What can you expect if you get a call from a COVID contact tracer?



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Tambri Housen, Australian National University

“Test, trace and isolate” has become the catch cry of the COVID-19 pandemic. It’s recognised as an essential strategy for containing the spread of the virus.

The “trace” part, of course, refers to contact tracing — the process of identifying people who may have come into contact with an infected person, so we can prevent further transmission of the virus.

Contact tracing can only be successful if three things happen:

  1. the contact tracer asks the right questions

  2. the person who has tested positive provides detailed and accurate information on whom they’ve had contact with

  3. every person identified as a close contact can be reached and quarantines as requested.

So what can you expect if a contact tracer calls you?




Read more:
Explainer: what is contact tracing and how does it help limit the coronavirus spread?


The contact tracer’s puzzle

If you’ve tested positive for COVID-19, a public health officer will call to interview you. The contact tracer is interested in two specific time periods.

The first piece of the contact-tracing puzzle is the time from two days before you developed your first symptoms until the time you began your isolation. This is known as the “infectious period”.

If you didn’t develop symptoms, you will be asked about the two days prior to your test and the period after you were tested until you began isolating.

Contact tracers are interested in the infectious period because this is when someone who has tested positive is most likely to infect others.

A group of adults clinking wine glasses.
Contact tracers seek to find out who you might have passed the virus onto.
Shutterstock

Contact tracers will ask you to recall everywhere you went during your infectious period, whom you were with, what type of contact you had with each person, and for how long.

For example, if you went to the pub for dinner you’re likely to be asked:

  • where did you sit?

  • who was with you?

  • how long were you at the pub for?

  • did the staff serve at the table or did you order at the bar?

  • did you go to the bathroom?

  • was there social distancing?

  • did you talk to anyone else (other than the people you were with)?

There might be more questions too.

Based on all this information, contact tracers will determine who meets the definition of a close contact and therefore needs to be called, asked to quarantine, and followed up to check if they develop symptoms.




Read more:
How long are you infectious when you have coronavirus?


The second piece of the puzzle is the “incubation period”. Experts believe the incubation period for COVID-19 is up to 14 days. This means if you’re going to develop COVID symptoms, it’s likely to happen within 14 days of you being exposed to the virus.

So, if you test positive, contact tracers will also ask you where you’ve been and whom you were with for the 14 days before you developed symptoms.

For contact tracers this information is essential. It can be the difference between being able to stop the spread or seeing many more people become infected with the virus.

When two or more people who have tested positive for COVID-19 report being at the same place at the same time, this leads to a more in-depth epidemiological investigation, and can help identify other people who may have also been exposed to the virus at this place and time.

Essentially, the first piece of the puzzle is about ascertaining to whom you might have spread the virus, whereas the second is more concerned with whom you might have picked it up from.

What if I can’t remember?

Many of us can’t remember what we did two days ago, let alone every day for 14 days. Contact tracers may use a variety of tools to help you remember where you were and what you were doing.

They may ask you to look up your bank statements to recall where you used your debit or credit card (they won’t ask to see this, but it can help jog your memory). They may also ask you to check your text messages, social media posts and photos you’ve taken on your phone as a way of helping you remember.

What about my right to privacy?

It’s not usual to be asked about where you were every minute of every day. On top of dealing with the diagnosis of COVID-19, this can be a confronting experience. It can feel like an invasion of privacy and it might feel threatening.

Some people may be involved in things they don’t want others, including people close to them, to know about. For example, a teenager may not want their parents to find out they were somewhere they shouldn’t have been; an adult having an affair or taking part in an illegal activity may want to keep their movements private.

There are many reasons people may not feel comfortable disclosing their exact movements at every moment of the day to a stranger on the phone.

However, if you are in this position, to keep your loved ones and community safe, it’s essential you answer the contact tracer’s questions honestly and to the very best of your ability.

Contact tracers are not there to judge you, report you or get you into trouble. They’re bound by the Privacy Act 1988, which sets out that health information can only be used for the primary purpose for which it is collected. So information collected through contact tracing can only be used for contact tracing.

A woman sits on a couch, wrapped in a blanket, speaking on the phone. She has a laptop in front of her.
A contact tracing call can be confronting.
Shutterstock

Ensuring confidence in the process

It’s important to understand there may be many reasons why people make decisions to disclose or not disclose particular things.

Last week, authorities made judgemental statements and revealed the gender, nationality and place of work of the person in South Australia who tested positive for COVID-19 and didn’t fully disclose their movements. This “blame game”, which spread to the media and onto social media, is not OK.

We need to build a culture of trust so people feel comfortable disclosing personal and private information, knowing they won’t be judged or punished as a result. This is how we’ll get the best results from contact tracing.




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Hating on the Woodville Pizza guy won’t fix a problem that was entirely foreseeable


The Conversation


Tambri Housen, Epidemiologist | Senior Research Fellow, National Centre for Epidemiology and Population Health, Australian National University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Exponential growth in COVID cases would overwhelm any state’s contact tracing. Australia needs an automated system


C Raina MacIntyre, UNSW

The people at highest risk of getting infected with SARS-CoV-2, the virus that causes COVID-19, are close contacts of infected cases. So tracking these close contacts, and quarantining them so they can’t infect others, is key to efficient epidemic control. Sometimes we also have to track contacts who attend venues where super-spreading occurs.

Victoria’s second wave prompted the National Cabinet to order a review into contact tracing, which became a flashpoint during the crisis.

The report, by Australian Chief Scientist Alan Finkel and released on Friday, broadly makes the following recommendations:

  • establish performance metrics on the speed of testing and contact tracing

  • states and territories should pursue their own contact tracing systems, but have a national digital data exchange mechanism

  • invest in technology, automation and digital systems for outbreak management

  • strengthen the public health workforce, training and career tracks, as well as surge capacity for outbreaks

  • go hard, go early and never fall behind

  • maintain other public health measures such as social distancing, personal hygiene and early testing; and use waste-water surveillance for early warning of community transmission

  • engage and communicate with communities, including those in higher risk groups and those with with diverse cultural or language needs.

We must invest in the public health workforce

The report recognises the efforts of all jurisdictions in continually improving mechanisms for control of COVID. It also recognises some of the challenges posed by confusing and inconsistent terminology, and also in differing testing protocols between jurisdictions.

It also reviews various digital technologies used to help with outbreak management across Australia, some of which are linked to pathology testing, and others to attendance at public venues, schools or workplaces. In Western Australia, for example, the G2G app enables facial recognition and mobile phone location data to help police to enforce quarantine.

Another strength of the report is the recognition of the public health workforce as a distinct and equally important part of the pandemic response as the clinical workforce.

Early in the pandemic, we did well to expand ICU beds and ventilator capacity. However, the requirements for public health capacity during pandemics has long been neglected. Victoria was under-resourced compared to other states and had fewer trained personnel for contact tracing and outbreak response, so when clusters began occurring in June, authorities were unable to stamp them out as NSW had done.

The report recommends surge capacity but no specific strategies. One strategy could involve harnessing the thousands of Bachelors or Masters of Public Health students and graduates around Australia. A course on contact tracing and surveillance within these degrees could create a large surge capacity of people with more baseline public health knowledge, compared with other options used in Victoria.




Read more:
Where did Victoria go so wrong with contact tracing and have they fixed it?


Manual contact tracing can’t keep up with exponential growth

However, while Victoria was compared to NSW unfavourably, NSW has not yet been stressed with substantial daily community case numbers, and may also be unable to keep up without digital tracing.

This is actually the crux of the problem. If an epidemic grows too large, no city or state — no matter how well-resourced — will be able to keep up with contact tracing using manual methods such as whiteboards, phone calls or SMS.

What the report doesn’t make clear is the enormous human resources requirement for contact tracing, how rapidly it increases and becomes unfeasible, and the critical importance of digital contact tracing methods which will automate the identification of contacts.

Every person with COVID will have 10-20 contacts to trace, which means if you have 100 cases a day, you need to trace 1,000-2,000 contacts within 24-48 hours. If you don’t trace them rapidly, you will miss the window of opportunity to prevent them infecting others. If you don’t trace them all, you will face a growing backlog and lose control of the epidemic.

Compounding this is the exponential growth of epidemics. New cases per day can grow from 20 to 700 in a matter of weeks, as we saw in Victoria, so the task of keeping up with contact tracing becomes more and more difficult as an epidemic grows.

Even in Wuhan, the human resource capacity for contact tracing was exceeded when the outbreak reached thousands of new cases a day – equating to tens of thousands of contacts to be traced every day, and hundreds of thousands being monitored in quarantine at any one time. So authorities used digital contact tracing to keep up.

Australia should expand public health workforce and implement automated contact tracing

Of the different digital tools discussed in the report, automated contact tracing is only mentioned fleetingly, but is essential.

This could be done with QR codes and a colour-coded alert system, as was used in China. With their QR code, people receive a colour code – if they are green, they are free to move about; if orange or red, they must quarantine.

We’ve heard many stories of restaurants and entertainment venues breaching requirements for recording patron details, so that when an outbreak occurs, we have no information to enable contact tracing.

To use QR codes successfully, there has to be enforcement and substantial disincentives to noncompliance.

Australia’s COVIDSafe App, in contrast, was an opt-in app that users had to download themselves, and has had low uptake and some technical issues. Other automated methods that do not require people to actively opt in include harnessing location data from mobile phones, credit card use and other digital footprints. However, many of these raise privacy issues, which is likely why they have been used less in Western countries than in Asia.

The bottom line is that finding all cases and tracing their contacts are the most important strategies to mitigate epidemic growth. We need to have methods to scale up vastly and rapidly with both manual and digital tracing in the event of an epidemic blowout.




Read more:
South Australia’s COVID outbreak: what we know so far, and what needs to happen next


The Conversation


C Raina MacIntyre, Professor of Global Biosecurity, NHMRC Principal Research Fellow, Head, Biosecurity Program, Kirby Institute, UNSW

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Where did Victoria go so wrong with contact tracing and have they fixed it?


Catherine Bennett, Deakin University

Victoria’s contact tracing system has faced criticism in the past for being inefficient, with officials flying to NSW in September to learn from that state.

Comparisons are difficult in a pandemic because each outbreak has its own unique characteristics. That said, there are some key features that underpin the differing responses of NSW and Victoria when it comes to contact tracing.

Fundamentally, NSW’s system of decentralised local area health districts meant when the second wave hit, that state was able to draw on teams embedded in their local communities to manage contact tracing. These teams worked independently but also in concert under the mothership of NSW Health.

In Victoria, a legacy of cuts left the Department of Health and Human Services under-resourced and highly centralised, meaning there was a smaller base upon which to build the surge contact tracing capacity (with some contact tracers coming from interstate).

This was further challenged with the rapid rise in daily new cases, from 65 to 288 in one week alone in July. Systems had to be developed quickly to manage large quantities of data and feed it back to a central hub. The state had to “build the aeroplane while flying”.

Much has changed since then, and for the better. Some hard lessons have been learned along the way but the contact tracing system in Victoria is now very comprehensive and increasingly robust.




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Community engagement, local knowledge

Community engagement and local knowledge might seem like buzzwords but in a pandemic, they’re vital to ring-fencing a cluster.

NSW’s system of devolved public health units and teams meant when local outbreaks occurred, locally embedded health workers were at an advantage. They’re already linked with local area health providers for testing, they already have relationships with community members and community leaders, and they know the physical layout of the area.

If you’re doing a contact tracing interview with someone and they’re talking about a key landmark at a certain time of day, you can visualise it and understand what it means in terms of risk.

What’s crucial is a nuanced understanding of local, social, and cultural factors that may facilitate spread or affect how people understand self-isolation and what’s being asked of them. It can also make a critical difference in encouraging people to come forward for testing.

It’s not just about making sure you have materials printed in the right language. It’s about understanding how people view the health system from their context. If you have people who come from a part of the world with a health system that operates differently to ours, they will bring that understanding with them.

If local health workers and contact tracers are already part of a community, they can bring that expert knowledge into the mix; they can make sure public health messaging is meaningful for local communities.

When NSW’s second wave came with the cases at the Crossroads Hotel, they were on high alert, with a system ready to jump on it and chase down every lead.

Victoria had to build its contact tracing capacity on the hop. That local knowledge had to be developed and integrated as they went, often when dealing with large and complex local clusters.




Read more:
Victoria’s coronavirus contact tracing is about to get faster. Let’s make it the first step in a larger digital boost


Evolution is underway

Since August, the Australian Department of Health has published the Common Operating Picture, which provides a weekly traffic light report of the coronavirus situation across Australia.

In the earlier part of the second wave, you can see Victoria gets an amber or red light for some elements relating to case notifications and outstanding case interviews — in other words, its system was under stress. That’s understandable; when an outbreak gets to a certain size, strain is inevitable.

It has been impressive to see Victoria’s more recent progression to green, meaning the system is coping well.

Coronavirus common operating picture – 8 October 2020.
Common Operating Picture/Australian Department of Health

In fact, the contact tracing system in Victoria is now so comprehensive that in Kilmore the department trialled a system of tracing “close contacts of close contacts”. When a confirmed case is identified, the contact tracers track down that person’s close contacts (people with whom they’ve spent 15 minutes or more). They then also track down the close contacts of each of those close contacts.

It’s incredibly resource- and labour-intensive, but it’s also a game-changer that will allow outbreaks to be contained quickly. Hopefully, this will be the standard approach state-wide where the circumstances permit and, combined with good cooperation from the public in getting tested early, it’s likely to be very effective.

Victoria has also got better over time at naming exposure sites clearly (in earlier days it could be quite vague).

You can see the evolution of the system happening. What’s admirable in Victoria is they did set about rebuilding their response, including creating regional hubs, while case numbers were high.

Public co-operation matters

I have faith in the design of Victoria’s contact tracing system now, and Kilmore is showing us how it can be rolled out to good effect. Half the latest batch of contact tests results came back on Tuesday, all negative.

There will always be room for improvement and we will learn as we go.

Key to the system working is people cooperating with masks, hygiene and personal distancing, along with broader critical rules limiting home visits and not leaving home if unwell.

Most important is getting tested early, whether you have symptoms or have been at a known exposure site, do it and do it fast. This is how we limit the risk of spread, and reduce the risk families and immediate close contacts will even need to be isolated, much less deal with being infected.

People on the frontline are working incredibly hard within a system being rebuilt around them. They are engaging with people in the community who are frustrated and getting mixed messages.

It pays for all of us to remember the effectiveness of our public health system and Victoria’s public health response is down to the sum of people’s contributions. We all have a role to play.




Read more:
Vital Signs: batch testing and contact tracing are the two keys to stop the lockdown yo-yo


The Conversation


Catherine Bennett, Chair in Epidemiology, Deakin University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Vital Signs: batch testing and contact tracing are the two keys to stop the lockdown yo-yo




Richard Holden, UNSW

Back in March and April I (and many other economists) argued for lockdowns to get COVID-19 infections under control and to give health systems time to put in place testing and tracing regimes to contain the virus in the longer term.

This was done pretty effectively everywhere in Australia except for Victoria. But if things go to plan, all states will be back on the same page by the end of October.

Or will they?

Concerns about Victoria’s contact-tracing regime remain, and although there is a lot of testing, how it is being done might not be as effective as possible.

More still needs to be done to avoid the “yo-yoing” Victorian premier Dan Andrews has warned about – in which relaxation of distancing rules leads to yet another outbreak big enough to require reimposing restrictions.

There is room for not just incremental improvement but dramatic improvement of testing and tracing.

Keeping the reproduction rate below 1

The key to avoiding the need for lockdown (unless and until a vaccine is widely deployed) is to keep what epidemiologist call the “effective” reproduction rate (R) below 1.

That is, on average each person infected with the virus must give it to less than one other person (R<1).

If R>1 infections will grow exponentially, overwhelming human contact-tracing systems and eventually the hospital system.

To keep the reproduction rate below 1 requires testing and contact tracing to be incredibly fast and effective.

Effective contact tracing

Victoria’s contact-tracing system is generally regarded as having performed poorly compared with systems such as in New South Wales.

The clunky system includes notifications of new infections still being sent by fax.

Only now is the state moving to adopt a more automated approach, using a data management system developed by IT giant Salesforce. The Victorian government rejected the system earlier in the year, on the grounds the state was too swamped by the first wave to implement and bed down a new system.

My University of NSW colleague, epidemiologist Raina MacIntyre, has observed that Victoria’s health system was less prepared than NSW because of 20 years of governments “stripping the health system bare”, and that:

No health workforce in the world, no matter how organised, well-resourced and efficient, can do manual contact tracing successfully when an epidemic becomes too large.

We could go down the more aggressive digital contact-tracing path akin to South Korea. But as the Financial Times has noted, the Korean systems:

include an extensive trawl of data from other sources, such as security cameras and credit card transactions, as well as smartphone apps that use wireless signals to detect who might have encountered an infected individual.

Given the relatively low voluntary uptake of the Australian government’s COVIDSafe smartphone tracing app, getting enough people to use it to make it effective will also require strong incentives – or compulsion.

Now, I’m strongly for such incentives (as well as smarter testing). But given the amount of bedwetting about the existing COVIDSafe app from the libertarian right and some elements of the soft left (who are paranoid about every smart light bulb spying on us), this is unlikely to happen.




Read more:
Vital Signs: Modelling tells us the coronavirus app will need a big take-up, economics tells us how to get it


Batch testing

The other crucial tool to keep R below 1 is efficient and large-scale testing.

Australia did well early in the pandemic ramping up testing capacity. Test results have been typically returned within a few days, though there have also been reports of results taking more than five days.



What we have not done is embrace the benefits of targeted batch testing.

Batch testing is a way to cost-effectively test large numbers of people by pooling together samples – say by postcode.

If the pooled sample comes back negative, then everyone who contributed to the batch is cleared. If it is positive, more targeted testing is done, using smaller batches (by suburb, then residential block, then by household).




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As I’ve noted before, the optimal batch size depends on the base rate of the virus in the community. But this general idea has been around since World War II and is well understood. It is a way to stretch resources to test more of the population more often.

For Australia at this point of the pandemic, this kind of testing would enable rapid detection and isolation of any new infections, allowing social and economic activity to get back to a new normal.

The strategy going forward

Once the Victorian outbreak is under control, we need to reopen Australia’s internal borders. Then we can start thinking about easing external border restrictions with places such as New Zealand.

All of this will require keeping the reproduction rate below 1, which means catching any new infections fast. Really fast.

Yo-yoing lockdowns are costly and to be avoided if at all possible.

Automated contact tracing could help a lot, as could smart and aggressive batch testing. We should be doing both until a vaccine is deployed.

Some commentators talk about “living with this virus” which is basically code for letting it rip. Instead, what we need to do is engage in “relentless suppression” to keep the reproduction rate low and our economy open.The Conversation

Richard Holden, Professor of Economics, UNSW

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Victoria’s coronavirus contact tracing is about to get faster. Let’s make it the first step in a larger digital boost


Karin Verspoor, University of Melbourne; Nic Geard, University of Melbourne, and Wendy Chapman, University of Melbourne

Victoria’s health authorities are now looking overseas for a reprieve following the federal government’s criticism of the state’s coronavirus response.

The state government has enlisted US cloud-based software company Salesforce to administer a data management system in the health department to accelerate contact-tracing efforts.

The government also plans to roll out five new “suburban response units” throughout Melbourne, using local insights and connections to speed up contact tracing.

Secretary of the federal Department of Health, Brendan Murphy, on Monday said an “integrated and very effective tracing regime” could help bring Victoria safely out of lockdown.

But the federal government’s widely touted but unsuccessful COVIDSafe app has shown how technology alone may not be a solution for public health challenges. So what’s different about the latest digital boost for Victoria?

Streamlined contact tracing is key

Contact tracing involves interviewing patients who have tested positive for COVID-19, to find out who else they came in contact with while infectious.

It’s a vital part of containing an outbreak, as it enables potentially infected people to be tested and isolated before they can infect others.

However, it is labour-intensive, particularly when the number of cases is large. When the capacity of contact-tracing teams is exceeded, delays ensue and effectiveness drops.




Read more:
Explainer: what is contact tracing and how does it help limit the coronavirus spread?


How could the new system help?

Victorian Premier Daniel Andrews said the upcoming Salesforce system would run in conjunction with the state’s 2,600 contact tracers, saving time otherwise spent on manual data entry.

Salesforce building logo
US-based software company Salesforce already has more than 150,000 corporate users globally.
zz/STRF/STAR MAX/IPx

The system would provide an electronic interface on which patients and case managers can upload details about where the patient has been, as well as the names, phone numbers and email addresses of their contacts.

The contacts can then be automatically notified by SMS or email, before being approached by the case manager for a more detailed discussion.

The system’s data collection and storage would be targeted at known cases. It would offer several advantages, such as:

  1. contacts can be notified more quickly about their potential exposure to the virus and will know to stay home

  2. suburban response units could more efficiently coordinate their efforts by assigning contacts to specific workers and providing contact logs. This would reduce the risk of multiple case managers following up with the same contacts, or of contacts being missed.

  3. health authorities could have a more up-to-date view of the contact-tracing progress

  4. potential overlaps between cases could be identified and used to prioritise which contacts should be followed up first.

Does the upgrade go far enough?

While the Salesforce system will undoubtedly make contact tracing more efficient and robust, it’s only one of a series of steps that could be automated to help manage outbreaks.

For instance, the system only starts when a person tests positive and health officials are notified. For maximum productivity, this could be done in real time by configuring pathology lab systems to automatically send test results to officials.

This could let them assess the test results of person A against those of their close contacts to better understand how the virus is spreading. Some factors to consider may include:

  • how many contacts of person A actually got sick (which means negative results matter too)

  • what kinds of contacts are getting sick. For example, is it only people with whom person A spent a lot of time in close quarters, or also people who happened to be in the same place at the same time?

Also, connecting the system to patient administration systems in hospitals would allow appointments to be automatically scheduled for patient follow-ups, or for testing close contacts.

And integrating the system with electronic records in clinics and hospitals could provide critical insight into how different people respond to the disease.

Answering questions such as “does a patient from a clinic get admitted to hospital?”, “do they have mild or severe illness?” and “how do they respond to treatment?”, would improve doctors’ ability to care for patients.

This level of sophisticated data-sharing goes beyond the current digital capabilities of Victoria’s health-care system. But capturing case information in digital form is a first step towards this vision.

Is it too late to change?

Since experiencing a second wave of COVID-19, Victoria has boosted its contact-tracing workforce. Victorian Chief Health Officer Brett Sutton has reassured people the state can now reach case contacts within 24 hours.

Andrews confirmed the state had rejected an earlier proposal from Salesforce in March, saying:

Sometimes when you are swamped, it is not a great time to move to a new IT platform.

However, the upcoming system is based on Salesforce’s core customer relationship management platform in development since 1999.

It has already been used in Western Australia, South Australia, New Zealand and 35 US states. This suggests a mature product with the kinks worked out.

Even if the system doesn’t end up being crucial in this pandemic, it could make a huge difference in future epidemics, especially as we enter what US infectious disease scientist Anthony Fauci has described as a “pandemic era”.

Data security and earning the public’s trust

The Robodebt saga has already made us sceptical using automated algorithms on personal data.

To safeguard Australian’s personal data, authorities must go the extra mile to make sure the system is foolproof. Some ways to do this could be:

  • requiring two-factor authentication from all parties that access the system

  • putting regulations and safeguards in place to ensure data in the system is stored in Australia, only accessible to contact-tracing staff and only used only for intended purposes

  • opening the system up for assessment by cybersecurity experts before it’s implemented (potentially by providing the software source code)

  • keeping audit logs of who accessed the data and when, so any breach can be rapidly traced.

If governments want the public to accept technological solutions for public health challenges, they must first show they take our data privacy seriously.

Doing so will be a worthwhile investment – not only for outbreak management but towards digital innovation in public health.

Young girls gets a coronavirus test in a clinic.
As of September 9, Victoria recorded a total number of 19,688 cases and 694 deaths, according to the state Department of Health and Human Services.
James Ross/AAP



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Coronavirus: digital contact tracing doesn’t have to sacrifice privacy


The Conversation


Karin Verspoor, Professor, School of Computing and Information Systems, University of Melbourne; Nic Geard, Senior Lecturer, School of Computing and Information Systems, University of Melbourne; Senior Research Fellow, Doherty Institute for Infection and Immunity, University of Melbourne, and Wendy Chapman, Associate Dean, Digital Health & Informatics, University of Melbourne

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Why New Zealand needs to ramp up genome sequencing to trace the source of its new COVID-19 outbreak



Shutterstock/Syuzann

David Welch

Genetic surveillance — a technology that uses the genetic fingerprint of a virus to track its spread — is part of the public health response to New Zealand’s new COVID-19 community outbreak and could help pinpoint its source.

There are now 17 cases of community transmission, all in Auckland, and health officials are treating the group as a single cluster, with an expectation that case numbers will grow.

Ideally, we should be sequencing all positive test swabs, regardless of whether they are found at the border or in the community. The community cases could then be compared to all other cases to find a close match. This would suggest a likely chain of transmission, help with contact tracing and reveal the sequence of the outbreak.

But not all samples are currently sequenced. In total, New Zealand had 1225 confirmed cases of COVID-19, and about 700 of the positive samples have been sequenced.

I argue the Ministry of Health should now make genetic sequencing mandatory. Here’s why.

Tracking epidemics using genomes

Genetic surveillance of infectious diseases is a maturing technology that has played a major role in the effort to control the Ebola and Zika epidemics, and now the COVID-19 pandemic.

We can now obtain a complete viral genome quickly and cheaply to identify mutations that provide clues about transmission chains.

Cases that are part of the same transmission chain will have genomes that look very similar: they share the same mutations compared to a reference genome. Cases from different transmission chains have genomes with differing patterns of mutations.

SARS-CoV-2, the virus that causes COVID-19, does not have a particularly high mutation rate. It acquires mutations at about half the rate of seasonal influenza, but it mutates fast enough to leave a signal of where it has come from.




Read more:
‘Genomic fingerprinting’ helps us trace coronavirus outbreaks. What is it and how does it work?


This brings us to how this is helping in our efforts to control the current community outbreak.

There are four main theories about where the new cases could have come from:




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The genomes of the new cases could identify the first scenario of a quarantine leak if we found a match between viral genomes from people in quarantine and in the new cluster. This relies on comprehensive sequencing of all cases in quarantine, but currently, there are still gaps.

Similarly, in the unlikely scenario of a transmission chain that has persisted since New Zealand’s first wave, we’d expect a match with one of the cases sequenced during the first outbreak, although the genomes would have diverged somewhat over that period of time.

The scenarios of transmission through goods or an undetected border case are more difficult to decipher using genomic methods. We would be looking to match the viral genome from the new local cases to one of more than 80,000 publicly available genomes that have been sampled worldwide. This would point to a country of origin but not necessarily distinguish between the scenarios.

Early results from sequencing of the first four cases from the new Auckland cluster suggest no link to a known (sequenced) New Zealand case, and the UK as the closest match. For now, this leaves all possibilities still open.

A global map of cumulative cases of COVID-19.
Johns Hopkins University

Ongoing surveillance

With widespread testing now underway, new cases will be identified in the community over the coming weeks. It is important that they are rapidly sequenced to determine whether they belong to the same transmission chain.

Genomic analysis will tell us whether we are dealing with a single or multiple clusters. Even the best contact tracing cannot be sure of the origin of an infection, and supplementing it with genomic data is crucial.

But genomic analysis is not limited to establishing transmission chains. It can also tell us about the overall size of an outbreak, which is directly related to the genomic diversity of the virus. We can also date events to establish when transmission started within a cluster, provided there is sufficient diversity in the cluster.

The genomes we have so far in New Zealand show a huge diversity of cases, with many introductions from around the globe. Indeed, the diversity of early samples largely reflects the diversity of the virus globally, with most cases that led to further transmission coming from North America and Australia in line with travel patterns to New Zealand.

This graph shows how COVID-19 travelled to New Zealand (see research https://www.medrxiv.org/content/10.1101/2020.08.05.20168930v2)
Author provided

Most introductions did not result in further community transmission. This shows how effective New Zealand’s first lockdown was, when transmission rates declined dramatically soon after level 3 and 4 measures were put in place.

Genomes were also used in real time during the first outbreak to help attribute cases to clusters. Retrospectively, this has shown that contact tracing was effective, with relatively few cases being wrongly attributed.

But genome analysis is neither foolproof nor a panacea. Sometimes positive samples are found that cannot be sequenced because they contain only a small amount of viral material. The rather slow rate of mutation of Sars-COV-2 means many cases are essentially carrying identical copies of the virus, even across different countries.

This greatly reduces our ability to attribute an infection to a particular outbreak. There are also real computational bottlenecks – data is generated faster than we can sensibly analyse it.

Despite these limitations, genomic surveillance gives us near real-time insights into the spread of COVID-19 that were not possible in any previous pandemic. That’s why I argue it’s time for the Ministry of Health to now make immediate genetic sequencing mandatory for all positive test swabs in New Zealand, not just some.The Conversation

David Welch, Senior lecturer

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Mapping COVID-19 spread in Melbourne shows link to job types and ability to stay home



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Melanie Davern, RMIT University; Mary-Louise McLaws, UNSW, and Ori Gudes, UNSW

COVID-19 provides a stark reminder of inequity and the spread of disease. These aren’t new ideas and can be traced back to John Snow’s cholera maps and Charles Booth and his colour-coded maps of occupation types and poverty in the 19th century. Today, as case numbers soar in Melbourne, large clusters of COVID-19 cases have been identified across the northern and western suburbs, raising questions about occupation types and socio-economic differences across the city.

One of the most important messages from government during the pandemic has been to work from home if you can. Though what happens if your work isn’t suited to this?




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Two weeks into Melbourne’s lockdown, why aren’t COVID-19 case numbers going down?


Snow and Booth were forefathers of modern geographical information systems (GIS) analysis. It’s a powerful tool for mapping and visualising differences or inequities across cities and the spread of disease. We mapped the connection between occupation types, indicating the ability to work from home, and the locations of COVID-19 cases across Melbourne in the recent second wave.

Why is equity a health issue?

Hotspot suburbs were first identified and ring-fenced in early July. A hard lockdown was applied to the 3,000 residents of nine high-density public housing estates in inner Melbourne.

Ring fencing is a powerful method of containing a disease. It’s most appropriate where a specific location has a distinctive pattern of risk. It should also be applied without bias.

As the public housing towers lockdown reminded us, there is an inequity in health.




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Many people associate equality with treating everyone the same regardless of their needs. This is very different to equity, which is about treating people according to their needs. Unlike equality, equity is providing people with extra help when it is needed.

The picture below makes the concept of equity easier to understand.

Illustration of equity by showing how standing on crates enables children of different heights to look over the people in front of them and see the action on a sports field.

Craig Froehle/Medium, CC BY

In the context of this pandemic, a recent discussion of housing affordability raised the issue of equality versus equity.




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Overcrowding and affordability stress: Melbourne’s COVID-19 hotspots are also housing crisis hotspots


We see a stark difference between the initial transmission of COVID-19 and the second wave. The earliest cases were concentrated in Melbourne’s wealthier areas and associated with international travel. In the second wave we have seen a different pattern of spread across disadvantaged areas of Melbourne.

This pattern is possibly linked to inequity associated with living and work conditions. People with higher education tend to work in occupations that often enable them to work from home, making it easier to self-isolate.

Outer areas of Melbourne have had more cases of COVID-19 cases in the second wave and this might be associated with job types and education levels. Residents living in inner areas of Melbourne are more likely to hold tertiary qualifications needed for occupations more suited to working from home.

What does mapping reveal?

We analysed Australian Bureau of Statistics Census data on employment types from the Australian and New Zealand Standard Classification of Occupations. We identified 93 major occupation types suitable for working from home.

We linked and mapped these occupation data along with COVID-19 incidence according to local government areas. The map below shows data from July 16.

Map of incidence of COVID-19 cases across Melbourne and proportion of people in occupations able to work from home by local government area.

Data: DHHS, July 16, Author provided
Legend for map: size of red dots shows number of COVID-19 cases, darker areas indicate more people in occupations able to work from home.

The map reveals lower proportions (shown by lighter-coloured areas) of people employed in occupations suitable for working from home in many outer northern and western areas of Melbourne. In particular, the proportion is low in Hume, one of the local government areas where COVID-19 cases have been concentrated.

In the inner and outer eastern areas of Melbourne, residents are more likely to be able to work from home. Nillumbik in the outer north-east has the highest proportion of people able to work remotely. It has very few cases of COVID-19.

Greater Dandenong is an exception to this pattern. As a manufacturing hub for Melbourne, it has a low proportion of people in occupations suitable from working from home, but has few cases.

COVID-19 is spread through community transmission or close contact with others who are infected, as happened in meatworks factory clusters in northern and western Melbourne. Greater Dandenong may have been protected by the small number of cases across south-eastern Melbourne where more residents have occupations suitable for working from home.

The Victorian Department of Health and Human Services updates COVID-19 incidence data hourly. We first sourced data on July 16, a week after the Melbourne-wide lockdown began, to understand the patterns of occupation types and COVID-19 clusters as they evolved. To continue monitoring, we have developed a data dashboard, which is shown below.

Data dashboard showing incidence of COVID-19 cases by local government areas

Ori Gudes, Author provided

We hope this data dashboard will be released in coming days with updated data.

Using inclusive data to protect everyone

The related patterns of occupations and COVID-19 incidence remind us of the importance of the well-known relationships between health and place.




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This pandemic takes advantage of inequity and our most vulnerable communities. It shows us why we must include the full spectrum of society (not only those we know best) when we make decisions, communicate and ask people to work from home.

Many workers are engaged in casual and insecure employment and work is a critical determinant of health. Our mapping provides evidence that can help authorities decide where and how to focus preventive measures when planning public health interventions.

These methods of GIS analysis and easily understood maps should be freely available. The community will then be able to interrogate the data so they can realise in close to real time the rationale for public health directives.

These same principles have been used to understand health and liveability in cities though the Australian Urban Observatory to inform city planning.


We thank Weijia Liu of UNSW for assisting with data collection in this study.The Conversation

Melanie Davern, Senior Research Fellow, Director Australian Urban Observatory, Co-Director Healthy Liveable Cities Group, Centre for Urban Research, RMIT University; Mary-Louise McLaws, Professor of Epidemiology Healthcare Infection and Infectious Diseases Control, UNSW, and Ori Gudes, Senior Research Fellow, Geospatial Health Lab, University of Canberra, and Adjunct Senior Lecturer, School of Public Health and Community Medicine, UNSW

This article is republished from The Conversation under a Creative Commons license. Read the original article.

‘Genomic fingerprinting’ helps us trace coronavirus outbreaks. What is it and how does it work?



United Nations COVID-19 Response/Unsplash

Rebecca Rockett, University of Sydney

If you had told me in January that “genomics” would become a buzzword in 2020, I’d have thought you were crazy.

But the COVID-19 pandemic has brought medical science to the top of our nightly news bulletins. And now, it seems, everyone is talking about genomics.

During Australia’s first wave of COVID-19, genomic sequencing of the earliest Sydney clusters was crucial to identifying the difference between imported cases and local community transmissions.

And now with a second wave lapping at the New South Wales border, genomic sequencing traced the origin of the Crossroads Hotel cluster back to Victoria, just as Victorian scientists were able to trace the Melbourne outbreaks back to hotel quarantine cases.

Genomic sequencing offers us a key to unlocking the puzzle of local transmission of COVID-19.

But what is it and how does it work?




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Mapping the COVID-19 ‘family tree’

Genomics is the study of the genetic materials within an organism — DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

Genomic sequencing effectively takes a “genetic fingerprint” of an organism and maps how the DNA or RNA inside it is ordered.

COVID-19 is an RNA virus, and by looking at the genetic sequence of different cases, we can detect minute differences in each new infection.

This allows us to create a genetic “family tree” to show which COVID-19 cases are closely related, and to identify and track clusters.

The more fingerprints we take, the easier it becomes to identify whether someone contracted COVID-19 from a known cluster or case.

SARS-CoV-2, the coronavirus that causes COVID-19, is an RNA virus.
Shutterstock

Born in a tent: the COVID-19 genomic sequencing test

Late in January, travellers returning from overseas hotspots were showing symptoms of this new coronavirus — but the virus was so new we didn’t yet have a genomic sequencing test developed to prove where the virus was coming from.

On a family camping holiday north of Sydney over the Australia Day long weekend, I sat in a tent with my laptop, designing NSW’s first genomic sequencing test for COVID-19.

Meanwhile, my colleagues from the University of Sydney and NSW Health Pathology were working in the lab at Westmead Hospital testing and collating data to see whether it worked.




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From that point, we collected genetic material from positive COVID swab tests in NSW, and using the sequencing test we designed, we were able to generate genetic data from 209 COVID-19 cases.

Our study published recently in Nature Medicine reveals how we used genomic sequencing and mathematical modelling to give important insights into the “parentage” of cases and likely spread of the disease in NSW during the first ten weeks of COVID-19 in Australia.

Our secret weapon: rockmelons

Remember the rockmelon recall of 2018? Supermarkets across Australia pulled the fruits (otherwise known as cantaloupes) from shelves due to a deadly outbreak of listeria.

Genomic sequencing was used to help trace the source of that listeria outbreak, and over many years we’ve used it to trace other food poisoning outbreaks, as well as transmission of tuberculosis.




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When COVID-19 hit Australia we had to move quickly, so we began to adapt these tests to this new coronavirus — and it worked.

Very early on in our research we were able to discover cases which weren’t linked to a known cluster or case.

We identified that one-quarter of COVID-19 positive samples were local transmissions and were able to identify clusters such as those in nursing homes.

Comparing our genomic sequences against an international database, we also identified which countries the virus in Australia was being imported from.

We reported genomic sequencing to NSW Health to supplement epidemiological information from contact tracing and inform and improve public health follow-up of COVID-19 cases.

This knowledge community transmission was occurring led to the closure of the country’s international borders, revision of testing policies, and other federal and state government measures designed to minimise further spread of the virus.

Sequencing is key as we continue the battle against COVID-19

We know genomic data from Australia’s first wave of coronavirus infections proved vital to understanding the trajectory of the disease, and it continues to help us crack the codes of the second wave’s clusters.

With an effective vaccine still many months away at best, and with a resurgence of infections in Australia, it’s critical we continue to invest in this research to advance our ability to contain the virus in the long-term.




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The Conversation


Rebecca Rockett, Virologist, University of Sydney

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Victoria’s coronavirus contact tracers are already under the pump. What happens next?



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Gerard Fitzgerald, Queensland University of Technology

The emergence of significant community transmission of COVID-19 in Melbourne over the past week is greatly concerning to the whole of Australia.

Earlier this week, Victoria’s chief health officer Brett Sutton said the state was struggling to cope with the volume of contact tracing required for more than 2,500 people in self-isolation, who must have all their close contacts traced and contacted:

[…] we’re at the limits of managing that number.

Since then, the number of cases in Victoria has risen further still.

What options are available for increasing the pool of contact tracers in Victoria, or any other state that finds itself handling significant rises in COVID-19 cases?




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Remind me, what are contact tracers?

The key strategy to preventing further community transmission is to identify all cases through extensive testing, isolate people who test positive, and then trace their close contacts.

These contacts require initial testing to see if they are also potential spreaders, but more importantly they need to be isolated and closely monitored. Should they develop symptoms, they also need to be tested.

The process of identification of cases, ensuring isolation and monitoring, identifying contacts and following up each of those requires extensive effort.




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Explainer: what is contact tracing and how does it help limit the coronavirus spread?


Every patient who tests positive needs to be interviewed to identify where they have been during the potentially infective stage of the disease, and who they may have come into contact with.

In some circumstances, this may be limited to family members, while in others it may involve following up others who may have been in the same locations, such as workplaces, restaurants, shops or public transport.

All these people need to be made aware of the risk and followed up. This is challenging in a free society. It requires cooperation from the community. It also requires understanding that some who may be spreading the disease are not aware they are doing so.




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This task is traditionally the role of public health workers — including doctors, nurses and those with specific public health qualifications — called contact tracers.

They are the real heroes of this effort, doing mundane work below the radar to keep the community protected.

In normal circumstances, these staff monitor diseases that are present in the community and identify and follow up notifiable disease such as measles, HIV, hepatitis or tuberculosis.

These public health workers have been working desperately hard for months and now those in Victoria are being asked to step up to the mark again.




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By persisting with COVIDSafe, Australia risks missing out on globally trusted contact tracing


How can we expand the pool of contact tracers?

The public health workforce needs to be expanded rapidly to handle the increased workload. There are several ways to do this, some of which have already been implemented in Victoria.

We could reallocate people from other public health functions, which could immediately provide a ready and well-trained workforce.

But this will impact other vital public health protections, including surveillance of other disease, health promotion, screening, early diagnosis and intervention. Diverting staff from these efforts may also have long-term health consequences.




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Staff could be deployed from other agencies, including the Australian Defence Force.

While readily available and well-disciplined for the task, only some of these people have the necessary expertise to identify cases and trace contacts. Others may need to serve in support roles.

Options include calling in the Australian Defence Force to add to the pool of contact tracers (Department of Defence Australia).

Other states and territories could provide support. However, this may require people to relocate to Victoria with the personal disruption implied, as well as the enhanced risk to them and to their families and communities when they return.

This sharing of public health resources across state borders requires significant national cooperation, which has been evident in other parts of Australia’s COVID-19 response.

Finally, people may be recruited from the pool of partly trained people (public health students). While they may lack the practical skills, they will at least bring theoretical knowledge to perform some targeted tasks with specific training. For instance, they could work with experienced personnel to help maintain records or identify contacts.

We have a lot at stake

This new outbreak in Victoria threatens to overwhelm the system’s public health capacity. If that occurs, we can expect large numbers of deaths to follow. We are not there yet, but this outbreak in Victoria is placing the whole country at risk.

So public health workers need all the help and support the Australian community can provide.The Conversation

Gerard Fitzgerald, Emeritus Professor, School of Public Health, Queensland University of Technology

This article is republished from The Conversation under a Creative Commons license. Read the original article.

By persisting with COVIDSafe, Australia risks missing out on globally trusted contact tracing


Ritesh Chugh, CQUniversity Australia

Australia has ruled out abandoning the government’s COVIDSafe contact tracing app in favour of the rival “Gapple” model developed by Google and Apple, which is gaining widespread support around the world. Deputy Chief Medical Officer Nick Coatsworth told The Project the COVIDSafe app was “a great platform”.

In the two months since its launch, COVIDSafe has been downloaded just over 6.4 million times – well short of the government’s target of 40% of the Australian population.

Its adoption was plagued by privacy, security and backwards compatibility concerns, and further exacerbated by excessive battery consumption. And despite being described as a vital tool in the response to COVID-19, it is reportedly yet to identify a single infection that hadn’t already been tracked down by manual contact tracing.




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It seems the app has failed to win the public’s trust. Software downloads are based on the perceptions of risk and anticipated benefits. In this scenario, the risks appear to outweigh the benefits, despite the dangers of a second coronavirus wave taking hold in our second most populous city.

COVID-19 cases in Melbourne continue to surge. But more broadly, the relatively low number of overall cases in Australia and the lack of adequate buy-in among the public make it difficult for COVIDSafe to make a meaningful contribution.

Is there another way?

Some 91% of Australians have a smartphone, whereas a rough calculation based on the 6.4 million downloads suggests only 28% have downloaded COVIDSafe.

For digital contact tracing to be effective, an uptake of around 60% of the population has been suggested – well beyond even the 40% target which COVIDSafe failed to hit.

The logic is straightforward: we need a system that 60% of people are willing and able to use. And such a system already exists.

Tech giants Apple and Google have collaboratively developed their own contact-tracing technology, dubbed the “Gapple” model.

How does Gapple work?

Gapple is not an app itself, but a framework that provides Bluetooth-based functionality by which contact tracing can work. Crucially, it has several features that lend it more privacy than COVIDSafe.

In simple terms, it allows Android and iOS (Apple) devices to communicate with one another using existing apps from health authorities, using a contact-tracing system built into the phones’ operating systems.

The system offers an opt-in exposure notification system that can alert users if they have been in close promixity to someone diagnosed with COVID-19.

Gapple’s exposure notification system.

Gapple’s decentralised exposure notification system offers more privacy and security than many other contact-tracing technologies, because:

  • it does not collect or track device location

  • data is collected on the users’ phones rather than a centralised server

  • it does not share users’ identities with other people, Apple or Google

  • health authorities do not have direct access to the data

  • users can continue to use the public health authority’s app without opting into the Gapple exposure notifications, and can turn the notification system off if they change their mind.

The system meets many of the basic principles of the American Civil Liberties Union’s criteria for technology-assisted contact tracing. And its exposure notification settings appear in recent updates of both Android and iOS devices. But without an app that uses the Gapple framework, the exposure notification system cannot be used.

COVID-19 Exposure Notification System.

Gapple going global

Global support for the Gapple model is growing. The United Kingdom, many parts of the United States, Switzerland, Latvia, Italy, Canada and Germany are abandoning their native contact-tracing technologies in favour of a model that could achieve much more widespread adoption worldwide.

The ease of communication between different devices will also make Gapple a crucial part of international contact tracing once borders are reopened in the future, and people start to travel.

In this light, it is hard to see why Australia resisted the calls to ditch COVIDSafe and adopt the Gapple model.

Can Australians use Gapple anyway?

No, they can’t, because the Gapple model requires users to download a native app from their region’s public health authority which uses the Gapple exposure notification system. Australia’s decision means that won’t be happening here any time soon.

In grappling with the dilemma between citizens’ civil rights and curbing the growth of the fatal COVID-19 virus, the Gapple model is a trade-off to encourage higher uptake of contact-tracing technologies.




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Ultimately, the Gapple model will be a step forward in the world’s fight against COVID-19, because it will encourage significant numbers of people to use it.

The decision to persist with the COVIDSafe app, rather than adopting an emerging global model, could have severe repercussions for Australians. For any digital contact-tracing technology to work effectively, a large number of people must use it, and COVIDSafe has fallen short of that basic requirement.The Conversation

Ritesh Chugh, Senior Lecturer/Discipline Lead – Information Systems and Analysis, CQUniversity Australia

This article is republished from The Conversation under a Creative Commons license. Read the original article.