Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression

More than 300,000 mammalian virus species are estimated to cause disease in humans. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infection is vital to understanding its impact on human health and to make accurat...

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Bibliographic Details
Published inbioRxiv
Main Authors Luebbert, Laura, Sullivan, Delaney K, Carilli, Maria, Hjorleifsson, Kristjan Eldjarn, Alexander Viloria Winnett, Chari, Tara, Pachter, Lior
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 12.12.2023
Subjects
Amino acids
Gene expression
Genomes
Next-generation sequencing
Peripheral blood mononuclear cells
RNA viruses
Transcriptomics
Tropism
Viral infections
Viruses
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Summary:More than 300,000 mammalian virus species are estimated to cause disease in humans. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infection is vital to understanding its impact on human health and to make accurate predictions to limit adverse effects, such as future epidemics. The increasing use of high-throughput sequencing methods in research, agriculture, and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus-disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on highly conserved amino acid domains, which enables the detection of RNA viruses covering up to 10^12 virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We applied our method to identify novel viruses in rhesus macaque PBMC data that display cell type specificity and whose presence correlates with altered host gene expression.Competing Interest StatementThe authors have declared no competing interest.
DOI:10.1101/2023.12.11.571168