APHL 2022 POSTER ABSTRACTS
COVID-19
Utilizing the Terra . Bio Platform to Rapidly Develop and Distribute Resources for SARS-CoV-2 Sample Characterization and Genomic Epidemiology to Public Health Laboratories
K Libuit 1 , F Ambrosio 1 , R Petit 1 , 2 , C Kapsak 1 , J Sevinsky 1 , E Smith 1 ;
1
Theiagen Genomics , 2 Wyoming Public Health Laboratory
SARS-CoV-2 ( SC2 ) sample characterization and genomic epidemiological analysis has become an increasingly critical function for public health laboratories . Integration of these practices , however , has been a major challenge due to the technical workforce and compute infrastructure development required to access the many SC2 bioinformatics solutions . Bestpractice approaches for SC2 sample characterization and genomic epidemiology were captured into a series of workflow description language ( WDL ) workflows--deemed the Titan workflow series . The Titan workflow series was made accessible through the Terra . Bio platform , a bioinformatics web application that connects nontechnical users to bioinformatics WDL workflows and dynamic cloud compute resources through a clean and intuitive graphical user interface . Public health scientists were introduced and trained on the Titan workflows to enable routine SC2 sample characterization and genomic epidemiological analysis in laboratories with otherwise limited bioinformatics capabilities . The Titan workflow series has been adopted in over 40 public health laboratories in the United States and over 15 countries internationally . To date , the US laboratories have analyzed an estimated 400,000 SC2 samples using the Titan workflows on the Terra platform .
Use of WDL workflows and the Terra . Bio platform has allowed various public health laboratories to overcome the major barriers to accessing advanced bioinformatics solutions for SC2 genomic analysis . Continued use of the Terra . Bio platform may also provide value in developing and distributing bioinformatics solutions for other pathogens of concern .
Presenter : Kevin Libuit , Theiagen Genomics , kevin . libuit @ theiagen . com using synthetic controls or heat-killed virus . Library preparation was performed manually or on the Ion Chef™ , sequenced on GeneStudio™ S5 or Genexus™ sequencers , and evaluated for sequencing uniformity , variant calling and consensus sequence assembly with built-in plugins . Automated workflows reduce handson time to as little as 45 minutes using the Ion Chef™ system or 5 minutes with the turnkey Ion Torrent™ Genexus™ sequencing system , reducing the risk of operator induced errors . With the 540 chip on Ion GeneStudio™ S5 , up to 80 samples can be multiplexed for high throughput . The panel exhibited strong targeted sequencing performance , with on-target reads above 95 % and coverage uniformity above 90 %. The panel also demonstrated high analytical sensitivity , with a limit of detection for variant calling and lineage assignment as low as 20 viral copies . The high sensitivity of the assay allows for sample inputs as low as 1 ng total RNA , increasing the eligibility of low viral load samples . Using the Ion AmpliSeq™ SARS-CoV-2 end-to-end analysis solution , we successfully detected known variants in synthetic controls and assembled the genomes from heat-killed virus . The Ion AmpliSeq™ SARS-CoV-2 Research panel requires minimal sample input and as little as 24 hours turnaround time with the Genexus system for comprehensive genomic analysis , genome assembly and variant annotation . Together , this uniquely positions the Ion AmpliSeq™ SARS-CoV-2 assay to provide rapid , high-quality results for tracking viral spread and evolution with robust performance across viral variants . To date , over 124k sequences have been deposited into GISAID using these workflows , including over 81k Delta genomes and 3.8k Omicron genomes with on average ≥99 % sequence identity . The panel has proven to be robust to natural variation , making it usable in a wide array of applications including contact-tracing and viral spread with a diversity of sample types such as nasopharyngeal swabs , wastewater and post-mortem FFPE tissue .
For Research Use Only . Not for use in diagnostic procedure .
Presenter : Anna McGeachy , Thermo Fisher Scientific , anna . mcgeachy @ thermofisher . com
Rapid Next Generation Sequencing of the Complete SARS- CoV-2 Genome using the Ion AmpliSeq SARS-CoV-2 Insight Research Assay
A McGeachy , N Li , W Zhang , X Duan , L Pickle , J Ni , X Meng , L Guo , Y Zhong , S Ambriz , Y Lin , B Hsaw , S Roman , A Shah and F Hyland , Thermo Fisher Scientific
Whole genome sequencing of SARS-CoV-2 is essential to monitoring the emergence and spread of variants such as Delta and Omicron . The Ion AmpliSeq SARS-CoV-2 Insight Research Assay is a targeted NGS solution that enables specific amplification , analysis and monitoring of the complete SARS-CoV-2 genome . We report the intelligent design for robust performance and utility in a wide variety of SARS-CoV-2 research applications . The design covers 99.6 % of the total bases of SARS-CoV-2 genome . Approximately 62 % of the viral genome is covered with two independent amplicons , giving the panel exceptionally robust performance in the face of naturally occurring variation . Amplicons were designed to cover all serotypes of SARS-CoV-2 with high analytical specificity and demonstrate no crosstalk to other Coronaviruses . Panel performance was assayed
Rapid , High-frequency SARS-CoV-2 Wastewater Sequencing with the Genexus™ Integrated Sequencer
J Ni 1 , R Knight 2 , S Karthikeyan 2 , D Merrill 1 ; 1 Thermo Fisher Scientific ,
1
University of California , San Diego
Environmental wastewater surveillance is becoming a powerful and minimally invasive genomic sequencing tool to monitor the emergence and spread of SARS-CoV-2 variants such as Delta and Omicron . A key advantage of wastewater sequencing is its ability to potentially provide early , comprehensive surveillance data within a community , especially with frequent sampling and sequencing . Rapid sequence data availability offers the potential for earlier public health messaging , advice , or interventions to help decrease the severity of outbreaks . However , current approaches are hindered by pooled sampling and long sequencing turnaround times , which can delay results . Wastewater sequencing can also be impacted by poor sample quality due to degradation , low viral titers and mixed samples for analysis . To address these challenges , we report a protocol for SARS-CoV-2 wastewater surveillance using the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Integrated Sequencer . Data were obtained by sequencing archival wastewater samples from University of