4.2 The rise of the variants: Delta and Omicron Te putanga ake o ngā rerekētanga: Delta me Omicron
4.2 The rise of the variants: Delta and Omicron | Te putanga ake o ngā rerekētanga: Delta me Omicron
Like other coronaviruses, the virus that caused the COVID-19 pandemic (SARS-CoV-2) evolved rapidly, with significant changes occurring over timescales of months to years. Evolution in viruses is driven by the rate at which mutations are generated and spread through host populations. Their ability to spread will depend on differences in infectiousness, and in the timing, nature and intensity of symptoms (such as coughing) that help spread the virus to others.
Most mutations do not provide any evolutionary advantages and soon disappear. Those that have the potential to pose an increased risk to public health are characterised as 'variants of concern' by the World Health Organization.⁹
We can identify which variants are prevalent in the population though the use of gene sequencing. In New Zealand, this is done by the New Zealand Institute for Public Health and Forensic Science (formerly Institute of Environmental Science and Research (ESR)). Figure 11 shows the prevalence of SARS-CoV-2 variants from August 2021 through to February 2024.
At any point in time there is usually one variant that dominates the test samples. The green area from August 2021 is the Delta variant (also denoted 'B.1.617.2'). At the beginning of 2022, a new set of variants, collectively called 'Omicron', emerged. First the BA.1 and then the BA.2 variant became the most prevalent in the population.
Figure 11: Prevalence of SARS-CoV-2 variants in New Zealand
7-day rolling average for the number of genomes sequenced from a given variant, August 2021 to February 2024
Source: New Zealand Institute for Public Health and Forensic Science (formerly Institute of Environmental Science and Research (ESR)), 'Prevalence of SARS-CoV-2 Variants of Concern in Aotearoa New Zealand', https://github.com/ESR-NZ/nz-sars-cov2-variants
In Figure 12, we can see that the Delta variant started becoming the major variant in Australia, the United Kingdom and China, earlier than it did in the United States, Sweden, Italy, and Japan. In each country, Delta surged to become the dominant strain. The Delta share began to fall in these countries between December 2021 and February 2022 (with a short-lived resurgence in China in February), as early Omicron variants emerged.
Figure 12: Share of Delta variant in SARS-CoV-2 sequences
Percentage of Delta variant in all analysed SARS-CoV-2 sequences in the preceding two weeks, April 2021 to June 2022
Source: Our World in Data, using data from GISAID, via CoVariants.org
Notes:
1. Shares may not reflect the complete breakdown of cases, since only a fraction of all cases are sequenced. Recently discovered or actively monitored variants may be over-represented, as suspected cases of these variants are likely to be sequenced preferentially or faster than other cases.
2. The uneven spacing of months along the X axis reflect that the data frequency is two-weekly, so some months have two datapoints whereas others have three.
Omicron quickly took over as the prevalent variant in all the countries in our comparison group (Figure 13). It reached a 50% share of the strains in circulation in New Zealand in mid-January 2022.
Figure 13: Share of Omicron variant in SARS-CoV-2 sequences
Percentage of Omicron variant in all analysed SARS-CoV-2 sequences in the preceding two weeks, November 2021 to April 2022
Source: Our World in Data, using data from GISAID, via CoVariants.org
Notes:
1. This share may not reflect the complete breakdown of cases, since only a fraction of all cases are sequenced. Recently discovered or actively monitored variants may be over-represented, as suspected cases of these variants are likely to be sequenced preferentially or faster than other cases.
2. The uneven spacing of months along the X axis reflect that the data frequency is two-weekly, so some months have two datapoints whereas others have three.
In 2022, the highly infectious Omicron variant arrived in New Zealand and spread quickly. Cumulative confirmed cases of COVID-19 jumped from two to 100 per million in the two weeks between 17ᵗʰ and 31ˢᵗ of March 2022 (Figure 14). Island countries in Figure 14 avoided major outbreaks until the start of 2022.
Figure 14: Cumulative COVID-19 cases, 2020–2022
Confirmed cases per million people
Source: Our World in Data, World Health Organization, https://ourworldindata.org/explorers/covid?time=2020-03-01..2023-01-01&[link truncated, click for complete URL]
Notes: Due to limited testing, the number of confirmed cases is lower than the true number of infections.
When looking at these numbers, it is important to be aware that the number of confirmed cases will be lower than the actual number, as not all people are tested, and not all test results are reported. This is particularly the case when testing moved out of the medical environment, as was the case when Rapid Antigen Tests (RATs) became widely available.
An alternative way to estimate the pr wastewater as it flows into a treatment plant provides a way to test for the presence of traces of the virus in the population served by the plant, without the need for testing individual people. We compare the results of wastewater testing in the New Zealand population with the confirmed cases reported for individuals in Figure 15.
Figure 15: Comparison of wastewater sampling for COVID-19 with reported cases in New Zealand
June 2021 to June 2024
Source: New Zealand Institute for Public Health and Forensic Science Ltd (PHF Science), 'Aotearoa New Zealand Wastewater COVID-19 Surveillance Programme', https://github.com/ESR-NZ/covid_in_wastewater
Notes: The wastewater data shows the average of the SARS-CoV-2 genome copies per person per day. It is calculated as an average of results from the previous 7 days. SARS-CoV-2 genome copies results are normalised by (a) catchment for population covered by testing and (b) wastewater flow into the wastewater treatment plant per day.
The two lines in Figure 15 show very similar patterns until mid-2023. As rates of test reporting declined, wastewater sampling continued – showing a higher prevalence of COVID-19 in the population than reported cases from mid-2023.
9 World Health Organization, 'Tracking SARS-CoV-2 variants', last updated 5 December 2025, https://www.who.int/activities/tracking-SARS-CoV-2-variants