Browsing by Author "Geoghegan JL"

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    A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease.
    (2023-02) Wierenga JR; Morgan KJ; Hunter S; Taylor HS; Argilla LS; Webster T; Dubrulle J; Jorge F; Bostina M; Burga L; Holmes EC; McInnes K; Geoghegan JL
    Yellow-eyed penguins (Megadyptes antipodes), or hoiho in te reo Māori, are predicted to become extinct on mainland Aotearoa New Zealand in the next few decades, with infectious disease a significant contributor to their decline. A recent disease phenomenon termed respiratory distress syndrome (RDS) causing lung pathology has been identified in very young chicks. To date, no causative pathogens for RDS have been identified. In 2020 and 2021, the number of chick deaths from suspected RDS increased four- and five-fold, respectively, causing mass mortality with an estimated mortality rate of >90%. We aimed to identify possible pathogens responsible for RDS disease impacting these critically endangered yellow-eyed penguins. Total RNA was extracted from tissue samples collected during post-mortem of 43 dead chicks and subject to metatranscriptomic sequencing and histological examination. From these data we identified a novel and highly abundant gyrovirus (Anelloviridae) in 80% of tissue samples. This virus was most closely related to Gyrovirus 8 discovered in a diseased seabird, while other members of the genus Gyrovirus include Chicken anaemia virus, which causes severe disease in juvenile chickens. No other exogenous viral transcripts were identified in these tissues. Due to the high relative abundance of viral reads and its high prevalence in diseased animals, it is likely that this novel gyrovirus is associated with RDS in yellow-eyed penguin chicks.
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    COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study
    (Elsevier Ltd, 2021-10) Nguyen T; Adnan M; Nguyen BP; de Ligt J; Geoghegan JL; Dean R; Jefferies S; Baker MG; Seah WKG; Sporle AA; French NP; Murdoch DR; Welch D; Simpson CR
    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 Reff<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 Reff 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.
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    Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
    (Springer Nature Limited, 2022-07-12) Jelley L; Douglas J; Ren X; Winter D; McNeill A; Huang S; French N; Welch D; Hadfield J; de Ligt J; Geoghegan JL
    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.
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    Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus.
    (Elsevier B.V., 2023-11-01) Wierenga JR; Grimwood RM; Taylor HS; Hunter S; Argilla LS; Webster T; Lim L; French R; Schultz H; Jorge F; Bostina M; Burga L; Swindells-Wallace P; Holmes EC; McInnes K; Morgan KJ; Geoghegan JL
    First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as causative agents yet, due to inconsistent cultures and inconclusive pathogenicity, their role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of inquiry to investigate its potential association with DS.
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    Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border
    (Springer Nature Limited, 2022-10-29) Douglas J; Winter D; McNeill A; Carr S; Bunce M; French N; Hadfield J; de Ligt J; Welch D; Geoghegan JL
    In the second quarter of 2022, there was a global surge of emergent SARS-CoV-2 lineages that had a distinct growth advantage over then-dominant Omicron BA.1 and BA.2 lineages. By generating 10,403 Omicron genomes, we show that Aotearoa New Zealand observed an influx of these immune-evasive variants (BA.2.12.1, BA.4, and BA.5) through the border. This is explained by the return to significant levels of international travel following the border's reopening in March 2022. We estimate one Omicron transmission event from the border to the community for every ~5,000 passenger arrivals at the current levels of travel and restriction. Although most of these introductions did not instigate any detected onward transmission, a small minority triggered large outbreaks. Genomic surveillance at the border provides a lens on the rate at which new variants might gain a foothold and trigger new waves of infection.
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    Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
    (F1000 Research Limited, 2021-09-17) O'Toole Á; Hill V; Pybus OG; Watts A; Bogoch II; Khan K; Messina JP; COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Tegally H; Lessells RR; Giandhari J; Pillay S; Tumedi KA; Nyepetsi G; Kebabonye M; Matsheka M; Mine M; Tokajian S; Hassan H; Salloum T; Merhi G; Koweyes J; Geoghegan JL; de Ligt J; Ren X; Storey M; Freed NE; Pattabiraman C; Prasad P; Desai AS; Vasanthapuram R; Schulz TF; Steinbrück L; Stadler T; Swiss Viollier Sequencing Consortium; Parisi A; Bianco A; García de Viedma D; Buenestado-Serrano S; Borges V; Isidro J; Duarte S; Gomes JP; Zuckerman NS; Mandelboim M; Mor O; Seemann T; Arnott A; Draper J; Gall M; Rawlinson W; Deveson I; Schlebusch S; McMahon J; Leong L; Lim CK; Chironna M; Loconsole D; Bal A; Josset L; Holmes E; St George K; Lasek-Nesselquist E; Sikkema RS; Oude Munnink B; Koopmans M; Brytting M; Sudha Rani V; Pavani S; Smura T; Heim A; Kurkela S; Umair M; Salman M; Bartolini B; Rueca M; Drosten C; Wolff T; Silander O; Eggink D; Reusken C; Vennema H; Park A; Carrington C; Sahadeo N; Carr M; Gonzalez G; SEARCH Alliance San Diego; National Virus Reference Laboratory; SeqCOVID-Spain; Danish Covid-19 Genome Consortium (DCGC); Communicable Diseases Genomic Network (CDGN); Dutch National SARS-CoV-2 surveillance program; Division of Emerging Infectious Diseases (KDCA); de Oliveira T; Faria N; Rambaut A; Kraemer MUG
    Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.