Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and SARS-CoV-2 variants

The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present microfluidic CARMEN (mCARMEN), a cost-effective virus and variant detection platform that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) and demonstrated its diagnostic-grade performance on 533 patient specimens in an academic setting and then 166 specimens in a clinical setting. We further developed a panel to distinguish 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 106 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of viral copies in samples. mCARMEN enables high-throughput surveillance of multiple viruses and variants simultaneously.

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Prevalence of Co-Infections With Respiratory Viruses in Individuals Investigated for Sars-Cov-2 in Ontario, Canada

10.20944/preprints202012.0258.v1 ◽

2020 ◽

Author(s):

Adriana Peci ◽

Vanessa Tran ◽

Jennifer L Gurtherie ◽

Ye Li ◽

Paul Nelson ◽

...

Keyword(s):

Respiratory Symptoms ◽

Patient Management ◽

Respiratory Virus ◽

Severe Disease ◽

Respiratory Viruses ◽

Single Infection ◽

Clinical Testing ◽

Routine Testing ◽

Wide Range ◽

Bacteria And Fungi

Background: Co-infections of SARS-CoV-2 with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. Objectives: We asses s the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. Methods: Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. Results: Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. Conclusions: Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other viruses may assist with patient management.

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Rainbowarray Microsphere-Based Gene Detection Assay

SLAS TECHNOLOGY Translating Life Sciences Innovation ◽

10.1177/2472630319882319 ◽

2019 ◽

Vol 25 (3) ◽

pp. 258-266

Author(s):

Ying Xu ◽

Pei Zhang ◽

Fan Yi ◽

Jing Wei ◽

Quan Du

Keyword(s):

Target Detection ◽

High Throughput ◽

Quantitative Measurement ◽

Clinical Testing ◽

Multiplex Detection ◽

Gene Detection ◽

Microrna Regulation ◽

Detection Assay ◽

Cost Efficient ◽

High Throughput Manner

Here, we have developed a set of fluorophore-labeled microspheres named rainbowarray microspheres. Based on the spectrally encoded microspheres, we further developed a liquid hybridization approach for multiplex target detection. Different from the prototype Luminex xMAP array, this technology enables feasible, flexible, and cost-efficient microsphere labeling and multiplex detection in a timely and high-throughput manner. To demonstrate the practicability of this technology, quantitative measurement of microRNA regulation was performed during the differentiation of 3T3-L1 cells, in which the expression of two microRNAs was determined at a 2 h interval during a process of 2 days. The flexibility and the timely and high-throughput properties of the technology enable it to be widely implemented in clinical testing.

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Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR

Journal of Clinical Microbiology ◽

10.1128/jcm.01704-16 ◽

2016 ◽

Vol 55 (1) ◽

pp. 226-233 ◽

Cited By ~ 33

Author(s):

Young-gon Kim ◽

Seung Gyu Yun ◽

Min Young Kim ◽

Kwisung Park ◽

Chi Hyun Cho ◽

...

Keyword(s):

Real Time ◽

Reverse Transcription ◽

Respiratory Virus ◽

Direct Sequencing ◽

Virus Detection ◽

Cost Effective ◽

Respiratory Viruses ◽

Nasopharyngeal Swab ◽

Virus Species ◽

Rt Pcr

ABSTRACT Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens ( P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens ( P = 0.1574). Adenovirus was detected more frequently in saliva samples ( P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens ( P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies.

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Prevalence of co-infections with respiratory viruses in individuals investigated for SARS-CoV-2 in Ontario, Canada

10.22541/au.160588464.45020441/v1 ◽

2020 ◽

Author(s):

Adriana Peci ◽

Vanessa Tran ◽

Jennifer L Guthrie ◽

Ye Li ◽

Paul Nelson ◽

...

Keyword(s):

Respiratory Symptoms ◽

Patient Management ◽

Respiratory Virus ◽

Severe Disease ◽

Respiratory Viruses ◽

Clinical Testing ◽

Routine Testing ◽

Wide Range ◽

Respiratory Virus Infection ◽

Bacteria And Fungi

Background: Co-infections of SARS-CoV-2 with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. Objectives: We assess the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. Methods: Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. Results: Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single respiratory virus infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. Conclusions: Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other respiratory viruses may assist with patient management.

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Prevalence of Co-Infections with Respiratory Viruses in Individuals Investigated for SARS-CoV-2 in Ontario, Canada

Viruses ◽

10.3390/v13010130 ◽

2021 ◽

Vol 13 (1) ◽

pp. 130

Author(s):

Adriana Peci ◽

Vanessa Tran ◽

Jennifer L. Guthrie ◽

Ye Li ◽

Paul Nelson ◽

...

Keyword(s):

Respiratory Symptoms ◽

Patient Management ◽

Respiratory Virus ◽

Severe Disease ◽

Respiratory Viruses ◽

Single Infection ◽

Clinical Testing ◽

Routine Testing ◽

Wide Range ◽

Bacteria And Fungi

Background: Co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. Objectives: We assess the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. Methods: Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. Results: Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. Conclusions: Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other viruses may assist with patient management.

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Respiratory viral testing and antibacterial treatment in patients hospitalized with community-acquired pneumonia

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.1312 ◽

2020 ◽

pp. 1-9

Author(s):

Michael Klompas ◽

Peter B. Imrey ◽

Pei-Chun Yu ◽

Chanu Rhee ◽

Abhishek Deshpande ◽

...

Keyword(s):

Retrospective Cohort ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Community Acquired Pneumonia ◽

Blood Cultures ◽

Antibacterial Treatment ◽

Viral Pathogens ◽

Antimicrobial Utilization ◽

Viral Testing ◽

Virus Testing

Abstract Objective: Viruses are more common than bacteria in patients hospitalized with community-acquired pneumonia. Little is known, however, about the frequency of respiratory viral testing and its associations with antimicrobial utilization. Design: Retrospective cohort study. Setting: The study included 179 US hospitals. Patients: Adults admitted with pneumonia between July 2010 and June 2015. Methods: We assessed the frequency of respiratory virus testing and compared antimicrobial utilization, mortality, length of stay, and costs between tested versus untested patients, and between virus-positive versus virus-negative patients. Results: Among 166,273 patients with pneumonia on admission, 40,787 patients (24.5%) were tested for respiratory viruses, 94.8% were tested for influenza, and 20.7% were tested for other viruses. Viral assays were positive in 5,133 of 40,787 tested patients (12.6%), typically for influenza and rhinovirus. Tested patients were younger and had fewer comorbidities than untested patients, but patients with positive viral assays were older and had more comorbidities than those with negative assays. Blood cultures were positive for bacterial pathogens in 2.7% of patients with positive viral assays versus 5.3% of patients with negative viral tests (P < .001). Antibacterial courses were shorter for virus-positive versus -negative patients overall (mean 5.5 vs 6.4 days; P < .001) but varied by bacterial testing: 8.1 versus 8.0 days (P = .60) if bacterial tests were positive; 5.3 versus 6.1 days (P < .001) if bacterial tests were negative; and 3.3 versus 5.2 days (P < .001) if bacterial tests were not obtained (interaction P < .001). Conclusions: A minority of patients hospitalized with pneumonia were tested for respiratory viruses; only a fraction of potential viral pathogens were assayed; and patients with positive viral tests often received long antibacterial courses.

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COVID-19 mitigation strategies were associated with decreases in other respiratory virus infections

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab105 ◽

2021 ◽

Author(s):

Sinha Pranay ◽

Katherine Reifler ◽

Michael Rossi ◽

Manish Sagar

Keyword(s):

Respiratory Virus ◽

Respiratory Infections ◽

Respiratory Viruses ◽

Mitigation Strategies ◽

Virus Infections ◽

Time Period ◽

Viral Respiratory Infections ◽

Respiratory Virus Infections ◽

Viral Respiratory

Abstract Detection of diverse respiratory viruses in Boston was around 80% lower after practices were instituted to limit COVID-19 spread compared to the same time period during the previous five years. Continuing the strategies that lower COVID-19 dissemination may be useful in decreasing the incidence of other viral respiratory infections.

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