Viruses are responsible for more than 50% of all health-care associated gastroenteritis. Of those, norovirus is the leading cause of viral gastroenteritis and adenovirus which  can cause a wide range of clinical diseases. Molecular surveillance of these viruses is essential to identifying prevalent strains that link to epidemics. This is the first Australian study to assess population-level epidemiology of norovirus and adneovirus, highlighting the benefits of using both clinical and environmental samples for surveillance of viruses circulation within the population. A better understanding of the viral strains’ distribution enhances the development of successful vaccines.

PhD Thesis completed by Jennifer Hoi Yin Lun in August 2018.

The protozoan parasites, Cryptosporidium and Giardia represent a major public health concern of water utilities in developed nations. In Australia, marsupials, cattle and sheep are the dominant animals inhabiting water catchment areas and contribute a large volume of manure to catchments. Cryptosporidium fayeri, one of the main species identified in marsupials, was identified in a 29-year-old woman in Sydney in 2009 with identical subtypes found in marsupials in the area. There have also been reports of C. parvum and C. hominis (the most common species found in humans), in kangaroos, a wallaby, possums and bandicoots by independent groups, as well as high prevalence’s of zoonotic genotypes of Giardia in marsupials.

This project conducted a comprehensive study of genotypes of Cryptosporidium and Giardia present in marsupials, pre-weaned cattle and sheep and STP sites, over a three-year period to gain a more thorough understanding of the zoonotic risk these parasites pose to humans. In addition to cataloguing the genotypes present using next generation sequencing technologies, researchers also enumerated the numbers of Cryptosporidium and Giardia (oo)cysts present in samples and conducted a survey of farming practices to determine if particular management practices were associated with a higher or lower prevalence of zoonotic genotypes in pre-weaned cattle and sheep.

This project formed the Mekong node of the Collaboration on Sewage Surveillance for SARS-CoV-2 “ColoSSoS” project after Water Research Australia and the Australian Water Association identified that technology transfer within Australia’s broader region was a logical extension of the local project.

This project transferred leading Australian innovation in the environmental surveillance of SARS-CoV-2 to support the Governments of five countries in the Mekong River Delta (including Vietnam, Cambodia, Laos, Myanmar, and Thailand) to prepare, respond and recover from the COVID-19 pandemic. It established partnerships between Australia and these five countries and transferred SARS-CoV-2 environmental surveillance methods established in Australia by WaterRA and partners. The transfer of these methods has supported each Government’s efforts to monitor SARS-CoV-2 prevalence in water environments (primarily sewage and stormwater), to inform COVID-19 control strategies of the Governments and add to their COVID-19 resilience toolbox. Through developing the set-up for potential cost-effective earlier warning detection systems for COVID-19 outbreaks in each country, the project has supported the long-term strengthening of health security, systems, stability, social cohesion and economic recovery across the Mekong region.

The Collaboration on Sewage Surveillance of SARS-CoV-2 (ColoSSoS) project combined the expertise of more than 50 Australian organisations in R&D activities that have enabled health departments across the country to integrate quantitative measurements of SARS-CoV-2 virus detected in sewage with human clinical PCR test data for COVID-19. This subproject trialled a series of molecular tests to identify the best laboratory protocols for the reliable retrieval of SARS-CoV-2 virus from sewage samples, extraction of the viral RNA and the amplification of viral sequences that can distinguish between SARS-CoV-2 and other closely related types of viruses. Laboratory test control and validation methods were also established. These methods have been implemented in the Victorian state wastewater monitoring programme and are also the foundation for the ongoing development of genome sequencing methods which will be applied to detect and identify emerging variants in the future.

Recycled stormwater has a range of possible uses that have different levels and types of human exposure. Before systems to collect and re-use stormwater are established it is important to identify and measure the risk stormwater poses to human health and the environment. This research collected samples from two sites after 12 rainfall events. Low levels of herbicides and other chemicals were found in all samples, lower than the threshold considered safe by the Australian Guidelines for Drinking Water (ADWG), but higher than levels Environment Protection Agencies permit for injection into natural acquifers. These low levels probably caused some of the toxic effects observed in the in vitro cell culture tests. There were very low levels of pathogens that can infect humans in some samples. It was concluded that stormwater should be treated before being re-used for a range of applications which might include replenishing acquifers and that it would be sensible to survey stormwater catchments and in some cases treat stormwater from specific contaminated sites because this would be more cost-effective than treating the entire stormwater outflow.

Recycled water usually contains extremely low levels of many different chemicals. The Australian Guidelines for Water Recycling (AGWR) require that some of these cannot exceed levels that would pose a risk to health, safety or the environment but there are concerns that one or more of these, or other, unmonitored micropollutants, might present a risk, or that chemicals that individually are harmless might add together and have undesirable effects. This research measured 300 organic micropollutants (listed by the AGWR) in a range of recycled waters and conducted a series of laboratory experiments. It was concluded that the toxic effects of individual chemicals often do add together but that this can be predicted accurately in most cases. Some disinfecting processes used to recycle water produce new micropollutants and it will never be possible to completely analyse the thousands of chemicals in any one water sample. These results led to the recommendation that classical chemical analytical measurement techniques should be complimented by a suite of bioassays which can quantify the total toxicity of all the mixed chemicals within recycled water.

In 2006, strict restrictions on using tap water for gardening or car-washing were imposed in Melbourne but relaxed in 2010-2011 as rainfall replenished depleted reservoirs. During this five-year period residents collected their own greywater from washing machines and laundry, showers, baths, and kitchens. The problem with this is that people with diarrhoea and gastrointestinal illness might soil bed linen or clothes, or have an accident in the bathroom, and inadvertently transfer pathogens into the greywater. The worst-case scenario is that greywater containing infectious pathogens is used to water lettuce in a way that transmits infection to those eating unwashed leaves. The Environmental Protection Agency of Victoria (EPAV) published Guidelines (2008) designed to minimise harm to health or the environment. This research examined 1621 households and concluded that although half knew the guidelines existed, they were not following the advice, but nevertheless, although this study was limited, there appeared to be no significant increase in gastrointestinal illness. This research recommended that future housing design incorporate integrated water management strategies to enable safe greywater collection.