Next-Generation Sequencing for Confronting Virus Pandemics

Abstract

Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.

Expedited retrieval of high-quality Usutu virus genomes via Nanopore sequencing with and without target enrichment

“…10.3389/fmicb. 2022.1044316 Frontiers in Microbiology frontiersin.org opened the door to an array of approaches including viral evolution, metagenomics, and transcriptomics in the study of quasispecies (Radford et al, 2012;Quer et al, 2022). These are genetically closely related viruses that can exist concurrently in a susceptible vector or host due to the high mutation rate of RNA viruses.…”

“…Through mass parallelization of sequencing reactions, NGS decreased the necessary costs and turnaround time per sample and revolutionized genomics ( Margulies et al, 2005 ). It opened the door to an array of approaches including viral evolution, metagenomics, and transcriptomics in the study of quasispecies ( Radford et al, 2012 ; Quer et al, 2022 ). These are genetically closely related viruses that can exist concurrently in a susceptible vector or host due to the high mutation rate of RNA viruses.…”

“…An advantage of SGS is the high throughput with fairly low error rates (≈1–2.4%) compared to TGS (≈10–15%). The disadvantage is linked to the shorter read lengths (75–600 nt/read) compared to TGS (60 K–2 M bp), which can limit the detection of mutations (deletions or insertions) as well as the characterization of repetitive genomic regions ( Quer et al, 2022 ). In this study, however, both the SGS (Illumina) and the TGS techniques via amplicons (MinION; excluding direct sequencing) produced similar results with high identity levels of 98–99%.…”

Current strategies for SARS-CoV-2 molecular detection

“…129,130 However, the main limitations do impose restrictions on the application of mNGS that minority sequences that share little identity with the reference sequences are inclined to be overlooked, leading to erroneous mapping. 125…”

“…123,124 It has been drawn from the pandemic that promptly identifying and characterizing the causal agent is essential for understanding the likelihood of a mutant gaining dominance and the investigation of the transmission route, which can be helpful for the authorities to take sound preventive action. 125 Nextgeneration sequencing (NGS) technologies for targeted deepsequencing, metagenomics, and whole-genome sequencing (WGS) are among the most ubiquitous methods to date in continuously monitoring the variants and relevant mutations in many countries. 125,126 Metagenomic NGS (mNGS), an NGS-based analysis, have been widely introduced in diagnosing the SARS-COV-2 infection, which aligns Q-PCR-conrmed cases with the GenBank nucleotide database to discern viral genomes in samples.…”