Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

BACKGROUND: New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. METHODS: We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. RESULTS: We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. CONCLUSION: Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Concurrent warming and browning eliminate cold-water fish habitat in many temperate lakes.

Cold-water species in temperate lakes face two simultaneous climate-driven ecosystem changes: warming and browning of their waters. Browning refers to reduced transparency arising from increased dissolved organic carbon (DOC), which absorbs solar energy near the surface. It is unclear whether the net effect is mitigation or amplification of climate warming impacts on suitable oxythermal habitat (<20 °C, >5 mgO/L) for cold-loving species because browning expands the vertical distribution of both cool water and oxygen depletion. We analyzed long-term trends and high-frequency sensor data from browning lakes in New York's Adirondack region to assess the contemporary status of summertime habitat for lacustrine brook trout. Across two decades, surface temperatures increased twice as fast and bottom dissolved oxygen declined >180% faster than average trends for temperate lakes. We identify four lake categories based on oxythermal habitat metrics: constrained, squeezed, overheated, and buffered. In most of our study lakes, trout face either seasonal loss (7 of 15) or dramatic restriction (12 to 21% of the water column; 5 of 15) of suitable habitat. These sobering statistics reflect rapid upward expansion of oxygen depletion in lakes with moderate or high DOC relative to compression of heat penetration. Only in very clear lakes has browning potentially mitigated climate warming. Applying our findings to extensive survey data suggests that decades of browning have reduced oxythermal refugia in most Adirondack lakes. We conclude that joint warming and browning may preclude self-sustaining cold-water fisheries in many temperate lakes; hence, oxythermal categorization is essential to guide triage strategies and management interventions.

Summary of National Surveillance Data on Vaccine Preventable Diseases in Australia, 2016-2018 Final Report.

Erratum Two tables within this report, as originally published, contained errors which are notified and corrected here.

Species trait diversity sustains multiple dietary nutrients supplied by freshwater fisheries.

Species, through their traits, influence how ecosystems simultaneously sustain multiple functions. However, it is unclear how trait diversity sustains the multiple contributions biodiversity makes to people. Freshwater fisheries nourish hundreds of millions of people globally, but overharvesting and river fragmentation are increasingly affecting catches. We analyse how loss of nutritional trait diversity in consumed fish portfolios affects the simultaneous provisioning of six essential dietary nutrients using household data from the Amazon and Tonlé Sap, two of Earth's most productive and diverse freshwater fisheries. We find that fish portfolios with high trait diversity meet higher thresholds of required daily intakes for a greater variety of nutrients with less fish biomass. This beneficial biodiversity effect is driven by low redundancy in species nutrient content profiles. Our findings imply that sustaining the dietary contributions fish make to people given declining biodiversity could require more biomass and ultimately exacerbate fishing pressure in already-stressed ecosystems.

A new national health system: the opportunity to address data quality issues in maternal immunisation coverage.

AIM: Maternal immunisation coverage is suboptimal in Aotearoa New Zealand. Our objective was to highlight discrepancies resulting from how maternal immunisation coverage for pertussis and influenza is measured in Aotearoa New Zealand. METHOD: A retrospective cohort study of pregnant people was undertaken using administrative datasets. Maternity and immunisation data from three sources (National Immunisation Register [NIR], general practice [GP], and pharmaceutical claims) were linked to determine the proportion of immunisation records not recorded in the NIR but captured in claims data, and to compare this with coverage data available from Te Whatu Ora - Health New Zealand. RESULTS: We found that while increasing numbers of maternal immunisations are being captured in the NIR, around 10% remain unrecorded on the NIR, but within claims datasets. CONCLUSION: Accurate maternal immunisation coverage data is important for public health action. Implementation of the whole-of-life Aotearoa Immunisation Register (AIR) is an important opportunity to improve completeness and consistency of maternal immunisation coverage reporting.

Ear health and hearing in urban Aboriginal children.

OBJECTIVE: Evaluate ear health and hearing among urban Aboriginal children and quantify relationships with child, family and social factors. METHODS: Baseline questionnaire and ear health examinations from 1430 children with diagnoses (0.5-18 years) attending Aboriginal Health Services enrolled in SEARCH. Ear health outcomes were Otitis Media (OM), and hearing loss (three-frequency average hearing loss >20dB) diagnosed using pneumatic otoscopy, tympanometry, and audiometry. RESULTS: Half the children 0.5-3 years had OM (51.5%, 136/264). One third 0.5-18 years (30.4%; 435/1430) had OM, including 1.8% (26/1430) with perforation (0.8% chronic suppurative OM, 0.6% dry perforation and 0.4% acute OM with perforation). One quarter 0.5-18 years (25.7%; 279/1087) had hearing loss; 12.4% unilateral, 13.2% bilateral (70.6% with bilateral loss had concurrent OM). OM was associated with: younger age (0.5-<3 years versus 6-18 years) age-sex-site; adjusted prevalence ratio (aPR)=2.64, 95%, 2.18-3.19); attending childcare/preschool (aPR=1.24, 95%CI, 1.04-1.49); foster care (aPR=1.40, 95%CI, 1.10-1.79); previous ear infection/s (aPR=1.68, 95%CI, 1.42-1.98); and ≥2 people/bedroom (aPR=1.66, 95%CI, 1.24-2.21). Hearing impairment was associated with younger age (0.5-<6 years vs. ≥6 years aPR=1.89, 95%CI, 1.40-2.55) and previous ear infection (aPR=1.87, 95%CI, 1.31-2.68). CONCLUSIONS: Half the urban Aboriginal children in this cohort had OM and two-thirds with hearing impairment had OM. IMPLICATIONS FOR PUBLIC HEALTH: Findings highlight importance of early detection and support for ear health, particularly in pre-school-aged children with risk factors.

Incremental effectiveness of 23-valent pneumococcal polysaccharide vaccine against pneumonia hospitalisation among Australian Indigenous children: A record linkage study.

BACKGROUND: The impact of pneumococcal conjugate vaccines (PCVs) on pneumonia in children is well-documented but data on 23-valent pneumococcal polysaccharide vaccine (PPV23) are lacking. Between 2001 and 2011, Indigenous children in Western Australia (WA) were recommended to receive PPV23 at 18-24 months of age following 3 doses of 7-valent PCV. We evaluated the incremental effectiveness of PPV23 against pneumonia hospitalisation. METHODS: Indigenous children born in WA between 2001 and 2012 who received PCV dose 3 by 12 months of age were followed from 18 to 60 months of age for the first episode of pneumonia hospitalisation (all-cause and 3 subgroups: presumptive pneumococcal, other specified causes, and unspecified). We used Cox regression modelling to estimate hazard ratios (HRs) for pneumonia hospitalisation among children who had, versus had not, received PPV23 between 18 and 30 months of age after adjustment for confounders. RESULTS: 11,120 children had 327 first episodes of all-cause pneumonia hospitalisation, with 15 (4.6%) coded as presumptive pneumococcal, 46 (14.1%) as other specified causes and 266 (81.3%) unspecified. No statistically significant reduction in all-cause pneumonia was seen with PPV23 (HR 1.11; 95% CI: 0.87-1.43), but the direction of the association differed for presumptive pneumococcal (HR 0.47; 95% CI: 0.16-1.35) and specified (HR 0.89; 95% CI: 0.49-1.62) from unspecified causes (HR 1.13; 95% CI: 0.86-1.49). During the baseline period before PPV23 vaccination (12-18 months), all-cause pneumonia risk was higher among PPV23-vaccinated than unvaccinated children (RR: 1.73; 95% CI: 1.30-2.28). CONCLUSION: In this high-risk population, no statistically significant incremental effect of a PPV23 booster at 18-30 months was observed against hospitalised all-cause pneumonia or the more specific outcome of presumptive pneumococcal pneumonia. Confounding by indication may explain the slight trend towards an increased risk against all-cause pneumonia. Larger studies with better control of confounding are needed to further inform PPV23 vaccination.

When should a longer needle be used for intramuscular injection in obese patients? A combined analysis of New Zealand data.

AIM: To estimate thresholds for Body Mass Index (BMI) and arm circumference above which a longer needle is needed to ensure intramuscular (IM) delivery of a vaccine in the deltoid muscle at the site recommended by New Zealand (NZ) immunization guidelines. METHODS: A combined analysis of two studies, including 442 adults, with measurements of arm circumference, BMI and skin to deltoid muscle distance (SDMD) at the NZ immunization guideline-recommended IM injection site. Receiver Operator Characteristic curves identified arm circumference and BMI cut-points that gave 100% sensitivity for SDMD thresholds. These thresholds were: SDMD of 20 mm, accounting for a minimal penetration of 5 mm into muscle with the standard needle; and 25 mm, which is the length of a standard needle for IM injection, representing the depth this can reach. RESULTS: Cut-point values for arm circumference, at which a longer needle would be required, were higher for males than females: 35 cm versus 30 cm for the 20 mm cut-point, and 40 cm versus 36.7 cm for the 25 mm cut-point respectively. The BMI cut-points were also higher for male than females: 24.6 kg/m2 versus 23.7 kg/m2 for the 20 mm cut-point, and 38.2 kg/m2 vs 31.6 kg/m2 for the 25 mm cut-point respectively. CONCLUSION: Arm circumference and BMI cut-points provide practical measures from which to choose a needle length that increases the chance of successful IM vaccination. Based on our data, an arm circumference of 35 cm for men and 30 cm for women should prompt selection of a longer needle to ensure intramuscular injection at the deltoid site. Thresholds for the different skin to deltoid sites proposed internationally should be determined to enable successful IM vaccination in clinical practice beyond NZ.

Optimal age targeting for pneumococcal vaccination in older adults; a modelling study.

Invasive pneumococcal disease (IPD) risk increases with age for older adults whereas the population size benefiting from pneumococcal vaccines and robustness of immunogenic response to vaccination decline. We estimate how demographics, vaccine efficacy/effectiveness (VE), and waning VE impact on optimal age for a single-dose pneumococcal vaccination. Age- and vaccine-serotype-specific IPD cases from routine surveillance of adults ≥ 55 years old (y), ≥ 4-years after infant-pneumococcal vaccine introduction and before 2020, and VE data from prior studies were used to estimate IPD incidence and waning VE which were then combined in a cohort model of vaccine impact. In Brazil, Malawi, South Africa and England 51, 51, 54 and 39% of adults older than 55 y were younger than 65 years old, with a smaller share of annual IPD cases reported among < 65 years old in England (4,657; 20%) than Brazil (186; 45%), Malawi (4; 63%), or South Africa (134, 48%). Vaccination at 55 years in Brazil, Malawi, and South Africa, and at 70 years in England had the greatest potential for IPD prevention. Here, we show that in low/middle-income countries, pneumococcal vaccines may prevent a substantial proportion of residual IPD burden if administered earlier in adulthood than is typical in high-income countries.

Environmental footprints of farmed chicken and salmon bridge the land and sea.

Food production, particularly of fed animals, is a leading cause of environmental degradation globally.1,2 Understanding where and how much environmental pressure different fed animal products exert is critical to designing effective food policies that promote sustainability.3 Here, we assess and compare the environmental footprint of farming industrial broiler chickens and farmed salmonids (salmon, marine trout, and Arctic char) to identify opportunities to reduce environmental pressures. We map cumulative environmental pressures (greenhouse gas emissions, nutrient pollution, freshwater use, and spatial disturbance), with particular focus on dynamics across the land and sea. We found that farming broiler chickens disturbs 9 times more area than farming salmon (∼924,000 vs. ∼103,500 km2) but yields 55 times greater production. The footprints of both sectors are extensive, but 95% of cumulative pressures are concentrated into <5% of total area. Surprisingly, the location of these pressures is similar (85.5% spatial overlap between chicken and salmon pressures), primarily due to shared feed ingredients. Environmental pressures from feed ingredients account for >78% and >69% of cumulative pressures of broiler chicken and farmed salmon production, respectively, and could represent a key leverage point to reduce environmental footprints. The environmental efficiency (cumulative pressures per tonne of production) also differs geographically, with areas of high efficiency revealing further potential to promote sustainability. The propagation of environmental pressures across the land and sea underscores the importance of integrating food policies across realms and sectors to advance food system sustainability.

Extensive global wetland loss over the past three centuries.

Wetlands have long been drained for human use, thereby strongly affecting greenhouse gas fluxes, flood control, nutrient cycling and biodiversity1,2. Nevertheless, the global extent of natural wetland loss remains remarkably uncertain3. Here, we reconstruct the spatial distribution and timing of wetland loss through conversion to seven human land uses between 1700 and 2020, by combining national and subnational records of drainage and conversion with land-use maps and simulated wetland extents. We estimate that 3.4 million km2 (confidence interval 2.9-3.8) of inland wetlands have been lost since 1700, primarily for conversion to croplands. This net loss of 21% (confidence interval 16-23%) of global wetland area is lower than that suggested previously by extrapolations of data disproportionately from high-loss regions. Wetland loss has been concentrated in Europe, the United States and China, and rapidly expanded during the mid-twentieth century. Our reconstruction elucidates the timing and land-use drivers of global wetland losses, providing an improved historical baseline to guide assessment of wetland loss impact on Earth system processes, conservation planning to protect remaining wetlands and prioritization of sites for wetland restoration4.

Mapping the planet's critical natural assets.

Sustaining the organisms, ecosystems and processes that underpin human wellbeing is necessary to achieve sustainable development. Here we define critical natural assets as the natural and semi-natural ecosystems that provide 90% of the total current magnitude of 14 types of nature's contributions to people (NCP), and we map the global locations of these critical natural assets at 2 km resolution. Critical natural assets for maintaining local-scale NCP (12 of the 14 NCP) account for 30% of total global land area and 24% of national territorial waters, while 44% of land area is required to also maintain two global-scale NCP (carbon storage and moisture recycling). These areas overlap substantially with cultural diversity (areas containing 96% of global languages) and biodiversity (covering area requirements for 73% of birds and 66% of mammals). At least 87% of the world's population live in the areas benefitting from critical natural assets for local-scale NCP, while only 16% live on the lands containing these assets. Many of the NCP mapped here are left out of international agreements focused on conserving species or mitigating climate change, yet this analysis shows that explicitly prioritizing critical natural assets and the NCP they provide could simultaneously advance development, climate and conservation goals.

Real world impact of 13vPCV in preventing invasive pneumococcal pneumonia in Australian children: A national study.

BACKGROUND: We aimed to assess the direct protective effect of 13 valent pneumococcal conjugate vaccine (13vPCV) against invasive pneumococcal pneumonia (IPP; including pneumonia and empyema) in children using a nation-wide case-control study across 11 paediatric tertiary hospitals in Australia. METHODS: Children < 18 years old admitted with pneumonia were eligible for enrolment. IPP was defined as Streptococcus pneumoniae (SP) cultured or detected by polymerase chain reaction (PCR) from blood or pleural fluid. Causative SP serotype (ST) was determined from blood or pleural fluid SP isolates by molecular methods in PCR positive specimens or else inferred from nasopharyngeal isolates. For each IPP case, 20 population controls matched by age and socio-economic status were sampled from the Australian Immunisation Register. Conditional logistic regression was used to estimate the adjusted odds ratio (aOR) of being fully vaccinated with 13vPCV (≥3 doses versus < 3 doses) among IPP cases compared to controls, adjusted for sex and Indigenous status. RESULTS: From February 2015 to September 2018, we enrolled 1,168 children with pneumonia; 779 were 13vPCV-eligible and were individually matched to 15,580 controls. SP was confirmed in 195 IPP cases, 181 of whom had empyema. ST3 and ST19A were identified in 52% (102/195) and 11% (21/195) of IPP cases respectively. The aOR of being fully vaccinated with 13vPCV was 0.8 (95% CI 0.6-1.0) among IPP cases compared to matched controls. CONCLUSION: We failed to identify a strong direct protective effect of 13vPCV against IPP among Australian children, where disease was largely driven by ST3.

Acute Flaccid Paralysis in Australian Children from 2007 to 2017.

INTRODUCTION: Acute flaccid paralysis (AFP) surveillance continues globally as part of the World Health Organization's goal to eradicate poliomyelitis. The Australian Paediatric Surveillance Unit (APSU), Paediatric Active Enhanced Disease Surveillance (PAEDS) network, and National Enterovirus Reference Laboratory (NERL) collaborate in AFP surveillance in Australia, capturing and reviewing cases of AFP for all aetiologies in order to exclude poliovirus. We aimed to describe the AFP epidemiology in childhood over an 11 year period. METHODS: Data were reported nationally by paediatricians via prospective APSU surveillance, PAEDS surveillance nurses at five tertiary paediatric hospitals and NERL from 2007 to 2017. Children aged 0-15 years with AFP were included. We combined APSU, PAEDS, and NERL datasets, analysed epidemiological trends, and described clinical features and investigations for major diagnoses. RESULTS: Of 590 AFP-compatible cases, 49% were male; 47% were aged 0-4 years, 9% aged <1 year. Annual incidence of AFP was 1.3 cases per 100,000 children aged <15 years. Lower limb paralysis was the most frequent presenting symptom. The most frequent diagnoses were Guillain-Barre syndrome (GBS; 36%), transverse myelitis (TM; 17%), and acute disseminated encephalomyelitis (ADEM; 15%). No secular trend was seen in frequency of AFP cases nor amongst major diagnoses. Seasonality was observed with ADEM occurring more frequently in winter. We observed periods of increased AFP frequency in 2013 and 2016, coinciding with increased reporting of non-polio anterior horn cell disease (AHCD) and detection of non-polio enterovirus (NPEV). CONCLUSIONS: Estimated incidence of GBS, ADEM, and TM in Australian children was comparable with international rates. There was stable incidence of AFP in Australian children between 2007 and 2017. GBS, ADEM, and TM are the major causes of AFP. We observed clustering of cases associated with NPEV that emphasises a need for ongoing vigilance in surveillance given continue emerging infectious disease threats.

Estimating the excess burden of pertussis disease in Australia within the first year of life, that might have been prevented through timely vaccination.

BACKGROUND: Previous Australian studies have shown that delayed vaccination with each of the three primary doses of diphtheria-tetanus-pertussis-containing vaccines (DTP) is up to 50 % in certain subpopulations. We estimated the excess burden of pertussis that might have been prevented if (i) all primary doses and (ii) each dose was given on time. METHODS: Perinatal, immunization, pertussis notification and death data were probabilistically linked for 1 412 984 infants born in two Australian states in 2000-12. A DTP dose administered >15 days after the recommended age was considered delayed. We used Poisson regression models to compare pertussis notification rates to 1-year of age in infants with ≥1 dose delayed (Aim 1) or any individual dose delayed (Aim 2) versus a propensity weighted counterfactual on-time cohort. RESULTS: Of all infants, 42% had ≥1 delayed DTP dose. We estimated that between 39 to 365 days of age, 85 (95% CI: 61-109) cases per 100 000 infants, could have been prevented if all infants with ≥1 delayed dose had received their three doses within the on-time window. Risk of pertussis was higher in the delayed versus the on-time cohort, so crude rates overestimated the excess burden (110 cases per 100 000 infants (95% CI: 95-125)). The estimated dose-specific excess burden per 100 000 infants was 132 for DTP1, 50 for DTP2 and 19 for DTP3. CONCLUSIONS: We provide robust evidence that improved DTP vaccine timeliness, especially for the first dose, substantially reduces the burden of infant pertussis. Our methodology, using a potential outcomes framework, is applicable to other settings.

Can preserved museum specimens be used to reconstruct fish mercury burden and sources through time?

To evaluate the utility of preserved fishes for reconstructing historical and spatial patterns of mercury (Hg) exposure, we experimentally tested the stability of Hg concentrations and Hg stable isotope ratios under standard museum practices of specimen preservation. We found that loss of unidentified constituents during preservation increased Hg concentrations in fish muscle. Low-Hg fish reared in the laboratory were susceptible to exogenous contamination with inorganic mercury (iHg) when preservative fluids were intentionally spiked or iHg leached passively from contaminated wild fishes in the same container. This contamination impacted Hg isotope values of total Hg, but the conservative nature of methylmercury allows us to quantitatively correct for iHg contamination. Our findings validate the potential to use fishes from the world's museums to generate spatiotemporal baselines for the Minamata Convention on Mercury, but we recommend a set of precautions to maximize inference strength. Selecting the largest specimens of a target species helps dilute any iHg contamination. Specimens should be drawn from lots that were not comingled with fishes from other collections to minimize risk of iHg transfer among fish with different contamination histories. Finally, focusing on low-lipid species will enhance the comparability of Hg concentrations between historical and contemporary collections.

Effectiveness of influenza vaccination in reducing influenza-like illness and related antibiotic prescriptions in adults from a primary care-based case-control study.

BACKGROUND: Evidence on the effectiveness of influenza vaccine in preventing antibiotic prescriptions for influenza-like illness (ILI) in adults is limited. METHODS: A primary care-based case-control study was conducted to estimate influenza vaccine effectiveness (VE) against influenza-like illness (ILI) and antibiotic prescribing for ILI in adults aged ≥40 years. Cases were patients diagnosed with ILI from 1st June to 30th September in each year, 2015-2018; a subset of those with ILI prescribed antibiotics was also defined. Controls were patients attending a practice who did not receive an ILI diagnosis. Generalised estimating equations were used to calculate adjusted VE overall, by age (<65 versus ≥65 years) and comorbidity status. RESULTS: The number of ILI cases varied from 558 in 2018 to 2901 in 2017 and controls from 86618 in 2015 to 136763 in 2017. Over 4 years the pooled estimate of VE was 24% (95%CI, 11% to 34%) against ILI and 15% (95%CI, -3% to 29%) against antibiotic prescription for ILI. Influenza vaccine was effective in reducing ILI with an associated antibiotic prescriptions in patients aged <65 years (VE=23%, 95%CI, 3% to 38%) and if no comorbidities were recorded (VE=22%, 95%CI, 1% to 39%) but not in other subgroups. CONCLUSIONS: Influenza vaccine reduced the likelihood of antibiotic prescriptions for ILI in low-risk adults (40-64 years and those without comorbidities).

Body size has primacy over stoichiometric variables in nutrient excretion by a tropical stream fish community.

Ecological Stoichiometry (ES) and the Metabolic Theory of Ecology (MTE) are the main theories used to explain consumers' nutrient recycling. ES posits that imbalances between an animal's body and its diet stoichiometry determine its nutrient excretion rates, whereas the MTE predicts that excretion reflects metabolic activity arising from body size and temperature. We measured nitrogen, phosphorus and N:P excretion, body N:P stoichiometry, body size, and temperature for 12 fish species from a Brazilian stream. We fitted competing models reflecting different combinations of ES (body N:P, armor classification, diet group) and MTE (body size, temperature) variables. Only body size predicted P excretion rates, while N excretion was predicted by body size and time of day. N:P excretion was not explained by any variable. There was no interspecific difference in size-scaling coefficients neither for N nor for P. Fitted size scaling coefficients were lower than the MTE prediction of 0.75 for N (0.58), and for P (0.56). We conclude that differences in nutrient excretion among species within a shared environment primarily reflect contrasts in metabolic rates arising from body size, rather than disparities between consumer and resource stoichiometry. Our findings support the MTE as the primary framework for predicting nutrient excretion rates.