COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study

Background: COVID-19 elimination measures, including border closures have been applied in New Zealand. We have modelled the potential effect of vaccination programmes for opening borders. Methods: We used a deterministic age-stratified Susceptible, Exposed, Infectious, Recovered (SEIR) model. We minimised spread by varying the age-stratified vaccine allocation to find the minimum herd immunity requirements (the effective reproduction number R_eff<1 with closed borders) under various vaccine effectiveness (VE) scenarios and R₀ values. We ran two-year open-border simulations for two vaccine strategies: minimising R_eff and targeting high-risk groups. Findings: Targeting of high-risk groups will result in lower hospitalisations and deaths in most scenarios. Reaching the herd immunity threshold (HIT) with a vaccine of 90% VE against disease and 80% VE against infection requires at least 86•5% total population uptake for R₀=4•5 (with high vaccination coverage for 30-49-year-olds) and 98•1% uptake for R₀=6. In a two-year open-border scenario with 10 overseas cases daily and 90% total population vaccine uptake (including 0-15 year olds) with the same vaccine, the strategy of targeting high-risk groups is close to achieving HIT, with an estimated 11,400 total hospitalisations (peak 324 active and 36 new daily cases in hospitals), and 1,030 total deaths. Interpretation: Targeting high-risk groups for vaccination will result in fewer hospitalisations and deaths with open borders compared to targeting reduced transmission. With a highly effective vaccine and a high total uptake, opening borders will result in increasing cases, hospitalisations, and deaths. Other public health and social measures will still be required as part of an effective pandemic response. Funding: This project was funded by the Health Research Council [20/1018]. Research in context.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

New Zealand, Australia, Iceland, and Taiwan all saw success in controlling their first waves of Coronavirus Disease 2019 (COVID-19). As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19. We employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of Severe acute respiratory syndrome coronavirus 2 in these four countries. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contact tracing strategies. We estimated the effective reproduction number of COVID-19 as 1-1.4 during early stages of the pandemic and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country and that introductions slowed down markedly following the reduction of international travel in mid-March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data. We have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics and for contact tracing.

Exposure of Human Skin Models to KrCl Excimer Lamps: The Impact of Optical Filtering†

Far‐UVC radiation is a promising technology that is potentially both effective at killing airborne microbes such as coronaviruses and influenza, and being minimally hazardous to the skin and eyes. Our previous studies on health risks from far‐UVC have employed a krypton‐chloride (KrCl) excimer lamp, emitting principally at 222 nm, supplemented with an optical filter to remove longer wavelength emissions inherent to these lamps. This study explores KrCl lamp health hazards by comparing filtered and unfiltered KrCl lamps using effective spectral irradiance calculations and experimental skin exposures. Analysis of effective irradiances showed a notable increase in allowable exposure when using a filter. Induction of DNA dimers (CPD and 6‐4PP) was measured in human skin models exposed to a range of radiant exposures up to 500 mJ cm⁻². Compared to sham‐exposed tissues, the unfiltered KrCl lamps induced a statistically significant increase in the yield of both DNA lesions at all the radiant exposures studied. Conversely, filtered KrCl lamps do not induce increased levels of dimers at the current daily TLV exposure limit for 222 nm (23 mJ cm⁻²). This work supports the use of filters for far‐UVC KrCl excimer lamps when used to limit disease transmission in occupied locations.

Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing

Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.

Improved Ultraviolet Radiation Film Dosimetry Using OrthoChromic OC-1 Film†

There is growing interest in far-UVC lighting, defined as wavelengths from 200 to 230 nm, because research has demonstrated these wavelengths to be an effective antimicrobial technology while posing a minimal hazard to human health. Far-UVC lighting is now being installed to directly irradiate spaces where humans are present, and it will be important to perform measurements to verify far-UVC lighting installations are operating within widely accepted exposure guidelines. In this work, we explore the use of a commercially available film, known as OrthoChromic OC-1, to measure ultraviolet radiation exposure. The film was tested with a variety of ultraviolet wavelengths and irradiance conditions, and the color change of the film was analyzed for increasing levels of radiant exposure. The film response extended over a dynamic range that was greater than the recommended exposure limits for far-UVC radiation so it can potentially be useful for health hazard monitoring. The spectrum of the incident ultraviolet radiation strongly affected the response of the film; therefore, for accurate measurements we recommend the measured spectrum match the spectrum used for calibration. Overall, dosimetry with this film provides a simple, accurate, and inexpensive method of quantifying ultraviolet radiation exposure that is suitable for far-UVC measurements.

Proton Irradiation Platforms for Preclinical Studies of High-Dose-Rate (FLASH) Effects at RARAF

Limited availability of proton irradiators optimized for high-dose-rate studies makes the preclinical research of proton FLASH therapy challenging. We assembled two proton irradiation platforms that are capable of delivering therapeutic doses to thin biological samples at dose rates equal to and above 100 Gy/s. We optimized and tested dosimetry protocols to assure accurate dose delivery regardless of the instantaneous dose rate. The simplicity of the experimental setups and availability of custom-designed sample holders allows these irradiation platforms to be easily adjusted to accommodate different types of samples, including cell monolayers, 3D tissue models and small animals. We have also fabricated a microfluidic flow-through device for irradiations of biological samples in suspension. We present one example of a measurement with accompanying preliminary results for each of the irradiation platforms. One irradiator was used to study the role of proton dose rate on cell survival for three cancer cell lines, while the other was used to investigate the depletion of oxygen from an aqueous solution by water radiolysis using short intense proton pulses. No dose-rate-dependent variation was observed between the survival fractions of cancer cells irradiated at dose rates of 0.1, 10 and 100 Gy/s up to 10 Gy. On the other hand, irradiations of Fricke solution at 1,000 Gy/s indicated full depletion of oxygen after proton doses of 107 Gy and 56 Gy for samples equilibrated with 21% and 4% oxygen, respectively.

Differential Immune Modulation With Carbon-Ion Versus Photon Therapy

PURPOSE

Radiation therapy (RT) modulates the immune characteristics of the tumor microenvironment (TME). It is not known whether these effects are dependent on the type of RT used.

METHODS AND MATERIALS

We evaluated the immunomodulatory effects of carbon-ion therapy (CiRT) compared with biologically equivalent doses of photon therapy (PhRT) on solid tumors. Orthotopic 4T1 mammary tumors in immunocompetent hosts were treated with CiRT or biologically equivalent doses of PhRT. Seventy-two hours after RT, tumors were harvested and the immune characteristics of the TME were quantified by flow cytometry and multiplex cytokine analyses.

RESULTS

PhRT decreased the abundance of CD4+ and CD8+ T cells in the TME at all doses tested, with compensatory increases in proliferation. By contrast, CiRT did not significantly alter CD8+ T-cell infiltration. High-dose CiRT increased secretion of proinflammatory cytokines by tumor-infiltrating CD8+ T cells, including granzyme B, IL-2, and TNF-α, with no change in IFN-γ. Conversely, high-dose PhRT increased CD8+ T-cell secretion of IFN-γ only. At most of the doses studied, PhRT increased proliferation of immunosuppressive regulatory T cells; this was only seen with high-dose CiRT. Cytokine analyses of bulk dissociated tumors showed that CiRT significantly increased levels of IFN-γ, IL-2, and IL-1β, whereas PhRT increased IL-6 levels alone.

CONCLUSIONS

At low doses, lymphocytes differ in their sensitivity to CiRT compared with PhRT. Unlike PhRT, low-dose CiRT is generally lymphocyte-sparing. At higher doses, CiRT is a more potent inducer of proinflammatory cytokines and merits further study as a modulator of the immunologic characteristics of the TME.

The Epidemiology of Noise Sensitivity in New Zealand

BACKGROUND

Sensitivity to noise, or nuisance sounds that interrupt relaxation and task-related activities, has been shown to vary significantly across individuals. The current study sought to uncover predictors of noise sensitivity, focussing on possible social and cultural determinants, including social position, education, ethnicity, gender, and the presence of an illness.

METHOD

Data were collected from 746 New Zealand adults residing in 6 areas differentiated by social position. Participants responded to questions probing personal characteristics, noise sensitivity, illness, neighbourhood problems, and noise annoyance. It was hypothesized that those in high-deprivation areas and/or experiencing illness report higher levels of noise sensitivity.

RESULTS

Approximately 50 and 10% of the participants reported being moderately or very noise sensitive, respectively. Significant predictors of noise sensitivity included age, length of residence, level of social deprivation, and self-reported illness.

CONCLUSION

There is evidence of social determinants of noise sensitivity, including social position and residential factors.

Music Listening as Coping Behavior: From Reactive Response to Sense-Making

Coping is a survival mechanism of living organisms. It is not merely reactive, but also involves making sense of the environment by rendering sensory information into percepts that have meaning in the context of an organism's cognitions. Music listening, on the other hand, is a complex task that embraces sensory, physiological, behavioral, and cognitive levels of processing. Being both a dispositional process that relies on our evolutionary toolkit for coping with the world and a more elaborated skill for sense-making, it goes beyond primitive action-reaction couplings by the introduction of higher-order intermediary variables between sensory input and effector reactions. Consideration of music-listening from the perspective of coping treats music as a sound environment and listening as a process that involves exploration of this environment as well as interactions with the sounds. Several issues are considered in this regard such as the conception of music as a possible stressor, the role of adaptive listening, the relation between coping and reward, the importance of self-regulation strategies in the selection of music, and the instrumental meaning of music in the sense that it can be used to modify the internal and external environment of the listener.

Estimating Epidemic Incidence and Prevalence from Genomic Data

Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth–death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here, we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model parameters from genomic sequences and case count data in a manner consistent with the underlying birth–death model. After demonstrating the accuracy of this method on simulated data, we use it to assess the prevalence through time of the early 2014 Ebola outbreak in Sierra Leone.

Forensic STR allele extraction using a machine learning paradigm

We present a machine learning approach to short tandem repeat (STR) sequence detection and extraction from massively parallel sequencing data called Fragsifier. Using this approach, STRs are detected on each read by first locating the longest repeat stretches followed by locus prediction using k-mers in a machine learning sequence model. This is followed by reference flanking sequence alignment to determine precise STR boundaries. We show that Fragsifier produces genotypes that are concordant with profiles obtained using capillary electrophoresis (CE), and also compared the results with that of STRait Razor and the ForenSeq UAS. The data pre-processing and training of the sequence classifier is readily scripted, allowing the analyst to experiment with different thresholds, datasets and loci of interest, and different machine learning models.

Identifying hearing care access barriers among older Pacific Island people in New Zealand: a qualitative study

OBJECTIVES

Hearing loss is one of the most prevalent conditions affecting older people. In addition, there is little known about the factors influencing the uptake of hearing services among underserved communities. Our objective was to identify the barriers to accessing hearing care services among older Pacific Island people in New Zealand.

SETTINGS

Eligible participants from Auckland City, New Zealand.

PARTICIPANTS

Individual face-to-face in-depth interviews were conducted with 36 older Pacific Island people who were experienced hearing difficulties.

METHODS

A Pacific Island research methodology (Talanoa) and the 'Health Care Access Barriers' (HCAB) model, which identifies modifiable barriers to healthcare, was used as a theoretical framework for this research. The interviews were transcribed and analysed using a deductive approach to identify HCAB themes and subthemes experienced by older Pacific Island people.

RESULTS

Identified themes aligned with HCAB's themes of financial, structural and cognitive barriers and subthemes described Pacific Island perspectives related to hearing care access in New Zealand. The financial barriers related to the high cost of hearing care and the structural barriers included transportation difficulties, limited family support, preference for community-based services and the absence of hearing care delivered by family doctors. Community norms and attitudes, communication limitations and limited awareness of hearing care services formed cognitive barriers among older Pasifika people in this study.

CONCLUSION

We identified financial, structural and cognitive barriers that dissuaded older Pasifika people from accessing hearing care services. These modifiable barriers need to be eliminated or minimised to enable people to readily receive the hearing care assistance they need. It is essential to improve and develop culturally responsive models of hearing service delivery to ensure equitable access to hearing care, especially for underserved groups such as Pacific Island communities.

Music and Noise: Same or Different? What Our Body Tells Us

In this article, we consider music and noise in terms of vibrational and transferable energy as well as from the evolutionary significance of the hearing system of Homo sapiens. Music and sound impinge upon our body and our mind and we can react to both either positively or negatively. Much depends, in this regard, on the frequency spectrum and the level of the sound stimuli, which may sometimes make it possible to set music apart from noise. There are, however, two levels of description: the physical-acoustic description of the sound and the subjective-psychological reactions by the listeners. Starting from a vibrational approach to sound and music, we first investigate how sound may activate the sense of touch and the vestibular system of the inner ear besides the sense of hearing. We then touch upon distinct issues such as the relation between low-frequency sounds and annoyance, the harmful effect of loud sound and noise, the direct effects of overstimulation with sound, the indirect effects of unwanted sounds as related to auditory neurology, and the widespread phenomenon of liking loud sound and music, both from the point of view of behavioral and psychological aspects.

Use of Creative Writing to Develop a Semantic Differential Tool for Assessing Soundscapes

Exploring our understanding of soundscapes to understand why and how sound impacts people is important. The aim of this study was to develop a short quantitative questionnaire that would use terms generated by creative writers to assess people’s experiences of a soundscape. This process may provide different items for the questionnaire and thus, potentially, different dimensions or fuller definitions of dimensions that have already been identified. In the preliminary phase, a group of people identifying themselves as good writers listened to recordings of natural, traffic, and human sound environments and wrote about their impressions and responses to each. Qualitative analysis was used to extract themes from the writing. These themes were identified by key words, and scalar items were developed to form a short 17-item questionnaire. The questionnaire was administered to 228 people in Auckland City, New Zealand, with participants recruited from city streets and in a central-city park. Respondents were comfortable to use the questionnaire. Factor analysis revealed patterns of responding with five dimensions: Calming, Protecting, Hectic, Belonging, and Stability. There were correspondences between these and others previously reported in the literature, as well as differences. The use of items derived from creative writing provided interesting insights into the soundscape, including spirituality, the sense of time passing, and physical wellbeing. The park soundscape was measurably better than the street soundscapes on all dimensions, and streets with less vehicular traffic tended to be experienced as more Calming and Protecting, and less Hectic. This implies that there is validity in the scales generated. In future, it would be valuable to test the questionnaire in more varied environments, to add greater variability to the soundscapes.

Health-related quality of life is impacted by proximity to an airport in noise-sensitive people

INTRODUCTION

The aim of the study was to determine whether those who are noise sensitive are more adversely affected by airport noise than those who are not noise sensitive.

PARTICIPANTS AND METHODS

One area was very close to Wellington International Airport and the other was distant from the airport and any other major sources of noise such as motorways and railways. Noise sensitivity was self-rated on a three-point scale as follows: non-noise sensitive, moderately noise sensitive, or highly noise sensitive. Statistical analysis consisted of analyses of variance using the domains of the WHOQOL score with the year, area (airport or the control), and noise sensitivity as covariates.

RESULTS

Noise-sensitive people were found to have a significantly poorer HRQOL than others when they lived near an airport, but not when they lived in the control area. The same effect was present at both of the time points investigated, suggesting that it is a general finding.

DISCUSSION

This finding is consistent with similar studies using the WHOQOL-BREF for investigating noise from road traffic, suggesting consistency in effect across transport noise sources.

Effect of far ultraviolet light emitted from an optical diffuser on methicillin-resistant Staphylococcus aureus in vitro

Drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are a target for new antimicrobial technologies. Far-UVC technology is an emerging disinfection method that directly kills microorganisms using light. In contrast with conventional UV sterilization, far-UVC light has antimicrobial capabilities without apparent harm to mammalian cells. This study examines the application of 224 nm far-UVC light delivered from a laser using an optical diffuser towards the goal of protecting against bacterial invasion around skin penetrating devices. Delivery of far-UVC using a laser and optical fibers enables exposure to unique geometries that would otherwise be shielded when using a lamp. Testing of the bactericidal potential of diffusing the far-UVC laser output over a large area was tested and yielded qualitative area killing results. The killing of MRSA using this method was also examined using an in vitro survival assay. Results followed a classic log-linear disinfection model with a rate constant of k = 0.51 cm2/mJ, which corresponds to an inactivation cross section of D90 = 4.5 mJ/cm2. This study establishes far-UVC delivered from a laser through an optical diffuser as a viable solution for disinfection of susceptible regions such as around catheters, drivelines, or other skin penetrating medical devices.

The Evolution of Soundscape Appraisal Through Enactive Cognition

We propose a framework based on evolutionary principles and the theory of enactive cognition ("being by doing"), that addresses the foundation of key results and central questions of soundscape research. We hypothesize that the two main descriptors (measures of how people perceive the acoustic environment) of soundscape appraisal ('pleasantness' and 'eventfulness'), reflect evolutionarily old motivational and affective systems that promote survival through preferences for certain environments and avoidance of others. Survival is aimed at ending or avoiding existential threats and protecting viability in a deficient environment. On the other hand, flourishing occurs whenever survival is not an immediate concern and aims to improve the agent's viability and by co-creating ever better conditions for existence. As such, survival is experienced as unpleasant, and deals with immediate problems to be ended or avoided, while flourishing is enjoyable, and therefore to be aimed for and maintained. Therefore, the simplest, safety-relevant meaning attributable to soundscapes (audible safety) should be key to understanding soundscape appraisal. To strengthen this, we show that the auditory nervous system is intimately connected to the parts of our brains associated with arousal and emotions. Furthermore, our theory demonstrates that 'complexity' and 'affordance content' of the perceived environment are important underlying soundscape indicators (measures used to predict the value of a soundscape descriptor). Consideration of these indicators allows the same soundscape to be viewed from a second perspective; one driven more by meaning attribution characteristics than merely emotional appraisal. The synthesis of both perspectives of the same person-environment interaction thus consolidates the affective, informational, and even the activity related perspectives on soundscape appraisal. Furthermore, we hypothesize that our current habitats are not well matched to our, evolutionarily old, auditory warning systems, and that we consequently have difficulty establishing audible safety. This leads to more negative and aroused moods and emotions, with stress-related symptoms as a result.

Far-UVC light prevents MRSA infection of superficial wounds in vivo

Background

Prevention of superficial surgical wound infections from drug-resistant bacteria such as methicillin resistant Staphylococcus aureus (MRSA) currently present major health care challenges. The majority of surgical site infections (SSI) are believed to be caused by airborne transmission of bacteria alighting onto the wound during surgical procedures. We have previously shown that far-ultraviolet C light in the wavelength range of 207–222 nm is significantly harmful to bacteria, but without damaging mammalian cells and tissues. It is important that the lamp be fitted with a filter to remove light emitted at wavelengths longer than 230 nm which are harmful.

Aims

Using a hairless mouse model of infection of superficial wounds, here we tested the hypothesis that 222-nm light kills MRSA alighting onto a superficial skin incisions as efficiently as typical germicidal light (254 nm), but without inducing skin damage.

Methods

To simulate the scenario wherein incisions are infected during surgical procedures as pathogens in the room alight on a wound, MRSA was spread on a defined area of the mouse dorsal skin; the infected skin was then exposed to UVC light (222 nm or 254 nm) followed by a superficial incision within the defined area, which was immediately sutured. Two and seven days post procedure, bactericidal efficacy was measured as MRSA colony formation unit (CFU) per gram of harvested skin whereas fixed samples were used to assess skin damage measured in terms of epidermal thickness and DNA photodamage.

Results

In the circumstance of superficial incisions infected with bacteria alighting onto the wound, 222-nm light showed the same bactericidal properties of 254-nm light but without the associated skin damage.

Conclusions

Being safe for patient and hospital staff, our results suggested that far-UVC light (222 nm) might be a convenient approach to prevent transmission of drug-resistant infectious agents in the clinical setting.