Tracking the true spread of Covid – Expert Reaction

Scientists have had to adapt to track trends in the Omicron outbreak, as infections soar across Aotearoa.

Now that the Health Ministry cautions against relying on the daily Covid case count to estimate virus spread, what can alternative data tell us? Hospital numbers and wastewater testing can play a part in more closely estimating the actual level of infection, as can monitoring groups like incoming travellers and border workers.

The SMC asked Covid-19 surveillance testing experts to comment.

Professor Mike Bunce, Principal Scientist, Genomics Lead, and Dr Joep de Ligt, Lead Bioinformatics & Genomics, Institute of Environmental Science and Research, comment:

How is New Zealand’s use of genomics changing in light of rising Covid-19 infections?

“The Omicron wave has seen a change in how we deploy the whole genome sequencing (WGS) toolkit across Aotearoa. Rather than genome sequence each case, we are now focusing on a country-wide approach to see: what variants are where; what variants turn up in hospital; and are new variants appearing at our borders? In other words, we are now in a genomics surveillance mode; in the past genomics was also deployed to assist in contact tracing.”

What should we be looking out for in the genomics data – and what does this tell us about the spread of infection?

“The interplay of BA.1 and BA.2 lineages is one of the key pieces of data that ESR is monitoring across NZ. For the first time this week BA.2 cases outnumbered BA.1 in our sequenced genomes. This was expected as BA.2 appears to have a transmission advantage over BA.1. With less stringent border restrictions we expect to see new lineages of viral genomes – genomics enables us to watch these closely. We are also keeping an eye out for Delta cases, although they are becoming hard to spot within the Omicron wave.”

What else can be done to get closer to the actual number of infections?

“Wastewater testing is also changing in response to the Omicron wave. For the first time in this pandemic, the case numbers are sufficient to enable quantitation of the virus in wastewater. Previously we were at the limits of detection which prevented a gauge on how much virus was present – it was always low.

“However, we stress that extrapolating wastewater concentrations into case numbers is difficult and imprecise, primarily due to differences in flow rates, and stormwater and population density differences between catchments. Trends in wastewater concentrations over a few weeks do provide an indication if COVID-19 is increasing, stable, or falling within a given catchment. It is hoped that when used with other data (case positivity rates and case numbers) that wastewater monitoring will play an increasing part in tracking infection waves.”

How is NZ monitoring new arrivals from Australia under the new MIQ-free arrangements?

“We have strong collaboration with Australia through the Communicable Disease Genomics Network, where all Australian and New Zealand data are shared on a integrated platform to allow detection of potentially linked cases.”

How is NZ monitoring Covid patients to help track any emerging new variants?

“Hospital cases are a priority for genome sequencing. The genomic surveillance plan also calls for multiple samples to be taken from patients that have a prolonged infection with COVID-19. The risk here is that the virus, if not ‘cleared’, can accumulate mutations; we can monitor this by taking samples over time and seeing if key parts of the virus (such as the spike protein) are changing.

“New variants can also emerge in long-haul (long Covid) patients, and there is an increasing awareness of this on the international stage.”

No conflict of interest declared.

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

How important is it for people to report RAT results – both positive and negative?

“Reporting any positive RAT results, and filling out the contact tracing form at the link that should then be sent to you (or calling the 0800 numbers if the online option doesn’t work for any reason), is incredibly important as it’s the only way that the different government agencies and health organisations will know about your situation. The above steps are how you are able to indicate whether you need any support to isolate, like food deliveries, payments from work and income, etc. And it also helps to flag anyone with high-risk health needs where more regular health check ins would be prioritised. This is also the only way that local/central agencies would have an estimate of the impact, and what resources will be needed.

“Reporting negative tests through time, especially in close/household contacts or recent border arrivals, is also incredibly valuable for informing public health guidelines around the duration of isolation, testing frequency, etc. We need this data to be able to answer questions like ‘what proportion of household contacts will go on to get infected?’ and ‘for household contacts that get infected, how soon would we expect to detect the infections using RATs?’.”

How is NZ monitoring new arrivals from Australia under the new MIQ-free arrangements?

“Arrivals from Australia are provided with three RATs on arrival, and instructions to take them on day 0/1 and day 5/6, or if any symptoms develop. Due to the lower sensitivity of RATs, and the more narrow time window in which they work, this will not catch all infections, but will hopefully detect the majority. Additionally, infection rates are now much lower in Australia than in NZ, so these arrivals are more likely to be infected after arrival, and present lower risk, at least initially, than people who have been out and about in NZ.

“The main reason for trying to detect as many of these border cases as possible, is so that they can be prioritised for a PCR test and genome sequencing, in order to monitor for new variants. In order to increase the likelihood of detecting infections, if any of these travellers have brought their own RATs, due to higher availability in Australia, then it would be great if they could do the RATs more like every day or every 2 days during the first 5 days, but ideally the NZ govt should supply 5 tests instead of 3 to enable this.”

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.

Andrew Sporle, Deputy Director, Healthier Lives National Science Challenge; and Director, iNZight Analytics Limited, comments:

“I would like to see both RAT and PCR tests for all arrivals at the airport, as PCR tests are much more accurate than RAT tests and they would be able to detect the potential introduction of a new variant.”

No conflict of interest declared.

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

How is NZ’s tracking of trends changing in light of rising Covid-19 infections?

“It’s important to remember that the case numbers that get reported and recorded are the confirmed cases that we know about, not the number of actual infections in the community. With rising numbers of confirmed cases, and with changes in the testing processes and the related advice around seeking testing and the consequences of being a confirmed case, or the close contact of one, the only thing that is certain is that our case ascertainment rate — the fraction of infections that are recorded as a known case — will be changing over time. It’s most likely that this is falling due to people’s difficulty or reluctance to seek a test. In order to accurately estimate what that case ascertainment rate is, and hence how the true number of infections is tracking, we really need an ONS-style infection prevalence survey like in the UK. Without one, decision makers and public health officials are flying blind and modelling results become less valuable without being able to verify their underlying assumptions.”

What should we be looking out for in the data – and what does this tell us about the spread of infection?

“Putting aside the issue of uncertainty in case ascertainment, one of the patterns to be looking for is the geographic extent of spread. To date the outbreak has been dominated by cases in Auckland. These are possibly close to a peak, with growth rates starting to slow, at least in some communities. Other regions are still in the earlier stages of the outbreak and may be yet to reach the period of rapid growth rates. Another important pattern to be looking for is the details of who is getting infected. Both modelling and overseas experience show that initial cases are dominated by younger people who have more interactions and are more likely to experience milder symptoms. This is conducive to high initial growth rates. As infections continue to spread they will move in to older populations where health consequences of infection are worse. This can mean that not only to hospitalisations peak later than cases (even after adjusting for the lag from case confirmation to hospitalisation) but they can also stay high for longer. Essentially, we expect to see hospitalisation rates increase in the later stages of the outbreak.”

What else can be done to get closer to the actual number of infections?

“While hospitalisation numbers can help to give information about how many new infections occurred in the recent past, they are a dangerously lagged indicator. Looking at hospitalisations to measure infections means that by the time we see hospitalisations reach a number where we might need to act, it is already too late to prevent additional hospitalisations from coming. The infections that correspond to those additional hospitalisation have already occurred over the past couple of weeks. Waste water testing can be used to give a broad indication of how the number of infections in the community are tracking but have limitations when it comes to relating the amount of virus in waste water to the true number of infections, and importantly, to who is infected. The gold standard in determining infection numbers is an ONS-style infection prevalence survey, as in the UK, that is designed to directly estimate the number of infections in the population.”

How important is it for people to report RAT results – both positive and negative?

“We need people to report positive RAT results to better estimate the number of infections that are in the community and to understand which communities are being affected. This helps us to predict where we are likely to see future growth and where more support might be needed. Reporting negative RAT results is important, especially if we know the reason for testing, as it helps us to estimate the rate of infection. Knowing things like the fraction of close contacts who didn’t become infected is important for estimating the effect of changes to policies like isolation rules.”

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.

Professor Nigel French, Co-Director, One Health Aotearoa; and Chief Scientist, NZ Food Safety Science and Research Centre, comments:

“Given the current situation it’s very difficult to tell how we are tracking in terms of new infections in the community. Under-reporting is likely to have increased markedly with the change to widespread use of RATs and self-reporting. If we rely on community case data alone we are likely to have a very inaccurate picture of how the Omicron outbreak is progressing – and this is not good for planning how best to respond.

“Other measures of the scale and time-course of the outbreak are likely to be more useful. The number of new hospitalisations with Covid is likely to be a more reliable indicator of the extent of the outbreak, but this is a ‘lag’ indicator due the delay between infection and hospital admission. Wastewater testing, population-based surveillance and test positivity rates can provide earlier and less-biased indicators of the extent of community transmission, but this relies on having effective, representative and rapid surveillance in place, and for individuals to rapidly report both positive and negative tests. Targeted genomic surveillance will also help us to determine what variants are currently circulating and rapidly identify any new variants that cross the border.

“For us to plan effectively, we need these multiple strands of data to be readily available to analysts and decision makers. This will enable us to determine more accurately the true force of infection in the community, identify when new community cases have peaked, and how hospitalisations are likely to track over time. Such information is essential for planning and implementing measures to reduce the impact of this Omicron wave.”

Conflict of interest statement: “I’m the co-director of One Health Aotearoa, and receive research funding from MBIE.”