Sewage testing is no magic bullet in our fight against COVID-19. But it can help

Posted on November 22, 2020 by particularkev

Cobus Gerber, University of South Australia and Rietie Venter, University of South Australia

We’re often hearing alerts for different areas after traces of coronavirus are found in the wastewater, or sewage.

Most recently, fragments were detected at Benalla, in Victoria’s north, and at Portland, not far from the South Australian border. The Victorian government subsequently closed the border to South Australia, and urged anyone in these areas to get tested if they developed symptoms.

The idea of testing sewage to track the presence of a virus is not new. Scientists in Israel used it to monitor a polio outbreak in 2013.

While it is a useful tool for COVID-19 disease surveillance, it’s not entirely foolproof.

From drug use to COVID-19

We commonly use wastewater monitoring to estimate levels of illicit drug use in Australia. This is the sort of work our teams do, although this year we shifted our focus to look at methods of testing wastewater for COVID-19.

A virus monitoring program uses the same principle as wastewater monitoring for drugs. Microbes such as SARS-CoV-2, the virus that causes COVID-19, are passed mainly through a person’s gut, then come out in their stool, and enter the sewerage system after a toilet flush.

This process, called viral shedding, depends on the severity of the infection (generally, people who have a more severe infection shed more of the virus, though this isn’t always the case) and can occur for several weeks after symptoms have disappeared.

Although the virus doesn’t stay viable in the sewage for very long — you’re not likely to catch it if you come into contact with sewage containing virus — remnants of its genetic material may remain intact. When a daily sample is collected at a treatment plant, we can recover the RNA fragments.

Some research groups have suggested this approach may be able to detect a single
infected person in a catchment of 100,000.

Wastewater samples in a laboratory. — Wastewater testing is being used in many places around the world during the pandemic, not only Australia.
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The technique is important

A variety of techniques can be used to recover the genetic material before we measure how much virus is present. The more virus there is in a sample, the easier it is to detect.

Currently, there are no agreed standard approaches — different teams testing wastewater for COVID in different places do it differently.

This is partly because we’re still working out the best method — each has its own strengths. Our research, currently under review, shows a method may be very sensitive in some cases but not in others.

Wastewater from a suburban area may contain mainly household effluent, whereas a sample from a more industrial area could contain various chemicals that may interfere with detecting the viral RNA. Wastewater is not homogeneous and its contents can even vary depending on the time of day.

We’re working on developing more robust methods that are less prone to being influenced by the wastewater source. In the meantime, we need to be a bit cautious when interpreting results from wastewater testing.

What happens when a sample is positive?

Once traces of SARS-CoV-2 show up in wastewater, it’s a likely indication that infected people live in, or have visited, the sewer catchment. However, it’s important that more than one indicator confirming virus RNA is included in the tests to minimise the risk of false positives.

Even then, a result may simply be a case of people who are recovering from illness, shedding virus after they’ve completed their quarantine, when they will no longer be infectious.

It’s important to carry out ongoing surveillance to determine if the signal peters out, or if the level of virus detected at the location increases. The latter would suggest an underlying spread of infections, and the need to step up targeted testing. This is arguably the strength of wastewater surveillance.

Conversely, when the results are negative, it may imply there are no infected people in the catchment. However, this could also mean the testing method is insufficiently sensitive to pick up infections. It’s possible infected people are located far from the sampling point, and no identifiable virus remnants remain in the sample by the time it’s collected.

There’s also the issue that many people in regional areas have their own septic tanks.

So like testing people for COVID, wastewater testing carries a risk of both false positives and false negatives.

There are strengths and weaknesses

Sewage surveillance can’t give us specific information, such as the location of the infected people or the number of infections. But as long as we understand its strengths and weaknesses, it’s a valuable complementary approach to guide targeted testing.

It can provide authorities with evidence that may inform whether they can relax restrictions in some communities, instead of applying blanket lockdowns. If we had COVID wastewater monitoring across South Australia (currently it’s only operating in Adelaide), it might have been able to indicate there were no cases in regional areas, and perhaps they could have avoided this week’s harsh lockdown.

With so much uncertainty about when and where the next outbreak might occur, monitoring wastewater could provide an early warning signal.

People in Benalla in Portland should be aware and get tested if they have any symptoms, according to public health advice. But at this stage, there’s no need for alarm.

Cobus Gerber, Associate Professor, University of South Australia and Rietie Venter, Associate professor, Clinical and Health Sciences, University of South Australia

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

Blaming the ‘worried well’ for long COVID testing queues won’t help anxious South Australians. This will

Posted on November 21, 2020 by particularkev

Bridget Haire, UNSW and Jane Williams, University of Sydney

It’s been a big week for South Australia. First, the announcement of a six-day lockdown to limit the spread of COVID-19. Then today we heard this lockdown may have not been needed, after a man lied to contact tracers, prompting an early lifting of restrictions.

In between, South Australians have been waiting in queues for up to ten hours for COVID-19 tests. And the state’s chief public health officer Nicola Spurrier warned the “worried well” not to clog up important public health services.

Labelling people anxious about COVID-19 the “worried well” isn’t helping, especially in a climate of uncertainty, as South Australia has experienced this week. It might also discourage people with mild symptoms to come forward.

So who are the “worried well”? And what should we really be doing to encourage the right people to get tested?

Who are the ‘worried well’?

The “worried well” is a term invented to describe apparently healthy people who think they might have a disease or medical problem, so see a doctor or have testing.

The term carries the whiff of a sneer, along with the implication such people are wasting health resources.

It shouldn’t be confused with hypochondria, which is chronic anxiety about your health to the level it may be considered a psychiatric illness.

The “worried well”, in contrast, are often responding to a situation that asks people to be paying special attention to an aspect of their health.

They might attend more regularly than required for cancer screening, for example. They are also more likely to believe it is important to take responsibility for their own health — a concept public health messaging actually reinforces.

We can’t dismiss people’s real anxiety

Dismissing people who seek medical attention for vague ailments or unsubstantiated risks as the “worried well” ignores the very real problem of the anxiety created by attention to particular illnesses.

Anxiety can cloud health perceptions and judgements, and prompt people to seek reassurance.

In the face of a global pandemic, where an invisible pathogen is transmitted often through pre-symptomatic or asymptomatic people, many of us are a bit anxious.

Vigilance can be useful for achieving compliance with the COVID-safe rules that have restructured our daily habits, such as physical distancing, avoiding touch and regularly washing our hands.

Anxiety is less useful if it results in people who have no known exposure and no COVID symptoms presenting for testing, particularly if there is a concern testing services may be stretched by demand.

However, applying a stigmatising label to such people is counterproductive.

Yes, it can be frustrating

In the context of an outbreak where there is urgent need to test people who have been exposed, and where testing capacity is being overwhelmed, reference to the “worried well” may be a symptom of public health officials’ understandable frustration.

It is, after all, a delicate balancing act to get everyone deemed at risk to test in a timely manner, without their ranks being swelled by those seeking reassurance who believe they were at risk but who have no clear or likely route of exposure.

But that doesn’t make the “worried well” a fair or useful label, and may work against achieving the widespread testing needed to control infection.

We’d be better off promoting testing as doing the ‘right thing’

New South Wales and Victoria have promoted COVID testing as doing the “right thing”. Both emphasise people with COVID-like symptoms should be tested regardless of whether they have had a known exposure.

Similarly, the South Australian government is asking everyone with COVID-like symptoms to be tested, regardless of whether the symptoms are mild.

One of the risks of a phrase like the “worried well” is different people can interpret it in different ways. So if someone with mild COVID-like symptoms is
worried they might be called one of the “worried well”, they might second-guess themselves and not get tested.

We have seen the dire consequences of people underestimating a sniffle, or mild respiratory illness, in the terrible tragedy of the Newmarch House aged-care cluster in New South Wales earlier this year.

Clear, consistent, targeted public health messaging works

The best way to ensure the right people get tested is by using very clear, consistent and targeted public health messaging.

Currently, in South Australia this means people with symptoms, people who have been identified through contact tracing, and people who have visited sites listed on the contact tracing website where exposure may have occurred.

Clear and consistent repetition of these groups is needed throughout relevant media, including the broadcast media, internet and social media.

Have the ‘worried well’ really clogged up testing?

It is not possible to assess how many of the more than 617,000 COVID tests conducted in the state so far met the criteria of credible risk according to the published criteria.

But if there is serious concern there is unnecessary testing, this needs to be swiftly addressed by explaining who needs testing and why. This needs to be repeated in multiple places, including being visible where people queue to test.

Clear and accessible pathways also need to be provided for people with COVID anxiety who don’t meet testing criteria, which the state government is beginning to address.

This is so people can be reassured in ways that do not involve unnecessary testing, and if necessary learn how they can address their concerns using the appropriate designated mental health services.

Bridget Haire, Postdoctoral Research Fellow, Kirby Institute, UNSW and Jane Williams, Researcher at the Centre for Values, Ethics and the Law in Medicine (VELiM), University of Sydney

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

Infecting volunteers with coronavirus may be one way to test potential vaccines. But there are risks

Posted on October 16, 2020 by particularkev

Euzebiusz Jamrozik, Monash University; Kanta Subbarao, The Peter Doherty Institute for Infection and Immunity, and Michael Selgelid, Monash University

Researchers are considering using “human challenge studies” to accelerate COVID-19 vaccine research and development. This would involve giving an experimental vaccine to healthy volunteers, then deliberately exposing them to the virus to see whether they’re protected from infection.

Challenge studies can also allow scientists to monitor the progress of infectious diseases from the moment they begin, and to study infection and immunity more closely than other types of research.

These studies can answer scientific questions in a short time. They recruit small numbers of participants — up to around 100 volunteers per study — usually young, healthy adults.

However, deliberate infection with SARS-CoV-2, the virus that causes COVID-19, involves risks to volunteers.

How do these studies differ from standard, larger studies?

Standard “field” trials for some COVID-19 vaccine candidates have already begun. Each aims to recruit at least 10,000 people. Usually, half or two-thirds receive the experimental vaccine and the rest might receive a placebo or a vaccine against another disease.

Participants then go about their daily lives. Scientists observe whether those who received the COVID-19 vaccine are less frequently infected with the virus than the other group, allowing them to determine how effective the vaccine is.

Two scientists in a lab look at a syringe. — Human challenge studies involve fewer participants than standard field trials.
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In large epidemics, field trials can quickly reveal whether a vaccine works. But proof may be delayed when there’s less community transmission, for example due to local public health measures.

If current field trials identify a highly effective vaccine, there might be less need for human challenge trials. However, if the first vaccines fail, or turn out to be only moderately effective, challenge studies could be used to select the next most promising candidates for future field trials.

Challenge studies need extra preparation

First, scientists need to prepare a strain of SARS-CoV-2 in the laboratory to administer to volunteers. The strain needs to be similar to the virus circulating in the community.

There’s also a need for special research facilities with health-care support and capacity to isolate participants.

Volunteers may have to remain in these facilities for 2–3 weeks to be closely monitored, and so they are not released into the community while they may be infectious.

Past experience and recent developments

While COVID-19 challenge trials are now making news, scientists have previously conducted these kinds of experiments with many different types of microorganisms.

Such studies have been used to develop vaccines against malaria, typhoid and cholera. They have also provided unique insights into immunity to influenza and “common cold” coronaviruses.

One research centre in London has announced a plan to conduct challenge studies with SARS-CoV-2. Another centre in the United States is also preparing a strain of the virus.

Ethical and scientific questions

The World Health Organisation (WHO) convened two advisory groups, in which we were involved, to consider COVID-19 human challenge studies. One focused on ethics, the other on scientific and technical aspects.

The ethics group identified eight criteria proposed challenge studies would need to meet before going ahead.

These included the need for researchers to consult and engage with the general public before, during, and after the trials. There would also need to be careful independent expert review, and demonstration that expected benefits are likely to outweigh risks.

Relevant risks might be especially hard to predict for SARS-CoV-2, partly because it’s a new pathogen.

While young, healthy people generally fare better with COVID-19 than older adults with pre-existing conditions, there are exceptions. For example, a multisystem inflammatory syndrome has been reported in rare cases among previously healthy adults after they contracted COVID-19.

Members of WHO’s science group agreed on a number of technical requirements for COVID-19 challenge studies to maximise volunteers’ safety and prevent wider spread of infection.

These included recruiting only healthy young adults, conducting the studies under strict biosafety procedures (for example, isolating participants), giving the virus via the nose to mimic natural infection, and carefully increasing the dose of the virus.

Group of young adult students outside looking at books and papers, studying — Only young adults without underlying health conditions could volunteer for these studies.
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However, the experts were split on other issues, such as whether:

challenge studies would actually accelerate vaccine approval
results in young healthy adults would demonstrate whether or not a vaccine works for older people
challenge trials should begin before a proven and highly effective treatment for COVID-19 becomes available.

What next?

To design an ethically acceptable challenge study, it’s important to minimise the risks to study volunteers, research staff, and the wider community.

In the future, there may be additional ways scientists can reduce the risks. They may be able to better identify those at lowest risk of severe infection, develop a weakened strain of the virus, or have a highly effective treatment on hand to use if needed.

In the meantime, scientists could obtain results relevant to COVID-19 by conducting less risky challenge studies with other viruses.

For example, challenge studies with “common cold” coronaviruses, which are being considered in Australia, could teach us about the types of immune responses that protect us against coronavirus diseases.

Research eventuating in safe and effective vaccines for COVID-19 could save many lives. However, whether the benefits of challenge studies in the current pandemic outweigh the risks depends on many factors.

We must carefully consider proposals for these studies in light of the current state of science and vaccine development, and update our evaluations as new data emerge.

Euzebiusz Jamrozik, Infectious Disease Ethics Fellow, Ethox & Wellcome Centre for Ethics and Humanities, Univeristy of Oxford. Adjunct, Monash University; Kanta Subbarao, Professor, The Peter Doherty Institute for Infection and Immunity, and Michael Selgelid, Professor of Bioethics, Monash Bioethics Centre, Monash University, Monash University

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

Why do some COVID-19 tests come back with a ‘weak positive’, and why does it matter?

Posted on October 11, 2020 by particularkev

Sheena G. Sullivan, WHO Collaborating Centre for Reference and Research on Influenza and Jennifer MacLachlan, The Peter Doherty Institute for Infection and Immunity

When we get a test result for a disease like COVID-19, we naturally expect it to be either positive or negative. But the results of these tests are not so black and white.

Polymerase chain reaction, or “PCR”, is the most common test to detect the presence or absence of SARS-CoV-2, the virus that causes COVID-19.

Recently, a “weak positive” case of COVID-19 was reported in the Northern Territory.

Let’s take a look at why someone might get a weak positive result.

Shouldn’t you just be ‘positive’ or ‘negative’?

PCR tests are used to detect a range of viruses and pathogens. They look for viral genetic material in a respiratory sample, such as a nose or throat swab or a saliva sample.

We identify a sample to be positive or negative based on the number of times we need to amplify the small segments of genetic material to detect the virus — and whether this number falls below or above a certain threshold.

When there’s a lot of virus present, we only need a few cycles of amplification to detect it. When there isn’t much virus, or there’s none, we need to amplify the sample several more times until finally we cross the threshold and deem the sample negative.

So in this process we can see the potential for a weak positive result. It would generally be a reading at or just above the threshold. And that threshold varies depending on the test used.

Importantly, thresholds are just the point at which we believe we’ve detected something. They’re not 100% precise. Sometimes results just above or below the threshold might be false negatives or false positives.

When might you have a weak positive result?

In most cases, the genetic material of a virus is only detectable when we’re infected and the virus is still replicating and shedding into our respiratory passages.

But sometimes, even when the virus is no longer alive and replicating, it can hang around and be detectable by PCR. In these cases, it’s unclear whether the virus is infectious.

A health worker dressed in PPE prepares to take a swab from a man in his car. — PCR tests for COVID-19 look for the genetic material of SARS-CoV-2.
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In the case of the NT man, he had earlier tested positive for COVID-19 in Victoria and recovered. Although he recorded a negative test before travelling to the NT, it’s likely he was still just shedding small amounts of the virus.

This may be more common among people with weaker immune systems, as it takes them longer to clear the virus from their system.

How do we handle weak positives?

A weak positive is treated as a “presumptive positive” result — we presume it to be positive, and generally classify it as such, until we have information to suggest otherwise.

National testing guidelines for COVID-19 recommend weak positive results be checked by testing the same sample again. They also recommend collecting another sample.

In some cases, retesting the original sample may give more confidence of an infection with SARS-CoV-2. But collecting and testing another sample can offer further confirmation.

The subsequent test might target a different region of the virus’ genetic material, or use a different type of test. Alternatively, the sample could be referred to a reference laboratory to verify the result using specialised tests.

We don’t know of any publicly available data which indicate how common weak positive results are. But we don’t think they’re unusual.

It’s one of the reasons the publicly reported case numbers for COVID-19 are sometimes revised downwards, as weak positives are later confirmed to be negative after retesting.

It’s also not unique to COVID-19 or PCR — many different tests, for a variety of diseases, can produce weak positives.

But the phenomenon has a unique impact when the infection is part of a pandemic.

The danger of assumption

During a pandemic, there are implications not just for the person being tested, but for their contacts, their workplace, and the whole population.

Incorrectly assuming a weak positive result isn’t COVID-19 could lead to a person continuing to transmit the disease to others. It could also prevent them receiving the proper monitoring and, if necessary, treatment.

Conversely, assuming a weak positive result is COVID-19 when it’s actually negative could lead to the person being unnecessarily quarantined, which has potential personal, psychological and financial effects.

A man wearing a mask looks out the open window of his home. — A weak positive result which turns out to be negative could see a person isolated unnecessarily.
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In the case in the NT, classifying this indeterminate result as a positive case would have meant the first COVID-19 infection in two months in that state.

While the man was isolated, NT authorities didn’t count him as a case based on advice from the health department that the result was likely due to residual virus from his previous infection. They said he didn’t have any symptoms and it was highly unlikely he was infectious.

When the elimination of community transmission is being used as a criteria for border closures, individual cases can have significant flow-on effects to the whole population.

For these reasons, it’s important to appreciate the complexities of COVID-19 testing. It’s not always as simple as “positive” or “negative”.

Sheena G. Sullivan, Epidemiologist, WHO Collaborating Centre for Reference and Research on Influenza and Jennifer MacLachlan, Epidemiologist, WHO Collaborating Centre for Viral Hepatitis, The Peter Doherty Institute for Infection and Immunity

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

The new 15-minute test has potential, but standard tests are still the best way to track COVID-19

Posted on September 27, 2020 by particularkev

Katherine Gibney, The Peter Doherty Institute for Infection and Immunity; Deborah Williamson, The Peter Doherty Institute for Infection and Immunity, and Jodie McVernon, University of Melbourne

Testing remains a vital component of Australia’s success in managing COVID-19.

We need to diagnose people infected with SARS-CoV-2, the virus that causes COVID-19, as early as possible so they can be isolated from others and their contacts quarantined. Testing also helps us understand to what degree the virus is present in the population, so we can tailor public health measures accordingly.

If you’ve had a COVID-19 test, in all likelihood you received a PCR test. That’s the one with the throat and nose swabs, and is regarded as the “gold standard” in COVID-19 testing.

But now the Therapeutic Goods Administration (TGA) has approved a new kind of COVID-19 test, which can produce results in as little as 15 minutes, as opposed to a day or more for standard tests.

So is this new rapid test set to revolutionise COVID-19 testing in Australia? Not quite yet.

The traditional tests

Nucleic acid tests, or PCR tests, can detect ribonucleic acid (RNA) of SARS-CoV-2 from a day or two before symptoms start, and for a week or more afterwards, as symptoms resolve. Of course, some people will test positive without ever having symptoms.

PCR tests have been the backbone of SARS-CoV-2 testing worldwide. Because of the vast global experience with PCR tests and their high performance, they’re considered the most reliable COVID-19 test.

PCR tests require specialised laboratory equipment and trained scientists and technicians to test the specimens; processing and testing take several hours.

Since January, we’ve performed an astonishing 7.4 million SARS-CoV-2 PCR tests in Australia, which has needed a massive upscaling of capacity in laboratories nationally.

An illustration of SARS-CoV-2, the coronavirus that causes COVID-19. — PCR tests detect SARS-CoV-2 viral RNA.
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At times, demand for PCR testing has exceeded capacity, occasionally resulting in delays of up to several days in getting results back to patients. Meanwhile, laboratories swamped with COVID-19 tests may be limited in their capacity to perform their routine business, including diagnostic testing for other infectious diseases.

As people are required to isolate until they receive a negative test result and their symptoms resolve, these delays may come at a cost to the person waiting, their family, and the economy.

Recognising these costs may lead some people to choose not to be tested, Victoria has offered financial compensation for people without leave entitlements awaiting test results.

But delayed case confirmation also increases the time to identification and quarantine of contacts, undermining public health efforts.

What can we expect from the antigen test?

Rapid antigen tests can diagnose COVID-19 in 15 minutes. They’re relatively inexpensive and require a swab from the nose.

These tests detect viral antigens, proteins on the surface of SARS-CoV-2. The immune system recognises these proteins as foreign, and responds by making antibodies to SARS-CoV-2 (“anti-gen” means antibody generator).

Antigen tests perform best early in the infection when the amount of virus in a person’s system is highest. For a person with symptomatic COVID-19, this would be in the first week of symptoms. So they only pick up current infections – unlike antibody tests, which can detect if a person was previously infected with SARS-CoV-2.

Four SARS-CoV-2 rapid antigen tests have been licensed for use in Australia in the past two months.

Unfortunately, rapid antigen tests for COVID-19 appear to be less sensitive than PCR tests, meaning they may give a negative result in someone who does actually have COVID-19. One of the recently licensed rapid antigen tests may give a false negative result in up to 18.3% of people with COVID-19 diagnosed by PCR.

While a positive rapid antigen test result is more reliable, widespread use of these tests in asymptomatic people will result in some false positive results — that is, a positive test result in someone who doesn’t have COVID-19.

At this stage, national COVID-19 guidelines don’t include information on antigen tests. So a person with a positive antigen test would need to undergo a PCR test to be counted in Australia’s official COVID-19 case numbers.

Considering the pros and cons

We’re faced with a trade-off between the potential benefits of the rapid antigen tests — the ability to test larger numbers of people, consuming fewer laboratory resources, and quicker results — and the potential to miss a few cases because of the lower test sensitivity.

Despite the lower sensitivity, increasing testing rates might result in an overall net increase in the proportion of COVID-19 cases diagnosed, and therefore a public health benefit by preventing onward transmission from these cases.

One possible strategic use of these tests may be in screening people without symptoms to detect asymptomatic and pre-symptomatic infection that might otherwise go undetected. This could include people in workplaces where ongoing exposure to colleagues and the public is unavoidable, including sectors of the food supply chain or other essential services.

Because of the lower test sensitivity for the rapid antigen test, a PCR test remains most appropriate for people with symptoms, those at greater risk of poor outcomes from COVID-19, and people working in high-risk settings like aged care and health care.

While rapid antigen tests show promise, we’ll need to evaluate their efficacy in Australia before we can determine their role in our fight against COVID-19.

Katherine Gibney, NHMRC early career fellow, The Peter Doherty Institute for Infection and Immunity; Deborah Williamson, Professor of Microbiology, The Peter Doherty Institute for Infection and Immunity, and Jodie McVernon, Professor and Director of Doherty Epidemiology, University of Melbourne

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

Posted on September 13, 2020 by particularkev

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.

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).

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.

Richard Holden, Professor of Economics, UNSW

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

Worried you might test positive and put a spanner in Victoria’s COVID roadmap? Here’s why you should get tested anyway

Posted on September 13, 2020 by particularkev

Breanna Wright, Monash University

Victoria’s much-anticipated roadmap out of lockdown was released on Sunday, bringing with it a clear outline of how (and provisionally when) Victoria will see an easing of restrictions.

The plan is transparent about the case numbers, or lack of them, required for the state to move to each progressive stage. For example, moving to the second step, provisionally scheduled for September 28, will require an average of 30-50 new cases per day over a 14-day period.

Victorians are suffering from lockdown fatigue. They’re exhausted and drained. The reopening of playgrounds, the singles bubble, shortening the curfew, and an extra hour of daily exercise are all gestures to keep them going during this difficult time. But many people are still desperate for the lockdown to end.

Lockdown won’t be over until the number of positive cases falls. And there’s a risk that a desire to end restrictions might discourage Victorians from getting tested, for fear of adding to the numbers and prolonging the lockdown.

Not getting tested?

The way society views an illness affects how people who have it or might have it feel and behave. Since the beginning of the pandemic, terms such as “COVID suspect” or “superspreader” have risked creating a sense of shame for those who contract the virus.

Those feeling unwell may not want to be seen as “part of the problem”. We know from other diseases, when there is stigma attached to being sick, people with symptoms are less likely to seek care. No Victorian will want to be blamed for restrictions lasting any longer than they have to.

Testing is still vital

Nevertheless, it is crucial people continue to get tested. Without this information, it will be impossible for the government to negotiate a safe path out of restrictions. Gaps in our knowledge could mean the decision-makers don’t have enough confidence to progress to the next step.

Analysts already know when there are gaps in our understanding. Earlier this week, evidence of the coronavirus was found in sewage from Apollo Bay, about 200 kilometres southwest of Melbourne, despite no one in the area having tested positive.

Test results are just one piece of data — albeit a crucial one — that informs our understanding of the situation. Testing actually helps us move forward faster, not slower.

How to encourage testing

There are several ways to ensure the number of COVID-19 tests remains high. More than 2,403,388 tests have now been done in Victoria, 12,938 on Sunday.

1. Create a sense of pride in getting tested

Obviously, low numbers of positive tests are good. But high numbers of negative tests are much more informative than no test results at all. Telling your friends you’ve been tested, or posting it on social media, should be a source of pride that you’re doing your bit for Team Victoria.

2. Remove the stigma and shame

We should also work to remove the stigma of contracting COVID-19 — no one is catching it on purpose, after all. Campaigns such as Melbourne Strong aim to help people who are struggling in lockdown, and we should extend this kind of support to those going through COVID-19 itself.

3. Promote positive messaging

It’s important to remember how far we’ve come since the peak of Victoria’s second wave. On July 30 there were 723 new cases; on Monday we had 41. We also now know the targets we need to hit to end the restrictions, and Premier Daniel Andrews has raised the possibility they could even be lifted early. Influential community messengers can help reinforce this message of hope.

4. Make testing easier

The Victorian government has tried to make testing as easy as possible, through measures such as mobile testing, incentive payments and research into faster tests. They should also consider keeping information on wait times for different testing sites up to date, as for many places it is not currently available.

There’s no easy road out of this pandemic, but now we have the roadmap and we know where we need to get to. So if you have COVID-19 symptoms, don’t hesitate to get tested. You’ll be doing yourself and the whole state a favour.

Breanna Wright, Research fellow, BehaviourWorks Australia, Monash Sustainable Development Institute, Monash University

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

Goodbye, brain scrapers. COVID-19 tests now use gentler nose swabs

Posted on August 20, 2020 by particularkev

Craig Lockwood and Lucy Crawford

Early COVID-19 images of swabbing from Wuhan, China, looked more like an Ebola news story — health-care workers fully encased in personal protective equipment (PPE), inserting swabs so deeply that brain injury seemed imminent.

As COVID-19 (and testing) spread around the world, there were reports of “brain scraping”, “brain stabbing” or “brain tickling” swabs. Perhaps this was your experience early in the pandemic. Perhaps these stories have put you off getting tested so far.

But if you go to a drive-through clinic today, you’re likely to have a different swab, one that’s briefly inserted and not so far up as before.

So if fear of the swab itself is holding you back from getting tested, here’s what you need to know about these gentler swabs.

‘Brain scrapers’ not used so much in drive-through clinics

The swabs that gave COVID-19 testing its reputation are the nasopharyngeal swabs. Although these are considered the “gold standard” of testing, they are undeniably uncomfortable.

You remove your mask and blow your nose to clear your nasal passages. Then you try not to sneeze, cough or gag while a health worker inserts a long, flexible shaft about 12cm up your nose and into the back of your throat (until there’s resistance). They then swivel the swab against the back of your throat.

The distance for insertion is significant. Close your eyes and imagine a thin shaft being inserted the length of the space between your nostrils and the outer opening of the ear. The health worker needs to rotate the swab to maximise contact with the contents in the back of the nose before removing it.

The swab may cause your eyes to water, a reflex cough or sneeze. Because of this risk, staff must wear full PPE to avoid risk of being exposed to and inhaling infectious particles and aerosols.

This type of swab is still used in some clinics, and different jurisdictions around the world have different testing policies.

You’ll be pleased to hear, things changed

As the pandemic evolved, so have methods of testing, with evidence accumulating about how well they work.

For instance, some Australians have had their saliva tested, including Victorians towards the start of the state’s second wave.

But more widely used now in a typical drive-through clinic are a combined swab of the throat and nose.

You’ll be pleased to know the health worker swabs your throat first before using the same swab up your nose (and not the other way around)! This is the so-called oropharyngeal/nasal swab.

First the health worker will use a tongue depressor to keep your tongue down, then swab the area behind and next to the tonsils. Then they will take a nose swab.

If they take a superficial nose swab, they will ask you to look straight ahead before gently inserting the swab upwards until there’s some resistance. Then they will hold the swab in place for 10-15 seconds while rotating it, before repeating this in the other nostril.

If they take a mid-turbinate nasal (also known as a deep nasal) swab, you will tilt your head back slightly. The health worker will then insert the swab horizontally (instead of vertically) until there’s resistance (about two to three centimetres). They will then gently rotate the swab for 10-15 seconds before repeating on the other side.

Why did the swabs change?

If someone is going to stick a swab stick up our collective noses, the test needs to be accurate and reliable.

But what if other options were almost as good, without so much invasion, coughing and increased exposure risk for health-care workers?

So from late March and into April, organisations including the US Food and Drug Administration and US Centers for Disease Control, and Australia’s Public Health Laboratory Network,
announced they would move away from the deeper nasopharyngeal swabs to using nasal swabs for this type of testing.

The recommendation in Australia is to use a combined throat/deep nasal swab but if the health worker thinks it necessary, a nasopharyngeal swab.

Since then, studies suggest the gap between absolute best (nasopharyngeal) and avoiding a gag or cough-inducing reflex (nasal) might not matter as much as once thought.

Comparative studies show throat/nasal swabs are as sensitive as nasopharyngeal to detect SARS-CoV-2, the virus that causes COVID-19.

Other studies show throat/nasal swabs are practical, cheap, accurate and reliable.

Still not convinced? Your brain really is safe

The accumulating evidence suggests the newer nasal swabs are safe, reliable, cheaper to complete, and less unpleasant. They also save expensive, higher grade PPE for where it is needed — in our health-care facilities.

So with testing rates down in Victoria and calls for more testing in New South Wales, this is a reminder we must continue to test, test, test, as well as practise hand hygiene, social distancing, and wearing masks.

Craig Lockwood, Associate Professor Implementation Science, JBI and Lucy Crawford, Clinical Lecturer

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

Making coronavirus testing easy, accurate and fast is critical to ending the pandemic – the US response is falling far short

Posted on July 28, 2020 by particularkev

There are functional tests for coronavirus, but not enough of them are being done.
AP Photo/Paul Sancya

Zoë McLaren, University of Maryland, Baltimore County

For many people in the U.S., getting tested for COVID-19 is a struggle. In Arizona, testing sites have seen lines of hundreds of cars stretching over a mile. In Texas and Florida, some people were waiting for five hours for free testing.

The inconvenience of these long waits alone discourages many people from getting tested. With the surge in cases, many public testing sites have been reaching maximum capacity within hours of opening, leaving many people unable to get tested for days. Those that do get tested often face a week-long wait to get their test results.

Every person who isn’t tested could be spreading COVID-19 unknowingly. These overstretched testing programs are a weak link in the U.S. pandemic response.

I study public health policy to combat infectious disease epidemics. The key to overcoming this pandemic is to slow transmission of the virus by preventing contagious people from infecting others. A widespread quarantine would accomplish this, but is economically and socially burdensome. Testing offers a way to identify contagious people so they can be isolated to prevent the spread of the disease. This is especially important for COVID-19 because an estimated 40% or more of all people infected with SARS-CoV-2 have few or no symptoms so testing is the only way to identify them.

Some states are doing much better than others. But as a whole, the U.S. is falling far short of the amount of testing needed to control the pandemic. What are the challenges the U.S. is facing? And what is the way forward?

A lab technician using a swab to put a sample into a rapid test machine. — Currently, rapid tests that take about 15 minutes to process are a quick and easy way to diagnose COVID-19 infections, but there are concerns about accuracy.
AP Photo/Carlos Osorio

Testing should be free, easy, fast and accurate

The ultimate goal of testing is for everyone, regardless of symptoms, to know at all times whether they are infected with the coronavirus. To achieve this level of testing, tests should be free, very easy to perform and provide accurate results quickly.

Ideally, free COVID-19 tests would be delivered to everyone directly. The tests would be simple to perform – like a saliva test – and would give a perfectly accurate result within minutes. Everyone could test themselves weekly or anytime they were going to be in close contact with other people.

In this ideal scenario, most, if not all, contagious people would be detected before they could spread the virus to others. And because of the rapid results, there would be no burden of quarantining between doing the test and getting the result.

Researchers are working on better-quality tests, but access is a problem of infrastructure, not science. Right now, nowhere in the U.S. comes close to meeting surging demand for testing.

A line of people waiting in cars in front of a sign for COVID-19 testing. — Long lines, slow turnaround times for results and shortages of testing capacity all make Texas one of the worst places to get a test in the U.S.
AP Photo/David J. Phillip

One of the worst cases: Texas

The difficulty of getting a COVID-19 test varies by state, but currently, people in Texas face some of the biggest obstacles, which results in far fewer tests being done than is needed to control the pandemic.

First, Houston – which is experiencing a surge in cases – and many testing sites across the state recommend or offer testing only to people who have symptoms, were exposed to a COVID-19 case or are a member of a high-risk group.

Even people recommended for testing still face challenges. It is possible to request an appointment for a free COVID-19 test, but testing facilities can handle only so many patients a day and testing slots fill up quickly. Even if someone gets an appointment, they may face an hours-long wait at the testing site.

Finally, public health experts recommend that people who may have been exposed to COVID-19 should quarantine at home for 14 days or until they receive a negative test result. In Texas, patients are supposed to get results through an online portal in three to five days, but many labs have been taking seven to nine days to return results. These long delays mean people face a much higher burden of quarantining while waiting for results.

All of these challenges make it clear that Texas is simply not testing enough people to keep the spread of COVID-19 in check.

To gauge the success of COVID-19 testing programs, epidemiologists use a measure called test positivity. This is simply the percentage of tests that come back positive. The lower the test positivity, the better, because that means very few cases are going undetected. A high test-positivity rate is usually a sign that only the sickest people are getting tested and many cases are being missed.

The World Health Organization guidelines say that if more than 1 out of 20 COVID-19 tests comes back positive – a test positivity of more than 5% – this is an indication that a lot of cases are not diagnosed and the epidemic is not under control. Texas currently has a test-positivity of around 16%, which means that a lot of infected people are not getting tested and may be unknowingly spreading the disease.

A doctor using a nasal swab to test a state senator of New Mexico. — In New Mexico, it is relatively easy to get a test, so more people are getting tested.
AP Photo/Cedar Attanasio

One of the best cases: New Mexico

In stark contrast to Texas is New Mexico, which has one of the strongest testing programs in the U.S.

First, public health officials there encourage everyone to get tested for COVID-19 regardless of symptoms or exposure. The state has also prohibited health providers from charging patients for tests. People seeking a test have the option to walk in or to make an appointment ahead of time, whichever is more convenient.

All of this relatively good access to testing has resulted in one of the highest per capita testing rates in the country, at over 20,000 tests per 100,000 people, and a test-positivity rate of around 4%. New Mexico’s testing program is diagnosing a relatively high proportion of cases despite the state experiencing a recent surge.

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New Mexico still has room for improvement. Long lines, wait times and limited capacity are becoming more common as cases surge, but the foundation of a strong testing program has helped the state cope with the increase in cases.

The big-picture problems

The pre-pandemic infectious disease testing capabilities in the U.S. are clearly unable to meet the current demand. A nationwide response is needed, and there are three things that Congress, the federal government and local governments can do to help ensure COVID-19 tests will be easy to get, fast and accurate.

First, Congress can provide funding to stimulate the testing supply chain, scale up existing testing programs and promote innovation in test development. Second, governments can improve the management and coordination of testing programs to more efficiently use existing resources. And third, innovative testing methods that reduce the need for lab capacity – like paper-strip tests and pooled testing – need be approved and implemented more quickly.

Every little improvement in testing capabilities means more COVID-19 cases can be caught before the virus is transmitted. And slowing the spread of the virus is the key to overcoming the pandemic.

Zoë McLaren, Associate Professor of Public Policy, University of Maryland, Baltimore County

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

Victoria hits bleak record of 484 new cases, NSW at a critical point — if you feel sick, get tested then stay home

Posted on July 22, 2020 by particularkev

Hassan Vally, La Trobe University

Too many people are going out while experiencing COVID-19 symptoms or while awaiting test results, Victorian Premier Daniel Andrews said on Wednesday, after the state hit a bleak new record of 484 new cases. The state’s previous worst daily case number was 428 last Friday.

It’s always a shock to see a new record number, and certainly these numbers are bigger than we would have hoped. While it’s a psychological blow, it’s not cause for panic. Thankfully, we are not seeing a doubling or tripling of case numbers, which really would ring alarm bells.

Too many people going out while sick

Andrews chastised people for taking too long to get tested after first experiencing symptoms, which include fever, cough and sore throat. He said:

From 3,810 cases, which are the cases between July 7 and July 21, I’m very unhappy and very sad to have to report that nearly nine in ten – or 3,400 cases – did not isolate between when they first felt sick and when they went to get a test […]

That means people have felt unwell and just gone about their business. They have gone out shopping, they have gone to work, they have been at the height of their infectivity and they have just continued on as usual […] The one and only thing that you can and must do when you feel sick is to go and get tested. Nothing else is acceptable.“

He also said 53% those 3,810 cases “did not isolate, that is, did not stay at home and have no contact with anybody else — between when they had their test taken and when they got the results of that test.”

Unless people stay home when unwell and isolate while awaiting test results, the case numbers will continue to climb, Andrews said.

The premier noted self-isolation would leave some people with no income, and urged people in that situation to call 1800 675 398 to apply for an emergency A$1500 payment.

It’s good to see the premier acknowledge income as one of the major drivers for these behaviours; people may not always have the financial flexibility to do the right thing.

Hopefully, making more people aware of the emergency payment option will help counteract this.

The government may have to work harder to ensure people know to self-isolate, and that the emergency payment is available, and I suspect this will be promoted more widely.

NSW at a critical point

In New South Wales, Premier Gladys Berejiklian said there were 16 new cases in the 24 hours to 8pm last night, all traced to known clusters. She called on people to avoid crowded places, wash hands, stay home if unwell and get tested if they have even mild symptoms.

Berejiklian said from Friday, NSW businesses breaking rules on COVID-Safe registration, and breaching caps on group bookings, would “be fined — worse than that, if you breach again you will be shut down”.

NSW is on especially high alert. Despite this, it’s somewhat reassuring to know the state’s new cases can be traced to known outbreaks. However NSW residents are not out of the woods yet.

Speculation is rife that further lockdowns might be on the way in NSW. While nothing should be off the table, it doesn’t appear NSW is anywhere near this point yet. The state has more than enough capacity to bring things under control from where the numbers sit now.

Today’s news serves as a grim reminder we must all follow the golden rules of pandemic management: get tested if you experience even mild symptoms, stay home if unwell or awaiting test results, wash your hands often, physically distance from others, limit social gatherings, and wear a mask if you can’t physically distance (face-coverings will be mandatory for residents of metropolitan Melbourne and Mitchell Shire as of midnight Wednesday).

As to where things move from here, much of that is in our hands as individuals. Each of us, by doing everything we can to prevent the spread of the virus, can make a massive contribution to saving lives and defeating COVID-19.

The silver lining is that we know what’s needed. What we’re being asked to do is not easy, but we do know how to bring this coronavirus pandemic under control. We’ve done it before and we can do it again.

Hassan Vally, Associate Professor, La Trobe University

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

Sharing my thoughts with the world from a Particular Baptist perspective

From drug use to COVID-19

The technique is important

What happens when a sample is positive?

There are strengths and weaknesses

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Who are the ‘worried well’?

We can’t dismiss people’s real anxiety

Yes, it can be frustrating

We’d be better off promoting testing as doing the ‘right thing’

Clear, consistent, targeted public health messaging works

Have the ‘worried well’ really clogged up testing?

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How do these studies differ from standard, larger studies?

Challenge studies need extra preparation

Past experience and recent developments

Ethical and scientific questions

What next?

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Shouldn’t you just be ‘positive’ or ‘negative’?

When might you have a weak positive result?

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The danger of assumption

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The traditional tests

What can we expect from the antigen test?

Considering the pros and cons

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Keeping the reproduction rate below 1

Effective contact tracing

Batch testing

The strategy going forward

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Not getting tested?

Testing is still vital

How to encourage testing

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‘Brain scrapers’ not used so much in drive-through clinics

You’ll be pleased to hear, things changed

Why did the swabs change?

Still not convinced? Your brain really is safe

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Testing should be free, easy, fast and accurate

One of the worst cases: Texas

One of the best cases: New Mexico

The big-picture problems

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Too many people going out while sick

NSW at a critical point

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