APHL 2022 POSTER ABSTRACTS
COVID-19 or better than , WT control nucleocapsid protein . Specifically , the recombinant point mutations identified gave relative signal / cutoff ( S / C ) values of 110-380 % compared to WT . Additionally , the fully mutated Omicron nucleocapsid protein was tested , carrying its three mutations and a single three-residue deletion . As was the case with the individual recombinant point mutations tested , the Omicron nucleocapsid protein was detected with higher S / C than the WT control .
Conclusion : The performance of the VITROS Immunodiagnostic Products SARS-CoV-2 Antigen assay is unaffected by mutations found among emerging variants to date , up to and including the Gamma , Delta and Omicron variants .
* For EUA only RD-00024
Presenter : Brett Hirsch , Ortho Clinical Diagnostics , brett . hirsch @ orthoclinicaldiagnostics . com
HiFiViral SARS-CoV-2 : A Mutation Tolerant , Fully-kitted Solution for COVID-19 Surveillance
M Ashby 1 , T Hon 1 , J Wilson 1 , I McLaughlin 1 , Z Kronenberg 1 , J Harting 1 , T Dahlen 1 , J Zeigle 1 , K Koprowski 2 , S Lee 2 , C Waddling 2 , S Finckbeiner 2 , P Lomax 2 , S Kingan 1 ; 1 Pacific Biosciences , 2 SPT Labtech Ltd .
The COVID-19 pandemic is an ongoing global challenge , with the repeated emergence of new variants that are more contagious , more virulent , drug resistant or evade vaccine-induced immunity . In response , the HiFiViral SARS-CoV-2 kit was developed as a scalable solution with increased resilience against virus mutations , designed for use on the Sequel IIe system . Unlike PCR-based amplicon methods , the HiFiViral SARS-CoV-2 kit relies on ~ 1,000 , densely tiled Molecular Inversion Probes ( MIPs ) such that every genomic position is covered by ~ 22 probes , resulting in robust genome coverage of all circulating variants , including the mutation-dense Omicron lineage , across a broad range of Ct values . The HiFiViral kit offers many benefits for high-throughput surveillance . Sequencing 675 bp fragments with highly accurate HiFi reads enables comprehensive variant detection , including single nucleotide variants , indels , structural variants and identification of multi-strain samples . The kit is scalable , containing all reagents needed to enrich and barcode 384 samples , in batches ranging from 24 – 384 , for sequencing in one SMRT bell library . For high throughput labs , up to 8 SMRT Cells may be loaded on an instrument with no subsequent touch points , for up to 3,072 samples per run . The enrichment assay is also simpler to execute than PCR-based assays , consisting of just 4 add-only , color-change indicated steps . Barcoding primers come pre-mixed in a 384-well , resealable plate . The simple assay design uses fewer plastics , limiting the impact of supply chain issues . In addition , methods for running the HiFiViral kit were established on a mosquito ® HV Genomics pipetting robot and assessed for their performance . Finally , SMRT Link data analysis is one touch , and reports include variant calling , genome coverage , multi-strain detection and a plate performance summary . File outputs include consensus sequences ready for database submission and reads and consensus sequences aligned to the Wuhan reference . In this study , we demonstrate consistent recovery of > 95 % complete SARS-CoV-2 genomes using the commercially available HiFiViral kit at 4 different sites performing routine genomic surveillance . The evaluation runs included a broad range of sample
Ct inputs across control and nasopharyngeal samples in batches up to 384 . The runs also demonstrated consistent performance against Alpha , Delta , Omicron and other variant lineages , without the need for probe updates . In summary , the HiFiViral for SARS-CoV-2 kit is a cost-effective , convenient , accurate method for viral sequencing and well-suited for scalable surveillance of a rapidly evolving virus to inform public health decision making .
Presenter : Meredith Ashby , Pacific Biosciences , mashby @ pacificbiosciences . com
Extraction-free Nucleic Acid Detection by DirectDetect™ Technology on Gargle Samples
Z Lu , C Mcginnis , M Miller , M Veling , E Dougherty , G Filippov , T Perroud and Y Tong , PerkinElmer
Background : Nasal or throat swab followed by nucleic acid extraction , RT-qPCR is the most common procedure for diagnosis of COVID-19 . This report provides a feasible and non-invasive sample collection , extraction-free method for SARS-CoV-2 detection .
Methods : Saline gargle samples were self-collected and stored at 4oC . Samples were processed the same day using PerkinElmer ’ s DirectDetect™ technology without any nucleic acid extraction or additional heat lysis steps . Inactivated SARS-CoV-2 virus was spiked in pooled negative gargle samples for performance evaluation .
Results : The technology can reach detection sensitivity ( limit of detection ) as 5,400 cp / mL . Conclusion : The method takes ~ 2hrs from sample input to results . It provides a cost-efficient screening solution for SARS-CoV-2 with a non-invasive sample collection procedure .
This product is under development .
Presenter : Michael Miller , PerkinElmer , michael . miller @ perkinelmer . com
A Convenient Nucleic Acid Extraction Procedure for Wastewater-based Epidemiology
S Mondal , N Feirer , B Saul , S Moorji , S Goueli , J Cali , Promega Corporation
The COVID-19 pandemic has spurred investigation on the use of wastewater-based epidemiology ( WBE ) as a tool for monitoring the appearance and spread of COVID-19 in communities . The SARS-CoV-2 genetic signal is present at low concentrations in wastewater , making sample concentration a prerequisite . Most of the existing viral concentration and processing methods were originally developed to concentrate non-enveloped viruses . We hypothesized that since the SARS-CoV-2 genetic material in the wastewater is primarily present in nucleoprotein complexes and not in intact virions , a direct capture method that renders total nucleic acid conducive to binding to affinity resin may be able to overcome cumbersome viral concentration steps . This led to development of a simple , rapid and modular alternative to existing purification methods from wastewater . In this approach , chaotropic agents are added to raw sewage allowing nucleic acid binding to a silica matrix . The captured nucleic acid is then washed by successive alcohol washes to remove inhibitors that may have co-purified , followed by subsequent elution with water . The eluted