Fitzpatrick Amy H, Rupnik Agnieszka, O'Shea Helen, Crispie Fiona, Keaveney Sinéad, Cotter Paul
Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland.
Shellfish Microbiology, Marine Institute, Oranmore, Ireland.
Front Microbiol. 2021 Feb 22;12:621719. doi: 10.3389/fmicb.2021.621719. eCollection 2021.
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.
本综述旨在评估并推荐针对多种样本基质中RNA病毒进行靶向和非靶向高通量测序的方法。高通量测序（HTS）也被称为深度测序、下一代测序和第三代测序；它为环境病毒学领域提供了很多帮助，因为其增加的测序深度规避了为进行桑格测序而克隆环境分离株的问题。然而，需要考虑方法选择可能给测序结果带来的挑战和偏差。在此，根据RNA提取、逆转录到文库制备等方法选择对RNA病毒检测或表征的影响进行比较。
