5.3 What happened: activating public health and infection control measures in response to COVID-19 I aha: te kōkiri i ngā whakaritenga hauora tūmatanui me te whakahaere pokenga ki te KOWHEORI-19

5.3.1 The early health system response

The Ministry of Health took the first steps in the Government’s pandemic response as soon as the World Health Organization sent member states a disease outbreak alert about the situation in Wuhan, China on 5 January 2020. The following day, the Ministry issued its first National Health Advisory to district health boards and general practitioners, setting out advice on how to reduce the general risk of acute respiratory infections. Monitoring teams began following developments. The first media briefing about what was now an emerging global pandemic took place on 27 January 2020, fronted by the Director-General of Health Dr Ashley Bloomfield and the Director of Public Health Dr Caroline McElnay.

As emergency management preparations ramped up across government throughout February 2020 (see Chapter 2), the Ministry established several expert groups to gather information and advise ministers and the health sector about the SARS-CoV-2 virus.

Chief among these was the COVID-19 Technical Advisory Group, comprising 14 epidemiologists, virologists and laboratory science experts. In addition, four sub-groups were established to help the system prepare for the COVID-19 threat.

Health officials engaged closely with international scientific networks and information sources, especially with state and federal agencies in Australia. The relationship with Australia was particularly valuable when COVID-19 testing began: until New Zealand established its own COVID-19 testing capability in early February 2020, the first samples taken here were sent to a Melbourne laboratory for processing.

The Ministry’s emergency operations centre, the National Health Coordination Centre, was pivotal in the early part of the health system response. It was activated on 28 January 2020 (as intended in the pandemic plan) and used the Coordinated Incident Management System approach, which Aotearoa New Zealand followed in all kinds of emergencies (see Chapter 2 for more about the wider emergency management response).

Health officials engaged closely with international scientific networks and information, especially with Australia.

With the National Health Coordination Centre in place to coordinate system-wide preparedness and response, the Ministry of Health next established an Incident Management Team^vii to deal with COVID-19 incidents and outbreaks. If a community case was identified, this team would be activated and became the point of contact for public health units, district health boards, ministers, the Ministry’s own leadership team, and other stakeholders.¹⁰

In light of the escalating public health risk, the Ministry advised Cabinet to make the novel coronavirus a notifiable infectious disease – a legal mechanism that would help with the detection of cases by making it compulsory to report them. This came into effect on 30 January 2020.

By the end of January 2020, there were an estimated 98 cases globally, outside of China. At this stage, officials considered it was very likely one or more imported cases were already in Aotearoa New Zealand, given there were regular direct flights between here and China. Twenty percent of the confirmed cases in China had become severely ill, and the mortality rate there was around 2–3 percent. The Ministry of Health was part of an all-of-government effort to repatriate New Zealanders in China; officials were deployed to Wuhan to help with a repatriation flight on 5 February 2020, and managed the quarantine of passengers once they reached Auckland.

As described in Chapter 2, the New Zealand Influenza Pandemic Plan 2017 was at this point the blueprint for the Ministry’s response. Given the potential severity of the threat COVID-19 presented, the focus was now on the ‘Keep It Out’ and ‘Stamp It Out’ stages set out in the Plan.

Ministry of Health officials considered at the time (and since) that a precautionary approach was warranted to buy the country some time. In providing evidence to the Inquiry, the Ministry noted that:

“More time allowed us to gain a deeper understanding of the virus, including the best way to manage the disease, to prepare to mobilise further responses in the health sector and other sectors, and to reinforce public understanding of appropriate hygiene measures.”

On 16 March 2020, Professors Nick Wilson and Michael Baker from the University of Otago in Wellington provided the Ministry with a report modelling potential health outcomes if COVID-19 were to spread through the New Zealand population.¹¹ This was essentially a ‘thought experiment’ about what might potentially occur if no public health or social measures were introduced to mitigate or suppress the virus. (As the authors acknowledged, the absence of any social measures was unrealistic – people would change their behaviour on a voluntary basis, even if no mandatory measures were introduced – but the modelling was intended to give a sense of the potential health impacts for different levels of infectiousness.)

Suppression of the virus would be insufficient to prevent the health system from being overwhelmed with the burden of illness falling disproportionately on Māori, Pacific people, people with disabilities and older communities.

The report outlined two potential scenarios. Under the less severe scenario (if COVID-19 turned out to be only moderately infectious), the model suggested there could be a total of 92,500 hospitalisations, 6,480 people requiring ventilation in intensive care units (ICU) and 8,190 deaths. Under the more severe scenario (i.e. if COVID-19 was highly infectious), the model suggested there could be 124,000 hospitalisations, 8,690 people requiring ventilation, and 10,983 deaths. In both scenarios the vast majority of deaths (87 percent) would be in the 65+ age group. On the basis of these projected health outcomes, the report concluded there was justification for putting ‘substantive societal and government resources’ into what was then referred to as a suppression strategy.

Along with another modelling study from the United Kingdom, this analysis not only demonstrated the potential impact of COVID-19 on the health system, but also prompted health officials to recognise the need to step up Aotearoa New Zealand’s response and make critical decisions quickly.

By 19 March 2020, global case numbers were growing exponentially; it had taken only 12 days for 100,000 reported cases to become more than 200,000. The same thing was happening on a smaller scale in Aotearoa New Zealand, where cases had nearly doubled overnight, from 11 to 20. It was now clear that managing the virus through suppression¹² (‘flattening the curve’) would not be sufficient to prevent the health system from being overwhelmed. Moreover, as the Ministry of Health noted to the Inquiry:

“the burden of this failure would fall disproportionately on Māori, Pacific, disability, and older communities. We therefore needed to prevent COVID-19 from escaping beyond the border and into the community as far as possible and eliminate chains of transmission in the community as soon as they emerged.”

Border restrictions took effect that night.

5.3.2 Strengthening public health and infection control functions to respond to the virus

With a global pandemic now in full swing, the Ministry of Health and district health boards were responsible for ensuring Aotearoa New Zealand’s health system response was effective and coordinated.¹³ The actions to be taken by each part of the health and disability sector were set out in the Ministry’s COVID-19 Health and Disability Response Plan (published in April 2020), which emphasised the importance of ‘strong leadership across the sector’.¹⁴

The health system’s response was two-pronged. First, public health functions necessary to limit and stamp out transmission – testing, isolation of identified cases, contact tracing and quarantine of close contacts – were stepped up. These matters are covered in this section. Second, hospitals and other healthcare facilities implemented changes to help them care safely for COVID-19 cases and prepare for a potentially large influx of patients. (These matters are covered in section 5.4.)

5.3.2.1 Contact tracing

During an outbreak of a notifiable infectious disease, contact tracing can be a key tool to stamp out or slow down transmission. Once a new case of infection has been identified, contact tracing can identify other people who might also have been exposed, and notify them so that they can isolate themselves and/or access treatment. If contact tracing is successful, contacts will be isolated before they have a chance to infect others, thus limiting the spread of an infectious disease.¹⁵

Importantly, contact tracing is only effective if undertaken quickly (as soon as possible after someone is newly diagnosed with infection), and if there is a reasonable time delay between someone being exposed to infection and becoming infectious themselves (the incubation period).^viii The initial variant of the COVID-19 virus had an incubation period of about five days. This meant there was sufficient time to identify and isolate ‘contacts’ of newly diagnosed cases before they became infectious and passed the virus on to others. In other words, effective contact tracing and isolation could prevent further spread of infection.

Contact tracing in Aotearoa New Zealand is generally carried out by public health units.^ix When someone is diagnosed with a notifiable disease, unit staff trace and interview people with whom the confirmed case has recently been in contact. Under ‘normal circumstances’, contact tracing happens on a modest, localised scale (for example, to stamp out a measles outbreak in a particular community). But in a pandemic, contact-tracing capacity needs to be scaled-up quickly and expanded to cover multiple locations. The higher the case numbers, the more contact tracers are required, and the bigger their task.

Aotearoa New Zealand’s contact-tracing capacity was very limited at the start of the pandemic – the Director-General of Health, Sir Ashley Bloomfield, described it to us as a ‘cottage industry’. Its limited capacity was confirmed in April 2020 when a rapid audit by Dr Ayesha Verrall (then a public health academic, and not yet a member of parliament or minister) found public health units would need to scale-up their contact-tracing capacity ‘three to four fold’ to deal with COVID-19.¹⁶

Initially, public health units in regions with high COVID-19 case numbers were boosted by extra staff brought in from units in regions with no cases. Then in March 2020, the Ministry of Health established a National Close Contact Service to provide centralised coordination and nationally consistent processes. This service was staffed by a broad range of health professionals, including those who had recently retired, students, or professionals who normally worked in private healthcare. The Service evolved as the Ministry sought to enhance the coordination, consistency and scale of contact tracing: it became the National Investigation and Tracing Centre later in 2020 and the National Case Investigation Service in November 2021.

The national telehealth service provider Whakarongorau Aotearoa was also deployed as part of the effort to rapidly scale-up contact-tracing capacity. It recruited and trained large numbers of contact tracers who would work remotely. (See section 5.5.3.3 for more on the activities of Whakarongorau Aotearoa during the pandemic response.)

As well as rapidly growing the contact-tracing workforce, the Ministry of Health sought to improve contact-tracing capacity by creating a new digital platform. Over the course of a few weeks, the Ministry’s digital team developed the National Contact Tracing Solution to store details about COVID-19 cases, close contacts, and their management (what advice they had been given about self-quarantining, for example).

The NZ COVID Tracer app

Developing and piloting a smartphone app to assist with contact tracing was one of the key recommendations made by Dr Verrall in her early capacity audit.¹⁷ The Ministry of Health moved quickly to implement the recommendation, partnering with Auckland-based design company RUSH Digital to develop the NZ COVID Tracer app. Its purpose was to create a virtual diary of people’s activities and interactions.

The Privacy Commissioner was consulted during the app’s development, and publicly endorsed it as ‘a privacy-friendly solution for contact tracing which New Zealanders should feel secure in downloading and using’.¹⁸ It was launched on 20 May 2020 as a voluntary contact-tracing measure. While the app’s use was never mandated, the Government later made it compulsory for businesses and event organisers to display QR codes so people could ‘scan’ into their premises,¹⁹ and for certain businesses and organisers to keep records of who had attended²⁰ – both of which were most easily accomplished via the app. (These measures are discussed further in Chapter 8.)

The app’s functions were built iteratively, with arguably its most useful function – the ability to consent to sharing location data via QR code scanning – added as part of an update in June 2020. Bluetooth capability, which theoretically allowed people to be directly notified when they had been in close proximity with a confirmed case, was added in December 2020. Between 1 July 2020 and 30 June 2021, an average of 807,000 scans were made each day using the app.

5.3.2.2 Testing

Testing is a vital component of any pandemic response, both for identifying who is infected and for confirming who is not. From early in 2020, people with respiratory and other symptoms were encouraged to undergo diagnostic testing to assess whether they were infected with COVID-19. Groups considered to be at higher risk of having contracted the virus – including people entering Aotearoa New Zealand from other countries, workers whose jobs brought them into contact with overseas arrivals, and healthcare workers – underwent regular testing.

Two main types of COVID-19 tests were used in Aotearoa New Zealand at different stages of the COVID-19 pandemic: Polymerase Chain Reaction (PCR) tests,^x which identified genetic material from the virus in the form of ribonucleic acid (RNA), and Rapid Antigen Tests (RATs), which detected protein from the virus, both via nasal swab.

PCR tests

PCR tests were the first form of testing available in Aotearoa New Zealand, and the most accurate. They had to be administered by health professionals^xi and processed in laboratories. It could take hours or days to get a result. Workforce and laboratory capacity constraints limited the number of PCR tests that could be carried out.

One response to these constraints was the ‘pooling’ of samples (when a large number of samples are all tested together). This approach is very efficient if there are very low levels of infection in the population: if the whole ‘pool’ returns a negative result, a single test provides results for 50 (or whatever the pool size) people. However, if the ‘pool’ returns a positive result, each sample must be re-tested individually to determine which ones were positive.

While this approach was used effectively through 2020 and 2021, it started to become problematic in early 2022 when the arrival of the Omicron variant led to widespread community infection. Community case numbers soared, severely straining laboratory capacity.

Since testing of ‘pooled’ samples was no longer efficient, the surge in positivity rates caused by the Omicron outbreak led to an effective reduction in testing capacity just as population testing rates increased. As a result, laboratories were unable to process tests in a timely manner. By late January 2022, PCR test results were taking up to a week to return. By early March, laboratories had a backlog of approximately 30,000 samples more than five days old; these were assigned for destruction due to their reduced clinical relevance.²¹

These capacity issues were eventually resolved by the transition to RAT tests.

RAT tests (or RATs)

While less accurate than PCR tests, RAT tests^xii could be self-administered and processed and gave results within 15 minutes.²² From early in the pandemic, RAT tests were widely used overseas to test for COVID-19. But they were not authorised for use (or importation) in Aotearoa New Zealand until early 2022, due to concerns about their lower accuracy.²³ In the context of the elimination strategy, some health experts felt the greater accuracy of PCR tests was necessary to ensure as many cases of COVID-19 were detected and isolated as possible. Officials also had concerns about the poor quality of some RAT test kits available internationally.

With the decision to move out of the elimination strategy in October 2021 (see Chapter 2), the ban on RAT tests was modified to allow importation and use of tests approved by the Ministry of Health.²⁴ A ministry advisory team had by this time evaluated over 600 different RAT tests, of which 25 were eventually approved for use. The transition from PCR to RAT tests did not go smoothly, however. While importation was now permitted, supplies were limited. The Ministry worked to source and distribute RAT tests to those that needed them,²⁵ but their ability to do so was impaired by global supply shortages and the time taken for orders to reach Aotearoa New Zealand. An external review later found a lack of forward planning had delayed the transition to RAT testing and necessitated a continued reliance on PCR testing – contributing to testing capacity being overwhelmed in early 2022 (as described in the previous section).²⁶

By mid-March 2022, RAT tests were the primary COVID-19 testing modality²⁷ and were freely available from GPs, pharmacies, schools and other community locations. In its evidence to our Inquiry, the Ministry of Health described ‘significant effort’ to ensure equitable access to tests, including the establishment of a ‘Māori-provider distribution channel’ in February 2022 that created ‘a network of over 1,000 community partners to ensure that Māori have good access to tests’.

5.3.2.3 Surveillance and wastewater testing

Accurate information about COVID-19 case numbers was a critical input for Cabinet decisions about alert level changes and the addition, removal, or alteration of other public health and social measures throughout the pandemic. The Ministry of Health therefore put significant effort into providing accurate daily counts of newly diagnosed cases throughout the pandemic period.

Early on, this ‘surveillance’ of the virus was based on individual case notifications. In 2020, surveillance involved routine testing of border workers and new arrivals in managed isolation and quarantine (MIQ), as well as wider efforts prompted by specific outbreaks: comprehensive contact tracing and testing during the initial outbreak in March/April 2020 and focused efforts in response to localised outbreaks like that which prompted a short national lockdown in August 2020. Case identification relied on case PCR testing, while genome sequencing was undertaken on positive tests to identify specific COVID-19 variants.

These efforts were later supplemented with regular wastewater testing, using methods developed by ESR during the COVID-19 response.²⁸ This involved routine sampling to reveal whether the virus was present in municipal wastewater. If detected, it indicated the presence of COVID-19 infection in the community (possibly without the knowledge of those infected). These approaches were formalised in a comprehensive COVID-19 Surveillance Strategy in January 2021.

5.3.2.4 Facemask guidance

Outside of healthcare settings, the routine use of facemasks as a precaution against catching or transmitting infectious diseases was not normal practice in Aotearoa New Zealand before COVID-19. Nor was there a culture of wearing masks when ill.

This changed dramatically during the pandemic response, in which masks played an important – and sometimes controversial – role. The widespread use of masks was important for protecting people who were vulnerable to the virus. From being rarely seen in public settings in Aotearoa New Zealand before 2020, facemasks became ubiquitous, especially during the second half of 2021 and early 2022. For many, they are now an instantly evocative symbol of the COVID-19 experience.

Evidence about the effectiveness of masks to prevent COVID-19 transmission evolved over the course of the pandemic, and the way they were used as a public health tool varied accordingly.^xiii On 6 April 2020, the World Health Organization issued guidance recommending workers in healthcare settings wear masks – but only to prevent the transmission of COVID-19 from medical procedures involving infected patients. This was updated on 5 June 2020, and while the updated guidance applied more broadly than just to medical procedures, it was still focused on health workers.²⁹ It took longer for the World Health Organization to recognise that COVID-19 was spread by airborne particles,^xiv often but not always between people within 1 metre of each other.³⁰

By August 2020, officials at the Ministry of Health were satisfied there was enough evidence to support mask use for them to play a significant part in the response to the community outbreak of that month. As well as their direct role in preventing transmission, there was evidence that mask wearing enhanced other behaviours that discouraged spread, with studies suggesting people were more likely to follow social distancing guidelines when around a person wearing a mask or if they were wearing a mask themselves. They began to be mandated in some settings from 19 August 2020 (see Chapter 8).