Abstract
The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.
Highlights
Host subtraction is the bioinformatics process of filtering reads derived from host DNA and RNA (Daly et al, 2015)
Host subtraction resources are needed for human cell lines that are widely used for RNA virus propagation
Using low-coverage short-read sequencing of genomic DNA, we generated cell line contigs (CLCs) from reads that did not map to the human genome reference (GRCh38)
Summary
Host subtraction is the bioinformatics process of filtering reads derived from host DNA and RNA (Daly et al, 2015). Host subtraction resources are needed for human cell lines that are widely used for RNA virus propagation. This includes three human cell lines Jurkat, HuH-7, and HepG2 commonly used to grow viruses or to amplify viruses suspected to be present in clinical isolates. The Jurkat line, derived from human T cells, supports replication of HIV and some Herpesviruses. The HuH-7 and HepG2 lines, both derived from liver cells, are widely used for virus research among multiple virus families. These cell lines are permissive to the growth of several RNA viruses. SeV is extensively used as a model to study virus-host interactions since it has a similar genomic organization to pathogenic viruses that include Ebola, Marburg, Hendra and Nipah Virus
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