Introduction by Croakey: Data linkage, wastewater surveillance, mystery tracking and genomics programs have all proved critical in guiding Victoria’s COVID-19 response and more novel programs are in the pipeline, say Victorian experts.
In her latest article from the recent World Congress of Epidemiology, Nicole MacKee reports for the Croakey Conference News Service on some of Victoria’s innovative epidemiology-driven public health programs and other COVID research presented at the Congress.
Nicole MacKee writes:
Wastewater surveillance and a “turbocharged” data linkage program are among the many innovative tools Victoria has deployed in the battle against COVID-19, say experts.
Introducing a session at the World Congress of Epidemiology last week, Professor Benjamin Cowie, Acting Chief Health Officer of Victoria’s Department of Health, said innovative thinking was needed to “collectively stay ahead of the curve” of COVID.
Wastewater surveillance, for example, was still in its infancy last year but is now central to the state’s COVID-19 response.
“[Wastewater detections] have become a core part of what we review on a daily basis,” Cowie said, noting this tool “could not be more critical” in providing both early and targeted warnings of potential COVID outbreaks.
“If you have a positive detection in a [public housing] tower where you don’t have a known case we can reflex in with testing, [and] it allows us to engage with the communities regarding vaccination,” Cowie said.
“Sometimes it gives us significant lead time in what otherwise would be a disastrous public health outcome, and on other occasions it has proven to be prescient, for instance, in Shepparton, we had 11 days of detections before we got our first case.”
Dr Monica Nolan, Epidemiologist Lead, Wastewater Surveillance for SARS-CoV-2 with the Department of Health, said it could be as little as two hours between a wastewater SARS-CoV-2 detection and review and advising the deputy Chief Health Officer’s office or public health unit for action.
“In the social housing example, we had boots on the ground and testing within 10 hours [of the wastewater detection],” Nolan said. “It’s amazingly quick in the way we are able to integrate data and inform that response.”
Cowie added that wastewater detections were also being used in press conferences as a call to action to COVID-19 boost testing rates in areas of concern.
Rachael Poon of the Victorian Department of Health said the development of the wastewater surveillance program had been a matter of “learning by doing”, with ColoSSoS (Collaboration on Sewage Surveillance of SARS-CoV-2), a collaboration between water utilities researchers and the Health Department, established in February 2020.
Poon said the highly sensitive surveillance methods enable the detection of virus at very low levels. “It’s also very specific, so we know that when we get a detection, it’s SARS-CoV-2.”
The surveillance program is also adaptive to risk, she said. “We have surveillance at both metropolitan and regional settings, and we increase the frequency of sampling depending on what’s happening in terms of dynamic risk and exposure sites,” she said.
Localised testing was also critical and in recent weeks the program had zeroed in on social housing, aged care facilities, and industry sites, Poon said.
Turbocharging data linkage
Dr Stacey Rowe, Director of the COVID-19 Response division of Victoria’s Department of Health, said prior to the pandemic, data linkage – the bringing together of records from the same individual from separate datasets – was already used across several areas, including evaluating the effectiveness of maternal influenza and pertussis vaccination programs in preventing these infections in infants.
“During Victoria’s COVID-19 response, we turbocharged our existing linkage program and established daily, near automated, enduring linkage with several key datasets,” Rowe said.
“Enhanced linked data has been used in several ways including understanding people’s pathways from testing to diagnosis, hospitalisation and death, understanding risk factors for severe disease, and identifying potential hospital-acquired disease.”
Also, Rowe said, linked data has been used to cross-check individuals’ residential address to ensure adherence to isolation orders.
“We were able to monitor emergency department and hospitalisation use,” she said, adding that intensive care unit admissions and ventilator use relative to the onset of illness have also been tracked.
“We see peak ICU and ventilation use occurring between days seven and 21 following illness,” Rowe noted.
Data linkage has also improved the completeness of mortality data.
In the future, Rowe said, data linkage could play a role in exploring the complications associated with SARS-CoV-2 infections.
“Importantly,” she said, “our mortality surveillance program is primed and ready to go to monitor the impact of other events of public health importance, such as influenza and extreme weather events.
“Data saves lives,” she said.
Cowie agreed but added that data only saves lives when it was “appropriately collected, analysed, reported and then acted upon by the decision-makers”.
Rowe highlighted how the COVID-19 response has brought epidemiologists and decision-makers together in real time.
“COVID-19 has put epidemiology and public health onto the world stage, all for the wrong reasons, but I think a benefit of that is we are closer to that decision-making process and making sure that the data and intelligence and the information that is generated through the analyses of epidemiologists is getting into the hands of the people who can make a real difference.”
Cracking mystery cases
Dr Jose Canevari, Manager, COVID-19 Response division of the Victorian Department of Health, outlined the development of a “government secret weapon” to combat the spread of COVID-19.
Canevari led the development of a “Mystery Case Tracker” tool to help identify COVID-19 cases with no known source of acquisition (no link to previous cases or exposure sites).
Mystery cases were a major cause of concern, said Canevari, noting that increasing numbers of such cases indicated that surveillance and contract tracing systems were under stress.
The Mystery Case Tracker used real-time surveillance data to generate reports showing cases, their contacts and exposure sites, and mapping that information against a timeline of the infectious periods of linked cases in the network, he said.
“Not only does this allow us to visualise links and movements that were entered into our database, it can also impute potentially missing links,” he said. “If two individuals have been to nearby places, this tool can detect that proximity and suggest the links we may have missed.”
He said operational epidemiologists have found the tool so useful that a COVID wastewater browser – enabling the mapping of wastewater detections of SARS-CoV-2 – was now under development.
Genomics in COVID
Dr Benjamin Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) and Director of the Doherty Centre for Applied Microbial Genomics, said it had become clear over the past 5-10 years that genomics was the “future for public health microbiology”.
“Genomics provides a higher resolution characterisation of pathogens; it leads to more accurate source attribution and identification of outbreaks,” Howden said.
“There is a global shift to using genomics for public health. It leads to better and more rapid characterisation of antimicrobial resistance and the datasets generated … provide powerful information for understanding the spread of pathogens more broadly.”
He said genomics had key played a role in detection of several recent Victorian outbreaks requiring a public health response, including a 2016 outbreak of Meningococcal W disease; the 2018 listeria outbreak linked to rockmelon; multidrug resistant gonorrhoea in Australia in 2018; and the identification of buruli ulcer bacteria in inner western Melbourne in 2021. It had also proved critical in detecting antimicrobial resistance and in the state’s COVID-19 response.
Howden said the next step was a complete transition to genomics-enabled public health laboratory in Victoria, as well as implementing new approaches to data analysis, including machine learning and genomic modelling. Efforts were also underway to enhance national and international engagement, he said.
“There is no going back. The legacy methods are no longer available for some pathogens and there is an expectation – built partly on the success of technology in COVID-19 – for genomics to be available for infectious disease pathogens of significance in Australia.”
Syndromic surveillance plans
Victoria has more innovative tools in the pipeline, including the Syndromic Surveillance (SynSurv) program. The system has broad aims, from providing early warning of a thunderstorm asthma event to detecting a single severe adverse event following vaccination.
Dr Jim Black, Principal Epidemiologist with the Department of Health, said SynSurv aimed to detect events of public health significance as early as possible, increasing the capacity to respond.
“We have a good notifiable diseases system but often by the time we get enough notifications to know that an event is happening, it’s too late to do very much about it,” Black said.
“SynSurv tries to push the point at which we know about events as early in the illness course as possible, and the sweet spot for us is the point at which the patient first seeks care.”
There was important trade-off, however, between sensitivity and specificity, Black noted.
“The earlier we can get a signal, the earlier we can public health action and potentially resolve a problem with the smallest possible outbreak. So, we don’t want to miss things,” he said. “But, at the same time, we don’t want to waste a lot of people’s time on false alarms, so we are trying to [find] that balance and that is one of the big challenges.”
Croakey’s coverage of the WCE will continue this week.
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