Sequencing the pandemic: rapid and high-throughput processing and analysis of COVID-19 clinical samples for 21st century public health

Abstract

Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks. Here, we report two genomic sequencing and analysis strategies for rapid-turnaround or high-throughput processing of metagenomic samples. The rapid-turnaround method was designed to provide a quick phylogenetic snapshot of samples at the heart of active outbreaks, and has a total turnaround time of <48 hours from raw sample to analyzed data. The high-throughput method was designed for semi-retrospective data analysis, and is both cost effective and highly scalable. Though these methods were developed and utilized for the SARS-CoV-2 pandemic response in Arizona, U.S, and we envision their use for infectious disease epidemiology in the 21st Century.

Methods for sequencing the pandemic: benefits of rapid or high-throughput processing

“…Lines 122-123: Consensus genomes generated using these methods include those from Ladner et al 19 . and are similar to those in Peng et al 43 and Stoddard et al 44 Comment 5: What is the quality of assembled genomes based on read coverage?…”

“…Underlying data Zenodo: Supplementary Data for "Sequencing the Pandemic: Rapid and High-Throughput Processing and Analysis of COVID-19 Clinical Samples for 21st Century Public Health" DOI: 10.5281/zenodo.5822962 44 . This project contains the following underlying data:…”

Genomic investigation of a household SARS-CoV-2 disease cluster in Arizona involving a cat, dog, and pet owner

“…Whole genome sequencing of specimens obtained from the cat, dog, and pet owner using previously documented methods [ 12 ] produced viral genomes with 95%, 84%, and 97% breadth of coverage of the Wuhan reference genome, respectively. The Pango-lineage for all three genomes was identified as B.1.575, which has been reported in >30 countries, with the majority of genomes (90%) originating in the US [ 13 ].…”

Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona

“…RNA was extracted using previously described methods (11,12) and prepared for whole genome sequencing. SARS-CoV2 cDNA was amplified following the nCoV-2019 sequencing protocol V.124 and using the ARTIC v3 primer set, prepared for sequencing with plexWell384 (SeqWell), and sequenced on a NextSeq 550 with v2 chemistry and 150 X 150 base-pair reads (Illumina).…”

“…SARS-CoV2 cDNA was amplified following the nCoV-2019 sequencing protocol V.124 and using the ARTIC v3 primer set, prepared for sequencing with plexWell384 (SeqWell), and sequenced on a NextSeq 550 with v2 chemistry and 150 X 150 base-pair reads (Illumina). Data were processed and virus genome consensus sequences were built using the Amplicon Sequencing Analysis Pipeline (ASAP) (12). Maximum likelihood phylogenetic trees containing the outbreak genomes and a subset of other Arizona genomes for context were generated using the Wuhan-1 genome as a reference using NextStrain (13,14).…”