Automation and Pathogen Surveillance: Scaling Up

In early 2020, it was difficult to imagine what would be achieved in laboratories across the globe as the pressure to increase testing capacity and understand the viral lineages of SARS-CoV-2 grew exponentially.

Register for this 3-part webinar, during which there will be presentations from researchers who have transformed their labs, expanded their teams, and implemented automation to show what can be expected for the future of pathogen surveillance.

Part 1: Creating and Adapting our Public Health Laboratory in COVID-19.

Speaker: Jennifer Toner, The George Washington University

The Public Health Laboratory (PHL) at the George Washington University was started in July 2020 after a small COVID-19 surveillance study showed potential for greater impact.

The unimaginable was achieved, starting with expansion of the team from 5 to 20 and repurposing a borrowed space into a high-throughput clinical testing lab. Fortunately, PHL were able to work closely with suppliers to secure liquid handling instruments, RNA extraction kits, and PCR light cyclers to provide campus-wide testing coverage. Early on, the lab had started automating almost all process.

A breakthrough in the automation journey came in with introduction to SPT Labtech and their instruments. With the addition of mosquito and dragonfly, researchers no longer manually add master mix and RNA to 384-well plates, allowing them to get samples on the light cycler in less amount of time.

Currently, with a drop in COVID-19 testing, PHL is fully armed and open to new opportunities to take on other viral and RNA–based testing while remaining agile and adaptive.

Part 2: mosquito HV genomics and Dragonfly Discovery Enable a COVID-seq Project at UF ICBR.

Speaker: Yanping Zhang, UF Interdisciplinary Center for Biotechnology Research

With a pursuit of evaluating the molecular epidemiology of COVID-19 in Florida, the UF Interdisciplinary Center for Biotechnology Research set out to understand viral lineages of SARS-CoV-2 circulating in Florida. Further, also to determine how the cases in different regions of Florida are gnomically related and to assess effect of vaccination on transmission clusters.

To achieve the goal, 764 samples needed to be completed from DNA extraction to final sequencing data analysis on a weekly based. SPT Labtech’s mosquito HV genomics (mosquito) made this project possible, and we went on to add dragonfly discovery to our solution. Using a combination of both instruments has enabled us to have library construction of one 384-well plate completed in a day.

First, we tested COVID library construction with different input (10ng, 25ng and 50ng) with a full and a quarter reaction. The result showed that we can get libraries from ¼ reaction with 10ng input. After water test for mosquito protocol, we process the first 235 samples on mosquito with 1/5 reactions. The sequencing data showed that each sample consistently has over 1 million reads, and average coverage on the COVID-SARS-2 genome is over 5000x. However, the percentage of viral load for some of the samples is low. Thus, we increased the reads number per sample to 4-5 million, which gives us a better viral load percentage.

Part 3:  The future of pathogen surveillance

Speaker: Paul Lomax, SPT Labtech

During the past year we have worked closely several high-profile customers who have led the global charge in Covid-19 surveillance. Understanding the spread of the virus has become a vital tool to inform and execute public health policies. In this short presentation, we explore the thoughts of leading scientists in this field and their visions of the future of Pathogen surveillance.

Speakers

Jennifer Toner, Laboratory Supervisor, The George Washington University, School of Medicine and Health Sciences, Public Health Laboratory

Jennifer Toner first joined the Public Health Laboratory shortly after it’s creation in August 2020 as a laboratory assistant. In February 2021, she assumed the position of supervisor which meant handling constant supply chain issues and searching for new equipment to make the lab more efficient. It was through this searching that they found SPT Labtech and the robots they offered that could enhance the company workflow. Today, Jennifer and her team happily use the Dragonfly and mosquito on a regular basis and everyone’s pipetting-hands are thankful! Before working in this lab, Jennifer worked in a breast cancer research lab in Salt Lake City, Utah where the bulk of her work included cell culture in 3D matrixes and murine work. Before that, she spent two years working in both primary and emergency medicine as a scribe in Vermont. Ultimately, Jennifer wishes to be in the clinic but will always be involved with clinical research and rely on what she has learned in PHL.

Message Presenter

Yanping Zhang, Scientific Director, ICBR (Interdisciplinary Center of Biotechnology Research) at University of Florida

Yanping Zhang is a Scientific Director for the Gene Expression Core at the Interdisciplinary Center for Biotechnology Research (ICBR) in University of Florida since 2010. She operates and manages the core to deliver best-in-class gene expression and genotyping services in a timely manner to researchers both within and outside UF. The main services the core offers are qPCR, ddPCR, QuantiGene assay, GeneTitan Axion genotyping analysis, whole genome wide transcriptome analysis using RNA-seq, 16s metagenomics analysis, single cell RNA-seq, single cell immune profiling, single cell CITE-seq, single cell ATAC-seq.

Yanping enjoys performing the experiments, identifying the problem and making new technologies to work. There is nothing better than utilizing her passions to assist scientists and make contribution to their research projects. The recently acquired SPTlabtech mosquito HV Genomics liquid handler and Dragonfly Discovery helps her customers for their COVID-seq project possible to be performed at the center.

Message Presenter

Paul Lomax, Product Manager, SPT Labtech

Paul Lomax is a product manager at SPT Labtech, responsible for liquid handling systems for applications in genomics. He has over 20 years’ experience in the automation of sample processing across a wide range of application areas in the academic, clinical, environmental, biotech, and pharmaceutical sectors.

Message Presenter