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Rako Science has detected Omicron and Stealth Omicron positive cases

Omicron is now in New Zealand, and we are all expecting a rapid increase in cases. As Laboratory Director for IGENZ, the laboratory contracted by Rako Science, I know that we are well prepared to meet the challenge of sustaining throughput and identifying Omicron and its sub-variants.

Other laboratories have issued stark warnings[1] about throughput reduction due to the inability to pool when the number of positive cases increase, just when increased capacity is required. Rako Science does not pool samples. Our throughput, turnaround times, and scalability performance are unaffected by the prevalence of positive samples.

Rako Science has already had initial Omicron cases come through our laboratory. Not only can we safely detect the Omicron variant, but we can rapidly differentiate and identify the specific lineages.

At the end of November, WHO designated the variant B1.1.529 a variant of concern named Omicron. Although social media would lead you to believe that Omicron is nothing more than a mild cold, the medical and scientific community are a little more reserved. Researchers in South Africa where it was first reported, along with researchers around the world are currently conducting studies to determine whether it is more transmissible compared to other variants such as Delta and to whether it causes more severe disease compared to infection with other variants. Initial reports of Omicron infections were among university students – younger individuals with more mild disease – leading to claims that it is less severe which need to be substantiated across all age groups. The early data is indicating fewer hospitalisations and deaths with Omicron which is excellent news. But for many not going to hospital does not mean the course of symptomatic disease isn’t seriously debilitating. For some it may be a mild cold but for others it can be like a bad case of influenza and can take you out of the workforce for at least a week.

Rako Science uses the ThermoFisher TaqPath™ COVID-19 Combo Kit for our saliva RT-PCR assay. This assay targets the nucleocapsid (N) protein, ORF1ab and the spike (S) protein. We require amplification of at least two of these to confirm a positive case. With the Delta strain of SARS-CoV-2 we see expression of all three genes, however with Omicron B1.1.529 we do not. Instead, we see only expression of the N gene and ORF1ab. The S gene shows what is termed “S gene target failure” (SGTF). It was SGTF that alerted scientists of the new variant. This is not surprising given that we now know that Omicron has ~30 mutations within the spike (S) protein. This feature allowed laboratories in Europe to differentiate between the Delta or the Omicron strain without having to employ other techniques such as genomic sequencing.

In the laboratory we can confirm whether a positive case is either the Delta or Omicron variant. This negates the need for genomic sequencing at the time of diagnosis to determine the variant. It also provides Public Health with critical information at the time of notification of a positive result which is important when prioritising contact tracing. Genomic sequencing can be subsequently used for epidemiological reasons but waiting for that to be completed results in delays which are outside the testing targets defined in the Verrall[2] report.

Just when laboratories using the ThermoFisher TaqPath™ COVID-19 Combo Kit were able to flag probable cases of Omicron another lineage of Omicron appeared that did not show SGTF. The so-called Omicron “stealth” variant or BA.2 was detected at the beginning of December and is currently designated a subvariant of Omicron and a “variant under investigation.” This Omicron variant has been reported in Denmark, India, the Philippines, Britain, Sweden and Singapore and it has also been detected in New Zealand.

The ThermoFisher TaqPath™ COVID-19 Combo Kit cannot distinguish between an individual with Delta or Omicron BA.2 as it can for B1.1.529, but we have other tools in the toolbox that can be employed. To differentiate between Delta and Omicron BA.2 we can run the ThermoFisher TaqMan™ SARS-CoV-2 mutation panel. This assay can be completed within two hours of detecting a positive result and, with the right primers, will demonstrate whether it is Delta or Omicron BA.2.

The ability to determine the variant within hours of a positive result could have improved the speed of contact tracing being experienced by the Prime Minister. Notification of a close contact of a suspected Omicron case seven days later is quite simply not fast enough. Knowing the variant and lineage of a positive case as fast as possible is important to break the chains of transmission in our essential workers and there is no more essential role in this country than that of Prime Minister.

[1] Warning labs can only cope with peak PCR test demand for up to a fortnight | RNZ News [2] Rapid Audit of Contact Tracing for COVID-19 in New Zealand | Ministry of Health NZ

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.

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