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Updated: Jun 29, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
RBD Amplicon Sequencing and Evolutionary Analysis of SARS-CoV-2 Variants from Wastewater Samples
Xingwen Chen1,2, Chunfu Zheng3, Fuqing Wu4,5
1Department of Environmental and Occupational Health Sciences, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA.
Abstract:
The surveillance of SARS-CoV-2 is significantly limited by the presence of numerous variants with distinct behaviors driven by rapid evolution. Although the conventional clinical genome sequencing method provides comprehensive data, it has limitations in capturing the epidemiological dynamics of the variants circulating in the community. In this chapter, we describe a protocol using RBD amplicon sequencing of wastewater samples. We present the detailed experimental procedure for wastewater sample processing, robust nested-PCR-based amplification of the target RBD sequence, and library preparation. Moreover, we describe a general pipeline of sequencing data processing and interpretation, showing the epidemiological and evolutionary trends of SARS-CoV-2 variants in the community.
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