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Phase 3 shakes up the pandemic response – Expert Reaction

With more than 6,000 cases of Covid-19 recorded today, the gears are shifting on the Omicron outbreak in New Zealand, and so is the government’s response.

After the move to Phase 3 at midnight, close contacts will no longer be required to isolate – unless they are in the same household as an infected case – and Rapid Antigen Tests (RATs) will become the primary testing method. RATs will also be available for the public to buy from next month, and people will be able to report their own results online.

The SMC asked experts to comment. 

Emily Harvey, Senior Researcher at Market Economics, Lead Researcher at COVID-19 Modelling Aotearoa, Principal Investigator with Te Pūnaha Matatini, comments:

“The shift to Phase 3 includes two main bundles of changes. The first is to the testing system, with the shift to RATs in place of PCR tests in many circumstances. The second is the change in isolation and testing requirements for non-household close contacts.

“Although PCR tests have a much higher sensitivity, the long delays seen in PCR testing due to capacity constraints has prevented them being useful in reducing onward transmission because of the delay in identifying close contacts of cases as soon as possible after exposure. The shift to using RATs which are less sensitive, but give a result almost immediately, will be a big help in identifying cases promptly and reducing onwards transmission from them and their close contacts.

“With the prevalence levels and test positivity rates we are seeing, the chance of false positives becomes very small for anyone with covid-like symptoms or known contact with a confirmed case, and the use of confirmatory PCR would be a waste of PCR testing capacity. More of a concern with RATs is that people will need to be aware of the possibility of false negatives, and there should be clear messaging about the importance of continuing to isolate if you have covid-like symptoms or are a close contact even if you test negative with a RAT.

“The second set of changes removes the isolation requirements for non-household close contacts, and only requires them to test if they develop symptoms. This change was included in the original announcement of the ‘Phases’ in order to manage the anticipated disruption to critical workers and supply chains due to a large number of people needing to isolate if they were close contacts. Since then, the Close Contact Exemption Scheme has been introduced, which enables close contacts to go to work as long as they test negative on daily RATs and are not symptomatic. This has removed the original reason for this change, and it is not clear why it is still being implemented.

“This change to isolation and testing requirements at Phase 3 will increase overall transmission risk. Although Minister Hipkins stated that people could still choose to isolate if they were a close contact, for many people this is not an option. This shift will exacerbate the already existing inequities in infection risk.

“Additionally, the increased transmission risk due to this shift can be expected to result in a steeper rise in case numbers, a higher peak, and a greater cumulative number of infections, hospitalisations, and deaths. These additional infections may in fact increase the level of disruption to critical services, due to having more confirmed cases in their workforce.”

Conflicts of interest: I, along with others from COVID-19 Modelling Aotearoa, am funded by the Department of Prime Minister and Cabinet to provide advice on the COVID-19 response and from a Health Research Council grant designed to help ensure equitable health and wellbeing outcomes for all New Zealanders during the COVID-19 pandemic, and future infectious disease threats in Aotearoa.

Phillip Wilcox, Senior Lecturer, Department of Statistics, University of Otago, comments:

“Overseas research has shown that severe Covid-19 has a heritable component. What this means is:

“If you have a close relative – including those living overseas – who is or has been severely affected, then chances are higher that you will too, more so if you are not vaccinated or recently boosted and/or have other risk factors.

“If you live with close relatives and become infected, then if possible, self-isolate away from them and follow the self-isolation guidelines provided by the Ministry of Health. Doing so will help protect your whānau.

“Keep in touch with close relatives during this time. Sharing experiences will forewarn whānau members so they can proactively take appropriate measures.

“Lack of infection is not necessarily an indicator of immunity: other factors could be contributing to lack of infection despite possible exposure, so even if close relatives are not affected it doesn’t mean you won’t be.”

No conflict of interest declared.

Dr David Welch, Senior Lecturer, Centre for Computational Evolution and School of Computer Science, University of Auckland, comments:

“We want to see some ongoing random sampling of people with PCR tests or a similar sample that is appropriate for genome sequencing.

“If we exclusively rely on RATs in all but the very vulnerable or hospitalised, we may be very slow to detect a new variant or reemergence of Delta circulating within a specific community or demographic.

“Random sampling of cases for sequencing could be obtained via less invasive means than the nasopharyngeal swabs that have been used to date.”

David Welch and his colleagues have also written a Conversation piece published yesterday on how the role of genome sequencing is changing due to reduced PCR testing.

No conflict of interest declared.

Dr Dion O’Neale, Project Lead, COVID Modelling Aotearoa; and Senior Lecturer, Physics Department, University of Auckland, comments:

Changes in isolation requirements:

“One of the big concerns with large numbers of cases is that so many people will need to isolate due to being infected, or close contacts, that there may be a period where there are not enough staff for essential services like healthcare, food supply, and managing critical infrastructure. To address this, the three phases of the original Omicron response set out increasingly narrow definitions of who would be considered a close contact, and the period that they would have to isolate for as case numbers increased. This approach makes the trade-off of doing less to prevent transmission (fewer people isolating for shorter times) with allowing more people to keep working, as case numbers, and hence risk, go up.

“Since that initial plan, the introduction of the ‘close contact exemption scheme’  businesses can now self-nominate roles as essential and where those staff who are close contacts can already return to work immediately if they are symptom free and return a daily negative RAT result  can be expected to relieve a large amount of the expected pressure on staffing critical roles. As such, the change in the close contact definition and isolation requirements have the potential to increase transmission risk without strong evidence being presented that staffing of critical roles can’t be managed under the close contact exemption scheme.

“Reducing self-isolation requirements to only confirmed cases and their household contacts increases the risk of onward transmission from any other contacts of confirmed cases that would previously have been classified as “close” until today. In addition to this, the expectation that people no longer covered by the phase 3 isolation requirements make their own judgements about whether they can, and should, isolate if they are the (non-household) contacts of confirmed cases, creates the familiar issue of large inequities between people who will have the financial resources, time, and necessary information to easily opt-in to isolating, in order to protect those around them in the community. The pattern of who is disproportionately affected by COVID around the world is well established  people with disabilities, indigenous populations, people of colour, and people on lower incomes or in precarious work bear the brunt of infections. The move in Aotearoa of people being expected to look after themselves as best they can will mean we move further down that path of driving infections towards the most vulnerable populations.

“Contacts of confirmed cases who would previously have been classified as “close”, and required to isolate accordingly, are now being told to watch for symptoms and only test if symptomatic. Given that a significant fraction of COVID cases are asymptomatic while infectious, particularly among younger people who also have the most interactions, this advice further increases the risk of onwards transmission with the shift to phase 3.”

Testing strategy shift – more Rapid Antigen Tests:

“In a high prevalence scenario like we are in with Omicron in Aotearoa, speed is key in returning test results to people so that they can use that information to modify their behaviour and isolate, if they are able to, or possibly required to. The sooner people can receive a positive test result, the sooner they can notify any of their recent contacts, so that those people can also isolate (though they won’t be required to unless they are in the same household).

“When prevalence is high, the risk of a false positive from a RAT is incredibly low, so the value in having a more sensitive PCR test is reduced compared with when we had lower case numbers. Conversely, there is a risk of false negative results on a RAT  for someone who either has symptoms, or is a close contact of a confirmed case, when prevalence in the community is high. In such cases the prudent course of action would be to take a second test – either another RAT, or a PCR test – and to assume that there is still a decent chance that you may be infected.

“People who have no known exposure to a confirmed case and no symptoms can be relatively confident in the accuracy of a negative result from a RAT. And of course, we would hope that anyone with COVID-like symptoms is isolating until they recover from whatever illness is causing those symptoms  COVID or otherwise.”

We will start to miss more Covid cases:

“The move to phase 3 acknowledges that infection and confirmed cases are becoming high enough that many of the processes that we use to monitor and plan for the outbreak will become stretched and may become inaccurate. As the number of infections rise in the community, we can expect the Case Ascertainment Rate or CAR to fall. The CAR is a measurement of the percentage of total infections at a point in time that we ever learn about as confirmed cases. i.e. given an observed number of confirmed cases, how many infections do we think are actually in the community, including those that are unconfirmed. This is important since as requirements around who must isolate as a close contact decrease fewer people will be eligible for testing, or people may test positive on a RAT but not report it.

“The only way to accurately estimate the Case Ascertainment Rate is through an Infection Prevalence Survey  similar to the ONS survey that runs in the UK and which has been one of the strongest aspects of their COVID response. This is a randomised survey that tries to directly measure the fraction of people who are infected at a point in time, for different demographic groups. Modelling can estimate the number of infections occurring over time in different populations, subject to different assumptions, but without an infection prevalence survey, or equivalent data, only confirmed cases can be directly observed. Since confirmed cases are only a fraction of total infections, and this fraction changes over time, it is important to be able to accurately estimate the underlying infection numbers since these are a leading indication for hospitalisations and are valuable for planning to adjust any processes or policies, such as testing or isolation.

“Measures such as the fraction of people admitted to hospital who test positive for COVID are an unreliable estimate of infection prevalence because they are biased by a large number of factors that are difficult to control for  namely that people rarely turn up at hospital for random reasons and that many of the same factors that might drive hospital admissions, even for reason not-directly linked to COVID, are none-the-less related to COVID infection risk.

“As an example in early January 2022, the UK recorded an average of around 200,000 daily confirmed cases. During that same period, the ONS infection prevalence survey estimated that there were just under 4 million people who were currently infected. Details around the length of the period for which someone might test positive during the survey period will affect the exact value of the CAR but the UK figures paint a picture of only a small fraction of infections being detected, even with RATs being provide freely and frequently to people in the UK.

“With access to testing in Aotearoa being more limited than that in the UK, we might expect our case ascertainment rate to be even lower, and hence the number of reported cases is likely to significantly undercount true infections.  But without an infection prevalence survey, exactly how much we are undercounting by is difficult to tell.”

Conflict of interest statement: I, along with others from COVID Modelling Aotearoa, am funded by the Department of Prime Minister and Cabinet to provide advice on the COVID response and from a Health Research Council grant to look at equity related to COVID in Aotearoa.

Dr Dianne Sika-Paotonu, Immunologist, Associate Dean (Pacific), Head of University of Otago Wellington Pacific Office, and Senior Lecturer, Pathology & Molecular Medicine, University of Otago Wellington, comments:

“Although today’s COVID-19 case figures represent the highest ever recorded new cases in the community in one day, it is important to note also that the actual COVID-19 case numbers in the community are likely to be much higher than this.

“High COVID-19 case numbers are already placing added strain onto our health and support systems in Aotearoa New Zealand, and we are still in the process of protecting vulnerable members of our communities that include our children, tamariki and tamaiki aged 5-11 years getting their COVID-19 vaccine, and helping people get their boosters to protect them from the highly transmissible Omicron variant.

“The Government’s Omicron response plan overall has already signalled a significant shift in managing COVID-19 moving forward, where self-management now features very strongly in the planned approach for dealing with COVID-19 in Aotearoa New Zealand. This 3rd Phase of the Government’s Omicron response plan aims to manage the current and predicted extraordinarily numbers of Omicron cases, and also the predicted escalation in COVID-19 case numbers.

“Persisting inequities with respect to Māori and Pacific peoples, tamariki and tamaiki aged 5-11 years remain evident in booster and vaccination levels. Of those children aged 5-11 years, 48.8% of the general population have received their first COVID-19 vaccine dose, and for Māori and Pacific tamariki and tamaiki, vaccination levels for first doses are at 29.1% and 40.6% respectively.

“For all those aged 18 years and over currently eligible for a booster dose, 68.2% have received theirs, and for Māori and Pacific, booster levels are at 57.5.1% and 55.0% respectively.

“COVID-19 boosters are not currently being offered to adolescents in Aotearoa New Zealand. They are available to adolescents in Israel, USA, Europe, UK, Switzerland and Australia

“We need to do everything we can to help our children, tamariki and tamaiki get vaccinated, and to for people to get boosted as well.

No conflict of interest declared.

Dr Andrew Chen, Research Fellow, Koi Tū – Centre for Informed Futures, University of Auckland, comments:

This is an excerpt from comments Dr Chen made last week.

“One of the critical challenges with contact tracing is system capacity. The key bottleneck is that under normal procedures, a human calls a case to inform them of their positive test result, and humans then have a conversation to collect information about their symptoms, where they have been, and who else they may have exposed to the virus. When we have thousands or tens of thousands of cases a day that is not tenable.

“The Ministry of Health has released a digital form that will allow people with COVID-19 to self-report a lot of this information digitally. They will be informed about their positive test result with a text from 2328, the same number that vaccine messages are sent from. The contact tracing form asks for a lot of the same information that would be provided in a verbal conversation, and guides people through different pages to provide that information. It is expected that on average the form will take 30 minutes to complete, which may seem like a burden but it is a shorter time than the verbal conversations usually last. People who don’t complete the form may still get a phone call or similar to follow up.

“Importantly, through this form cases will also have the opportunity to highlight their wellness and welfare requirements, such as needing food delivered to them so that they can continue to safely isolate. We know that in order for people to comply with isolation requirements it has to be made as easy as possible for them, and so this is one way to help identify challenges so that the system can respond. People will also be able to self-report their rapid antigen test (RAT) results via MyCovidRecord, both to have a central record of those results and to be able to report a positive result and trigger processes to ensure there is appropriate care.”

Conflict of interest statement: I have had interactions with the Ministry of Health around digital contact tracing in an academic capacity, but am not employed or paid by them.