AUTHOR=Hu Huan , Feng Zhen , Shuai Xinghao Steven , Lyu Jie , Li Xiang , Lin Hai , Shuai Jianwei 

TITLE=Identifying SARS-CoV-2 infected cells with scVDN

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1236653

DOI=10.3389/fmicb.2023.1236653

ISSN=1664-302X

ABSTRACT=Single-cell RNA sequencing (scRNA-seq) is a powerful tool for understanding cellular heterogeneity and identifying cell types. In virus-related research, scRNA-seq is widely used to investigate the host response to SARS-CoV-2 infection and cellular heterogeneity in infected tissues. However, direct identification of SARS-CoV-2infected cells at the single-cell level remains challenging, hindering the understanding of viral pathogenesis and the development of effective treatments. In this study, we propose a deep learning framework, the single-cell virus detection network (scVDN), to predict the infection status of single cells. The scVDN is trained on scRNA-seq data from multiple nasal swab samples obtained from several contributors with varying cell types. To objectively evaluate scVDN's performance, we establish a model evaluation framework suitable for real experimental data. Our results demonstrate that scVDN outperforms four state-of-the-art machine learning models in identifying SARS-CoV-2-infected cells, even with extremely imbalanced labels in real data. Specifically, scVDN achieves a perfect AUC score of 1 in four cell types. Our findings have important implications for advancing virus research and improving public health by enabling the identification of virus-infected cells at the single-cell level, which is critical for diagnosing and treating viral infections. To facilitate the application of scVDN to other single-cell virus-related studies, we make all source code and datasets publicly available on GitHub at https://github.com/studentiz/scvdn.