CovProfile: profiling the viral genome and gene expressions of SARS-COV2

SARS-COV2 is infecting more than one million people. Knowing its genome and gene expressions is essential to understand the virus.

Here, we propose a computational tool to detect viral genomic variations as well as viral gene expression from the sequenced amplicons with Nanopore devices of the multiplex reverse transcription polymerase chain reactions.

We applied our tool to 11 samples of terminally ill patients, and discovered that seven of the samples are infected by two viral strains. The expression of viral genes ORF1ab gene, S gene, M gene, and N gene are high among most of the samples. While performing our tests, we noticed the abundances of MUC5B transcript segments to be consistently higher than those of other genes in the host.