Current state of Omicron - global, local, positivity and turnaround

Updated: Feb 23

Rako Science data provides unique insights into the current state of the Omicron surge. First, we have the COVID-19 Modeller ( with the SIR+B method developed in conjunction with University of Illinois at Urbana Champaign. And second, Rako Science is monitoring the positivity rate across its collection network which provides real-time insights.

In this review, we look at New Zealand in the global context; the current New Zealand effective reproduction number; the positivity rate in the Rako network throughout February; and the Rako total test turnaround performance as volumes have substantially increased this month.

Global context

The COVID-19 modeller shows that only a handful of countries are now experiencing an Omicron surge. Countries coloured in light tan have effective reproduction numbers below 1.0 and those with an R0 value exceeding 2.2 are coloured in red. Countries like the UK have R0 < 1.0 but still have high daily case numbers at around 34,000 cases. Denmark which withdrew all COVID-19 mandates and restrictions has R0 = 1.0 and reports that Omicron BA.2 is now dominant and may have a higher virulence than BA.1. The Rako Science data team will be monitoring developments in this country with interest. Both Omicron variants are present in New Zealand and have been identified by Rako Science.

Figure 1 World map showing heatmap of R0 by country as of 22 February 2022. New Zealand (R0=2.8 CI 95% 2.2-3.2) is among a few countries with an R0 value exceeding 2.2 coloured in red. Other countries currently include China (R0 = 2.5), Myanmar (R0=3.1), Malaysia (R0=3.3), Indonesia (R0=3.3) and Oman (R0=2.3).

New Zealand current state

The COVID-19 modeller shows on 22 February 2022, using daily case data from 20 February that R0 = 2.8 and is plateauing at this high rate for over a week. The modeller identifies that 7 January was the moment that R0 exceeded 1.0 which is the beginning date for the surge. Figure 2 provides a graphical illustration of the significant differences between the first wildtype outbreak in March 2020 which was quickly eliminated; the Delta outbreak in August

2021 which was contained through lockdowns; and the current Omicron surge.

Figure 2 The calculation of the Effective Reproduction Number for New Zealand showing 3 distinct phases of COVID-19 outbreaks. These are the wildtype outbreak in March 2020 followed by elimination, until the delta outbreak starting in August 2021 and lockdown suppression in November 2021, and finally the Omicron outbreak starting in January 2022.

Rako Science network positivity rate

Rako Science is collecting samples from a range of sub populations across New Zealand. These include large and small workforces across the country, skewed towards South Auckland and Waikato businesses; iwi and community testing in Whanganui, Taranaki and West Auckland; most private hospital patients across New Zealand prior to admission; and people about to travel overseas or fly domestically. Rako is testing a largely asymptomatic population, whereas public health testing is currently targeting only symptomatic patients and close contacts. The Rako-tested population cannot be considered to be representative data, but the in absence of better information from public health it serves as a real-world data point for Aotearoa New Zealand. It does include sufficient populations of Pakeha, Māori and Pasifika to draw some approximate conclusions.

Figure 3 shows a steep increase in the positivity rate from 13 February onwards. Projected across the total New Zealand population it suggests that the positivity rate across New Zealand is approximately 3%, with a higher rate in South Auckland than the rest of the country at this time.

Figure 3 - Absence and Positivity Rate for all Rako Science testing in February 2022 focusing on the Omicron outbreak. The positivity Rate is shown in red columns with scale on the left-hand side. Absence rate is shown as the blue line with the scale on the right-hand side. The peak rate of 3.42% occurred on 22 February from samples collected on 22 February. This contrasts with the positivity rate of 12% reported in the public health network possibly due testing only symptomatic and close contact individuals.

Rako Science total turnaround time (from sample to result)

Rako Science’s total daily test volumes have grown significantly throughout February. Our 10,000 test capacity is based on simplex testing. We do not pool samples.

Higher positivity rates undermine pooled testing capacity. Remembering that if a pool tests positive you must repeat the testing on each individual sample to determine the origin of the positive result. If a lab is pooling at a rate of 5:1 a positivity rate of >X% means you must revert to simplex testing This results in an 80% collapse in testing capacity. This was seen in Australian laboratories in November last year. This is happening here in New Zealand now. This explains the media reports of 5 day waits for test results in Auckland and up to 7 day waits in Waikato. Recent news reports are linked here, here, and here.

Contrast this with Rako Science’s performance illustrated below in Figure 4. The box whisker chart shows average total test turnaround time consistently less than 10 hours on every day apart from one weekend when we had reduced hours in collection sites and the laboratory.

The Rako Science collection and laboratory processing systems were built to withstand pandemic scale events and will continue to perform strongly throughout the Omicron surge.

Figure 4 – Box-whisker plot of the Total Turnaround Time (TTAT) for the Rako Science Saliva Test by day in the month of February 2022. The average TTAT is consistently under 10 hours, only exceeding 10 hours on holiday weekends. On the Saturday 12th February the average TTAT was 15 hours due to weekend processing. The average TTAT for urgent samples is 4 hours (see 22 February). The most important feature of this graph is that the TTAT is unaffected by the increase in the positivity rate in the period starting 14 February 2022. The Rako Science test was designed to be scalable throughout the pandemic.

​Stephen Grice is a founder and director of Rako Science. Stephen has a PhD in Physical Chemistry and 30 years of experience working in the high tech, business and science sectors.

Stephen's work with University of Illinois Urbana Champaign on new mathematical methods for the epidemiology led to licensing and development of covidSHIELD in New Zealand and the implementation of the saliva test protocol by accredited New Zealand laboratory IGENZ.

Rako Science is a pathology company offering saliva based rt-qPCR tests. Rako Science uses the University of Illinois covidSHIELD saliva test that was diagnostically validated and accredited by IANZ and contracted to IGENZ Ltd. Rako Science’s test is the first saliva test accredited in New Zealand and remains the only diagnostically validated test in New Zealand.

Rako Science is also the first test that supports IATA Travel Pass.

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