Journal Articles

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    Severe weather events and cryptosporidiosis in Aotearoa New Zealand: A case series of space-time clusters.
    (Cambridge University Press, 2024-04-15) Grout L; Hales S; Baker MG; French N; Wilson N
    Occurrence of cryptosporidiosis has been associated with weather conditions in many settings internationally. We explored statistical clusters of human cryptosporidiosis and their relationship with severe weather events in New Zealand (NZ). Notified cases of cryptosporidiosis from 1997 to 2015 were obtained from the national surveillance system. Retrospective space-time permutation was used to identify statistical clusters. Cluster data were compared to severe weather events in a national database. SaTScan analysis detected 38 statistically significant cryptosporidiosis clusters. Around a third (34.2%, 13/38) of these clusters showed temporal and spatial alignment with severe weather events. Of these, nearly half (46.2%, 6/13) occurred in the spring. Only five (38%, 5/13) of these clusters corresponded to a previously reported cryptosporidiosis outbreak. This study provides additional evidence that severe weather events may contribute to the development of some cryptosporidiosis clusters. Further research on this association is needed as rainfall intensity is projected to rise in NZ due to climate change. The findings also provide further arguments for upgrading the quality of drinking water sources to minimize contamination with pathogens from runoff from livestock agriculture.
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    A review and analysis of cryptosporidiosis outbreaks in New Zealand.
    (Cambridge University Press, 2023-06-01) Garcia-R JC; Hayman DTS
    Cryptosporidium is a leading global cause of diarrhoea with many reported outbreaks related to water and zoonotic transmission. This study summarizes data from Public Health Surveillance reports since 2010 in New Zealand to describe exposures associated with human diarrhoea outbreaks caused by Cryptosporidium. We investigate the species and subtypes of cases involved in some of the outbreaks to elucidate transmission routes and the predominant aetiological agents of cryptosporidiosis. For the period 2010–2017, 318 cryptosporidiosis outbreaks were reported in New Zealand resulting in 1634 cases and 20 hospitalizations. The most important mode of transmission was person-to-person (primary infections and secondary or close contacts infections), relating to 260 outbreaks and 1320 cases, followed by 113 outbreaks associated with animals, resulting in 436 human cases. From 2018 to 2021, there were 37 cryptosporidiosis outbreaks associated with 324 cases. We identified the subtypes by using polymerase chain reaction targeting the gp60 gene and the likelihood of mixed subtype infections with the Tracking of Indels by DEcomposition (TIDE) algorithm. Subtype families Ib and Ig of Cryptosporidium hominis and IIa and IId of Cryptosporidium parvum were found among cases; however, C. hominis subtypes occurred in 8 of the 11 outbreaks reviewed where molecular data were available. Examination of the chromatograms showed no mixed subtype infections in the samples assessed. Subtyping data need to be routinely incorporated into national surveillance programmes to better understand the epidemiology, sources, transmission and extent of cryptosporidiosis outbreaks in New Zealand. Our study highlights the value of integrating epidemiological information and molecular typing to investigate and manage clusters of cryptosporidiosis cases.
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    Is transportation a risk factor for African swine fever transmission in Australia: a review
    (John Wiley and Sons Australia, Ltd on behalf of Australian Veterinary Association, 2021-11-02) Neumann EJ; Hall WF; Dahl J; Hamilton D; Kurian A
    African swine fever (ASF) is a viral disease of the pigs that was first described in Africa during the early part of the twentieth century. The disease has periodically occurred outside of Africa, including an ongoing epidemic in Europe and Asia that started in 2007; the disease has never occurred in Australia or New Zealand. Once introduced into a country, spread can occur through direct and indirect routes of transmission. Infected feral pig populations have the potential to act as a long-term reservoir for the virus, making eradication difficult. Just before and throughout the period of clinical signs, ASF virus is shed in oronasal fluids, urine, faeces and blood. This results in contamination of the pig's environment, including flooring, equipment and vehicles. Transportation-related risk factors therefore are likely to play an important role in ASF spread, though evidence thus far has been largely anecdotal. In addition to the existing AUSVETPLAN ASF plan, efforts should be made to improve transportation biosecurity, from the time a pig leaves the farm to its destination. Collection of data that could quantify the capabilities and capacity of Australia to clean and disinfect livestock trucks would help to determine if private and/or public sector investment should be made in this area of biosecurity. No peer-reviewed research was identified that described a specific process for cleaning and disinfecting a livestock truck known to be contaminated with ASF virus, though literature suggests that transportation is an important route of transmission for moving the virus between farms and countries.
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    Transmission models indicate Ebola virus persistence in non-human primate populations is unlikely
    (The Royal Society, 2022-02-02) Hayman DTS; Sam John R; Rohani P
    Infectious diseases that kill their hosts may persist locally only if transmission is appropriately balanced by susceptible recruitment. Great apes die of Ebola virus disease (EVD) and have transmitted ebolaviruses to people. However, understanding the role that apes and other non-human primates play in maintaining ebolaviruses in Nature is hampered by a lack of data. Recent serological findings suggest that few non-human primates have antibodies to EVD-causing viruses throughout tropical Africa, suggesting low transmission rates and/or high EVD mortality (Ayouba A et al. 2019 J. Infect. Dis.220, 1599-1608 (doi:10.1093/infdis/jiz006); Mombo IM et al. 2020 Viruses12, 1347 (doi:10.3390/v12121347)). Here, stochastic transmission models of EVD in non-human primates assuming high case-fatality probabilities and experimentally observed or field-observed parameters did not allow viral persistence, suggesting that non-human primate populations are highly unlikely to sustain EVD-causing infection for prolonged periods. Repeated introductions led to declining population sizes, similar to field observations of apes, but not viral persistence.
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    Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach
    (Elsevier Inc, 2018-03-29) Perez-Acle T; Fuenzalida I; Martin AJM; Santibañez R; Avaria R; Bernardin A; Bustos AM; Garrido D; Dushoff J; Liu JH
    Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which, when it comes to biological processes, could often lead to unrealistic models. Among others, model approaches based on differential equations entangle kinetics and causality, failing when complexity increases, separating knowledge from models, and assuming that the average behavior of the population encompasses any individual deviation. To overcome these limitations, simulations based on the Stochastic Simulation Algorithm (SSA) appear as a suitable approach to model complex biological systems. In this work, we review three different models executed in PISKaS: a rule-based framework to produce multiscale stochastic simulations of complex systems. These models span multiple time and spatial scales ranging from gene regulation up to Game Theory. In the first example, we describe a model of the core regulatory network of gene expression in Escherichia coli highlighting the continuous model improvement capacities of PISKaS. The second example describes a hypothetical outbreak of the Ebola virus occurring in a compartmentalized environment resembling cities and highways. Finally, in the last example, we illustrate a stochastic model for the prisoner's dilemma; a common approach from social sciences describing complex interactions involving trust within human populations. As whole, these models demonstrate the capabilities of PISKaS providing fertile scenarios where to explore the dynamics of complex systems.
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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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    Uncovering the genetic diversity of Giardia intestinalis in isolates from outbreaks in New Zealand
    (BioMed Central Ltd, 2022-12) Ogbuigwe P; Biggs PJ; Garcia-Ramirez JC; Knox MA; Pita A; Velathanthiri N; French NP; Hayman DTS
    BACKGROUND: Giardia intestinalis is one of the most common causes of diarrhoea worldwide. Molecular techniques have greatly improved our understanding of the taxonomy and epidemiology of this parasite. Co-infection with mixed (sub-) assemblages has been reported, however, Sanger sequencing is sometimes unable to identify shared subtypes between samples involved in the same epidemiologically linked event, due to samples showing multiple dominant subtypes within the same outbreak. Here, we aimed to use a metabarcoding approach to uncover the genetic diversity within samples from sporadic and outbreak cases of giardiasis to characterise the subtype diversity, and determine if there are common sequences shared by epidemiologically linked cases that are missed by Sanger sequencing. METHODS: We built a database with 1109 unique glutamate dehydrogenase (gdh) locus sequences covering most of the assemblages of G. intestinalis and used gdh metabarcoding to analyse 16 samples from sporadic and outbreak cases of giardiasis that occurred in New Zealand between 2010 and 2018. RESULTS: There is considerable diversity of subtypes of G. intestinalis present in each sample. The utilisation of metabarcoding enabled the identification of shared subtypes between samples from the same outbreak. Multiple variants were identified in 13 of 16 samples, with Assemblage B variants most common, and Assemblages E and A present in mixed infections. CONCLUSIONS: This study showed that G. intestinalis infections in humans are frequently mixed, with multiple subtypes present in each host. Shared sequences among epidemiologically linked cases not identified through Sanger sequencing were detected. Considering the variation in symptoms observed in cases of giardiasis, and the potential link between symptoms and (sub-) assemblages, the frequency of mixed infections could have implications for our understanding of host-pathogen interactions.
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    Psychosocial impacts of quarantine during disease outbreaks and interventions that may help to relieve strain
    (New Zealand Medical Association, 5/06/2009) Johal S
    The threat of outbreak of infectious disease such as non-seasonal influenza A (H1N1), commonly referred to as Swine Flu, can provoke the implementation of public health control measures such as quarantine. This paper summarises the psychosocial consequences that may follow for patients and health care and other front-line workers when using quarantine controls. Those affected by quarantine are likely to report distress due to fear and risk perceptions. This distress can be amplified in the face of unclear information and communication that is common in the initial period of disease outbreaks. This paper outlines recommendations for care of those in quarantine and those working with them, such as helping to identify stressors and normalising their impact as much as possible. This should take place at all levels of response, from public information and communication messages to individual face-to-face advice and support.