Tackling COVID-19 and Influenza Testing With Semi-Automation

The rapid transmission of contagious diseases always puts pressure on public health laboratories, but never more so than during the COVID-19 pandemic. The quick development of tests for COVID-19 was crucial to efforts to slow the spread of the disease, but it was the significant numbers of public health laboratories rolling hundreds or thousands, or even tens of thousands, of results out the door every day that were the backbone of this success. These laboratories were – and many still are – facing unprecedented pressures to scale-up their operations to meet record-breaking demands for COVID-19 and flu testing with limited staff members and resources. This extraordinary demand unavoidably took a toll on the well-being of staff, giving labs such as the New Hampshire Public Health Laboratory the impetus to evaluate the use of semi-automated workflows for performing the CDC influenza and SARS-CoV-2 rRT-PCR assays. This article discusses how semi-automation drastically improved the accuracy and precision of the lab’s results, and freed up its busy scientists to run other vital tests that had temporarily been forced to take a backseat.

New Hampshire Public Health Laboratory (NHPHL) – a member of the Association of Public Health Laboratories – carries out a huge array of testing for infectious diseases of public health significance, including influenza, measles, mumps, HIV, syphilis and hepatitis C. When the global pandemic hit in early 2020, the lab was suddenly required to perform high volume, fast turnaround COVID-19 testing on top of its routine tasks, quickly reaching 800 to 1,000 SARS-CoV-2 tests every day. Initially, staff were struggling to get through these enormous sample numbers using their existing manual pipettes, which created a testing backlog. NHPHL therefore implemented the ASSIST PLUS pipetting robot from INTEGRA Biosciences to automate the steps of specimen processing and nucleic acid transfer. This addition helped the laboratory to significantly increase its throughput, allowing the team to cope with the dramatic increase in their testing workload and meet the demand for rapid turnaround times.

The lab’s workload once again jumped drastically to around 2,000 tests a day in November 2020, with numbers remaining at this peak for several months. This placed a huge strain on facilities and personnel, and exceeded the throughput capacity of the lab’s existing workflow. To address this new challenge, NHPHL decided to introduce INTEGRA’s MINI 96 portable electronic pipette to accelerate its PCR plate set-up. This further automated laborious pipetting, speeding up the lab’s workflow and cutting down on errors and hands-on time.  

Staying ahead of the game with novel technology

In early 2022, NHPHL evaluated the possibility of using a newly launched single channel pipetting module for its pipetting robot running the CDC’s Influenza SARS-CoV-2 (Flu SC2) rRT-PCR multiplex assay. The team prepared serial dilutions of five previously tested SARS-CoV-2-positive specimens, using the ASSIST PLUS and INTEGRA’s new D-ONE single channel pipetting module to prepare and plate the master mix. Extracted RNA samples were then added using the MINI 96. Five replicates were tested over five days for a total of 125 tests, and PCR results were compared to results obtained from manual master mix preparation and plate set-up, performed using a handheld electronic pipette.

The trial showed that the D-ONE module on the ASSIST PLUS enabled robust and reliable automated influenza/SARS-CoV-2 master mix preparation, PCR plate set-up, and single step addition of 96 specimens to a PCR reaction plate. The platform demonstrated 100 percent accuracy and showed a coefficient of variation of 0.39 percent, compared to 0.52 percent for manual plate preparation. In addition, semi-automating the sample testing protocol reduced the total hands-on time by 27 percent, which freed up technicians to perform other tasks, while also reducing the risk of pipetting errors.

Improved ergonomics and intuitive software

INTEGRA’s user-friendly VIALAB software enabled the team to quickly and easily program the ASSIST PLUS, and the ability to control the platform from a laptop made it convenient to modify the number of master mix reactions according to variations in workload, as well as to produce post-run reports for quality assurance. Automation also improved the mental wellbeing of personnel, and helped to reduce the bodily strain caused by long periods of standing and performing repetitive tasks. The set-up further contributed to limiting the employees’ exposure to potential pathogens, reducing the risk of contamination and illness – a major priority for NHPHL.

Looking ahead

Semi-automating sample testing significantly streamlined the workflow of NHPHL, saving staff time and allowing them to perform other important tasks which would otherwise have been completely sidelined and impossible to carry out. Automated pipetting also yielded more accurate and precise results in comparison with the lab’s previous manual pipetting methods, while still maintaining short turnaround times and enabling the lab to handle relentlessly high numbers of samples. Overall, introducing automated pipetting platforms from INTEGRA Biosciences increased the productivity and throughput of NHPHL, as well as reducing the mental and physical strain on staff. The laboratory is now eager to use these new tools to automate its whole genome sequencing workflow, and plans to rely on them to continue fighting the battle against COVID-19 and other infectious diseases well into the future.

About the authors

Dr. Jessica L. Alexander, Virology/STD Laboratory Supervisor, NHPHL

Jessica earned her BSc in Biochemistry from the Rochester Institute of Technology, and then went on to graduate school at the Massachusetts Institute of Technology where she earned her PhD in Biology. After graduate school, Jessica worked at Lamplighter Brewing Co. as the Microbiologist and Quality Control Manager for three years. She then transitioned into public health in August 2020, when she was recruited to NHPHL during the COVID-19 pandemic. In February 2021, Jessica was pleased to accept the position of Virology & STD Unit Supervisor at NHPHL.

Pedro Tirado Velez, Virology Laboratory Scientist, NHPHL

Pedro earned his BA in Molecular Biology from Colorado College in May 2020. Freshly out of college, he was excited to join the NHPHL as a laboratory assistant during the COVID-19 pandemic, where he worked in the central receiving division verifying specimen integrity. In August 2020, Pedro was presented with the opportunity to expand his scientific techniques as a laboratory scientist in the Arbovirus and Virology unit at NHPHL. Here, he continues to assist the state with its efforts in surveying patient samples for SARS-CoV-2, Influenza A, and Influenza B.