Development of a new field-deployable RT-qPCR workflow for COVID-19 detection

Background:Outbreaks of coronavirus disease 2019(COVID-19)have been recorded in different countries across the globe.The virus is highly contagious,hence early detection,isolation,and quarantine of infected patients will play an important role in containing the viral spread.Diagnosis in a mobile lab can aid to find infected patients in time.Methods:Here,we develop a field-deployable diagnostic workflow that can reliably detect COVID-19.Instruments used in this workflow can easily fit in a mobile cabin hospital and also be installed in the community.Different steps from sample inactivation to detection were optimized to find the fastest steps and portable instruments in the detection of COVID-19.Each step was compared to that of the normal laboratory diagnosis setup.Results:From the results,our proposed workflow(80 min)was two times faster compared to that of the normal laboratory workflow(183 min)and a maximum of 32 samples could be detected at each run.Additionally,we showed that using 1%Rewocid WK-30 could inactivate the novel coronavirus directly without affecting the overall detection results.Comparison of our workflow using an in-house assay to that of a commercially acquired assay produced highly reliable results.From the 250 hospital samples tested,there was a high concordance 247/250(98.8%)between the two assays.The in-house assay sensitivity and specificity were 116/116(100%)and 131/134(97.8%)compared to that of the commercial assay.Conclusion:Based on these results,we believe that our workflow is fast,reliable,adaptable and most importantly,field-deployable.

Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19

As a respiratory tract virus,SARS-CoV-2 infected people through contacting with the upper respiratory tract first.Previous studies indicated that microbiota could modulate immune response against pathogen infection.In the present study,we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough.Through metagenomic analysis of the above two groups and a healthy group from the public data,there are 6502 species identified in the samples.Specifically,the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group.Combined with the linear discriminant analysis(LDA)and the generalized linear model,eighty-one bacterial species were found with increased abundance in the COVID-19 group,where 51 species were enriched more than 8 folds.The top three enriched genera were Streptococcus,Prevotella and Campylobacter containing some opportunistic pathogens.More interestingly,through experiments,we found that two Streptococcus strains,S.suis and S.agalactiae,could stimulate the expression of ACE2 of Vero cells in vitro,which may promote SARS-CoV-2 infection.Therefore,these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host’s immune system.