In the second in a series of opinion editorials by Dr Amanda Dixon-McIver she details another critical performance requirement in a COVID-19 testing laboratory – "Throughput".
In a pandemic, throughput - the number of samples processed per unit time - is critically important. The importance of throughput escalates as the number of positive cases in the community increase. Failure to have adequate throughput means that positive cases continue to transmit infection. The consequence is a reduced ability to break chains of transmission.
The importance of test design in a pandemic
Legacy COVID-19 testing methods based on nasopharyngeal (NP) swab test protocols have multiple challenges in achieving high throughput. Firstly, the collection of NP samples requires trained medical professionals. Medical professionals are a finite resource at the best of times, least of all during a pandemic. As we saw when community transmission happened in Auckland, there was simply not enough qualified health professionals to service the testing and vaccination needs of the community. Resources were redeployed from testing to staff the vaccination centres. In some instances, this meant that testing stations were closed. However, there are alternatives available that could have meant that you had the best of both worlds – testing stations open AND increased numbers of qualified staff available for vaccination programmes – RT-PCR saliva testing is one of them.
Almost all NP test protocols involve removal of a designated volume of the fluid surrounding the NP swab, followed by an RNA extraction step. The process is labour intensive and is a bottleneck in the test workflow. The RNA extraction step has been problematic throughout the pandemic because of worldwide supply chain issues with reagents, NP swabs and logistics.
Better Test Designs
Early last year, US researchers in both Yale and the University of Illinois Urbana Champaign (UIUC) developed new test protocols with improved test designs compared to existing NP protocols. These researchers considered saliva as a completely distinct sample type that could be self-collected and scaleable. They did not simply apply the existing methodology and protocols used for NP testing to saliva. The new tests now outperform NP testing in several ways. The ability to self-collect and the removal of the RNA extraction step are two simple changes that increase the number of tests undertaken and increase throughput. The new test designs are efficient and automated, which reduce both turnaround time and labour costs.
In New Zealand, the lack of understanding of saliva and the differences between saliva testing and the NP swab has resulted in misinformation about the accuracy of saliva testing. This is part of the reason that our current public response is still based on NP methodology. Our national laboratory COVID-19 test throughput is limited and with increasing samples numbers turnaround times for test results become delayed. This will continue to occur with every surge event.
Terry Taylor, the President of the New Zealand Institute of Medical Laboratory Science, has said:
“Before the most-recent Delta outbreak, only 2 to 3 per cent of laboratory work was testing for Covid-19. Now it was 20 to 30 per cent. In Auckland it could be as high as 40 per cent.” Not only is the diagnostic laboratory workforce required to process these samples, but they are also required to continue with the non-COVID testing that still continues to be performed.
This is echoed by a Medical Laboratory scientist in Auckland who recently posted on social media,
“We are being slammed!”.
How to increase test throughput?
One common strategy to increase test throughput is the pooling of samples.
Pooling samples requires adaptation of the existing protocol where samples are processed individually. It involves taking a specified amount from each of a number of different samples and mixing these samples together to form a “pool”. The pooled sample is then processed as one. Pooling allows you to process large numbers of samples within a shorter timeframe. However, there are drawbacks, including complicated workflow, lower sensitivity, and the need to repeat tests from positive pools. The reduction in sensitivity is an acceptable trade-off, along with the benefit of reagent conservation and cost reduction.
The use of pooling becomes less justified when you have significant community transmission. Ideally you want the most sensitive test possible to identify all positive individuals to break the chains of transmission as soon as possible. In this instance the need for timely results becomes crucial.
In New Zealand, sample pooling is routinely used for NP testing, but it is not currently used for saliva.
Laboratories using pooling are required to validate their protocols so that the loss of sensitivity of the pooled test is quantified. While validation data for laboratories who are pooling in New Zealand is not made public, it is known that NP laboratories testing for COVID-19 have typical pooling ratios of 4 or 5:1. At these ratios the reduction in CT values is between 1-4 cycles (dependent on the method being used). This is not an issue provided that the laboratory is aware of the exact loss of sensitivity and that pooling is being used in the appropriate clinical setting.
Pooled tests are best used where the highest sensitivity testing is not required, such as where the likelihood of detecting a positive result is low where there is no or minimal community transmission. However, if the purpose is asymptomatic surveillance in the context of wide-spread community transmission, you want the most sensitive test possible for early detection.
Saliva-based tests are already high throughput by design given the reduction in manual handling and the removal of the RNA extraction process. The Rako Science saliva process, due to significant automation, can test up to 10,000 individual saliva samples per day. Rako Science’s saliva test throughput can be increased still further with pooling.
Recently Yale have received FDA approval for sample pooling with their saliva protocols at a 5:1 ratio. Here is their key data.
Surveillance test with proven high sensitivity suitable for asymptomatic individuals in high prevalence populations.
Yale SalivaDirect (pooled)
Diagnostic test protocol which is suitable for high throughput.
Table 1: Test pooling data and performance for RT-PCR salivaDirect.
Currently there is no need for Rako Science to lower sensitivity of its test and deploy pooling. But if circumstances required and with appropriate validation, Rako Science could increase the throughput of their testing with existing robotics to 80,000 tests per day. This would double the current national laboratory throughput overnight.
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.