single source of the virus. Our findings highlight the need to develop approaches that account for relic RNA in environmental monitoring. IMPORTANCE Environmental monitoring of SARS-CoV-2 is rapidly becoming a key tool in infectious disease research and public health surveillance. Such monitoring offers a complementary and sometimes novel perspective on population-level incidence dynamics relative to that of clinical studies by potentially allowing earlier, broader, more affordable, less biased, and less invasive identification. Environmental monitoring can assist public health officials and others when deploying resources to areas of need and provides information on changes in the pandemic over time. Environmental surveillance of the genetic material of infectious agents (RNA and DNA) in wastewater became widely applied during the COVID-19 pandemic. There has been less research on other types of environmental samples, such as surfaces, which could be used to indicate that someone in a particular space was shedding virus. One challenge with surface surveillance is that the noninfectious genetic material from a pathogen (e.g., RNA from SARS-CoV-2) may be detected in the environment long after an infected individual has left the space. This study aimed to determine how long SARS-CoV-2 RNA could be detected in a room after a COVID-positive person had been housed there.

COVID-19 pandemic lesson learned- critical parameters and research needs for UVC inactivation of viral aerosols

The COVID-19 pandemic highlighted public awareness of airborne disease transmission in indoor settings and emphasized the need for reliable air disinfection technologies. This increased awareness will carry in the post-pandemic era along with the ever-emerging SARS-CoV variants, necessitating effective and well-defined protocols, methods, and devices for air disinfection. Ultraviolet (UV)-based air disinfection demonstrated promising results in inactivating viral bioaerosols. However, the reported data diversity on the required UVC doses has hindered determining the best UVC practices and led to confusion among the public and regulators. This article reviews available information on critical parameters influencing the efficacy of a UVC air disinfection system and, consequently, the required dose including the system's components as well as operational and environmental factors. There is a consensus in the literature that the interrelation of humidity and air temperature has a significant impact on the UVC susceptibility, which translate to changing the UVC efficacy of commercialized devices in indoor settings under varying conditions. Sampling and aerosolization techniques reported to have major influence on the result interpretation and it is recommended to use several sampling methods simultaneously to generate comparable and conclusive data. We also considered the safety concerns and the potential safe alternative of UVC, far-UVC. Finally, the gaps in each critical parameter and the future research needs of the field are represented. This paper is the first step to consolidating literature towards developing a standard validation protocol for UVC air disinfection devices which is determined as the one of the research needs.

SARS-CoV-2 surveillance in indoor and outdoor size-segregated aerosol samples

We aimed to determine the presence of SARS-CoV-2 RNA in indoor and outdoor size-segregated aerosol samples (PM_10-2.5, PM_2.5). Five outdoor daily samples were collected between November and December 2020 in an urban/industrial area with relatively high PM₁₀ levels (Maliaño, Santander, Spain) by using a PM impactor (air flowrate of 30 L/min). In a non-hospital indoor sampling surveillance context, 8 samples in classrooms and 6 samples in the central library-Paraninfo of the University of Cantabria (UC) were collected between April and June 2021 by using personal PM samplers (air flowrate of 3 L/min). Lastly, 8 samples in the pediatric nasopharyngeal testing room at Liencres Hospital, 6 samples from different single occupancy rooms of positive patients, and 2 samples in clinical areas of the COVID plant of the University Hospital Marqués de Valdecilla (HUMV) were collected between January and May 2021. N1, N2 genes were used to test the presence of SARS-CoV-2 RNA by RT-qPCR. SARS-CoV-2 positive detection was only obtained from one fine fraction (PM_2.5) sample, corresponding to one occupancy room, where a patient with positive PCR and cough was present. Negative results found in other sampling areas such as the pediatric nasopharyngeal testing rooms should be interpreted in terms of air sampling volume limitation and good ventilation.

Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples

The compositional analysis of 16S rRNA gene sequencing datasets is applied to characterize the bacterial structure of airborne samples collected in different locations of a hospital infection disease department hosting COVID-19 patients, as well as to investigate the relationships among bacterial taxa at the genus and species level. The exploration of the centered log-ratio transformed data by the principal component analysis via the singular value decomposition has shown that the collected samples segregated with an observable separation depending on the monitoring location. More specifically, two main sample clusters were identified with regards to bacterial genera (species), consisting of samples mostly collected in rooms with and without COVID-19 patients, respectively. Human pathogenic genera (species) associated with nosocomial infections were mostly found in samples from areas hosting patients, while non-pathogenic genera (species) mainly isolated from soil were detected in the other samples. Propionibacterium acnes, Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and jeikeium were the main pathogenic species detected in COVID-19 patients' rooms. Samples from these locations were on average characterized by smaller richness/evenness and diversity than the other ones, both at the genus and species level. Finally, the ρ metrics revealed that pairwise positive associations occurred either between pathogenic or non-pathogenic taxa.

SARS-CoV-2 detection in hospital indoor environments, NW Iran

This study aimed to investigate the potential contamination of SARS-CoV-2 in indoor settled dust and surfaces of Amir Al-Muminin hospital in Maragheh, Iran. Samples were taken from surfaces and settled dust using a passive approach and particulate matter (PM) using an active approach from different hospital wards. SARS-CoV-2 was detected in 15% of settled dust samples (N = 4/26) and 10% of surface samples (3/30). SARS-CoV-2 has been detected in 13.8% and 9.1% of the dust samples collected at a distance of fewer than 1 m and more than 3 m from the patient bed, respectively. SARS-CoV-2 was found in 11% of surface samples from low-touch surfaces and 8% from high touch surfaces. The relationship between PM_2.5, PM₁₀, humidity, temperature, and positive samples of SARS-CoV-2 was investigated. A positive correlation was observed between relative humidity, PM_2.5, and positive SARS-CoV-2 samples. Principal component analysis (PCA) suggested positive correlation between positive SARS-CoV-2 samples, relative humidity, and PM_2.5. Risk assessment results indicated that the annual mean infection risk of SARS-CoV-2 for hospital staff with illness and death was 2.6 × 10^-2 and 7.7 × 10^-4 per person per year. Current findings will help reduce the permanence of viral particles in the COVID 19 tragedy and future similar pandemics e.g., novel influenza viruses.

Detection of SARS-CoV-2 in exhaled breath from non-hospitalized COVID-19-infected individuals

The diagnosis of COVID-19 is based on detection of SARS-CoV-2 in oro-/nasopharyngel swabs, but due to discomfort and minor risk during the swab procedure, detection of SARS-CoV-2 has been investigated in other biological matrixes. In this proof-of-concept study, individuals with confirmed SARS-CoV-2 infection performed a daily air sample for five days. Air samples were obtained through a non-invasive electrostatic air sampler. Detection of SARS-CoV-2 RNA was determined with qRT-PCR. The association of positive samples with different exposures was evaluated through mixed-effect models. We obtained 665 air samples from 111 included participants with confirmed SARS-CoV-2 infection. Overall, 52 individuals (46.8%) had at least one positive air sample, and 129 (19.4%) air samples were positive for SARS-CoV-2. Participants with symptoms or a symptom duration ≤ four days had significantly higher odds of having a positive air sample. Cycle threshold values were significantly lower in samples obtained ≤ 4 days from symptom onset. Neither variant of SARS-CoV-2 nor method of air sampling were associated with a positive air sample. We demonstrate that SARS-CoV-2 is detectable in human breath by electrostatic air sampling with the highest detection rate closest to symptom onset. We suggest further evaluation of the air sampling technique to increase sensitivity.

Novel aerosol detection platform for SARS‑CoV‑2: Based on specific magnetic nanoparticles adsorption sampling and digital droplet PCR detection

The SARS‑CoV‑2 virus is released from an infectious source (such as a sick person) and adsorbed on aerosols, which can form pathogenic microorganism aerosols, which can affect human health through airborne transmission. Efficient sampling and accurate detection of microorganisms in aerosols are the premise and basis for studying their properties and evaluating their hazard. In this study, we built a set of sub-micron aerosol detection platform, and carried out a simulation experiment on the SARS‑CoV‑2 aerosol in the air by wet-wall cyclone combined with immunomagnetic nanoparticle adsorption sampling and ddPCR. The feasibility of the system in aerosol detection was verified, and the influencing factors in the detection process were experimentally tested. As a result, the sampling efficiency was 29.77%, and extraction efficiency was 98.57%. The minimum detection limit per unit volume of aerosols was 250 copies (10² copies/mL, concentration factor 2.5).

Definition of an Indoor Air Sampling Strategy for SARS-CoV-2 Detection and Risk Management: Case Study in Kindergartens

In the last two years, the world has been overwhelmed by SARS-CoV-2. One of the most important ways to prevent the spread of the virus is the control of indoor conditions: from surface hygiene to ventilation. Regarding the indoor environments, monitoring the presence of the virus in the indoor air seems to be promising, since there is strong evidence that airborne transmission through infected droplets and aerosols is its dominant transmission route. So far, few studies report the successful detection of SARS-CoV-2 in the air; moreover, the lack of a standard guideline for air monitoring reduces the uniformity of the results and their usefulness in the management of the risk of virus transmission. In this work, starting from a critical analysis of the existing standards and guidelines for indoor air quality, we define a strategy to set-up indoor air sampling plans for the detection of SARS-CoV-2. The strategy is then tested through a case study conducted in two kindergartens in the metropolitan city of Milan, in Italy, involving a total of 290 children and 47 teachers from 19 classrooms. The results proved its completeness, effectiveness, and suitability as a key tool in the airborne SARS-CoV-2 infection risk management process. Future research directions are then identified and discussed.

SARS-CoV-2 in Environmental Samples of Quarantined Households

The role of environmental transmission of SARS-CoV-2 remains unclear. Thus, the aim of this study was to investigate whether viral contamination of air, wastewater, and surfaces in quarantined households result in a higher risk for exposed persons. For this study, a source population of 21 households under quarantine conditions with at least one person who tested positive for SARS-CoV-2 RNA were randomly selected from a community in North Rhine-Westphalia in March 2020. All individuals living in these households participated in this study and provided throat swabs for analysis. Air and wastewater samples and surface swabs were obtained from each household and analysed using qRT-PCR. Positive swabs were further cultured to analyse for viral infectivity. Out of all the 43 tested adults, 26 (60.47%) tested positive using qRT-PCR. All 15 air samples were qRT-PCR-negative. In total, 10 out of 66 wastewater samples were positive for SARS-CoV-2 (15.15%) and 4 out of 119 surface samples (3.36%). No statistically significant correlation between qRT-PCR-positive environmental samples and the extent of the spread of infection between household members was observed. No infectious virus could be propagated under cell culture conditions. Taken together, our study demonstrates a low likelihood of transmission via surfaces. However, to definitively assess the importance of hygienic behavioural measures in the reduction of SARS-CoV-2 transmission, larger studies should be designed to determine the proportionate contribution of smear vs. droplet transmission.

SARS-CoV-2 in Environmental Samples of Quarantined Households

The role of environmental transmission of SARS-CoV-2 remains unclear. Thus, the aim of this study was to investigate whether viral contamination of air, wastewater, and surfaces in quarantined households result in a higher risk for exposed persons. For this study, a source population of 21 households under quarantine conditions with at least one person who tested positive for SARS-CoV-2 RNA were randomly selected from a community in North Rhine-Westphalia in March 2020. All individuals living in these households participated in this study and provided throat swabs for analysis. Air and wastewater samples and surface swabs were obtained from each household and analysed using qRT-PCR. Positive swabs were further cultured to analyse for viral infectivity. Out of all the 43 tested adults, 26 (60.47%) tested positive using qRT-PCR. All 15 air samples were qRT-PCR-negative. In total, 10 out of 66 wastewater samples were positive for SARS-CoV-2 (15.15%) and 4 out of 119 surface samples (3.36%). No statistically significant correlation between qRT-PCR-positive environmental samples and the extent of the spread of infection between household members was observed. No infectious virus could be propagated under cell culture conditions. Taken together, our study demonstrates a low likelihood of transmission via surfaces. However, to definitively assess the importance of hygienic behavioural measures in the reduction of SARS-CoV-2 transmission, larger studies should be designed to determine the proportionate contribution of smear vs. droplet transmission.

Longitudinal analysis of built environment and aerosol contamination associated with isolated COVID-19 positive individuals

The indoor environment is the primary location for the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), largely driven by respiratory particle accumulation in the air and increased connectivity between the individuals occupying indoor spaces. In this study, we aimed to track a cohort of subjects as they occupied a COVID-19 isolation dormitory to better understand the impact of subject and environmental viral load over time, symptoms, and room ventilation on the detectable viral load within a single room. We find that subject samples demonstrate a decrease in overall viral load over time, symptoms significantly impact environmental viral load, and we provide the first real-world evidence for decreased aerosol SARS-CoV-2 load with increasing ventilation, both from mechanical and window sources. These results may guide environmental viral surveillance strategies and be used to better control the spread of SARS-CoV-2 within built environments and better protect those caring for individuals with COVID-19.

Detection of SARS-CoV-2 contamination in the operating room and birthing room setting: a cross-sectional study

BACKGROUND

The exposure risks to front-line health care workers caring for patients with SARS-CoV-2 infection undergoing surgery or obstetric delivery are unclear, and an understanding of sample types that may harbour virus is important for evaluating risk. We sought to determine whether SARS-CoV-2 viral RNA from patients with SARS-CoV-2 infection undergoing surgery or obstetric delivery was present in the peritoneal cavity of male and female patients, in the female reproductive tract, in the environment of the surgery or delivery suite (surgical instruments or equipment used, air or floors), and inside the masks of the attending health care workers.

METHODS

We conducted a cross-sectional study from November 2020 to May 2021 at 2 tertiary academic Toronto hospitals, during urgent surgeries or obstetric deliveries for patients with SARS-CoV-2 infection. The presence of SARS-CoV-2 viral RNA in patient, environmental and air samples was identified by real-time reverse transcription polymerase chain reaction (RT-PCR). Air samples were collected using both active and passive sampling techniques. The primary outcome was the proportion of health care workers' masks positive for SARS-CoV-2 RNA. We included adult patients with positive RT-PCR nasal swab undergoing obstetric delivery or urgent surgery (from across all surgical specialties).

RESULTS

A total of 32 patients (age 20-88 yr) were included. Nine patients had obstetric deliveries (6 cesarean deliveries), and 23 patients (14 male) required urgent surgery from the orthopedic or trauma, general surgery, burn, plastic surgery, cardiac surgery, neurosurgery, vascular surgery, gastroenterology and gynecologic oncology divisions. SARS-CoV-2 RNA was detected in 20 of 332 (6%) patient and environmental samples collected: 4 of 24 (17%) patient samples, 5 of 60 (8%) floor samples, 1 of 54 (2%) air samples, 10 of 23 (43%) surgical instrument or equipment samples, 0 of 24 cautery filter samples and 0 of 143 (95% confidence interval 0-0.026) inner surface of mask samples.

INTERPRETATION

During the study period of November 2020 to May 2021, we found evidence of SARS-CoV-2 RNA in a small but important number of samples obtained in the surgical and obstetric operative environment. The finding of no detectable virus inside the masks worn by the health care teams would suggest a low risk of infection for health care workers using appropriate personal protective equipment.

A clinical observational analysis of aerosol emissions from dental procedures

Aerosol generating procedures (AGPs) are defined as any procedure releasing airborne particles <5 μm in size from the respiratory tract. There remains uncertainty about which dental procedures constitute AGPs. We quantified the aerosol number concentration generated during a range of periodontal, oral surgery and orthodontic procedures using an aerodynamic particle sizer, which measures aerosol number concentrations and size distribution across the 0.5-20 μm diameter size range. Measurements were conducted in an environment with a sufficiently low background to detect a patient's cough, enabling confident identification of aerosol. Phantom head control experiments for each procedure were performed under the same conditions as a comparison. Where aerosol was detected during a patient procedure, we assessed whether the size distribution could be explained by the non-salivary contaminated instrument source in the respective phantom head control procedure using a two-sided unpaired t-test (comparing the mode widths (log(σ)) and peak positions (DP,C)). The aerosol size distribution provided a robust fingerprint of aerosol emission from a source. 41 patients underwent fifteen different dental procedures. For nine procedures, no aerosol was detected above background. Where aerosol was detected, the percentage of procedure time that aerosol was observed above background ranged from 12.7% for ultrasonic scaling, to 42.9% for 3-in-1 air + water syringe. For ultrasonic scaling, 3-in-1 syringe use and surgical drilling, the aerosol size distribution matched the non-salivary contaminated instrument source, with no unexplained aerosol. High and slow speed drilling produced aerosol from patient procedures with different size distributions to those measured from the phantom head controls (mode widths log(σ)) and peaks (DP,C, p< 0.002) and, therefore, may pose a greater risk of salivary contamination. This study provides evidence for sources of aerosol generation during common dental procedures, enabling more informed evaluation of risk and appropriate mitigation strategies.

SARS-CoV-2 Detection in air samples from inside heating, ventilation, and air conditioning (HVAC) systems- COVID surveillance in student dorms

Background

The COVID-19 pandemic affected universities and institutions and caused campus shutdowns with a transition to online teaching models. To detect infections that might spread on campus, we pursued research towards detecting SARS-CoV-2 in air samples inside student dorms.

Methods

We sampled air in 2 large dormitories for 3.5 months and a separate isolation suite containing a student who had tested positive for COVID-19. We developed novel techniques employing 4 methods to collect air samples: Filter Cassettes, Button Sampler, BioSampler, and AerosolSense sampler combined with direct qRT-PCR SARS-CoV-2 analysis.

Results

For the 2 large dorms with the normal student population, we detected SARS-CoV-2 in 11 samples. When compared with student nasal swab qRT-PCR testing, we detected SARS-CoV-2 in air samples when a PCR positive COVID-19 student was living on the same floor of the sampling location with a detection rate of 75%. For the isolation dorm, we had a 100% SARS-CoV-2 detection rate with AerosolSense sampler.

Conclusions

Our data suggest air sampling may be an important SARS-CoV-2 surveillance technique, especially for buildings with congregant living settings (dorms, correctional facilities, barracks). Future building designs and public health policies should consider implementation of Heating, Ventilation, and Air Conditioning surveillance.

A review on measurements of SARS-CoV-2 genetic material in air in outdoor and indoor environments: Implication for airborne transmission

Airborne transmission of SARS-CoV-2 has been object of debate in the scientific community since the beginning of COVID-19 pandemic. This mechanism of transmission could arise from virus-laden aerosol released by infected individuals and it is influenced by several factors. Among these, the concentration and size distribution of virus-laden particles play an important role. The knowledge regarding aerosol transmission increases as new evidence is collected in different studies, even if it is not yet available a standard protocol regarding air sampling and analysis, which can create difficulties in the interpretation and application of results. This work reports a systematic review of current knowledge gained by 73 published papers on experimental determination of SARS-CoV-2 RNA in air comparing different environments: outdoors, indoor hospitals and healthcare settings, and public community indoors. Selected papers furnished 77 datasets: outdoor studies (9/77, 11.7%) and indoor studies (68/77. 88.3%). The indoor datasets in hospitals were the vast majority (58/68, 85.3%), and the remaining (10/68, 14.7%) were classified as community indoors. The fraction of studies having positive samples, as well as positivity rates (i.e. ratios between positive and total samples) are significantly larger in hospitals compared to the other typologies of sites. Contamination of surfaces was more frequent (in indoor datasets) compared to contamination of air samples; however, the average positivity rate was lower compared to that of air. Concentrations of SARS-CoV-2 RNA in air were highly variables and, on average, lower in outdoors compared to indoors. Among indoors, concentrations in community indoors appear to be lower than those in hospitals and healthcare settings.

SARS-CoV-2 RNA Recovery from Air Sampled on Quartz Fiber Filters: A Matter of Sample Preservation?

The airborne route of transmission of SARS-CoV-2 was confirmed by the World Health Organization in April 2021. There is an urge to establish standardized protocols for assessing the concentration of SARS-CoV-2 RNA in air samples to support risk assessment, especially in indoor environments. Debates on the airborne transmission route of SARS-CoV-2 have been complicated because, among the studies testing the presence of the virus in the air, the percentage of positive samples has often been very low. In the present study, we report preliminary results on a study for the evaluation of parameters that can influence SARS-CoV-2 RNA recovery from quartz fiber filters spotted either by standard single-stranded SARS-CoV-2 RNA or by inactivated SARS-CoV-2 virions. The analytes were spiked on filters and underwent an active or passive sampling; then, they were preserved at −80 °C for different numbers of days (0 to 54) before extraction and analysis. We found a mean recovery of 2.43%, except for the sample not preserved (0 days) that showed a recovery of 13.51%. We found a relationship between the number of days and the recovery percentage. The results presented show a possible issue that relates to the quartz matrix and SARS-CoV-2 RNA recovery. The results are in accordance with the already published studies that described similar methods for SARS-CoV-2 RNA field sampling and that reported non-detectable concentrations of RNA. These outcomes could be false negatives due to sample preservation conditions. Thus, until further investigation, we suggest, as possible alternatives, to keep the filters: (i) in a sealed container for preservation at 4 °C; and (ii) in a viral transport medium for preservation at a temperature below 0 °C.

Airborne concentrations of SARS-CoV-2 in indoor community environments in Italy

COVID-19 pandemic raised a debate regarding the role of airborne transmission. Information regarding virus-laden aerosol concentrations is still scarce in community indoors and what are the risks for general public and the efficiency of restriction policies. This work investigates, for the first time in Italy, the presence of SARS-CoV-2 RNA in air samples collected in different community indoors (one train station, two food markets, one canteen, one shopping centre, one hair salon, and one pharmacy) in three Italian cities: metropolitan city of Venice (NE of Italy), Bologna (central Italy), and Lecce (SE of Italy). Air samples were collected during the maximum spread of the second wave of pandemic in Italy (November and December 2020). All collected samples tested negative for the presence of SARS-CoV-2, using both real-time RT-PCR and ddPCR, and no significant differences were observed comparing samples taken with and without customers. Modelling average concentrations, using influx of customers' data and local epidemiological information, indicated low values (i.e. < 0.8 copies m-3 when cotton facemasks are used and even lower for surgical facemasks). The results, even if with some limitations, suggest that the restrictive policies enforced could effectively reduce the risk of airborne transmissions in the community indoor investigated, providing that physical distance is respected.

Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook

A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.

Expert elicitation on the relative importance of possible SARS-CoV-2 transmission routes and the effectiveness of mitigations

OBJECTIVES

To help people make decisions about the most effective mitigation measures against SARS-CoV-2 transmission in different scenarios, the likelihoods of transmission by different routes need to be quantified to some degree (however uncertain). These likelihoods need to be communicated in an appropriate way to illustrate the relative importance of different routes in different scenarios, the likely effectiveness of different mitigation measures along those routes, and the level of uncertainty in those estimates. In this study, a pragmatic expert elicitation was undertaken to supply the underlying quantitative values to produce such a communication tool.

PARTICIPANTS

Twenty-seven individual experts from five countries and many scientific disciplines provided estimates.

OUTCOME MEASURES

Estimates of transmission parameters, assessments of the quality of the evidence, references to relevant literature, rationales for their estimates and sources of uncertainty.

RESULTS AND CONCLUSION

The participants' responses showed that there is still considerable disagreement among experts about the relative importance of different transmission pathways and the effectiveness of different mitigation measures due to a lack of empirical evidence. Despite these disagreements, when pooled, the majority views on each parameter formed an internally consistent set of estimates (for example, that transmission was more likely indoors than outdoors, and at closer range), which formed the basis of a visualisation to help individuals and organisations understand the factors that influence transmission and the potential benefits of different mitigation measures.

Airborne SARS-CoV-2 in home- and hospital environment investigated with a high-powered air sampler

Background

The initial aim was to study the effects of face masks worn by recently infected individuals on the airborne spread of SARS-CoV-2, but findings motivated us to proceed with comparing the presence of SARS-CoV-2 in air samples near infected individuals at home with those near infected intensive care unit (ICU) patients.

Aim

To assess the presence of SARS-CoV-2 in the air of homes of infected individuals and in ICU rooms of critically ill patients with COVID-19 who were undergoing different forms of potential aerosol-generating medical procedures.

Methods

A high-volume air sampler method was developed that used a household vacuum cleaner with surgical face masks serving as sample filters. SARS-CoV-2 RNA was harvested from these filters and analysed by polymerase chain reaction. Fog experiments were performed to visualize the airflow around the air sampler. Air samples were acquired in close proximity of infected individuals, with or without wearing face masks, in their homes. Environmental air samples remote from these infected individuals were also obtained, plus samples near patients in the ICU undergoing potential aerosol-generating medical procedures.

Findings

Wearing a face mask resulted in a delayed and reduced flow of the fog into the air sampler. Face masks worn by infected individuals were found to contain SARS-CoV-2 RNA in 71% of cases. SARS-CoV-2 was detected in air samples regardless of mask experiments. The proportion of positive air samples was higher in the homes (29/41; 70.7%) than in the ICU (4/17; 23.5%) (P < 0.01).

Conclusion

SARS-CoV-2 RNA could be detected in air samples by using a vacuum cleaner based air sampler method. Air samples in the home environment of recently infected individuals contained SARS-CoV-2 RNA nearly three times more frequently by comparison with those obtained in ICU rooms during potential aerosol-generating medical procedures.

A critical review of heating, ventilation, and air conditioning (HVAC) systems within the context of a global SARS-CoV-2 epidemic

The Coronavirus disease (COVID-19) has spread over the world, resulting in more than 225 million patients, and 4.7 million deaths in September 2021. It also caused panic and terror, halted numerous activities, and resulted in the world economy deteriorates. It altered human behavior and compelled people to alter their lifestyles to avoid infection. Air conditioning systems are one of the most important sectors that must be considered because of the pandemic SARS-CoV-2 all over the world. Air is used as a heat transfer medium in heating, ventilation, and air conditioning (HVAC) systems. The air contains a variety of pollutants, viruses, and bacteria, all of which have an impact on and destroy human life. Significantly in summer, people spend more time in air conditioners which results in lower levels of vitamin D and melatonin which may affect the functioning of their immune system and are susceptible to receiving SARS-CoV-2 from other individuals. As an important component of air conditioning and ventilation systems, the air filter plays a significant role. As a result, researchers must work harder to improve its design to prevent the ultra-small particles loaded with COVID-19. This paper contributes to the design of existing HVAC systems in terms of their suitability and impact on the spread of the hybrid SARS-CoV-2 epidemic, as well as efforts to obtain a highly efficient air filter to remove super-sized particles for protection against epidemic infection. In addition, important guideline recommendations have been extracted to limit the spread of the SARS-CoV-2 throughout the world and to get the highest quality indoor air in air-conditioned places.

Evaluation of Residual Infectivity after SARS-CoV-2 Aerosol Transmission in a Controlled Laboratory Setting

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is mainly transmitted through respiratory droplets, aerosols, or direct contact with fomites from an infected subject. It has been reported that SARS-CoV-2 is stable and viable in aerosol up to 16 h in controlled laboratory conditions. However, the aerosolization conditions varied a lot between the studies. In this work, an experimental laboratory model of SARS-CoV-2 aerosolization was established, employing an impinger nebulizer, a cylindrical chamber for aerosol travel, and a SKC biosampler for the collection of particles. The efficiency of the system was assessed based on the molecular determination of the viral load in the nebulizer after the aerosolization and in the aerosol collected at the end of the travel. Moreover, the residual infectivity was tested in vitro on the Vero E6 cell line, through the observation of the cytopathic effect (CPE), and the quantification of the viral load in the supernatants at 7 days post inoculation (dpi). A high RNA viral load was found in the SKC biosampler after aerosolization, indicating that it was possible to transport a high virus titer through the 30-cm chamber with all the dilutions (initial 105, 104, 103 plaque forming unit-PFU/mL). At the 7 dpi, an increment of the RNA viral load was determined for the dilutions 105 and 104 PFU/mL tested, while only the initial 105 PFU/mL resulted in visible CPE. Our findings allowed us to achieve the resilience of SARS-CoV-2 in aerosol form, at a concentration comparable to those reported for clinical samples. This mode of transmission should be considered for the mitigation and preventive measures to counteract SARS-CoV-2 spreading.

An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks

Virus-related mortality and morbidity are due to cell/tissue damage caused by replicative pressure and resource exhaustion, e.g., HBV or HIV; exaggerated immune responses, e.g., SARS-CoV-2; and cancer, e.g., EBV or HPV. In this context, oncogenic and other types of viruses drive genetic and epigenetic changes that expand the tumorigenic program, including modifications to the ability of cancer cells to migrate. The best-characterized group of changes is collectively known as the epithelial–mesenchymal transition, or EMT. This is a complex phenomenon classically described using biochemistry, cell biology and genetics. However, these methods require enormous, often slow, efforts to identify and validate novel therapeutic targets. Systems biology can complement and accelerate discoveries in this field. One example of such an approach is Boolean networks, which make complex biological problems tractable by modeling data (“nodes”) connected by logical operators. Here, we focus on virus-induced cellular plasticity and cell reprogramming in mammals, and how Boolean networks could provide novel insights into the ability of some viruses to trigger uncontrolled cell proliferation and EMT, two key hallmarks of cancer.