Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing

Abstract

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Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification

“…This study compared the amplification rates of two different sequencing platforms, namely partial genome sequencing by the Sanger method and full genome by Illumina NextSeq2000 NGS, from the perspective of massive screening and SARS-CoV-2 variants identification. There are some reports on the comparison between the NGS and the Sanger strategies for mutation screening and genotype identification of hepatitis B virus (HBV) [ 24 ] and hepatitis C virus (HCV) [ 25 ], but reports on the SARS-CoV-2 virus are limited. Hence, a variety of methods were developed to identify the variants of concern, such as amplicon-based whole or partial genome sequencing, multiplex real-time polymerase chain reaction (RT-PCR) assays [ 26 ], S-gene target failure (SGTF) [ 27 ], screening single nucleotide polymorphism (SNP) assays [ 28 ], reverse transcription loop-mediated isothermal amplification (RT-LAMP) [ 29 ], transcription-mediated amplification (TMA) [ 30 ], among others.…”