scholarly journals Molecular Detection of SARS-Cov-2 in Exhaled Breath Using a Portable Sampler

2021 ◽  
Author(s):  
Tim Stakenborg ◽  
Joren Raymenants ◽  
Ahmed Taher ◽  
Elisabeth Marchal ◽  
Bert Verbruggen ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Respiratory Infections ◽  
Sample Volume ◽  
Nasopharyngeal Swab ◽  
Exhaled Breath ◽  
Sample Type ◽  
Viral Shedding ◽  
Current Test ◽  
Standard Sampling ◽  
Antigen Tests

Abstract The SARS-CoV-2 pandemic has highlighted the need for improved technologies to help control the spread of contagious pathogens. While rapid point-of-need testing plays a key role in strategies to rapidly identify and isolate infectious patients, a cornerstone for any disease-control strategy, current test approaches have significant shortcomings related to assay limitations and sample type. Direct quantification of viral shedding in exhaled particles may offer a better rapid testing approach, since SARS-CoV-2 is believed to spread mainly by aerosols. It potentially measures contagiousness directly, the sample is easy to obtain, its production can be standardized between patients, and the limited sample volume lends itself to a fast and sensitive analysis. In view of these benefits, we developed and tested an approach where exhaled particles are efficiently sampled using inertial impaction in a micromachined silicon chip, followed by an in-situ RT-qPCR molecular assay to detect SARS-CoV-2 shedding. We demonstrate that sampling subjects using a one-minute breathing protocol, yields sufficient viral RNA to detect infections with a sensitivity comparable to standard sampling methods. A longitudinal study revealed clear differences in the temporal dynamics of viral load for nasopharyngeal swab, saliva, breath, and antigen tests. Overall, after an infection, the breath-based test is the first to consistently report a negative result, putatively signaling the end of contagiousness and further emphasizing the potential of this tool to help manage the spread of airborne respiratory infections. 


scholarly journals Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Natalie N Kinloch ◽  
Aniqa Shahid ◽  
Gordon Ritchie ◽  
Winnie Dong ◽  
Tanya Lawson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Copy Number ◽  
Respiratory Infections ◽  
Nasopharyngeal Swab ◽  
Human Dna ◽  
Acid Recovery ◽  
Participant Experience ◽  
Nasal Anatomy ◽  
Adult Volunteers

Abstract Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.

scholarly journals Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1084
Author(s):  
Ho-Jae Lim ◽  
Jung-Eun Park ◽  
Min-Young Park ◽  
Joo-Hwan Baek ◽  
Sunkyung Jung ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Simultaneous Detection ◽  
Respiratory Viruses ◽  
Analytical Performance ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Significant Difference ◽  
Z Scores ◽  
Syncytial Virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

scholarly journals Influenza A and B viruses in the population of Vojvodina, Serbia

2014 ◽  
Vol 66 (1) ◽  
pp. 43-50 ◽  
Author(s):  
J. Radovanov ◽  
V. Milosevic ◽  
I. Hrnjakovic ◽  
V. Petrovic ◽  
M. Ristic ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Infections ◽  
Influenza Viruses ◽  
Influenza B Virus ◽  
Nasopharyngeal Swab ◽  
Influenza B ◽  
Influenza A Viruses ◽  
B Virus ◽  
Life Threatening ◽  
Seasonal Epidemic

At present, two influenza A viruses, H1N1pdm09 and H3N2, along with influenza B virus co-circulate in the human population, causing endemic and seasonal epidemic acute febrile respiratory infections, sometimes with life-threatening complications. Detection of influenza viruses in nasopharyngeal swab samples was done by real-time RT-PCR. There were 60.2% (53/88) positive samples in 2010/11, 63.4% (52/82) in 2011/12, and 49.9% (184/369) in 2012/13. Among the positive patients, influenza A viruses were predominant during the first two seasons, while influenza B type was more active during 2012/13. Subtyping of influenza A positive samples revealed the presence of A (H1N1)pdm09 in 2010/11, A (H3N2) in 2011/12, while in 2012/13, both subtypes were detected. The highest seroprevalence against influenza A was in the age-group 30-64, and against influenza B in adults aged 30-64 and >65.

scholarly journals Transmission dynamics of the delta variant of SARS-CoV-2 infections in Daejeon, South Korea

2021 ◽  
Author(s):  
Hari Hwang ◽  
Jun-Sik Lim ◽  
Sun-Ah Song ◽  
Chiara Achangwa ◽  
Woobeom Sim ◽  
...  
Keyword(s):  
South Korea ◽  
Symptom Onset ◽  
Credible Interval ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Strict Adherence ◽  
Virus Shedding ◽  
Viral Shedding ◽  
Asymptomatic Patients

Abstract Background The delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear. Methods We analyzed all case patients in local clusters and temporal patterns of viral shedding using contact tracing data from 405 cases associated with the delta variant of SARS-CoV-2 between 22 June and 31 July 2021 in Daejeon, South Korea. Results Overall, half of the cases were aged under 19 years, and 20% were asymptomatic at the time of epidemiological investigation. We estimated the mean serial interval as 3.26 days (95% credible interval 2.92, 3.60), and 12% of the transmission occurred before symptom onset of the infector. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63% (52/82). We estimated that 15% (95% confidence interval, 13–18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from asymptomatic patients, and the highest viral load was observed two days after symptom onset. The temporal pattern of viral shedding did not differ between children and adults (P = 0.48). Conclusions Our findings suggest that the delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, and strict adherence to public health measures are needed to mitigate the community transmission of the delta variant.

scholarly journals Self-collected Saline Gargle Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients

2021 ◽  
Author(s):  
David M. Goldfarb ◽  
Peter Tilley ◽  
Ghada N. Al-Rawahi ◽  
Jocelyn A. Srigley ◽  
Geoffrey Ford ◽  
...  
Keyword(s):  
Room Temperature ◽  
Positive Sample ◽  
Nasopharyngeal Swab ◽  
Sample Type ◽  
Mouth Rinse ◽  
Rna Detection ◽  
School Aged Children ◽  
Primary Sample ◽  
User Acceptability ◽  
Temperature Storage

Background: We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of SARS-CoV-2 in adults and school-aged children. Methods: Outpatients who had recently been diagnosed with COVID-19 or were presenting with suspected COVID-19 were asked to have a nasopharyngeal swab collected and provide at least one self-collected sample type. Participants were also asked about sample acceptability using a five point Likert scale. For those previously diagnosed with COVID-19, all samples underwent real-time PCR testing using a lab-developed assay, and the majority were also tested using an FDA-authorized assay. For those presenting with suspect COVID-19, only those with a positive nasopharyngeal swab sample went on to have other samples tested. Saline mouth rinse/gargle and saliva samples were tested daily at time zero, day one, and day 2 to assess nucleic acid stability at room temperature. Results: 50 participants (aged 4 to 71 years) were included; of these, 40 had at least one positive sample and were included in the primary sample yield analysis. Saline mouth rinse/gargle samples had a sensitivity of 98% (39/40) while saliva samples had a sensitivity of 79% (26/33). Both saline mouth rinse/gargle and saliva samples showed stable viral RNA detection after 2 days of room temperature storage. Mouth rinse/gargle samples had the highest (mean 4.9) and HCW-collected NP swabs had the lowest acceptability scores (mean 3.1). Conclusion: Saline mouth rinse/gargle samples demonstrated the highest combined user acceptability ratings and analytical performance when compared with saliva and HCW collected NP swabs. This sample type is a promising swab-independent option, particularly for outpatient self-collection in adults and school aged children.

scholarly journals Sub-nanoliter metabolomics via mass spectrometry to characterize volume-limited samples

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yafeng Li ◽  
Marcos Bouza ◽  
Changsheng Wu ◽  
Hengyu Guo ◽  
Danning Huang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Stromal Cells ◽  
Exhaled Breath Condensate ◽  
Sample Volume ◽  
Triboelectric Nanogenerator ◽  
Exhaled Breath ◽  
Nanoelectrospray Ionization ◽  
External Stimuli ◽  
Breath Condensate

Abstract The human metabolome provides a window into the mechanisms and biomarkers of various diseases. However, because of limited availability, many sample types are still difficult to study by metabolomic analyses. Here, we present a mass spectrometry (MS)-based metabolomics strategy that only consumes sub-nanoliter sample volumes. The approach consists of combining a customized metabolomics workflow with a pulsed MS ion generation method, known as triboelectric nanogenerator inductive nanoelectrospray ionization (TENGi nanoESI) MS. Samples tested with this approach include exhaled breath condensate collected from cystic fibrosis patients as well as in vitro-cultured human mesenchymal stromal cells. Both test samples are only available in minimum amounts. Experiments show that picoliter-volume spray pulses suffice to generate high-quality spectral fingerprints, which increase the information density produced per unit sample volume. This TENGi nanoESI strategy has the potential to fill in the gap in metabolomics where liquid chromatography-MS-based analyses cannot be applied. Our method opens up avenues for future investigations into understanding metabolic changes caused by diseases or external stimuli.

scholarly journals Co-Circulation and Excretion Dynamics of Diverse Rubula- and Related Viruses in Egyptian Rousette Bats from South Africa

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 37 ◽  
Author(s):  
Marinda Mortlock ◽  
Muriel Dietrich ◽  
Jacqueline Weyer ◽  
Janusz T. Paweska ◽  
Wanda Markotter
Keyword(s):  
South Africa ◽  
Temporal Dynamics ◽  
Virus Transmission ◽  
Sample Type ◽  
Limited Extent ◽  
Human Pathogens ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Viral Excretion

The Egyptian rousette bat (Rousettus aegyptiacus) has previously been implicated as the natural host of a zoonotic rubulavirus; however, its association with rubulaviruses has been studied to a limited extent. Urine, spleen, and other organs collected from the R. aegyptiacus population within South Africa were tested with a hemi-nested RT-PCR assay targeting a partial polymerase gene region of viruses from the Avula- and Rubulavirus genera. Urine was collected over a 14-month period to study the temporal dynamics of viral excretion. Diverse rubulaviruses, including viruses related to human mumps and parainfluenza virus 2, were detected. Active excretion was identified during two peak periods coinciding with the host reproductive cycle. Analysis of additional organs indicated co-infection of individual bats with a number of different putative rubulaviruses, highlighting the limitations of using a single sample type when determining viral presence and diversity. Our findings suggest that R. aegyptiacus can harbor a range of Rubula- and related viruses, some of which are related to known human pathogens. The observed peaks in viral excretion represents potential periods of a higher risk of virus transmission and zoonotic disease spill-over.

scholarly journals Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation

2021 ◽  
Author(s):  
Xianding Deng ◽  
Miguel A Garcia-Knight ◽  
Mir M. Khalid ◽  
Venice Servellita ◽  
Candace Wang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Cell Cultures ◽  
Spike Protein ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Wild Type ◽  
Antibody Neutralization ◽  
Protein Mutation ◽  
Viral Shedding

AbstractWe identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.

scholarly journals Temporal dynamics in viral shedding and transmissibility of COVID-19

2020 ◽  
Author(s):  
Xi He ◽  
Eric HY Lau ◽  
Peng Wu ◽  
Xilong Deng ◽  
Jian Wang ◽  
...  
Keyword(s):  
Viral Load ◽  
Disease Control ◽  
Symptom Onset ◽  
Temporal Dynamics ◽  
Temporal Patterns ◽  
Control Measures ◽  
Separate Sample ◽  
Viral Shedding ◽  
Index Disease

ABSTRACTWe report temporal patterns of viral shedding in 94 laboratory-confirmed COVID-19 patients and modelled COVID-19 infectiousness profile from a separate sample of 77 infector-infectee transmission pairs. We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset. We estimated that 44% of transmission could occur before first symptoms of the index. Disease control measures should be adjusted to account for probable substantial pre-symptomatic transmission.

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