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By Joe Rotter
How do you prepare for the unexpected? The COVID-19 pandemic has brought to light how challenging it is for labs and production facilities to scale up quickly in times of need. The sudden surge in demand for laboratory solutions at the very time that we are experiencing unprecedented constraints on the workforce and global supply chains is a wake-up call. This has put pressure on infrastructures in every sphere connected to the healthcare industry—from R&D and manufacturing to clinical diagnostics. Even relatively small labs and organizations have been required to rapidly shift focus and massively expand their outputs at an unprecedented rate.
There is, however, a silver lining: the current pandemic compels healthcare industry leaders to question the agility and scalability of their laboratory solutions—both now and in the future. With the advent of next-generation sequencing (NGS), the field of metagenomics has exploded in recent years, as scientists are now able to study microbes as communities instead of individual organisms. This has revolutionized our understanding of the relationships between microbiota, human health, and the environment.
The current pandemic is making healthcare industry leaders think more deeply about the agility and scalability of laboratory solutions—now and for the future.
An unprecedented challenge
The current COVID-19 pandemic represents one of the greatest global challenges of our time: a novel and highly contagious airborne virus with initially no diagnostic test and currently no vaccines. The pandemic strikes at a time when the world has never been more interconnected, meaning geographic barriers that previously may have provided a natural means to curb the spread are non-existent. The scale of the pandemic has put immense strain on laboratories conducting serological and PCR testing, as well as on those labs screening drug candidates for treatments and working to develop an effective vaccine as quickly as possible. The response of these laboratories has been remarkable and heroic in most cases, with great demonstrations of ingenuity and tireless devotion. An inspiring example is the UK Biocentre, who developed an automated sample handling and testing process from scratch in a matter of months. Manufacturers have also stepped up in addressing this unprecedented challenge, with molecular diagnostics companies like Cepheid, who have produced a test that can deliver results in under 45 minutes. While this is the first global pandemic of this scale, it is unlikely to be the last, and that forces us to reflect and consider what we can learn for the next time, and how can we be better prepared.
Rapid scale-up and custom solutions are essential
To meet such extreme challenges, both now and in the future, the ability to adapt quickly to novel threats and scale up operations accordingly is essential. With COVID-19, we have seen the potential cost of delay as well as the speed at which global situations can change. Clinical infrastructures and testing labs need sufficient agility to develop novel analysis methodologies and/or modify existing protocols. Scale-up capacity is critical to enable rapid test validation and processing of growing numbers of samples. At the same time, equipment manufacturers need to be ready to quickly interpret the current research needs and medical knowledge in order to deliver tailored and cost-efficient solutions as soon as possible.
The UK Government has recently identified five pillars critical for scaling up its testing programs, based on the available scientific research. Harvard University also published a document on ‘Pandemic Resilience’ which reported the need for fast scale-up of multiple levels of testing in order to control the pandemic. Rapid scale-up is no small feat, but modularity in design of laboratory solutions and test equipment may be key to achieving some of the goals outlined in these documents. By working with components, it means that no new solution has to be designed completely from scratch, which can dramatically improve time-to-market. A good example during COVID-19 was the rapid deployment of next generation sequencing (NGS) and PCR-based techniques to analyze patient samples. Modular workflows for efficient nucleic acid extraction and purification are allowing researchers to analyze thousands of isolates using a variety of downstream methods. As discussed by Dr. Christopher Mason, Associate Professor at Weill Cornell Medical College, a modular automation approach makes it easier for multiple types of experiments and functionalities to be carried out and integrated on the same platform. This allowed the Mason lab to add techniques such as RT-qPCR, isothermal assays and immunological profiling to their DNA purification to better understand heterogeneity in the viral populations.
Agility is key to scaling up…and scaling back down again
When scaling up or implementing a new analytical test or production process, it makes sense to establish and test new equipment and workflows when the pressure is off. That means installing and optimizing the set-up of laboratory solutions before the demand for its use is at a peak. This poses somewhat of a conundrum: if the lab is at low capacity now, how quickly will it be able to adapt and validate its operating procedures to enable effective, cost-efficient use of high-capacity automation equipment? Likewise, when demand later tapers off, will the lab be able to return to cost-efficient, low-capacity production using the same equipment, or will that new high-throughput system become a “white elephant” with a high depreciation cost?
An optimal solution is a lab automation setup and integrated accessories that function well at low capacity but can be seamlessly scaled up when capacity increases. Modular solutions—especially those that are purpose-built to be compatible with commonly used off-the-shelf kits—are especially well-suited for pandemic responses, when solutions need to be rolled out fast. For example, as the COVID-19 pandemic expands, laboratories have had to scale up testing using high-throughput approaches to isolate the viral RNA for downstream analysis. These workflows typically involve time-consuming steps such as scripting, protocol reconfiguration, and workflow optimization to ensure robust results. To avoid bottlenecks at this sample preparation stage, the entire process needs to be integrated into the overall workflow and scaled up quickly. Moreover, the automation solution needs to be compatible with preferred commercial kits, as well as being easily adaptable to accommodate new kits and protocols that may be introduced at a later time. Recently, Zymo Research and Tecan announced their partnership to launch a ready-to-go processing solution to streamline viral DNA/RNA extraction from nasopharyngeal swabs, oropharyngeal swabs, saliva, sputum, plasma, and serum. "Nucleic acid extractions can be one of the most challenging, frustrating, and time-consuming portions of a workflow to automate," said Ryan Kemp, Director of Nucleic Acid Solutions at Zymo Research. "With push-to-start sample purification, the DreamPrep™ NAP workstation is uniquely positioned to help labs around the world quickly and effectively scale their testing to accommodate a much larger number of tests and ultimately mitigate the spread of the virus."
The power of partnering
For organizations that are considering developing or scaling up production of a test kit, automated solution or other equipment for a rapid pandemic response, it is essential to have a thorough understanding of the full process workflow as well as an appreciation of the viewpoints of all relevant stakeholders involved in its use, purchase, validation and maintenance. Getting this information quickly can be challenging in times of crisis when resources and staff may be limited. One way to accelerate the process is to engage with an experienced partner who understands the industry, including the customer base and the regulatory landscape. There are many providers for various manufacturing and workflow optimization needs so it makes sense to research them and find out what they can really provide.
When considering potential partners, their manufacturing capabilities are an important piece of the puzzle, but not the only piece. Beyond conducting a thorough audit including a site evaluation, it is essential to find indicators that a manufacturing partner can be trusted to deliver. Service contracts, life cycle management and a vertically integrated business are all important factors to consider. A compatible culture and good communication mechanisms are also key to ensuring that a partner can correctly interpret the project requirements, even in the heat of a crisis. Of course, any manufacturing partner should also be able to provide tangible proof that they really can deliver. Ideally this should include years of industry experience, a demonstrated track record, and workable prototypes that can be validated and tested.
Since trust takes time to develop, it is best to start conversations with potential partners as early as possible—ideally before any crisis occurs—when there is still time to build strong relationships. This advanced groundwork gives a project with a manufacturing partner the best chance possible to hit the ground running when the time comes.
Traversing the changing regulatory landscape
In times of global crisis, regulatory guidelines and approval processes can often change quickly and unexpectedly; during the current pandemic, for example, the FDA posted multiple updates on their website on any given day. Many of these posts included regulatory implications for testing and manufacturing. It is therefore essential that partners are not just familiar with current regulations but are flexible and experienced enough to interpret new guidelines and legislation, and incorporate them seamlessly into an ongoing project, on the fly. This offers a huge advantage if you need to respond quickly to get laboratory solutions to market.
Remote monitoring and digital communication are no longer optional
The COVID-19 pandemic has increased the remote workforce. Working from home has been mandated in many countries to help reduce commuter travel and maintain physical distance. The workforce, at large, has done surprisingly well at adapting to this new remote work structure. However, laboratory personnel often don’t have the option to work from a distance due to a lack of automation and remote operation capability. Remote operation and monitoring features have quickly shifted from being a productivity gimmick to an essential feature to keep laboratory workers safe during a global pandemic. When incorporating remote working features into an automation project, look for providers who have a track record of these advanced features and can demonstrate their reliability.
Expecting the unexpected
The COVID-19 pandemic has highlighted the value of quality lab automation while illuminating some potential pitfalls. To cope with a rapidly spreading pathogen or other emerging global health threat, adaptable solutions need to be developed and rolled out more quickly than ever before. Key to being better prepared for the next crisis may be the availability of more modular end-to-end solutions, such as those developed for nucleic acid purification and NGS sample prep, with the capacity to scale up and down quickly to meet changing demands in the lab. With novel biological threats, the transition from research to in vitro diagnostics also has to be fast and seamless. This gives companies that can provide both a significant edge. In his recent online conference presentation, Dr. Christopher Mason explained the importance of scale-up and automation for his lab’s response to the COVID-19 pandemic. To find out more, watch the video.
The Verge. “Newly approved novel coronavirus test gives results in 45 minutes”. March 2020. https://www.theverge.com/2020/3/23/21191055/rapid-coronavirus-test-hospital-fda
Department of Health and Social Care. “COVID-19 - Scaling up our testing programmes”. April 2020. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/878121/coronavirus-covid-19-testing-strategy.pdf
Edmond J. Safra Center for Ethics - Harvard University. “Roadmap to Pandemic Resilience”. April 2020. https://ethics.harvard.edu/files/center-for-ethics/files/roadmaptopandemicresilience_updated_4.20.20.pdf
US. Food and Drug Administration. “Coronavirus Disease 2019 (COVID-19)”, May 2020. https://www.fda.gov/emergency-preparedness-and-response/counterterrorism-and-emerging-threats/coronavirus-disease-2019-covid-19