Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

Abstract

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

LINE-1 Retrotransposon-derived Proteins: The ORFull Truth?

“…In turn, the activated LINEs and their expressed products may help the virus integrate into the host. Others however have both questioned the methodology of the work [44] or found little evidence for SARS-CoV-2 integration into the genome of infected individuals [45] raising questions about the solidity of the other findings. Interestingly however, in terms of the ability of a virus to stimulate LINE-1 activity, previous studies examined the effect of the Kaposi's sarcoma (KS)associated herpesvirus (KSHV) on L1 retrotransposition [46,47].…”