Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay

Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets

BACKGROUND

Concentrations of the pathogenic microorganisms' DNA in biological samples are typically low. Therefore, DNA diagnostics of common infections are costly, rarely accurate, and challenging. Limited by failing to cover updated epidemic testing samples, computational services are difficult to implement in clinical applications without complex customized settings. Furthermore, the combined biomarkers used to maintain high conservation may not be cost effective and could cause several experimental errors in many clinical settings. Given the limitations of recent developed technology, 16S rRNA is too conserved to distinguish closely related species, and mosaic plasmids are not effective as well because of their uneven distribution across prokaryotic taxa.

RESULTS

Here, we provide a computational strategy, Shine, that allows extraction of specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets. Distinguished with simple concatenations with blast-based filtering, our method involves a de novo genome alignment-based pipeline to explore the original and specific repetitive biomarkers in the defined population. It can cover all members to detect newly discovered multicopy conserved species-specific or even subspecies-specific target probes and primer sets. The method has been successfully applied to a number of clinical projects and has the overwhelming advantages of automated detection of all pathogenic microorganisms without the limitations of genome annotation and incompletely assembled motifs. Using on our pipeline, users may select different configuration parameters depending on the purpose of the project for routine clinical detection practices on the website https://bioinfo.liferiver.com.cn with easy registration.

CONCLUSIONS

The proposed strategy is suitable for identifying shared phylogenetic markers while featuring low rates of false positive or false negative. This technology is suitable for the automatic design of minimal and efficient PCR primers and other types of detection probes.

Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes

To increase the throughput, lower the cost, and save scarce test reagents, laboratories can pool patient samples before SARS-CoV-2 RT-qPCR testing. While different sample pooling methods have been proposed and effectively implemented in some laboratories, no systematic and large-scale evaluations exist using real-life quantitative data gathered throughout the different epidemiological stages. Here, we use anonymous data from 9673 positive cases to model, simulate and compare 1D and 2D pooling strategies. We show that the optimal choice of pooling method and pool size is an intricate decision with a testing population-dependent efficiency-sensitivity trade-off and present an online tool to provide the reader with custom real-time 1D pooling strategy recommendations.

Risk Factors for Hospitalization Among Patients with COVID-19 at a Community Ambulatory Clinic in Massachusetts During the Initial Pandemic Surge

Among patients with COVID-19 evaluated in outpatient settings, factors associated with hospitalization remain poorly understood. Multivariable regressions were used to assess sociodemographic and clinical factors associated with increased odds of hospitalization among patients with confirmed COVID-19 between March 18, 2020 through April 25, 2020 at a community-based outpatient clinic in Massachusetts. Older age, BMI ≥ 25, self-reported dizziness/lightheadedness, temperature ≥ 99.5°F, tachycardia, and oxygen saturation < 95% were associated with increased odds of hospitalization after adjustment for age, sex, and BMI. There was also an association between speaking Spanish as primary language and increased odds of hospitalization (compared to English, adjusted OR = 2.99 [95% CI 1.39, 6.39]). Speaking Portuguese as primary language was not associated with increased odds of hospitalization (compared to English, adjusted OR = 1.83 [0.78, 4.28]). In addition to several clinical risk factors established among inpatients, our study found that primarily speaking Spanish, but not Portuguese, was a marker of hospitalization risk among a diverse outpatient cohort of patients with COVID-19.

Evaluation of the diagnostic accuracy of a new point-of-care rapid test for SARS-CoV-2 virus detection

BACKGROUND

The easy access to a quick diagnosis of coronavirus disease 2019 (COVID-19) is a key point to improve the management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to contain its spread. Up to now, laboratory real-time PCR is the standard of care, but requires a fully equipped laboratory and significant infrastructure. Consequently, new diagnostic tools are required.

METHODS

In the present work, the diagnostic accuracy of the point-of-care rapid test "bKIT Virus Finder COVID-19" (Hyris Ltd) is evaluated by a retrospective and a prospective analysis on SARS CoV-2 samples previously assessed with an FDA "authorized for the emergency use-EUA" reference method. Descriptive statistics were used for the present study.

RESULTS

Results obtained with the Hyris Kit are the same as that of standard laboratory-based real time PCR methods for all the analyzed samples. In addition, the Hyris Kit provides the test results in less than 2 h, a significantly shorter time compared to the reference methods, without the need of a fully equipped laboratory.

CONCLUSIONS

To conclude, the Hyris kit represents a promising tool to improve the health surveillance and to increase the capacity of SARS-CoV-2 testing.