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Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand.

ABSTRACT: New Zealand's COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

SUBMITTER: Jelley L

PROVIDER: S-EPMC9274967 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:New Zealand delayed the introduction of the Omicron variant of SARS-CoV-2 into the community by the continued use of strict border controls through to January 2022. This allowed time for vaccination rates to increase and the roll out of third doses of the vaccine (boosters) to begin. It also meant more data on the characteristics of Omicron became available prior to the first cases of community transmission. Here we present a mathematical model of an Omicron epidemic, incorporating the effects of the booster roll out and waning of vaccine-induced immunity, and based on estimates of vaccine effectiveness and disease severity from international data. The model considers differing levels of immunity against infection, severe illness and death, and ignores waning of infection-induced immunity. This model was used to provide an assessment of the potential impact of an Omicron wave in the New Zealand population, which helped inform government preparedness and response. At the time the modelling was carried out, the date of introduction of Omicron into the New Zealand community was unknown. We therefore simulated outbreaks with different start dates, as well as investigating different levels of booster uptake. We found that an outbreak starting on 1 February or 1 March led to a lower health burden than an outbreak starting on 1 January because of increased booster coverage, particularly in older age groups. We also found that outbreaks starting later in the year led to worse health outcomes than an outbreak starting on 1 March. This is because waning immunity in older groups started to outweigh the increased protection from higher booster coverage in younger groups. For an outbreak starting on 1 February and with high booster uptake, the number of occupied hospital beds in the model peaked between 800 and 3,300 depending on assumed transmission rates. We conclude that combining an accelerated booster programme with public health measures to flatten the curve are key to avoid overwhelming the healthcare system.

Project description:BACKGROUND:Injuries to tendons and ligaments make up a large portion of musculoskeletal injuries, and contribute to significant morbidity and healthcare costs. However, there is currently a poor understanding of the burden of these injuries at a population level. The purpose of this study was to quantify the burden and distribution of tendon and ligament injuries in the Aotearoa/New Zealand population. METHODS:Using the Accident Compensation Corporation (ACC, a no fault comprehensive compensation scheme encompassing all of Aotearoa/New Zealand; population in 2013 4.4 million) database, data specific to tendon and ligament injuries were identified between July 2010 and June 2016. The total number of claims made and the total cost of these claims per financial year were analyzed. Injuries were categorized by anatomical site, gender, ethnicity and age of the claimant. RESULTS:During the 6-year study period, the total number of tendon and ligament injury claims was 1,112,077, with a total cost of over $1.4 billion NZD. There was a 16.2% increase in the number of claims, and a 40% increase in the total cost of these injuries during this period. The majority of claims were made by people of European ethnicity, whilst the number of claims made by people of Asian ethnicity increased at the greatest rate; 52% (from 9047 claims in 2011) during the 6-year study period. Interestingly, Māori (Indigenous New Zealanders) maintained the highest average cost per claim ($1614.05 NZD); 13% more than the overall average cost per claim ($1262.12 NZD). The most common sites of injury were the shoulder and knee; these injuries were also the greatest contributors to overall cost. The total costs of injuries peaked in claimants aged 40-54, irrespective of the number of claims made for that age group. CONCLUSIONS:Health and economic burdens of tendon and ligament injuries in Aotearoa/New Zealand are rising. The high healthcare costs underscore the urgent need for multifaceted interventions to reduce the incidence and improve clinical outcomes of tendon and ligament injuries.

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Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand.

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