Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Oral and Faecal Viromes of New Zealand Calves on Pasture With an Idiopathic Ill-Thrift Syndrome(John Wiley and Sons Ltd, 2025-07-28) Grimwood RM; Darnley JA; O’Connell JP; Hunt H; Taylor HS; Lawrence KE; Abbott MBW; Jauregui R; Geoghegan JL; Zhai S-LSince 2015, an idiopathic ill-thrift syndrome featuring diarrhoea and, in some cases, gastrointestinal ulceration has been reported in weaned New Zealand dairy calves. Similar syndromes have been described in the British Isles and Australia, but investigations in New Zealand have yet to identify a specific cause. Notably, the viromes of affected calves remain understudied. We conducted metatranscriptomic analyses of oral and faecal viromes in 11 calves from a dairy farm in Taranaki, New Zealand, experiencing an outbreak of this syndrome. This included nine calves showing clinical signs. Our analysis identified 18 bovine-associated viruses across two DNA and three RNA viral families, including six novel species. Oral viromes were dominated by Pseudocowpox virus, which was detected in all calves with oral lesions. Faecal viromes were more diverse, featuring adenoviruses, caliciviruses, astroviruses and picornaviruses. Bovine bopivirus, from the Picornaviridae family and previously unreported in New Zealand, was significantly associated with calves showing oral lesions and diarrhoea, indicating a possible link to disease, though its role remains unclear. The diverse viral communities of the calves complicate the identification of a single causative agent. Importantly, no novel viruses were significantly associated with the syndrome, and the viromes closely resembled those found in cattle globally. These findings suggest the syndrome likely has a multifactorial origin involving nutritional, management and environmental factors rather than being driven primarily by known or novel viruses. Further, research across regions and seasons is recommended to clarify the role of viruses in idiopathic ill-thrift among New Zealand calves.Item Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.(Cold Spring Harbor Laboratory, 2024-07-17) Jelley L; Douglas J; O'Neill M; Berquist K; Claasen A; Wang J; Utekar S; Johnston H; Bocacao J; Allais M; de Ligt J; Ee Tan C; Seeds R; Wood T; Aminisani N; Jennings T; Welch D; Turner N; McIntyre P; Dowell T; Trenholme A; Byrnes C; SHIVERS investigation team; Webby R; French N; Winter D; Huang QS; Geoghegan JLHuman respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.Item Avian Influenza Virus Surveillance Across New Zealand and Its Subantarctic Islands Detects H1N9 in Migratory Shorebirds, but Not 2.3.4.4b HPAI H5N1(John Wiley and Sons Ltd, 2025-04) Waller SJ; Wierenga JR; Heremia L; Darnley JA; de Vries I; Dubrulle J; Robinson Z; Miller AK; Niebuhr CN; Melville DS; Schuckard R; Battley PF; Wille M; Alai B; Cole R; Cooper J; Ellenberg U; Elliott G; Faulkner J; Fischer JH; Fyfe J; Hay L; Houston D; Keys BC; Long J; Long R; Mattern T; McGovern H; McNutt L; Moore P; Neil O; Osborne J; Pagé A-S; Parker KA; Perry M; Philp B; Reid J; Rexer-Huber K; Russell JC; Sagar R; Ruru TT; Thompson T; Thomson L; Tinnemans J; Uddstrom L; Waipoua TA; Walker K; Whitehead E; Wickes C; Young MJ; McInnes K; Winter D; Geoghegan JLHighly pathogenic avian influenza (HPAI) virus subtype H5N1 has never been detected in New Zealand. The potential impact of this virus on New Zealand's wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of H5N1 during the annual 2023–2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.Item Preparing for the next pandemic: insights from Aotearoa New Zealand's Covid-19 response(Elsevier Ltd, 2025-03-18) French NP; Maxwell H; Baker MG; Callaghan F; Dyet K; Geoghegan JL; Hayman DTS; Huang QS; Kvalsvig A; Russell E; Scott P; Thompson TP; Plank MJIn 2020 Aotearoa New Zealand, like many other countries, faced the coronavirus pandemic armed with an influenza-based pandemic plan. The country adapted rapidly to mount a highly strategic and effective elimination response to the SARS-CoV-2 pandemic. However, implementation was hampered by gaps in pandemic preparedness. These gaps undermined effectiveness of the response and exacerbated inequitable impacts of both Covid-19 disease and control measures. Our review examines the Covid-19 response, reflecting on strengths, limitations and implications for pandemic planning. We identify three key areas for improvement: 1) development of a systematised procedure for risk assessment of a new pandemic pathogen; 2) investment in essential capabilities during inter-pandemic periods; and 3) building equity into all stages of the response. We present a typology of potential pathogens and scenarios and describe the evidence assessment process and core capabilities required for countries to respond fluidly, equitably, and effectively to a rapidly emerging pandemic threat.Item 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 JLIn 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.Item 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 JLNew 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.Item 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 JLYellow-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.