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

Kakuk, Balázs; Dörmő, Ákos; Csabai, Zsolt; Kemenesi, Gábor; Holoubek, Jiří; Růžek, Daniel; Prazsák, István; Dani, Virág Éva; Jankovics, I.; Torma, Gábor; Jakab, Ferenc; Tóth, Gábor Endre; Földes, Fanni; Zana, Brigitta; Lanszki, Zsófia; Harangozó, Ákos; Fülöp, Ádám; Gulyás, Gábor; Mizik, Máté; Kiss, A.; Tombácz, Dóra; Boldogkői, Zsolt

doi:10.1038/s41597-023-02149-4

Cited by 7 publications

(4 citation statements)

References 49 publications

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“…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.…”

Section: Efficiency Of Adaptive Sampling and Lineage Assignment Of Mp...supporting

confidence: 76%

“…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 .…”

Section: Discussionmentioning

confidence: 99%

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

Hewel,

Schmidt,

Runkel

et al. 2024

Journal of Medical Virology

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In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.

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Section: Efficiency Of Adaptive Sampling and Lineage Assignment Of Mp...supporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

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

Hewel,

Schmidt,

Runkel

et al. 2024

Journal of Medical Virology

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“…However, the complete genome of the monkeypox virus was assembled using only nanopore sequencing data [43]. Recently, the nanopore sequencing method resulted in a transcriptomic profile of the monkeypox virus and its host which provided critical information to investigate the virus-host interaction and viral infection [44].…”

Section: Nanopore Sequencing Technology In Pathogenic Diagnosticsmentioning

confidence: 99%

Implication of Nanopore Sequencing Technology for Pathogenic Diagnostics: A Mini-Review

Nguyen,

Nguyen

et al. 2024

tvujs

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DNA sequencing is the most critical technique to explore and study genomic data of human beings and surrounding environments. The history of DNA sequencing has rapidly grown since the first-generation DNA sequencing in 1977. Until now, emerging high-throughput sequencing technology has recently revolutionized omics areas, including genomics, transcriptomics, metagenomics, and metabolomics for the development of modern molecular biology. Besides the short-read sequencing method (Illumina platforms), the long-read sequencing technologies (including Pacific Biosciences and Oxford Nanopore Technologies) have been developed with the advantages of larger read sizes, portable devices, and diverse preparation kits. Consequently, the number of biological databases and study-related nanopore sequencing technologies has grown fast. This review paper summarized the principle and fundament of nanopore sequencing regarding their advanced applications in pathogenic diagnostics of different hosts. The most recent application of nanopore sequencing in the diagnostics of infectious diseases is highlighted and discussed to provide insights into the novelty of nanopore sequencing technology and its future perspectives.

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“…Whole genome sequencing is essential for researching and monitoring MPXV. Balázs Kakuk and companions have sequenced the transcriptome of MPXV and the infected cells by cDNA sequencing and direct RNA sequencing with nanopore technology [84]. This research provides an LRS (long read sequencing) dataset, comprising nearly 1.5 million viral sequences, which facilitates comprehensive and temporal analysis of the monkeypox transcriptome and the impact of viral infection on host gene expression.…”

Section: Diagnosis and Monitoring Of Virusesmentioning

confidence: 99%

The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research

Ji,

Feng,

Huang

et al. 2024

Viruses

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In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.

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

Cited by 7 publications

References 49 publications

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

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

Implication of Nanopore Sequencing Technology for Pathogenic Diagnostics: A Mini-Review

The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research

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