In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

Abstract

The recent Monkeypox outbreak showed the importance of studying the basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. Our direct cDNA and native RNA sequencing data enable the in-depth characterization of the transcriptomic architecture and dynamics of the gene expressions of monkeypox virus; and also the deeper understanding of the changes it causes in the host cells on a transcriptome level.

Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case

“…Next, we reannotated the SV parts specifically by downloading and realigning publicly available long read RNAseq data from a bio sample isolated during the recent outbreak in Prague. 20 This confirmed the expression of the two 128 bp SVs as a part of OPG015 and the expression of the 324 bp SV as a part of OPG208 (Figure 4). This highlights the importance of multiomic datasets and periodic re-sequencing to generate and maintain the highest level of genome annotation.…”

“…In contrast, we believe there is probable cause that this may be an artifact due to the main annotation method chosen, which seems to be an annotation transfer of gene features from a genome without the SV and therefore re‐mapping of a shorter gene model sans SV. Overlapping expression data from the current outbreak, shows SV1 expressed as part of OPG015 20 . OPG015 (or D1L) is frequently implicated as a gene participating in immune invasion and influencing monkeypox host range 31,32 .…”

Monkeypox virus genomic accordion strategies

“…5c). Thus, to demonstrate the biological relevance of our findings, we analyzed publicly available transcriptome data obtained at different times during the MPXV replication cycle, allowing for the identification of expression of viral transcripts 43 . We first identified the early and late putative MPXV promoters (Figure S6).…”

“…We utilized open-access RNA-seq data to examine alterations in the transcriptional profile of MPXV during infection 43 . We used these data to identify the top (e.g., 10 or more abundant transcripts) early and late expressed viral genes (see DESEQ results in Supplementary Data 8).…”

“…The original samples were subjected to total RNA isolation, library preparation, poly(A)+ enrichment, and RNA sequencing with ONT MinIon. The BAM files retrieved from SRA were preprocessed files from which reads have been aligned to MPXV ON563414.3 and human GCF_015252025.1 43 .…”