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Review
. 2022 Mar 14;14(3):600.
doi: 10.3390/v14030600.

Next-Generation Sequencing for Confronting Virus Pandemics

Josep Quer  1   2   3 , Sergi Colomer-Castell  1   2 , Carolina Campos  1   2 , Cristina Andrés  4 , Maria Piñana  4 , Maria Francesca Cortese  2   5 , Alejandra González-Sánchez  4 , Damir Garcia-Cehic  1   2 , Marta Ibáñez  1 , Tomàs Pumarola  4   6 , Francisco Rodríguez-Frías  2   3   5 , Andrés Antón  4   6 , David Tabernero  2   7
Affiliations
Review

Next-Generation Sequencing for Confronting Virus Pandemics

Josep Quer et al. Viruses. .

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.

Keywords: COVID-19; NGS; SARS-CoV-2; deep-sequencing; diagnostic tools; pandemics; variability; viruses; zoonosis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Week-by-week distribution of variants from March 2020 to present (February 2020). We have encircled the most prevalent variants in each pandemic wave. Pointed line with numbers (· · ·) indicate the amount of positive cases detected in Vall d’Hebron Hospital per week. Pointed and slashed line (· - · -) indicates vaccine coverage in Barcelona city with one dose and slashed line (- -) with double doses.
Figure 2
Figure 2
Most human pathogenic viruses in a clock-like classification scheme. Permission kindly provided by Todd N. Wylie; adaptation of Figure 1 of Wylie et al. [52].
Figure 3
Figure 3
General schematic methodologies for virus genome sequencing.
See this image and copyright information in PMC

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