Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes COVID-19 and is responsible for the ongoing pandemic. Screening of potential antiviral drugs against SARS-CoV-2 depend on in vitro experiments, which are based on the quantification of the virus titer. Here, we used virus-induced cytopathic effects (CPE) in brightfield microscopy of SARS-CoV-2-infected monolayers to quantify the virus titer. Images were classified using deep transfer learning (DTL) that fine-tune the last layers of a pre-trained Resnet18 (ImageNet). To exclude toxic concentrations of potential drugs, the network was expanded to include a toxic score (TOX) that detected cell death (CPETOXnet). With this analytic tool, the inhibitory effects of chloroquine, hydroxychloroquine, remdesivir, and emetine were validated. Taken together we developed a simple method and provided open access implementation to quantify SARS-CoV-2 titers and drug toxicity in experimental settings, which may be adaptable to assays with other viruses. The quantification of virus titers from brightfield images could accelerate the experimental approach for antiviral testing.
Highlights
IntroductionSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in 2019 as a pathogen responsible for the coronavirus disease 2019 (COVID-19), which in a proportion of cases causes severe symptoms such as shortage of breath and lung failure [1]
30 images of negative controls and 32 images showing SARS-CoV-2 mediated cytopathic effects (CPE) were split into 21/23 images for training, 5 images for validation, and 4 images for testing
We show that pretrained neural networks can classify SARS-CoV-2 cultures and can assist with quantification during drug screening
Summary
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in 2019 as a pathogen responsible for the coronavirus disease 2019 (COVID-19), which in a proportion of cases causes severe symptoms such as shortage of breath and lung failure [1]. SARSCoV-2 binds to the entry receptor ACE2, which triggers uptake and cleavage by the proteases Cathepsin B and TMPRSS2 [2]. If viruses cause no or low cytopathic effects (CPE), immunostaining is used to determine virus titers [3]. Viruses with strong CPE can be visualized by staining of residual cells, resulting in plaque forming units [4]. Plaque assays have been established, but effects depend on
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