Andrew Worlock, senior director development, diagnostic assay development for Hologic looks at lessons learnt from COVID-19 and how they will help public health leaders, government and the diagnostics sector prepare for future virus threats of pandemic proportions.
In 2019, the world faced the uncertainty of a new viral disease with COVID-19 outbreak. The complexity and spread of SARS CoV-2 meant that those working in the diagnostics industry had to overcome scientific and operational challenges at speeds never seen before. We achieved unprecedented levels of collaboration across health providers, labs, government, and agencies, such as the FDA, producing SARS-CoV-2 diagnostic assays in one to three months, rather than the usual development time of more than a year.
Over a year on it is an important time to reflect on what we’ve learnt and how this will help public health leaders, government and the diagnostics sector prepare for future virus threats of pandemic proportions.
Early decisions are vital
When faced with the unknown of a new virus, the early decisions you make are critical. For example, very early on we had to decide which region of the SARS CoV-2 virus genome to focus on. We chose the ORF-1 ab region rather than the spike protein as we knew it was under less evolutionary pressure and less likely to mutate. We also targeted dual regions of the virus, this means the assay has redundancy built in and can better deal with future mutations.
It has two chances to detect the presence of the virus and means if mutations affect one region, the other region still identifies the virus, providing further assurance and specificity.
Making these important, bold decisions early and facilitating discussions across the various teams within the organisation to gather the right intelligence and expertise are vital when responding to a crisis.
Monitoring a crisis
Data plays a key part in building understanding of a new virus and preparing for the future. The COVID-19 pandemic has precipitated unprecedented sharing of information and access to more genomic sequencing data. This helped us monitor in almost real-time the effect of mutations on the performance of our tests and confirm they were not affected.
Our bioinformatics team developed new computing tools to monitor public data and wrote programmes to analyse an overwhelming amount of information. Timelines were reinvented - analysing a set of 200,000 or more sequences used to take a week but the new process allows us to do this in a day or two.
Also, shortly after the release of the Aptima SARS CoV-2 assay we worked closely with customers who were generating thousands of test results using our assay, to analyse the data and ensure the assay was delivering the highest quality.
One of the key lessons learnt from the pandemic is not to ignore warning signs about emerging virus threats and to regularly monitor and share data. This continued monitoring should allow all parties to respond quickly and get ahead of any future threats and we have found that programming to expedite big data analysis has a key role to play in doing this.
Scaling up capacity
The fast transmission of the SARS CoV-2 virus meant testing millions of people was key and rapidly scaling up capacity to meet demand was essential. Hologic set up a cross-function team to deal with the logistics of the unprecedented level of scale up to provide the millions of tests needed worldwide. We increased production of some components of our diagnostic tests by three-fold in a matter of a few months
What we have learnt from the pandemic is developing a high-quality test is only half the battle. The bigger challenge is getting sufficient tests and the instruments to run them in the hands of the right people so they can make the right healthcare decisions. Then you need to sustain the effort and respond to supply challenges. To prepare for the future, some firms are creating extra manufacturing capacity, not necessarily using it immediately but having it available to scale up more quickly.
While the diagnostics industry and vaccine community can continue to scale faster, government and industry also need to better prepare for shortages. The whole sector was faced with unexpected shortages of key components to make COVID tests such as plastic and glass vials as demand skyrocketed. We saw great ingenuity during the pandemic, for example, we confirmed that customers could use many different tubes and workflows on our diagnostics systems helping to mitigate collection tube shortages by providing more options.
Creating stockpiles of tubes and plastics may work in future but they do have expiry dates, so preparedness also comes with a cost attached. Flexibility and the ability to adapt are also key components. What is needed is robust scenario planning from multidisciplinary teams so that challenges can be anticipated and modelled for future pandemics. Considering what the pain points are and how we can reasonably solve them is a sensible first step.
Testing and treatment scale up are important but so is protecting your workforce. Having enough personal protective equipment on hand for the first responders and hospital staff to do their job and stay safe is an essential consideration.
Looking ahead to future needs
Building resilience into the system needs to be a core component of anticipating future threats. Multiplex assays are likely to become more prevalent so labs and hospitals can test for respiratory viruses with similar symptoms such as SARS CoV-2, flu, and respiratory syncytial virus (RSV) simultaneously and treat the patient accordingly.
While the world is more prepared to face a future threat there are still big questions that remain and the choices that come next are difficult. What is clear from the COVID-19 pandemic is that it could happen again, and more government level planning and investment is needed to prepare for such future events.
