Supplemental Materials for: Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater

This is a collection of Supplemental Materials for the research article: Lin, X., et al. (2021) "Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater". mSystems

Data File S1: Multiplex Tiling PCR Primer Schemes for 150 bp, 400bp, and 1200 bp Amplicons.

Table S2: Results of RT-PCR inhibition test with VetMax Xeno Internal Positive Control (IPC) Assay and US CDC N1 assay. SARS-CoV-2 viral concentrations in primary sludge samples were quantified using the Reliance One-Step Multiplex RT-qPCR Mastermix (Bio-Rad Laboratories, Hercules, CA, USA) with the 2019-nCoV CDC RUO primers and probes targeting the N1 gene (Integrated DNA Technologies). RT-qPCR reactions were prepared as described by D’Aoust et al. (https://doi.org/10.1016/j.watres.2020.116560) and run in triplicate on a CFX96 Real-time System (Bio-Rad Laboratories).

Table S3: Single nucleotide variants (SNVs) associated with SARS-CoV-2 lineages of concern (or variants of concern). The mutations were identified by querying the GISAID database to find SNVs that were over 90% prevalent in the variants of concern, and were also not present above 10% prevalence in another lineage (see Text S1).