COVID-19 Research Response Report – August 2022 case studies

Through these trials, different processing methods to maximize the amount of ethanol which could be produced from Marlborough wineries’ waste products were investigated. BRI’s Research Winery undertook fermentation and distillation trials on several forms of grape marc.

Grape marc was collected and promptly frozen until fermentation trials could be conducted. Triplicated fermentations of each treatment were carried out in 17 L tanks under identical conditions.

Other methods included pulverising, enzymes, acid hydrolysis and ‘heap fermentation’, under various conditions.

Once ferments were completed, the tanks were drained, and the grape marc was pressed for full extraction. The subsequent liquid was distilled at a local distillery.

Other waste streams investigated included lees (sediment of dead yeast and grape remnants) from Sauvignon Blanc fermentations and red grape marc post fermentations, which were collected and steam distilled at the local distillery.

The trials produced more than 100 bottles of hand sanitiser from marc-derived alcohol, which was bottled and donated to local health care workers in the Marlborough region including St. Johns, Red Cross, and local medical centres. In addition, the wineries that donated grape marc were given bottles of the hand sanitiser for their staff to use.

This consolidated BRI’s position in the community, helping to build a sense of regional solidarity and a connection between the people of the Marlborough region and its most important economic sector. This was significant as the Research Winery had been open for only a year, and also served as publicity for the winery’s fermentation trial capability.

Research showed a positive finding of a reduction in the weight of grape marc post fermentation by up to 36%, when used to produce ethanol. While there is still a significant amount of remaining marc to be disposed of, this finding could benefit wineries that are paying for disposal based on weight.

A comprehensive business model to produce ethanol from winery grape waste was developed. In summary, the production cost may outweigh the benefit if the production of hand sanitiser is the only objective. This is offset by other economic, social, and environmental benefits.  In addition, the process’s economics may become more attractive if incorporated as part of an integrated system of multiple processes for treating the same waste.

Research findings were distributed via the NZ Winegrowers and BRI websites, internal newsletters, plus press releases and subsequent media articles.

The impact (in the short term) was the pilot scale production of hand sanitiser from marc-derived alcohol, as well as the development of a connection between the winegrowing industry and the programme to manage COVID-19 and other diseases, and technical data to support a scaled development. These will benefit the wine industry, and the Marlborough region, economically and environmentally.

The Marlborough winegrowing industry is looking for ways to manage and use the large volumes of marc produced. The motivation to treat marc differently is driven by environmental and regulatory pressures, with convictions already entered for illegal disposal methods, and by economic pressures as the industry seeks a cost-effective way to use or dispose of marc. The information dossier delivered by this project contributes to industry discussions about management of marc and will be used by BRI as it creates options for the industry through research and technical development. This is a complex mix of considerations and the information from this project is a valuable part of the process of finding a solution. 

 The full value proposition of this project goes beyond a low-cost ethanol source. For Marlborough, the NZ winegrowing industry and NZ, the benefits include:

• a product known to be effective in disease control
• diversification options for the NZ winegrowing industry
• an opportunity for the Marlborough winegrowing industry to connect with pandemic responses and community healthcare in a tangible way
• adding value to large waste streams that currently present problems to the winegrowing industry

Trialling technology which could be adapted to facilitate ethanol-based sanitiser production from other horticultural waste streams, such as those from the apple and pip fruit industries.

The winegrowing industry was fortunate to be considered ‘essential’ during the initial COVID-19 response, which meant that by following strict guidelines the harvests in autumn of 2020 and 2021 were able to go ahead. For the Research Winery this led to new ‘contactless’ ways of receiving grapes and interacting with clients and research partners. Some systems for clients to monitor progress of research remotely have been developed further and become routine.

Significantly, the procedure for freezing grapes or juice for later research was fully tested, extending the production cycle and capacity of the Research Winery.

Covid-19 research fund invests in grape waste(external link) — Bragato Research Institute

Project to explore turning waste into hand sanitiser(external link) — Stuff.co.nz

https://www.stuff.co.nz/business/121595580/project-to-explore-turning-waste-into-hand-sanitiser(external link)

The marc of a good sanitizer!(external link) — Winestate Magazine

Grapes to hands(external link) — Blemheim Marlborough Sun

The project went through several phases as the pandemic progressed in NZ. It began in 2020 by exploring transmission in all manner of public places including offices, buses, theatres and gyms. In early 2021, as community transmission ceased, we focussed on managed isolation and quarantine facilities (MIQFs), working with staff from MBIE, the Ministry of Health, DHBs and the Defence Force to understand ventilation and air treatment in MIQF corridors, bedrooms, and the vehicles used to transfer returnees from airport to MIQF. We used out methods to investigate the small number of cross-infection events which occurred in MIQFs, to aid the operators in preventing future infections.

This touched several aspects of MIQF operation, but most significantly:

• Modelling in lifts which supported findings from in-MIF investigations and this leading to the change in focus on lifts as a priority for HEPA filter installations.
• Modelling in facility hallways which assisted in identify number and location of placement of HEPA filters.
• Research into ventilations systems in buses which showed little cost benefit in retrofitting expensive HEPA filters into the vehicles.  

In mid 2021, we started working with the Ministry of Education and the Indoor Air Quality Research Centre to understand ventilation in schools and to advise on ventilation strategies to reduce the rate of spread of COVID in schools (flatten the curve). This has had spin-off benefits in better understanding how good air quality can be maintained in schools in the long term.

We developed tools to estimate infection risk based on: the rate at which the infectious person breathes out virus-carrying particles (when breathing, coughing, talking, singing etc.), the effect of different types of masks in intercepting these particles; ventilation air flows carrying and dispersing these particles, air cleaners using filters or other methods to remove virus-carrying particles, or inactivate the virus, and the inhalation of remaining particles by other people who might become infected (including the effect of masks). We have tools which assume the air in a room is well mixed (simple and fast calculations) and tools which simulate complex air flows due to ventilation, wind and thermal effects.

To test our methods, used particle detection instruments to conduct measurements of airborne particle removal rate in test rooms and in MIQFs, using the (non-infectious) particles which occur naturally in the air, and safe tracer particles from nebulizers and smoke generators.

To understand ventilation flows in real-world environments where cross-infection is likely, we measured ventilation flow rates in offices, hotel bedrooms and corridors, and school classrooms (the latter in a 2 stage NIWA led study preparing for summer and winter use of classrooms).

Many of the places where people gather together are naturally ventilated, i.e. fresh air is brought in through windows and doors. We built simple tools to estimate fresh-air flow rates such places, according to the temperature, wind and window openings. One such tool is now in use by the Ministry of Education’s property advisors.

We also built models to predict the heating requirements for spaces with improved fresh-air flow during winter.

We assisted in preparing ventilation advice distributed to all schools by the Ministry of Education in December; compiled advice on the use of CO2 monitors to assess ventilation levels; provided advice on the use of air cleaners to reduce risk in areas which cannot be effectively ventilated, and analysed and made suggestions for specific areas in schools which had been identified as of special interest.

In collaboration with Fisher and Paykel Healthcare, we modelled the air flow around patients undergoing different types of respiratory support, to understand the effect of the therapy-induced air flow on infection risk.

With collaborators at the University of Otago Faculty of Dentistry, we measured particle concentrations in the air around a mock patient undergoing various dental operations, to understand the infection risk for dentists and oral hygienists.

We also built a schlieren system for imaging subtle airflow and thermal currents around the human head, and published a paper on the effect of masks on airflow in front of a speaker's face (in Nature Scientific Reports. Dr Derrick, who led this work gave an invited talk at the American Association for the Advancement of Science (AAAS) annual meeting, and participated in an AAAS panel discussion on airborne transmission of infectious diseases. Leveraging on this work, we obtained a grant of $839,000 from the RSNZ Marsden Fund for the project "Multi-sensory speech perception and syllable structure".

Tools to model infection risk in indoor spaces, including the impact of ventilation, masks, air cleaners etc. optimized for COVID-19 but easily adaptable to any airborne pathogen.

Integration of this method into three dimensional models of air flow, including air cleaning devices, thermal currents due to body heat, and evaporation of water from exhaled particles

New data on exhalation currents by people wearing different facemasks, and respiratory therapies

Public advice: with other members of the IAQRC, we compiled advice for the public on the effective use of air cleaners, ventilation in homes for suppression of infection risk, and ventilation in general practice clinics (responding to a request from a GP network), freely available through the University of Otago Public Health Expert Blog and the IAQRC website.

• Mark Jermy (UC) and Guy Coulson (NIWA) joined the Ministry of Education Ventilation Technical Advisory Group (VTAG).
• Mark Jermy joined the World Health Organization Technical Working group "Airborne Risk Indoor Assessment" (ARIA), as one of 20 worldwide experts developing a new risk assessment tool for airborne infection.
• Mark Jermy advised a major NZ operator of aged care facilities to give advice on ventilation and air cleaning in preventative and mid-pandemic stages.
• Mark Jermy joined the Australian Research Council funded Linkage Project "Making Australia resilient to airborne infection transmission" (ARC LP200301123) which will take lessons learned during the pandemic forward for long term benefit

A new partnership between NIWA and Fisher and Paykel Healthcare has been established to measure and model the circulation of CO2 and particulates indoors.

We trust our major impact has been in assisting the MIQF system in delaying a major epidemic of COVID in NZ, and in ‘flattening the curve’ of infection rates during the current Omicron outbreak.

We expect our advice will be incorporated longer-term into design guidelines for school buildings.

The tools we developed, and the experience we have accumulated, are of value in reducing infection rates for any airborne pathogen, and will be of lasting value.

The information we disseminated on the role of natural ventilation on indoor air quality has value in reducing indoor CO2 levels (better comfort and alertness) and reducing exposure to indoor pollutants (mould spores, cooking and heating smoke, volatile organic compounds (VOCs). In particular, advice on how to use and adjust window openings to achieve fresh indoor air at a comfortable temperature in different weather conditions.

During the project, we feel we got better at:

• Finding new collaboration partners, outside our own technical areas
• Engaging with government
• Communicating with people in different disciplines
• Public dissemination of knowledge
• Applying academic knowledge directly to achieve short-term mitigation of complex, widespread problems.

Estimating risk of airborne trasnmission of Covid-19 in isolation hotels(external link) — YouTube

• Invited talk at the International Society of Indoor Air Quality and Climate conference, “Healthy Buildings 2021” 21-23 June 2021, in a workshop on the “Use of Infection Risk Calculators to Manage Building Occupancy Post-COVID”

Scientific Report – Speech air flow with and without face masks(external link) — Nature

• Derrick, D., Kabaliuk, N., Longworth, L., Pishyar-Dehkordi, P., and Jermy, M. (2022).

Ventilation in NZ schools during the Omicron wave – results from a preliminary study(external link) — Indoor Air Quality Research Centre of New Zealand (IAQRC)

Blog – Reducing the risk of Covid-19 transmission through the use of air purifiers(external link) — Otago University 

See also:

• Derrick, D. (2022). Human airflow while breathing, speaking, and singing with and without masks. In Association for the Advancement of Science Annual Meeting (AAAS2022) 
• Gick, B. (Moderator) Asadi, S., Bouvier, N.M., & Derrick, D. (Panel). Transmission of airborne pathogens through expiratory activities, Association for the Advancement of Science Annual Meeting (AAAS2022), Feb 19, 2022 
• Freeman J., Jermy M. and Chen J.,"Airborne transmission of SARS-CoV-2: natural experiments in the MIQ system", Bioengineering@Otago Showcase 14-15 Feb 2022.

Drawing on our team’s world-class expertise in this technology we:

• Utilised sequencing to accurately assign New Zealand cases to clusters and/or to the border;
• Determined the size of clusters and the extent of community transmission;
• Determined temporal changes in the reproduction number (R0) of SARS-CoV-2.

Genomic sequencing of positive COVID-19 cases has now been integrated into the Ministry of Health’s pandemic response.

By integrating real-time genomic sequencing of SARS-CoV-2 with epidemiological data we have, for example, prevented multiple Alert Level changes by identifying direct links between cases. By providing direct links of community cases with the border, this project has provided substantial economic savings to New Zealand’s economy.

This collaboration involved researchers from across the country and internationally, which meant working virtually the ensure success of the project. For example, we continue to communicate daily via Slack and have frequent zoom calls with the team.

List of scholarly outputs(external link) — Google Scholar

Video: Documentary on COVID-19 genome sequencing(external link) — Vimeo

Video: NZ COVID-19 Genomics Animation(external link) — YouTube

This study consisted of four parts:

1. An analysis of news media coverage of older people and COVID-19 during the first lockdown.
2. 44 interviews with older people, including 10 Māori, 5 Pacific, 2 Korean and 3 Chinese participants.
3. 870 letters received from 760 participants, including 36 poems and 120 pictures.
4. Provider survey with 19 Age Concerns across the country.

• Development of website to raise awareness about issues affecting older New Zealanders related to pandemic (www.haveoursay.org)
• Partnership with Age Concern NZ which will involve discussion of implications of our findings for their policy and practice
• Eight academic papers published/in press or under review.
• These focus on media framing of older people, intergenerational connection, loneliness, physical activity, older people’s contributions to the pandemic, older Chinese and Korean people’s experiences, social cohesion during the first pandemic response and family caregiving.
• We have begun developing media guidelines to support better reporting of older people’s experiences and views in relation to the pandemic.
• We are developing an archive with Auckland Museum to provide an enduring historical record of this unique time period. The archive will be an invaluable domestic and international resource regarding first-person, eyewitness accounts of the impact of the pandemic. It will not only be good for future pandemic preparedness, but also provide historical documents for historians and for families/whānau/descendants in future generations.
• Research training and mentoring of three students (2 Master’s and 1 summer student) working on projects which draw on this data.

The primary impact of this study has been to shift public perceptions of older people during the COVID-19 pandemic. We have successfully done so through publishing academic journal articles and news in the national press based on our findings. We have also presented our findings in a number of forums including at U3A events in Tauranga, Rotorua and Blenheim.

We have created an archive of letters akin to that compiled during NZ’s worse public health epidemic – the 1919-1920 influenza pandemic. By working with the Auckland War Memorial Museum most of these letters will be housed in a way that makes them available to the public and provides a historic resource for New Zealand’s both now and in the future to understand the impact of COVID-19. This archive has filled a gap in the Museum’s archive as they have very few documents of older New Zealander’s lives in general. In addition this large dataset will continue to be used by students for developing their qualitative research skills.

This study helps raise awareness around some very serious, and pre-existing public health issues such as loneliness and isolation. We have also identified some positive health and social impacts of the lockdown which we are keen to feedback into policy such as the range of contributions older people made to the pandemic relief, the notable ground-swell of intergenerational connection older people observed in their neighbourhoods and the novel ways older people stayed active despite lockdown measures.

Finally, we have begun developing media guidelines to support better reporting of older people’s experiences and views in relation to the pandemic.

• The emergence of COVID-19 was the reason we received funding and made ageism topical, so for this reason the pandemic positively impacted this particular study.
• The pandemic required us to think of innovative ways to collect data which is how we decided on a letter-writing strategy which greatly exceeded the amount of numbers we initially expected (approx. 100). Our participants shared that having the opportunity record their experiences of COVID-19 gave participants a positive thing to do whilst being lockdown.
• The pandemic also made ageism far more explicit in media reporting. As a response we developed a strategy to analyse New Zealand news media which resulted in two publications on this topic (Morgan, 2021a, 2021b).
• We found that using Zoom and the telephone for interviews with New Zealand European participants worked well, but this was not the preferred method for Māori, Chinese, Korean or Pacific participants. This meant that we had to wait for levels to change for some of the data collection in the East Cape to go ahead.

 Older New Zealanders have their say about the COVID-19 Lockdown(external link) — Have Our Say

Outputs from the project to date:

‘A strange time’: letters document Covid lockdown for New Zealand’s elderly(external link) — The Guardian 

The Panel with Zoe George and Neil Millar(external link) — Radio New Zealand

Other outputs:

• Morgan, T., Wiles, J., Williams, L., Gott, M. (2021a): COVID-19 and the portrayal of older people in New Zealand news media Journal of the Royal Society of New Zealand, 51(1), S127-S142.
• Morgan, T., Carey, M., Gott, M., Williams, L., Egli, V., Anderson, N. (2021b) More than mortality data: a news media analysis of COVID-19 deaths in Aotearoa, New Zealand, Kōtuitui: New Zealand Journal of Social Sciences Online, 16(2), 419-431.
• Morgan, T., Gott, M., Williams, L., Wiles, J., Moeke-Maxwell, T., Goodwin, H. (2020) Talking to - not at – older

• Co-design and development of a prototype evidence-based well-being app
• Open trial of this prototype app
• Refinement of the app and completion of a randomized controlled trial

Newly co-designed well-being app with seven evidence-based modules now freely available via app stores:

Whitu iOS app(external link) — iOS App Store

Whitu Android app(external link) — Google Play Store

• Excellent clinical results from app during trial
• Limited dissemination since launch due to lack of implementation funding and MoH funding alternative, less evidence-based e-health interventions for youth well-being.
• Adaptation of app for well-being education in high schools currently underway. Further trials planned.

• Recruitment for the two trials was undertaken via social media
• Focus groups were conducted via Zoom, instead of face-to-face

Whitu: 7 ways in 7 days(external link) —  Auckland Medical Research Foundation 

Update! Whitu: 7 ways in 7 days(external link) —  Auckland Medical Research Foundation 

We used digital technologies and cellphones to conduct serial interviews over a six week period with 23 Ngatiwai and Waikato kaumātua. We identified key themes in our qualitative material with the help of our kaumātua community researchers via Zoom meetings.

• Training events delivered (to the Ministry of Health senior officials concerned with Māori and COVID-19)
• Delivery of a report requested by the Ministry of Health containing findings from our study relevant to Māori attitudes to vaccination
• Conference presentations (New Zealand Psychological Society)
• Journal articles (Journal of the Royal Society of New Zealand;
• Considerable publicity for our findings (Māori TV, Māori radio stations, Newsroom, internal University of Auckland publicity)
• New domestic partnerships developed (the James Henare Centre team received a University of Auckland Research Excellence Medal, partly for this work, and this has opened up new partnerships across the University, currently in development.

• Greater understanding of Māori perspectives and tikanga relating to COVID and to epidemics; greater understanding of the role of kaumātua in Māori communities; greater understanding of kaumātua resilience and wellbeing
• What opportunities have been (or will be) created in our science sectors (such as healthcare, environmental science, primary industries, and biosecurity)
• Our study is a contribution to those involved in healthcare for kaumātua and Māori communities
• Consider describing the ‘pathway to impact’ in instances where long-term impacts have not yet been realised (e.g. collaboration with end users, and improvements in public policy)
• The pathway to impact of our study is via our direct involvement with the Ministry of Health to whom the study was reported in an invited seminar, and invited short report, and a long report at the conclusion of the study; and those in the health sector, particularly Māori health, who have become aware of our study. We expect that our study findings will become integrated into research and teaching literature on Māori health, anthropology and Māori ageing. All this will contribute to reducing inequities in kaumātua health.

• We conducted our research via Zoom (and occasionally telephone) interviews with individuals over a period of time, instead of via wānanga with small groups.
• What new challenges did you face as a result of COVID-19 in the context of your research?
• We were unable to hold kanohi ti kanohi (face to face meetings) and so we developed successful techniques for interviews via Zoom. These involved substantial input from research assistants in getting kaumātua and their supporters up to speed with our digital requirements; although many kaumātua used Facebook of Whatsapp to converse online, only a few had used Zoom. We were unable to consult with our community researchers in person, and this meant that we were able to include them in weekly hui over Zoom, which meant they made a far stronger contribution to the design details, conduct of interviews, and the analysis and theorisation of findings.

Journal article – Hongi, Harirū and Hau: Kaumātua in the time of COVID-19(external link) — Taylor & Francis Online

New article — Covid-19: Vital that tikanga adapts again(external link) — Newsroom

Development of a method for rapid, inexpensive genome sequencing of SARS-CoV-2 to allow rapid tracking of outbreaks, including in resource-poor areas.

We developed a new technique for rapid and inexpensive sequencing of the SARS-CoV-2 genome (the “Midnight method”). This method is now one of the primary methods used globally for whole genome sequencing of the virus that causes COVID-19. The paper describing this work was published and has >65 citations in less than 1.5 years. The open access detailed method on protocols.io has had over 31,400 accessions. 

• The impact of this method has been profound. The Midnight method has enabled countries with limited resources to establish whole genome sequencing at low cost to track the emergence of new COVID-19 variants. For example, many of the first whole genome sequences of omicron from South Africa were sequenced with the Midnight method. It is also regularly used by higher income countries (USA, New Zealand, Canada, UK, etc) to sequence and track variants of COVID-19. This method is the only method now used in New Zealand to sequence the genome of SARS-CoV2, which speaks to its ease of use, rapid turnaround, and low cost.
• A large part of the success of the Midnight method stems from two new international partnerships. The first is with IDT (Integrated DNA Technologies), which sells the primers, one of the custom components necessary for this technique. IDT have now sold the pooled primers for more than one million genome sequencing reactions in over 40 countries.

The second international partnership is with the world’s second largest DNA sequencing company Oxford Nanopore Technologies (ONT). ONT has worked to scale and distribute the Midnight method globally. The ONT midnight kit has been used in over 85 countries and is recommended by ONT as the best approach for COVID-19 genome sequencing. The Midnight method significantly contributed to ONT’s IPO, with the initial valuation of the company at close to £5 billion ($7.3 billion NZD).

Oxford Covid biotech firm makes stellar debut on London stock market(external link) — The Guardian

We developed this method during the first lockdown in 2020. The development was only possible due funding from HRC and rapid communication and collaboration with both international and national researchers. In many ways, this has fundamentally changed the accessibility of science in New Zealand, as this means the science community is necessarily less isolated from other communities in the world.

Original research article of the Midnight method, >65 citations.

Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding(external link) — Oxford Academic

IDT sequencing Midnight kit

xGen SARS-CoV-2-Midnight-1200 Amplicon Panel(external link) — Integrated DNA Technologies

Open access Midnight SARS-CoV-2 genome sequencing protocol, accessed >30,400 times

SARS-CoV2 genome sequencing protocol (1200bp amplicon "midnight" primer set, using Nanopore Rapid kit) V.6(external link) — Protocols.io

Oxford Nanopore Midnight sequencing method

COVID-19(external link) — Nanopore Technologies

Oxford Nanopore Midnight sequencing kit

COVID Maxi: 9216 samples(external link) — Nanopore Technologies

Summary of Midnight method

Genome sequencing assays for infectious disease surveillance(external link) — Drug Discovery World

Summary of Midnight method and profile

SARS-CoV-2: Massey Univ. Profs Develop Method To Quickly Sequence Genome(external link) — Cell & Gene

Announcement by Oxford Nanopore of new kits based on the Midnight method

Oxford Nanopore Midnight Kit for SARS-CoV-2 Sequencing(external link) — Genome Web

Midnight method used to help determine the source of the August COVID-19 2020 Auckland outbreak on Nextstrain.org

Re-emergence of community transmission in Aotearoa New Zealand - Genomic overview of the Auckland Outbreak(external link) — Nextstrain

Radio New Zealand Nights interview on the Midnight method

Sequencing the genome of COVID-19(external link) — New Zealand Geographic

NZ Herald profile of scientists who helped with COVID-19

Big Read: The scientists who helped NZ crush Covid-19(external link) — New Zealand Herald

Dr. Freed discussing how genome sequencing works

Video: Dr Nikki Freed - Covid-19 Testing | Massey University(external link) — YouTube

Massey article on the August 2020 Auckland outbreak

From nasal swab sample to polished genomes in 8 hours.

New method used to sequence COVID-19 genomes in Auckland outbreak(external link) — Massey University – Mō Te Kunenga ki Pūrehuroa

• To extend phylodynamic methods
• To use rich data from a range of sources to directly infer the reproduction number from genetic data using information from publicly available Apple mobility data
• To carry out forecast modelling to understand COVID-19 vaccination and the effect on the New Zealand population and outcomes
• To create an online interactive dashboard.

This project has contributed to improved track and trace capabilities through improvements in genomic sequencing and phylodynamic analysis of SARS-CoV-2.

A new public dashboard Shinyapps tool to easily navigate the results from a complex model has been developed.

COVID-19 Vaccination Modelling(external link) — Institute of Environmental Science and Research

New domestic and international partnerships have been created and include: Te Pūnaha Matatini and The University of Edinburgh, UK

• For our phylodynamic and forecast modelling work, we have been working closely with the Ministry of Health and Government policy makers throughout the Covid-19 pandemic to ensure that our findings were broadly understood and had maximum health impact. We also communicated our work to the general public though our writings (e.g. the Conversation, and as Nextstrain narratives) and via social and mass media where our work has been featured on television, radio, and in news press.
• We have developed a dashboard based on our Covid-19 forecasting work which is publicly accessible and has been used in policy development.
• Phylogenomic results of this project have been published in Nature Communications (with an Altmetric score of 2251 - top 5% of all outputs). A paper on Covid-19 modelling was published in Lancet Regional Western Pacific and was listed as one of the journal’s most-read.
• Surveillance of infectious disease (genomic and forecast modelling) is a rapidly growing area that has been accelerated by the pandemic. The tools, methods, and techniques we have developed as a part of this project, although early examples of their type, are immediately useful. The knowledge gained here indicates that real-time genomic surveillance and infectious disease forecasting can be practical and useful for a wide range of infectious disease outbreaks, and the tools for rapid analysis, inference and visualisation need further development to improve scale, precision, and automation.
• Genomic sequencing of COVID cases has been a key tool in Aotearoa's COVID response. The work done in this grant has helped us to interpret the data we get from genomic sequencing in real time so that it can rapidly inform the public health response. We have developed and refined methods to link cases to clusters, monitor how many cases are coming across the border, uncover cryptic chains of transmission, and track how fast the virus is spreading in the community. The tools and techniques developed here are being used in the ongoing fight against Covid-19 and can be applied to other virus infections such as influenza.
• We undertook modelling work to understand the possible impact of Covid-19 on the Aotearoa New Zealand population (including Māori and Pasifika populations). Under a scenario with an effective vaccine and the Covid-19 Delta variant, we found that very high uptake amongst most age groups is required to prevent outbreak (a population immunity threshold). Higher vaccination rates with a strategy of targeting high risk groups (older ages) lead to lower rates of peak hospitalisations and deaths. A strategy to target younger age groups to minimise the spread of disease leads to lower cases.

We have tested the use of machine learning techniques to support outbreak identification - during the study, we used the information from the three smaller outbreaks and also data available from secondary sources data such as Google trends. These new techniques we found to perform less well with the smaller outbreaks. Future work will refine these methods in the presence of larger outbreaks.

New approaches were needed to ensure systems in place for genomic surveillance were fit-for-purpose for the Covid-19 pandemic.  

New data platforms required development so that we could perform advanced analyses. However, data infrastructure and analytical resource and capability in Aotearoa New Zealand to cope with future pandemics remains inadequate.

Predict and Prevent COVID-19: a data driven innovation project(external link) — Health Research Council of New Zealand

New Zealand study highlights successful COVID-19 vaccination programme will help save lives(external link) — Institute of Environmental Science and Research

Vaccinating 90% much safer than 70% – modelling results 'stark'(external link) — 1 News