Additional file 1 of A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2
Creators: name: Gohl, Daryl M.
name: Garbe, John
name: Grady, Patrick
name: Daniel, Jerry
name: Watson, Ray H. B.
name: Auch, Benjamin
name: Nelson, Andrew
name: Yohe, Sophia
name: Beckman, Kenneth B.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Additional file 1: Supplemental Fig. S1. Samples for initial SARS-CoV-2 sequencing workflow tests. Samples with N1 and N2 Ct values ranging from approximately 20–40 chosen for testing of SARS-CoV-2 sequencing workflows. Supplemental Fig. S2. Coverage metrics by method for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. Percentage of genome coverage at 10x at different subsampled read depths for each sample when sequenced using the following approaches: A) Illumina Nextera DNA Enrichment; B) ARTIC v3 with TruSeq library preparation. C) Tailed amplicon v1 (2 pool amplification); D) Tailed amplicon v2 (4 pool amplification). Supplemental Fig. S3. Coverage metrics by sample for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. A) Percentage of genome coverage at 10x at different subsampled read depths for the indicated sample when sequenced using the indicated workflow. B) Percentage of genome coverage at 100x at different subsampled read depths for the indicated sample when sequenced using the indicated workflow. Supplemental Fig. S4. Performance metrics for Illumina DNA Flex Enrichment Protocol. Number of total reads generated per sample using the Illumina Nextera DNA Flex Enrichment workflow relative to: A) Sample N1 Ct value; B) Sample N2 Ct value. Percentage of reads aligned to a human reference genome using the Illumina Nextera DNA Flex Enrichment workflow relative to: C) Sample N1 Ct value; D) Sample N2 Ct value. Supplemental Fig. S5. ARTIC v3 amplicon relative abundance. A-F) Observed read depth for each of the expected amplicons for the indicated sample amplified with the ARTIC v3 protocol with TruSeq library preparation at a subsampled read depth of 100,000 raw reads. Supplemental Fig. S6. Tailed amplicon v1 amplicon relative abundance. A-F) Observed read depth for each of the expected amplicons for the indicated sample amplified with the tailed amplicon v1 protocol at a subsampled read depth of 100,000 raw reads. Supplemental Fig. S7. Tailed amplicon v2 amplicon relative abundance. A-F) Observed read depth for each of the expected amplicons for the indicated sample amplified with the tailed amplicon v2 protocol at a subsampled read depth of 100,000 raw reads. Supplemental Fig. S8. Primer dimer formation in tailed amplicon method. A) Agilent TapeStation trace for a library prepared from samples with N1 and N2 Ct values between ~ 20–40 using the tailed amplicon v1 (2 pool amplification) workflow. B) Mean read 1 quality score for samples prepared with the tailed amplicon v1 (2 pool amplification) workflow amplified for either 25 or 35 PCR cycles. C) Percentage of sequencing adapter observed for samples prepared with the tailed amplicon v1 (2 pool amplification) workflow amplified for either 25 or 35 PCR cycles. D) Agilent Bioanalyzer trace for a library prepared from samples with N1 and N2 Ct values between ~ 20–35 using the tailed amplicon v2 (4 pool amplification) workflow. E) Mean read 1 quality score for samples prepared with the tailed amplicon v2 (4 pool amplification) workflow. F) Percentage of sequencing adapter observed for samples prepared with the tailed amplicon v2 (4 pool amplification) workflow. G) 2% agarose gel showing the presence of primer dimers particularly in high N1/N2 Ct samples when indexed using different PCR cycling conditions. Arrow indicates primer dimers on gel. Supplemental Table 1. Percentage of genome coverage at 10x at different subsampled read depths for WA1 and UMGC SARS-CoV-2 isolates sequenced with different methods. For the ARTIC v3, tailed amplicon v1, and tailed amplicon v2 methods, samples were amplified for 35 PCR cycles in the first PCR reaction. Supplemental Table 2. Percentage of genome coverage at 100x at different subsampled read depths for WA1 and UMGC SARS-CoV-2 isolates sequenced with different methods. For the ARTIC v3, tailed amplicon v1, and tailed amplicon v2 methods, samples were amplified for 35 PCR cycles in the first PCR reaction. Supplemental Table 3. Percentage of genome coverage at 10x at different subsampled read depths for WA1 and UMGC SARS-CoV-2 isolates sequenced the tailed amplicon v1 method amplified for 25 PCR cycles in the first PCR reaction. Supplemental Table 4. Percentage of genome coverage at 100x at different subsampled read depths for WA1 and UMGC SARS-CoV-2 isolates sequenced the tailed amplicon v1 method amplified for 25 PCR cycles in the first PCR reaction.