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

PATHPOD - A loop-mediated isothermal amplification (LAMP)-based point-of-care system for rapid clinical detection of SARS-CoV-2 in hospitals in Denmark

Sensitive and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a vital goal in the ongoing COVID-19 pandemic. We present in this comprehensive work, for the first time, detailed fabrication and clinical validation of a point of care (PoC) device for rapid, onsite detection of SARS-CoV-2 using a real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) reaction on a polymer cartridge. The PoC system, namely PATHPOD, consisting of a standalone device (weight less than 1.2 kg) and a cartridge, can perform the detection of 10 different samples and two controls in less than 50 min, which is much more rapid than the golden standard real-time reverse-transcription Polymerase Chain Reaction (RT-PCR), typically taking 16-48 h. The novel total internal reflection (TIR) scheme and the reactions inside the cartridge in the PoC device allow monitoring of the diagnostic results in real-time and onsite. The analytical sensitivity and specificity of the PoC test are comparable with the current RT-PCR, with a limit of detection (LOD) down to 30-50 viral genome copies. The robustness of the PATHPOD PoC system has been confirmed by analyzing 398 clinical samples initially examined in two hospitals in Denmark. The clinical sensitivity and specificity of these tests are discussed.

Quantity of SARS-CoV-2 RNA copies exhaled per minute during natural breathing over the course of COVID-19 infection

SARS-CoV-2 is spread through exhaled breath of infected individuals. A fundamental question in understanding transmission of SARS-CoV-2 is how much virus an individual is exhaling into the environment while they breathe, over the course of their infection. Research on viral load dynamics during COVID-19 infection has focused on internal swab specimens, which provide a measure of viral loads inside the respiratory tract, but not on breath. Therefore, the dynamics of viral shedding on exhaled breath over the course of infection are poorly understood. Here, we collected exhaled breath specimens from COVID-19 patients and used RTq-PCR to show that numbers of exhaled SARS-CoV-2 RNA copies during COVID-19 infection do not decrease significantly until day 8 from symptom-onset. COVID-19-positive participants exhaled an average of 80 SARS-CoV-2 viral RNA copies per minute during the first 8 days of infection, with significant variability both between and within individuals, including spikes over 800 copies a minute in some patients. After day 8, there was a steep drop to levels nearing the limit of detection, persisting for up to 20 days. We further found that levels of exhaled viral RNA increased with self-rated symptom-severity, though individual variation was high. Levels of exhaled viral RNA did not differ across age, sex, time of day, vaccination status or viral variant. Our data provide a fine-grained, direct measure of the number of SARS-CoV-2 viral copies exhaled per minute during natural breathing-including 312 breath specimens collected multiple times daily over the course of infection-in order to fill an important gap in our understanding of the time course of exhaled viral loads in COVID-19.

Detection of SARS-CoV-2 RNA in exhaled breath and its potential for prevention measures

Background

To propose infection prevention measures it is essential to understand the dynamics of SARS-CoV-2 shedding, particularly in asymptomatic patients. This report compares the viral load progression in exhaled breath (EB) with the symptom severity. We aim to evaluate the adequacy of symptom assessment regarding the infectivity level of individuals.

Methods

We observed infected patients since their first positive test during hospitalization. EB samples were collected on days 1, 3, 5, 7, 10, 12 and 14 of hospitalization using a filter-based device. After extraction, viral loads were quantified with qRT-PCR. The infection trajectory was documented after symptom onset.

Case Presentation and Discussion

A 34-year old patient showed mild symptoms, e.g. fever, cough, headache, muscle pain and loss of taste and smell across trajectory of infection (Case 1). The viral loads emitted via exhaling were nearly constant and ranged from 8.6 x 103 and 4.1 x 104 RNA copies per hour. After the infection, the patient developed a pneumonia. The second case of a 65-year old patient depicted an asymptomatic infection trajectory for 14 days after the first diagnosis (Case 2). Nevertheless, the patient exhaled up to 2 x 105 SARS-CoV-2 virus copies hourly, approximately 10 fold higher than measured for Case 1.

Conclusion

Symptomatic and asymptomatic COVID-19 patients exhale distinctive amounts of SARS-CoV-2 not necessarily correlating with symptom severity. Particularly, asymptomatic patients might show higher EB viral shedding. Therefore, EB testing should be included in infection prevention measures as it has high potential to reveal the most infectious individuals regardless of their symptoms during infection.

Diagnostic performance of respirators for collection and detection of SARS-CoV-2

Respirators, called as face mask, have been used to protect the wearer from the outside harmful air environment and prevent any virus from being released to neighbors from potentially infected exhaled breath. The antiviral effectiveness of respirators has not only been researched scientifically, but has also become a global issue due to society's obligation to wear respirators. In this paper, we report the results of a study on the collection and detection of viruses contained in exhaled breath using respirators. The inner electrostatic filter was carefully selected for virus collection because it does not come in direct contact with either human skin or the external environment. In the study of a healthy control group, it was confirmed that a large amount of DNA and biomolecules such as exosomes were collected from the respirator exposed to exhalation, and the amount of collection increased in proportion to the wearing time. We conducted experiments using a total of 72 paired samples with nasopharyngeal swabs and respirator samples. Out of these samples, fifty tested positive for SARS-CoV-2 and twenty-two tested negative. The PCR results of the NPS and respirator samples showed a high level of agreement, with a positive percent agreement of ≥ 90% and a negative percent agreement of ≥ 99%. Furthermore, there was a notable level of concordance between RCA-flow tests and PCR when examining the respirator samples. These results suggest that this is a non-invasive, quick and easy method of collecting samples from subjects using a respirator, which can significantly reduce the hassle of waiting at airports or public places and concerns about cross-contamination. Furthermore, we expect miniaturized technologies to integrate PCR detection into respirators in the near future.

Diagnostic performance of eNose technology in COVID-19 patients after hospitalization

BACKGROUND

Volatile organic compounds (VOCs) produced by human cells reflect metabolic and pathophysiological processes which can be detected with the use of electronic nose (eNose) technology. Analysis of exhaled breath may potentially play an important role in diagnosing COVID-19 and stratification of patients based on pulmonary function or chest CT.

METHODS

Breath profiles of COVID-19 patients were collected with an eNose device (SpiroNose) 3 months after discharge from the Leiden University Medical Centre and matched with breath profiles from healthy individuals for analysis. Principal component analysis was performed with leave-one-out cross validation and visualised with receiver operating characteristics. COVID-19 patients were stratified in subgroups with a normal pulmonary diffusion capacity versus patients with an impaired pulmonary diffusion capacity (DLCOc < 80% of predicted) and in subgroups with a normal chest CT versus patients with COVID-19 related chest CT abnormalities.

RESULTS

The breath profiles of 135 COVID-19 patients were analysed and matched with 174 healthy controls. The SpiroNose differentiated between COVID-19 after hospitalization and healthy controls with an AUC of 0.893 (95-CI, 0.851-0.934). There was no difference in VOCs patterns in subgroups of COVID-19 patients based on diffusion capacity or chest CT.

CONCLUSIONS

COVID-19 patients have a breath profile distinguishable from healthy individuals shortly after hospitalization which can be detected using eNose technology. This may suggest ongoing inflammation or a common repair mechanism. The eNose could not differentiate between subgroups of COVID-19 patients based on pulmonary diffusion capacity or chest CT.

Size distribution of exhaled aerosol particles containing SARS-CoV-2 RNA

BACKGROUND

SARS-CoV-2 in exhaled aerosols is considered an important contributor to the spread of COVID-19. However, characterizing the size distribution of virus-containing aerosol particles has been challenging as high concentrations of SARS-CoV-2 in exhaled air is mainly present close to symptom onset. We present a case study of a person with COVID-19 who was able to participate in extensive measurements of exhaled aerosols already on the day of symptom onset and then for the following three days.

METHODS

Aerosol collection was performed using an eight-stage impactor while the subject was breathing, talking and singing, for 30 min each, once every day. In addition, nasopharyngeal samples, saliva samples, room air samples and information on symptom manifestations were collected every day. Samples were analyzed by RT-qPCR for detection of SARS-CoV-2 RNA.

RESULTS

SARS-CoV-2 RNA was detected in seven of the eight particle size fractions, from 0.34 to >8.1 µm, with the highest concentrations found in 0.94-2.8 µm particles. The concentration of SARS-CoV-2 RNA was highest on the day of symptom onset, and declined for each day thereafter.

CONCLUSION

Our data showed that 90% of the exhaled SARS-CoV-2 RNA was found in aerosol particles <4.5 µm, indicating the importance of small particles for the transmission of COVID-19 close to symptom onset. These results are important for our understanding of airborne transmission, for developing accurate models and for selecting appropriate mitigation strategies.

Advanced setup for safe breath sampling and patient monitoring under highly infectious conditions in the clinical environment

Being the proximal matrix, breath offers immediate metabolic outlook of respiratory infections. However, high viral load in exhalations imposes higher transmission risk that needs improved methods for safe and repeatable analysis. Here, we have advanced the state-of-the-art methods for real-time and offline mass-spectrometry based analysis of exhaled volatile organic compounds (VOCs) under SARS-CoV-2 and/or similar respiratory conditions. To reduce infection risk, the general experimental setups for direct and offline breath sampling are modified. Certain mainstream and side-stream viral filters are examined for direct and lab-based applications. Confounders/contributions from filters and optimum operational conditions are assessed. We observed immediate effects of infection safety mandates on breath biomarker profiles. Main-stream filters induced physiological and analytical effects. Side-stream filters caused only systematic analytical effects. Observed substance specific effects partly depended on compound's origin and properties, sampling flow and respiratory rate. For offline samples, storage time, -conditions and -temperature were crucial. Our methods provided repeatable conditions for point-of-care and lab-based breath analysis with low risk of disease transmission. Besides breath VOCs profiling in spontaneously breathing subjects at the screening scenario of COVID-19/similar test centres, our methods and protocols are applicable for moderately/severely ill (even mechanically-ventilated) and highly contagious patients at the intensive care.