In the third in a series of opinion editorials Dr Amanda Dixon-McIver details another critical performance requirement in a COVID-19 testing laboratory – Scalability.
Scalability for COVID-19 testing is a critical performance requirement because positive cases grow exponentially. It is not a case of working harder or even smarter, in the end all finite systems get overwhelmed. We should not be surprised - it is entirely predictable.
This happened last week in Auckland in the “public health laboratory network” – a group of state funded laboratories - when sustained demand for testing led to a blow out in turnaround times.
Laboratory operations are complex systems and are intrinsically difficult to manage. Complex systems research is an interdisciplinary endeavour that draws contributions from many fields. Each of these disciplines have made unique and vital contributions to system scalability. The University of Illinois covidShield test had contributors from over 150 experts from fields as diverse as sociology, psychology, social media, medicine, molecular biology, computer science, chemistry, physics, and mathematics. The Rako Science saliva test system leverages this vast knowledge base, and it has extended and localised that knowledge with its own New Zealand-based multi-disciplinary team of experts. The system has been built from registration to result to be scalable, sensitive and efficient. The total system was designed to assist with the suppression or elimination of COVID-19 and to break the chains of transmission in Aotearoa New Zealand.
So how has the Rako Science Saliva test system performed during the delta outbreak?
Below is a Histogram of Total Turnaround Times (TTAT) for the Rako Science Saliva Test dating from 1 September 2021 to 27 November 2021. These are the three months since the Delta outbreak began on 17 August. During this period demand for testing has surged and the average TTAT reduced from 22 hours in July 2021 to approximately 10 hours in November. The improvement in TTAT performance was achieved by tailoring the laboratory processing hours to coincide with the arrival of samples. We don’t currently work a night shift and our medical laboratory scientist workforce a maintains good work-life balance.
Figure 1 – Histogram of the Total Turnaround Time for Rako Science saliva test shown in bins of hours. The sample set was taken from 100,000 tests chosen at random from the period 1 June 2021 through 27 November 2021. The character of the distribution of total turnaround time by month has not changed despite a surge in demand for private testing beginning with the New Zealand delta outbreak starting on 17 August 2021. The average TTAT for this period is about 10 hours with a standard deviation of about 5 hours. More than 98% of the tests were completed within 24 hours.
The “public health laboratory network” has target metrics defined in the “Rapid Audit of Contact Tracing for Covid-19 in New Zealand” report written by Dr Ayesha Verrall, now Associate Minister of Health and Research, Science and Innovation. Her report was published in April 2020 before the emergence of the Delta variant of concern. That report defined a metric of “Time from Sampling to suspected case to test result” (TTAT) with an urgent priority of reporting 80% of the cases within 24 hours. The Rako Science Saliva test system met this metric in 98% of the cases. The “public health laboratory network” does not currently publish data against this metric however recent media reports have stated:
People waiting five days to find out if they have Covid has sparked concern Auckland's testing system is starting to break down. Covid 19 Delta outbreak: Auckland test results taking up to five days - NZ Herald
Rako Science Saliva test system is currently designed for a capacity of 10,000 tests per day.
Since 17 August 2021 all laboratories have seen a surge in demand for testing. Below is a graph showing the increase in testing volumes for the last six months relative to the total system design capacity. The system is currently running at 13% of design capacity which is 20 times the June 2021 volumes.
Figure 2 – Area graph of the System Capacity of the Rako Science test by month. The total design capacity of the Rako Science Saliva Test system is based on 10,000 tests per day. Over the period 1 June 2021 to 27 November 2021 the laboratory throughput has increased 20-fold.
To examine scalability in more depth we have characterised the distribution of turnaround times with a box and whisker plot in a time series in a period where the system has come under increasing load which is displayed below.
Figure 3 - Box and whisker plot of the Total Turnaround Time for the Rako Science saliva test shown by month. The sample set was taken from 100,000 tests chosen at random from the period 1 June 2021 through 27 November 2021. The average total turnaround time has decreased from 22.4 hours in June 2021 to 10.2 hours in November 2021. This is despite a surge in demand for private testing beginning with the New Zealand Delta outbreak starting on 17 August 2021. The minimum total turnaround time has decreased slightly from 2.7 hours in June 2021 to 2.3 hours in November 2021. The maximum turnaround time has decreased from 54.8 hours in June 2021 to 17.7 hours in November 2021. The inter quartile range (the light blue box) has reduced from 18.8 hours in June 2021 to 4.1 hours in November 2021.
The increased test throughput is negatively correlated to total turnaround time. In other words, throughput has increased at the same time as TTAT has decreased. Test volumes have increased 20-fold since June 2021 while TTAT has halved. The inter quartile range has also decreased from 18.8 hours to 4.1 hours. The range between the highest and lowest value has also reduced from 52.1 hours to 15.4 hours. The urgent test TTAT minimum has remained constant at 2.5 hours.
Scalability is a critical performance requirement in COVID-19 testing because it allows the laboratory to increase throughput while maintaining total turnaround time. It allows you to focus on what matters, the patient and stopping the chains of transmission. It allows you to shape public health testing policy based on the science of the virus and not on the limitations of testing.
We expect that throughput will continue to grow while TTAT values converge on an average of about 10 hours if volumes remain in the designed capacity of 10,000 test per day. If necessary, the Rako Science system can scale to 80,000 tests per day with a new pooling protocol which has been submitted for FDA EUA approval. More about that later…
Dr Amanda Dixon-McIver
Amanda Dixon-McIver is the Laboratory Director of IGENZ, the IANZ-accredited medical diagnostic laboratory contracted by Rako Science to perform the COVID-19 saliva testing at scale. She has 30 years of laboratory experience both here in Aotearoa New Zealand and overseas and has been involved in the NZ laboratory response to COVID since the start of the pandemic in 2020.