SARS-CoV-2 detection in bioaerosols using a liquid impinger collector and ddPCR

SERS-based lateral flow immunoassay for rapid and sensitive sensing of nucleocapsid protein toward SARS-CoV-2 screening in clinical samples

Early and accurate identification of SARS-CoV-2 infection is crucial for epidemic prevention and control. Lateral flow immunoassay (LFIA) has become the mainstream method for screening SARS-CoV-2 infection due to its rapid, simple and amenable for point-of-care detection (POCT), but still suffered from the poor sensitivity and accuracy. In this study, Au nanoparticles (NPs) with controllable Ag shell (Au@Ag) were manufactured via a seed-mediated growth method. The Au@Ag-based LFIA exhibited superb colorimetric (CM) signal and intense surface-enhanced Raman scattering (SERS) signal for dual-mode sensing of nucleocapsid protein (N protein), a naturally protein expression in vivo during SARS-CoV-2 infection. The limit of detection (LOD) of the SERS-LFIA mode was 2.16 pg/mL, which was around 150-time more sensitive than conventional visual CM-LFIA mode (300 pg/mL). More importantly, the proposed LFIA is capable of quantitatively detecting N protein-spiked real samples with satisfactory recoveries from 83 % to 91.4 %. Clinical pharyngeal swab samples of the infected patients (n = 20) and healthy subjects (n = 20) were effectively discriminated in the developed SERS-LFIA, where the negative accuracy rate was 100 % and the positive accuracy rate was 85 %, among which samples from P1, P18, and P19 were false-negative results. The results obtained from the LFIA immunoassay were in good agreement with the standard PCR method in clinic, and superior to those of the commercially colloidal gold strip by using the same antibodies. In conclusion, the LFIA proposed here can perform specific, rapid, and ultrasensitive analysis of N protein toward early warning of SARS-CoV-2 infection.

COVID-19 patient variables associated with the detection of airborne SARS-CoV-2

BACKGROUND

Understanding the COVID-19 patient characteristics that impact environmental SARS-CoV-2 load is essential for improving infection risk management. In this study, we analyzed the influence of patient variables on airborne SARS-CoV-2 genome detection.

METHODS

Sixty-nine COVID-19 patients were recruited across three independent studies with airborne SARS-CoV-2 genome assessed in individual hospital rooms using droplet digital PCR.

RESULTS

In the bivariate analysis, the odds of airborne SARS-CoV-2 detection were significantly higher for patients with obesity, chronic respiratory diseases, pneumonia at admission, sampling, and discharge, and lower lymphocytes count. No significant associations were found between airborne SARS-CoV-2 detection and symptoms presence or duration, nor with the results of the most recent positive nasopharyngeal PCR test prior to air sampling. In the multivariate analysis, the best-fit model included patient age, type of admission, and symptoms duration. Patient age significantly contributed to the risk of airborne SARS-CoV-2 detection in the multivariate analysis.

CONCLUSIONS

Our findings highlight the variability in individual responses to SARS-CoV-2 infection and suggest that factors linked to COVID-19 severity, symptomatology, and immunocompetence influence the airborne SARS-CoV-2 detection. Our results may support the development of more precise preventive measures in healthcare settings.

Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles

Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.

Comprehensive performance evaluation of six bioaerosol samplers based on an aerosol wind tunnel

Choosing a suitable bioaerosol sampler for atmospheric microbial monitoring has been a challenge to researchers interested in environmental microbiology, especially during a pandemic. However, a comprehensive and integrated evaluation method to fully assess bioaerosol sampler performance is still lacking. Herein, we constructed a customized wind tunnel operated at 2-20 km/h wind speed to systematically and efficiently evaluate the performance of six frequently used samplers, where various aerosols, including Arizona test dust, bacterial spores, gram-positive and gram-negative bacteria, phages, and viruses, were generated. After 10 or 60 min of sampling, the physical and biological sampling efficiency and short or long-term sampling capabilities were determined by performing aerodynamic particle size analysis, live microbial culturing, and a qPCR assay. The results showed that AGI-30 and BioSampler impingers have good physical and biological sampling efficiencies for short-term sampling. However, their ability to capture aerosols at low concentrations is restricted. SASS 2300 and BSA-350 wet-wall cyclones had excellent enrichment ratios and high microbial cultivability in both short-term and long-term sampling; however, they were not suitable for quantitative studies of aerosols. Polycarbonate filter samplers showed outstanding performance in physical and long-term sampling but lacked the ability to maintain microbial activity, which can be improved by gelatin filter samplers. However, limitations remain for some fragile microorganisms, such as E. coli phage PhiX174 and coronavirus GX_P2V. In addition, the effects of wind speed and direction should be considered when sampling particles larger than 4 µm. This study provides an improved strategy and guidance for the characterization and selection of a bioaerosol sampler for better measurement and interpretation of collected ambient bioaerosols.

Droplet digital PCR application for the detection of SARS-CoV-2 in air sample

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) may transmit through airborne route particularly when the aerosol particles remain in enclosed spaces with inadequate ventilation. There has been no standard recommended method of determining the virus in air due to limitations in pre-analytical and technical aspects. Furthermore, the presence of low virus loads in air samples could result in false negatives. Our study aims to explore the feasibility of detecting SARS-CoV-2 ribonucleic acid (RNA) in air samples using droplet digital polymerase chain reaction (ddPCR). Active and passive air sampling was conducted between December 2021 and February 2022 with the presence of COVID-19 confirmed cases in two hospitals and a quarantine center in Klang Valley, Malaysia. SARS-CoV-2 RNA in air was detected and quantified using ddPCR and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The comparability of two different digital PCR platforms (QX200 and QIAcuity) to RT-PCR were also investigated. Additionally negative staining transmission electron microscopy was performed to visualize virus ultrastructure. Detection rates of SARS-CoV-2 in air samples using ddPCR were higher compared to RT-PCR, which were 15.2% (22/145) and 3.4% (5/145), respectively. The sensitivity and specificity of ddPCR was 100 and 87%, respectively. After excluding 17 negative samples (50%) by both QX200 and QIAcuity, 15% samples (5/34) were found to be positive both ddPCR and dPCR. There were 23.5% (8/34) samples that were detected positive by ddPCR but negative by dPCR. In contrast, there were 11.7% (4/34) samples that were detected positive by dPCR but negative by ddPCR. The SARS-CoV-2 detection method by ddPCR is precise and has a high sensitivity for viral RNA detection. It could provide advances in determining low viral titter in air samples to reduce false negative reports, which could complement detection by RT-PCR.

Monitoring Prevalence and Persistence of Environmental Contamination by SARS-CoV-2 RNA in a Makeshift Hospital for Asymptomatic and Very Mild COVID-19 Patients

Objective: To investigate the details of environmental contamination status by SARS-CoV-2 in a makeshift COVID-19 hospital. Methods: Environmental samples were collected from a makeshift hospital. The extent of contamination was assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) for SARS-CoV-2 RNA from various samples. Results: There was a wide range of total collected samples contaminated with SARS-CoV-2 RNA, ranging from 8.47% to 100%. Results revealed that 70.00% of sewage from the bathroom and 48.19% of air samples were positive. The highest rate of contamination was found from the no-touch surfaces (73.07%) and the lowest from frequently touched surfaces (33.40%). The most contaminated objects were the top surfaces of patient cubic partitions (100%). The median Ct values among strongly positive samples were 33.38 (IQR, 31.69-35.07) and 33.24 (IQR, 31.33-34.34) for ORF1ab and N genes, respectively. SARS-CoV-2 relic RNA can be detected on indoor surfaces for up to 20 days. Conclusion: The findings show a higher prevalence and persistence in detecting the presence of SARS-CoV-2 in the makeshift COVID-19 hospital setting. The contamination mode of droplet deposition may be more common than contaminated touches.

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.

Efficiency and sensitivity optimization of a protocol to quantify indoor airborne SARS-CoV-2 levels

Background

Development of methodologies to quantify airborne micro-organisms is needed for the prevention and control of infections. It is difficult to conclude which is the most efficient and sensitive strategy to assess airborne SARS-CoV-2 RNA levels due to the disparity of results reported in clinical settings.

Aim

To improve our previously reported protocol of measuring SARS-CoV-2 RNA levels, which was based on bioaerosol collection with a liquid impinger and RNA quantification with droplet digital polymerase chain reaction (ddPCR).

Methods

Air samples were collected in COVID-19 patient rooms to assess efficiency and/or sensitivity of different air samplers, liquid collection media, and reverse transcriptases (RT).

Findings

Mineral oil retains airborne RNA better than does hydrophilic media without impairing integrity. SARS-CoV-2 ORF1ab target was detected in 80% of the air samples using BioSampler with mineral oil. No significant differences in effectiveness were obtained with MD8 sampler equipped with gelatine membrane filters, but the SARS-CoV-2 copies/m³ air obtained with the latter were lower (28.4 ± 6.1 vs 9 ± 1.7). SuperScript II RT allows the detection of a single SARS-CoV-2 genome RNA molecule by ddPCR with high efficiency. This was the only RT that allowed the detection of SARS-CoV-2 N1 target in air samples.

Conclusion

The collection efficiency and detection sensivity of a protocol to quantify SARS-CoV-2 RNA levels in indoor air has been improved in the present study. Such optimization is important to improve our understanding of the microbiological safety of indoor air.