High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Amy H Fitzpatrick; Agnieszka Rupnik; Helen O'Shea; Fiona Crispie; Sinéad Keaveney; Paul Cotter

doi:10.3389/fmicb.2021.621719

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Front Microbiol. 2021 Feb 22:12:621719. doi: 10.3389/fmicb.2021.621719. eCollection 2021.

Authors

Amy H Fitzpatrick^{1

2

3}, Agnieszka Rupnik², Helen O'Shea³, Fiona Crispie¹, Sinéad Keaveney², Paul Cotter¹

Affiliations

¹ Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland.
² Shellfish Microbiology, Marine Institute, Oranmore, Ireland.
³ Biological Sciences, Munster Technological University, Cork, Ireland.

Abstract

This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

Keywords: RNA depletion; RNA viruses; amplicon sequencing; capture based probe hybridization; environmental virology; high throughput sequencing; viral enrichment.

Publication types

Review