TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.

ABSTRACT:

Background

Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the human papillomavirus (HPV) DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method's flexibility to a broader range of viruses, both DNA and RNA.

Results

Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approxim

SUBMITTER: Hesselberg Lovestad A 

PROVIDER: S-EPMC9993372 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature