What’s the difference between mutations, variants and strains? A guide to COVID terminology



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Lara Herrero, Griffith University and Eugene Madzokere, Griffith University

Living through a global pandemic over the past year has seen all of us expanding our vocabularies. We now understand terms like PPE, social distancing and contact tracing.

But just when perhaps we thought we had a handle on most of the terminology, we’re faced with another set of new words: mutation, variant and strain.

So, what do they mean?

The genetic material of SARS-CoV-2, the coronavirus that causes COVID-19, is called ribonucleic acid (RNA). To replicate, and therefore establish infection, SARS-CoV-2 RNA must hijack a host cell and use the cell’s machinery to duplicate itself.

Errors often occur during the process of duplicating the viral RNA. This results in viruses that are similar but not exact copies of the original virus. These errors in the viral RNA are called mutations, and viruses with these mutations are called variants. Variants could differ by a single or many mutations.

Not all mutations have the same effect. To understand this better, we need to understand the basics of our genetic code (DNA for humans; RNA for SARS-CoV-2). This code is like a blueprint on which all organisms are built. When a mutation occurs at a single point, it won’t necessarily change any of the building blocks (called amino acids). In this case, it won’t change how the organism (human or virus) is built.

On occasion though, these single mutations occur in a part of the virus RNA that causes a change in a particular building block. In some cases, there could be many mutations that together alter the building block.




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A variant is a referred to as a strain when it shows distinct physical properties. Put simply, a strain is a variant that is built differently, and so behaves differently, to its parent virus. These behavioural differences can be subtle or obvious.

For example, these differences could involve a variant binding to a different cell receptor, or binding more strongly to a receptor, or replicating more quickly, or transmitting more efficiently, and so on.

Essentially, all strains are variants, but not all variants are strains.

A diagram depicting the evolution from mutation to variant to strain.
Viruses with mutations become variants. If the variant displays different physical properties to the original virus, we call it a new strain.
Lara Herrero, created using BioRender, Author provided

Common variants (which are also strains)

Three of the most common SARS-CoV-2 variants are what we’ve come to know as the UK variant (B.1.1.7), the South African variant (B.1.351) and the Brazilian variant (P.1). Each contains several different mutations.

Let’s look at the UK variant as an example. This variant has a large number of mutations in the spike protein, which aids the virus in its effort to invade human cells.

The increased transmission of the UK variant is believed to be associated with a mutation called N501Y, which allows SARS-CoV-2 to bind more readily to the human receptor ACE2, the entry point for SARS-CoV-2 to a wide range of human cells.

This variant is now widespread in more than 70 countries, and has recently been detected in Australia.

While we commonly call it the “UK variant” (which it is), it’s also a strain because it displays different behaviours to the parental strain.

We’ve got lots more to learn

There is some confusion around how best to use these terms. Given all strains are variants (but not all variants are strains), it makes sense the term variant is more common. But when the science shows these variants behave differently, it would be more accurate to call them strains.

Pleasingly, the World Health Organisation and health departments in Australia appear to be using the terms correctly in the context of SARS-CoV-2.




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The big question everyone is asking at the moment is how the new variants and strains will affect the efficacy of our COVID vaccines.

The scientific community is uncovering more information about emerging mutations, variants and strains all the time, and leading vaccine developers are testing and evaluating the efficacy of their vaccines in this light.

Some recently licensed vaccines appear to protect well against the UK variant but recent data from Novavax, Johnson & Johnson and Oxford/AstraZeneca indicates possible reduced protection against the South African variant.

Health authorities in South Africa recently paused their rollout of the Oxford/AstraZeneca vaccine for this reason. However, its too early to tell what impact, if any, this will have on Australia’s vaccine plans.

The vaccine rollout in Australia will assess all information as it comes to light and ensure optimal available protection for the population.




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The Conversation


Lara Herrero, Research Leader in Virology and Infectious Disease, Griffith University and Eugene Madzokere, PhD Candidate in Virology, Griffith University

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

Do you want to be resuscitated? This is what you should think about before deciding



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Barbara Jean Hayes, The University of Melbourne and Joseph Ibrahim, Monash University

Every day, in every hospital, doctors and nurses respond to “code blue” situations. This is an emergency alert for when a patient’s heart stops beating, called a cardiac arrest.

To save the patient’s life, medical and nursing staff will often administer cardiopulmonary resuscitation (CPR). CPR involves repeated chest compressions, artificial breathing, use of medications and an electric shock to jump-start the heart (defibrillation).

The aim is to restore a person’s heartbeat and blood pressure to normal, and in turn to restore life. CPR must be initiated quickly as brain cells rapidly die without blood and oxygen.

Patients admitted to hospital are often surprised when their doctors ask: “If your heart were to stop beating, would you want CPR or not?” But in every code blue doctors need answers to the same two questions. First, whether the clinical team considers CPR would be an effective treatment; and second, whether the patient wants CPR.

First response

If a person has a cardiac arrest outside hospital, it is usual, and expected, that bystanders begin CPR, use a defibrillator if available, and call an ambulance.

CPR is taught in first aid courses and defibrillators are widely available in public places such as airports and sports grounds. Time is of the essence, so having trained community members is important.

In a hospital setting, though, the decision to administer CPR is more nuanced. It’s built on a discussion around the patient’s medical condition and, importantly, takes into account their wishes.




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Clinicians in Australia have provided examples of some different perspectives on this discussion:

Some of [the patients’ relatives] are absolutely aghast that we might even suggest not to resuscitate […] they bring their loved one into hospital to get better.

A lot of people […] just say, ‘No, I’ve had a good innings, just let me die.’ […] Often I find it’s families who have the objection.

A bit of background

CPR was developed and initially applied to resuscitate people with specific medical conditions such as an acute myocardial infarction (a heart attack).

When a cardiac arrest occurs because of a heart attack or other heart condition, there’s a reasonable chance CPR will re-start the heart and save the person’s life. A recent Australian study looking at people who had a cardiac arrest in hospital showed 41.5% of people who were admitted due to heart problems survived with good neurological function.

Expanding the use of CPR more broadly to every disease that causes the heart to stop beating seems like common sense. But this is not necessarily the case.

Talking about whether you want to be resuscitated, although difficult, is important.
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For older hospitalised patients (aged over 67 years in this research) with chronic diseases — such as heart failure, kidney disease, cancer or diabetes — their chance of surviving a cardiac arrest and leaving the hospital alive is around 11-15%. Chances of survival are slightly better in older patients without a chronic illness (17%).

For patients in the late stage of their life, due to advanced illness or severe frailty, their chance of survival is almost zero.

CPR is not always an appropriate treatment. The decision to perform it needs to be made carefully, especially when it’s highly unlikely to restore a patient’s heartbeat.

Outcomes after CPR

Unlike the popular media portrayal of CPR, not every survivor of cardiac arrest returns to their previous level of functioning.

Patients may survive but with some brain damage. This could range from minor damage with trivial functional effects such as being forgetful; to moderate damage with serious functional effects such as a change in personality and needing help with everyday activities; to severe damage with catastrophic functional impairment eventually leading to death.

CPR may revive a heart that has stopped beating, but it doesn’t always restore a person back to a life they had or want. It may also do harm by reviving a person who does not want to continue living and would have preferred their disease to follow its natural course. When CPR is performed on a patient who doesn’t want it, it disrupts a gentler dying process, transforming it into an impersonal medical event.

When a cardiac arrest happens, there’s no opportunity to ask the patient what they want at that time. In hospital, it’s routine to provide CPR for patients in cardiac arrest unless there is a medical order to withhold it, or if the patient has completed an advance care directive refusing CPR. This is often referred to as a “do not rescusitate” order.




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Talk about it

Avoiding harm from inappropriate or unwanted CPR requires planning ahead and being prepared to have a difficult conversation.

We have launched an animated film, The Inappropriate Question, to help people better understand why these conversations are important.

Discussing CPR is upsetting for some patients, because raising the possibility of death is confronting. It’s also harder to discuss this when a person has just been admitted to hospital for treatment and is expecting to recover.

But patients have the right, and usually want, to be involved in their own treatment decisions. The challenge is how we reconcile this wanting to know and wanting to be involved in decisions, with not wanting to be upset by knowing.




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CPR is an important treatment. When used appropriately, it saves lives. But when applied injudiciously it can cause distress and avoidable harm.

Advance care planning is one way to start thinking about this long before a person is seriously ill. Particularly if you’re older and have chronic medical conditions, have that discussion with yourself, your loved ones and your medical team.The Conversation

Barbara Jean Hayes, Honorary Academic, The University of Melbourne and Joseph Ibrahim, Professor, Health Law and Ageing Research Unit, Department of Forensic Medicine, Monash University

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

What are nebulisers? And how could they help spread COVID-19?



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Brian Oliver, University of Technology Sydney

A nebuliser — a medical device that turns a liquid into a fine mist, typically to deliver inhaled medication — may have spread the coronavirus in Melbourne’s hotel quarantine.

Victoria’s Chief Health Officer Brett Sutton said earlier today this was the “working hypothesis” to explain why three people became infected at the airport’s Holiday Inn hotel.

How could this have happened? And what are the implications for people who use nebulisers outside hotel quarantine, such as those with asthma?




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What is a nebuliser?

A nebuliser creates a fine mist from a liquid, usually using compressed air or oxygen, or via ultrasonic vibration. A nebuliser is different to a vaporiser, which uses heat to produce a mist.

Nebulisers are often used to deliver life-saving drugs. Patients inhale them via a mask they put over their nose and mouth. Sometimes the mist alone is sufficient to provide a treatment. For example, nebulised saline is used to treat the lung condition cystic fibrosis. Sometimes people with asthma or chronic obstructive pulmonary disease are also treated with drugs via a nebuliser.




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How could a nebuliser potentially spread COVID-19?

When we breathe in and out, the very small airways and the air sacs in our lungs open and close. This generates particles. These particles, along with water vapour, are what are commonly referred to as exhaled aerosols. Think back to breathing out on a cold day; the mist was aerosols from your lungs.

When we have a viral respiratory infection, the virus can be contained in the particles we exhale, and this is how aerosol transmission occurs. It is now widely accepted that SARS-CoV-2, the virus that causes COVID-19, can be spread via aerosols, as well as via larger droplets when we cough and sneeze.

Any activity that increases the amount of aerosols, for example singing or exercising, can increase the amount of aerosolised virus, thereby increasing the risk of transmission.




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When people use a nebuliser, two things happen. The first is they often take in big breaths and exhale more forcefully than normal. This alone increases the amount of particles generated. The second is they breathe in a fine mist, not all of which is absorbed in the lung. This too is exhaled.

And when a nebuliser is used to loosen mucus in the lungs, this mucus could also be exhaled. This could be as particles or coughed out.

So whatever the mechanism, someone with COVID-19 who uses a nebuliser is at risk of inadvertently spreading the virus to others.




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Don’t we already know this?

We know that using a nebuliser in COVID-19 patients is not a good idea, especially as many drugs can be delivered in other ways.

For example, the Australian Commission on Safety and Quality in Health Care states:

Nebulisation is NOT recommended in patients with COVID-19 as it may contribute to the spread of the virus.

However, it acknowledges that in some circumstances using a nebuliser is unavoidable, for instance, in children.

Was a nebuliser responsible for the spread at the Holiday Inn?

This question is very difficult to answer definitively without making actual measurements.

For example, some so-called super spreaders are highly contagious.

However, if a COVID-positive person was using a nebuliser, and the spread of the virus was limited to those in relatively close proximity to that person, it is highly likely the nebuliser would have contributed to the spread.

In Sutton’s announcement earlier today, he said that in the case of transmission at the Holiday Inn, the theory that a nebuliser was the route of infection:

…makes sense in terms of the geography and it makes sense in terms of the exposure time.

So what does this mean for people using nebulisers?

People using a nebuliser for medical reasons should not be frightened by these developments. They should talk to their health-care provider about any concerns.

The bigger question relates to the use of nebulisers by people in hotel quarantine, which Western Australia says it will now ban.

However, it is highly likely a person using a nebuliser in hotel quarantine needs it to provide life-saving medication. So it’s not as simple as banning their use altogether. We’re more likely to see more consideration around how they are used in our quarantine hotels. For example, they might be restricted to particular areas or only used when there is no other medical alternative.The Conversation

Brian Oliver, Research Leader in Respiratory cellular and molecular biology at the Woolcock Institute of Medical Research and Professor, Faculty of Science, University of Technology Sydney

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

‘The disease of kings?’ 1 in 20 Australians get gout — here’s how to manage it



“The Gout”, by James Gillray.
Wikimedia Commons, CC BY

Andrew Brown, UNSW

I awoke one morning late last year to find a bright red bauble at the foot of my bed. It wouldn’t have looked amiss adorning a Christmas tree. But it felt ready to explode. It was my big toe, and this was my first encounter with gout.

In good company

With a history spanning more than 4,500 years, gout is among our earliest recorded diseases. Hippocrates, traditionally regarded as the father of medicine, called it “the unwalkable disease”, because it was very painful for people with gout to walk.

Many famous historical figures suffered with gout, including Christopher Columbus, Henry VIII, Benjamin Franklin and Beethoven. It became known as “the disease of kings”.

This moniker also reflects the fact gout has historically been associated with indulging in rich food and excessive alcohol. Scientific evidence today suggests this may have something to do with it, though the common belief drinking port specifically causes gout is unfounded.

Today, no longer just a disease of kings, the prevalence of gout is increasing around the world. Almost one in 20 Australians have had at least one attack of gout.

And some stigma still clings to the condition. Often gout is seen as being self-inflicted, a mark of overindulgence. But living with gout has far-reaching implications, hampering a person’s ability to participate in everyday life.




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What is gout?

Gout is the most common form of inflammatory arthritis. It’s caused by sodium urate crystals forming in the joints. While the big toe is particularly susceptible, gout can also affect the ankles, knees, elbows, wrists and fingers.

Urate, or uric acid, is an end-product of the breakdown of biochemicals called purines, which are both components of your DNA and absorbed into the body through the foods you eat. Urate levels reflect how much is made in the liver and how much is flushed out when you go to the toilet.

If your urate levels become too high, the urate turns into crystals. When urate crystals form in the fluid cushioning a joint, the body’s defence forces see them as foreign invaders. Inflammation and debilitating pain follow.

A main, appearing in pain, clutches his inflamed foot.
Gout can be incredibly painful.
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What causes gout?

A high level of urate in the blood is the greatest risk factor for gout. But what causes high levels of urate? While we don’t know exactly, several factors certainly contribute.

A tangled web links urate, gout and other metabolic diseases, including type 2 diabetes and high blood pressure. Being overweight is a common factor.

Gout can run in families, with genetics playing a key role in determining urate levels. For example, genetic differences can impair urate excretion, thereby increasing blood urate levels.

Gout is also more common in males — almost 80% of people with gout are male. One reason for this is the female sex hormone oestrogen lowers urate levels, and is therefore protective against gout in pre-menopausal women.

And gout is more common the older you get. It affects 0.2% of Australian men in their 20s, increasing to 11% over the age of 85.




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Management and prevention

You should ice and raise the affected joint and minimise contact with it — even a light bedsheet can cause excruciating pain.

Attacks of gout can last for days or weeks. If you think you have gout, you should see your doctor.

Anti-inflammatory drugs can ease gout attacks. Your doctor might prescribe colchicine, or you can get ibuprofen over the counter.

It’s easy to stop exercising, but swimming and cycling are two ways you can comfortably continue moving during a gout flare.

Many people who have one gout attack will go on to have more. In one study, 70% of people who had an attack of gout went on to have another within a year.

If you suffer two or more attacks, management of chronic gout involves taking a urate-lowering therapy such as allopurinol or febuxostat.

Two hands clinking beers.
Beer is often singled out as it’s relatively purine-rich. But it’s a good idea to cut back on all types of alcohol.
Shutterstock

If you’ve had gout once and want to prevent it coming back, it’s worth thinking about lifestyle changes. As with other metabolic diseases, losing weight helps.

You might also consider minimising consumption of purine-rich foods, which include meat, seafood and yeast products, like Vegemite.

But as with any diet, sticking to a low-purine diet can be challenging. Evidence for particular foods to favour or avoid for gout is weak, and overall, diet contributes very little to variation in urate levels.

So rather than purely focusing on purine-rich foods, consuming less in total can better control urate levels while improving your overall health. Limiting alcohol is also a good idea.

Epilogue

With a red bauble stuck on the end of your foot, you learn to appreciate how important your big toe is for mobility.

Eventually, I managed to drop my COVID kilos, by watching portion sizes, not going back for seconds, replacing unhealthy snacks with fruit, and cutting back on alcohol.

And with that, I’m hoping my first encounter with gout might be my last. Although keeping off the kilos will require constant vigilance, the memory of that painful red bauble should be a powerful motivator.




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The Conversation


Andrew Brown, Professor, School of Biotechnology and Biomolecular Sciences, UNSW

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

COVID vaccines have been developed in record time. But how will we know they’re safe?



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Nicholas Wood, University of Sydney and Kristine Macartney, University of Sydney

With the rollout of COVID-19 vaccines about to begin in Australia, people may be wondering if they’re safe (and effective) in the long term. What might be the health consequences a year after vaccination, or further into the future?

While it’s true COVID-19 vaccines have been developed in record time, the importance of tracking vaccine safety is not new. We routinely monitor the safety of all vaccinations, years after they’ve been used in millions of people.

And in guidance from the Therapeutic Goods Administration (TGA) this week, we have a clearer picture of how we’ll know about any unexpected, rare or long-term side-effects of the COVID-19 vaccines. In fact, we’ll use and build on many existing systems to look out for these.




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Vaccine trials only tell us so much

Late-stage vaccine trials in tens of thousands of people only last for a defined period of time, typically 12 months. Vaccine manufacturers present data on vaccine safety (and efficacy) for that time-frame to regulatory bodies. Safety data is rigorously assessed before a vaccine is approved for use.

But when approved vaccines are then given to the general public, we can monitor for any new events that may occur unexpectedly in both the short and longer term. Tracking potential side-effects in the real world in all people who have a vaccine, and outside the tightly controlled conditions of a trial, means we can ensure the vaccine is safe when given to millions — or billions — of people.




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So how might this work for COVID-19 vaccines? The Pfizer/BioNTech vaccine phase 3 trial reported safety data until about 14 weeks after the second dose. The Oxford/AstraZeneca trial reported safety data after about three months after the first dose, and two months after the second dose.

However, participants in both these large trials will continue to be followed up for both efficacy and safety until the end of the study from around 12 months after the first dose of vaccine.

COVID vaccine safety is also being monitored in several other ways, by individual countries, including Australia. Countries also share their vaccine safety monitoring data via a global database.




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Here’s how we’ll monitor COVID vaccine safety in Australia

The TGA has overall responsibility for monitoring the safety of medicines and vaccines in Australia. Just this week, the TGA released its plans for monitoring the safety of COVID-19 vaccines.

This includes the timely collection and management of reports of COVID-19 vaccine adverse events, an ability to urgently detect any safety concerns and to communicate safety issues to the public.

‘Passive’ surveillance

A cornerstone of the system Australia has had in place for decades to capture any possible vaccine reactions is “passive” surveillance. In practice, this means anyone can report a reaction to the TGA, the public included.

If your GP or nurse thinks you may have had a reaction they should report this to their state or territory health department, which then informs the TGA. This is mandatory in some jurisdictions but not in others.

Woman holding smartphone about to make a call
Consumers are being encouraged to report any suspected side-effects after their COVID vaccine.
www.shutterstock.com

The TGA is encouraging health professionals and consumers to report suspected side-effects to COVID-19 vaccines and there is a guide on its website on how to do this.

The TGA has a database that records any reported possible reactions. If there are any suspected safety issues, these are immediately investigated and necessary action is taken. For example, if necessary an immunisation program can be stopped or special precautions implemented. TGA can also issue safety alerts.

‘Active’ surveillance

Since 2014, Australia has also been actively looking for any safety concerns via the AusVaxSafety surveillance system, led by the National Centre for Immunisation Research and Surveillance, which we are affiliated with.

We send texts or emails to people asking them to fill out a survey on their health after being vaccinated. This system enables us to detect any suspected safety issues in near real time. Last year, AusVaxSafety surveyed nearly 290,000 people after they had the 2020 influenza vaccine and found more than 94% felt completely well. Others had mild and expected short-term side effects.

This system will be used to pick up any safety concerns when the COVID-19 vaccines roll out in the next few weeks. If you are vaccinated at selected sites, including GP practices and COVID-19 vaccine hubs, you will be told about this automated system. You don’t have to register or enrol but will be sent an SMS on day 3 and day 8 after each vaccine dose (you can decide whether to fill out the survey). Your anonymised results will be reported to your state or territory health department and the TGA.

This system will probably be in place to monitor safety of the COVID-19 vaccines for a few years. And as new vaccine brands come on board, we will continue to monitor those too.




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We can also learn from other countries

The United States has recently developed an equivalent system, V-safe. Safety data from this system from about two million people who have had a COVID-19 vaccine indicates the vaccines are safe. The short-term side-effects are very similar to those reported in the vaccine trials. The most common reactions include injection site pain, headache, tiredness and muscle aches, usually in the first two days and then resolving within a week after vaccination.

And worldwide, more than 150 million COVID-19 vaccine doses have already been given, with no unexpected safety concerns.




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In a nutshell

The potential benefits to us all from a mass vaccination program against COVID-19 far outweigh the potential side-effects, based on data from millions of people who have already been vaccinated around the world. Yet, we know all medicines, vaccines included, have the potential for side-effects.

However, by using, and building on, our already established safety surveillance system, we will be “on top” of rapidly identifying any possible safety concerns. That’s immediately after vaccination and into the longer term.The Conversation

Nicholas Wood, Associate Professor, Discipline of Childhood and Adolescent Health, University of Sydney and Kristine Macartney, Professor, Discipline of Paediatrics and Child Health, University of Sydney

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

Are vaccines already helping contain COVID? Early signs say yes, but mutations will be challenging


Maximilian de Courten, Victoria University; Maja Husaric, Victoria University, and Vasso Apostolopoulos, Victoria University

More than 130 million COVID vaccine doses have been administered worldwide already, according to the University of Oxford’s “Our World in Data” vaccination tracker.

Israel, the United Kingdom, the United States, the United Arab Emirates and China are leading this huge global effort.

COVID vaccines were initially tested and approved on their ability to reduce the severity of the disease.

However, the long-term goal of vaccination is to decrease infection rates and eliminate the virus.

Excitingly, early signs suggest vaccines are already helping drive down infection rates in some countries, including Israel and the UK.

In saying that, it’s early days, and some preliminary data suggest countries might have to update their vaccine strategies to deal with emerging variants of the virus.

Israel is leading the way

The US (43 million doses), China (40 million) and the UK (13 million) have administered the most doses in total.

However, these numbers don’t take into account population size, so looking at the number of doses injected per 100 people is more meaningful.

Here, the league table is currently topped by Israel, with around 67 vaccination doses administered per 100 people.

Almost 25% of the population are fully vaccinated with both doses. And all this in just five weeks.

Israel aims to vaccinate everyone over the age of 16 and reach at least 80% of its nine million people by May this year.

Reaching at least 70% of the population via vaccination (and/or natural infection) is needed for herd immunity for COVID, according to initial modelling by University of Chicago researchers in May last year.

However, given more infectious variants of the virus have emerged, we may need to vaccinate an even higher proportion of the population to reach herd immunity.

Infection rates are falling

So far, Israel is solely using the Pfizer/BioNTech vaccine. Interim reports from the country suggest the vaccine rollout is linked to a fall in infections in people over 60 years old.

It can be tricky to separate the effects of public health measures such as lockdowns versus the effects of vaccination.

But because the fall is most pronounced in older people who were first in line to receive the vaccine, data suggest this is also partly due to the vaccine, and not just the country’s current restrictions. A team of Israeli researchers found larger falls in infections and hospitalisations after the vaccinations than occurred during previous lockdowns.

Only 0.07% of the 750,000 over-60s vaccinated tested positive for COVID, according to Israeli Ministry of Health data released last week. And only 38 people, or 0.005%, fell ill and required hospitalisation. The chance of testing positive for COVID two weeks after receiving the first dose was 33% lower than in those not vaccinated.

The UK is also showing positive signs

The UK has administered 19.4 doses per 100 people. Around 13.2 million people (or one in five adults) have received the first dose, and 0.5 million have received the second dose.

It’s currently using both the Pfizer/BioNTech and Oxford University/AstraZeneca vaccines in its rollout.

The infection rate appears to be decreasing substantially. The current daily infection growth rate is falling by between 2-5%, and the R number is estimated to be between 0.7 and 1 (an R number of less than 1 means daily new cases will decrease over time).

However, it’s difficult to determine whether these numbers are due to the lockdown or vaccinations. It’s too early to tell whether vaccines are slowing transmission, but the signs are encouraging.

According to data from the Oxford/AstraZeneca vaccine group, released as a preprint with The Lancet last week and yet to be peer reviewed, its vaccine is showing signs of reducing transmission. The shot was associated with a 67% reduction in transmission among vaccinated volunteers in clinical trials in the UK.

It’s early days, but authors of the study suggest the vaccine may have a “substantial” effect on reducing rates of transmission in the future.

In saying that, preliminary data suggest it offers minimal protection against mild or moderate illness caused by the South African variant.




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What threatens the successful rollout of vaccines?

There are three main problems that might hinder the success of this global vaccination drive.

1. Vaccine development, manufacturing, distribution and delivery

The world’s population over the age of five is currently estimated at seven billion people. If we need to vaccinate at least 70% of them to achieve herd immunity, we need to reach around five billion people.

This is an enormous undertaking, so vaccine production and availability are crucial. Many countries face the massive challenge of producing or securing enough vaccines to immunise all their citizens.

Generally, wealthier countries that could afford to make advanced purchase agreements with vaccine producers — or who could manufacture a vaccine domestically — have been the first to start COVID vaccinations.

Unfortunately, partial vaccination of the world’s population won’t achieve herd immunity. One modelling study suggests if high-income countries exclusively acquire the first two billion doses without regard for vaccine equity, the number of COVID deaths could double worldwide.

2. Administering, monitoring, and reporting adverse effects

Vaccinating a large number of citizens quickly can’t be done with existing health institutions alone.

It’s urgent we enable alternative sites such as halls and sporting venues to be used as mass vaccination sites. We also need to allow a range of health professions such as medical students, public health officials and pharmacists to administer doses to help speed up the process.

And once vaccines have been administered, it’s crucial we monitor efficacy and report on any adverse effects, which will require additional resources.




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Australia must vaccinate 200,000 adults a day to meet October target: new modelling


3. Vaccine effectiveness and virus mutation

The effectiveness of vaccines can be hindered by mutations of the virus. COVID variants originating in Brazil, South Africa, and the UK have triggered huge concern worldwide.

There’s early evidence some of our current crop of COVID vaccines respond less effectively to certain variants, though most of these data are preliminary and are still emerging.




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UK, South African, Brazilian: a virologist explains each COVID variant and what they mean for the pandemic


If vaccines become less effective, new vaccines will need to be developed either including a booster dose incorporating the region of the mutated virus, or reformulating existing vaccines to include the mutated strains.

This, however, isn’t uncommon — flu vaccines are required to be updated regularly in order to increase protective capacity against new mutated strains.The Conversation

Maximilian de Courten, Professor in Global Public Health and Director of the Mitchell Institute, Victoria University; Maja Husaric, Senior Lecturer; MD, Victoria University, and Vasso Apostolopoulos, Professor of Immunology and Pro Vice-Chancellor, Research Partnerships, Victoria University

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

Yes, a 16-day incubation period for COVID is possible. But it’s extremely rare


Catherine Bennett, Deakin University

Over the past week, three returned travellers — one in New South Wales and two in Victoria — have tested positive to COVID-19 shortly after leaving hotel quarantine.

The cases in Victoria appear almost certainly to have been acquired in hotel quarantine. The individuals had quarantined at the Holiday Inn, where eight staff members and guests have been now infected. Authorities are investigating.

But genomic sequencing has now indicated the NSW case was not picked up in hotel quarantine. So it’s possible either the person was still shedding virus from an earlier infection they contracted overseas, or that they incubated the virus for longer than 14 days.

The incubation period is the time between the point at which someone is exposed to the virus and the onset of symptoms (bearing in mind of course that not everyone who tests positive to COVID-19 will develop symptoms).

Theoretically, it is possible for a person to incubate the virus for longer than 14 days. But how likely is it?

The evidence

Most people who are exposed to SARS-CoV-2, the virus that causes COVID-19, will not go on to develop an infection. Sometimes the dose is not high enough, and/or the person can mount a successful immune response to prevent the virus establishing itself in their system.

But of those who do develop an infection, the evidence suggests almost all will return a positive test within 14 days of being exposed to the virus. A review summarising data from 21 studies reported only 1% of people incubated the virus beyond two weeks.

It’s important to note this review is a preprint, so it hasn’t received the same scrutiny as other published research.




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But it found the average incubation period to be 5.9 days, which aligns with peer-reviewed research indicating the incubation period for COVID-19 is within the range of five to six days.

This is similar to other coronaviruses, notably SARS and MERS. Average incubation periods of other acute respiratory viral infections vary; 1.4 days for influenza A, 0.6 days for influenza B, and 12.5 days for measles.

A woman sits on the couch looking at a thermometer and about to take a tablet.
Different viruses have different incubation periods.
Shutterstock

The ‘day 16’ test

For the small minority of people who incubate the virus beyond 14 days, this can be related to underlying conditions, especially those that weaken a person’s immune response.

Over the weekend, NSW began testing returned travellers on day 16 — that is, two days after they finish hotel quarantine. This is how the latest case in NSW was detected.

The test is not compulsory and if the person doesn’t have symptoms, they don’t need to isolate until receiving their result.

This day 16 test is designed to pick up infections that may develop after the expected maximum 14-day incubation period on which Australia’s quarantine period is based.

Other states are reported to be considering implementing this measure too. This is a good safety net because, not only could it pick up the very rare case where a person might incubate the virus for longer, it could also catch missed cases of the virus being contracted in quarantine.




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


Some places even have a shorter quarantine period than 14 days. The UK, for example, has just started a hotel quarantine program to try to protect against arrival of other new variants. The quarantine period is ten days.

So Australia is erring on the more cautious end of the spectrum.

Could the new variants affect the incubation period?

Most of the data we have on the incubation period for COVID-19 don’t capture the emerging variants of the virus. For example, most of the studies included in the review I mentioned above were conducted in China, and all were carried out in June 2020 or earlier.

If anything, it’s possible the new variants might have a shorter incubation period.

An illustration of SARS-CoV-2, the coronavirus that causes COVID-19.
New variants can change the way the virus behaves.
Shutterstock

The accelerated rise in case numbers we’ve seen around the world with new variants means a greater proportion of people become infected following an exposure to these new strains, as we know these new variants can be more infectious. But a shortened incubation period could also be contributing.

These new variants are more efficient at establishing infections, we’re told, with the virus better at binding to, and invading, our cells. We might therefore assume a more efficient virus wouldn’t wait 14 days before establishing an infection. It would get on the job of replicating more quickly.

Although we need more information on these new variants before we can draw any conclusions, we can be reassured Australia’s two-week quarantine period should be ample time to detect the vast majority of cases.

This may change once we see what post quarantine testing reveals over the next while, but for now the priority must be making sure any cases within hotel quarantine don’t escape into the wider community.




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Another hotel worker tests positive in Melbourne. It’s time to move hotel quarantine out of cities


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.

UK, South African, Brazilian: a virologist explains each COVID variant and what they mean for the pandemic


Kirsty Short, The University of Queensland

Australia has recently seen SARS-CoV-2 (the virus that causes COVID-19) escape several times from hotel quarantine, including in Brisbane, Perth and Melbourne.

These incidents have been particularly concerning because they involved people infected with “variants” of the virus.

But what exactly are these variants, and how concerned should we be?

What’s a variant?

Viruses can’t replicate and spread on their own. They need a host, and they need to hijack the cells of the host to replicate. When they replicate in a host, they face the challenge of duplicating their genetic material. For many viruses, this isn’t an exact process and their offspring often contain errors — meaning they’re not exact copies of the original virus.

These errors are referred to as mutations, and viruses with these mutations are called variants. Often, these mutations don’t affect the biological properties of the virus. That is, they don’t have any effect on how the virus replicates or causes disease.




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Perth is the latest city to suffer a COVID quarantine breach. Why does this keep happening?


Some mutations can impair the virus’s ability to replicate and/or transmit. Variants with such mutations are quickly lost from the viral population.

Occasionally, however, variants emerge with an advantageous mutation, one that means it’s better at replicating, transmitting, and/or evading our immune system. These variants have a selective advantage (in biological terms, they are “fitter” than other variants) and may rapidly become the dominant viral strain.

There’s some concern we’re seeing a growing number of variants with advantageous mutations, contributing to the severity of the COVID-19 pandemic.

Here’s a look at the main three variants you might’ve heard about in the media.

The ‘UK variant’ — B.1.1.7

This variant was first detected in the United Kingdom towards the end of 2020. It has a large number of mutations, many of which involve the virus’ spike protein, which helps the virus invade human cells.

It has spread rapidly throughout the UK since it emerged, and to at least 70 other countries, including Australia.

The fact it has spread so rapidly, and quickly replaced other circulating variants, suggests it has some sort of selective advantage over other variants.

After examining the evidence surrounding the new variant, the UK New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) concluded it “had moderate confidence” the variant is substantially more infectious than other variants.

This may be the result of one of the mutations in the spike protein of the variant — a mutation called “N501Y”. One preprint manuscript, uploaded last month and yet to be peer reviewed, found N501Y is associated with increased binding of the virus to a receptor found on the surface on many of our cells, called “ACE2”. This could mean the variant is even more efficient at entering our cells.

Although initially the variant wasn’t associated with more severe COVID symptoms, more recent data have led NERVTAG to conclude there’s “a realistic possibility” that infection with the variant “is associated with an increased risk of death” compared with non B.1.1.7 viruses.

However, the group acknowledged there are limitations of the available data, and this remains an evolving situation.

The ‘South African variant’ — B.1.351

This variant was first detected in Nelson Mandela Bay, South Africa, in October 2020. Since then it has been found in more than 30 countries.

Similar to the UK variant, it quickly outcompeted other SARS-CoV-2 variants in South Africa. It now accounts for more than 90% of SARS-CoV-2 samples in South Africa that undergo genetic sequencing.

Like the UK variant, it also has the N501Y mutation in the spike protein, meaning it’s more efficient at gaining access to our cells to replicate. This may help to explain its rapid spread.

It also contains several other concerning mutations. Two of these, called “E484K” and “K417N”, are bad news for our immune system. They can reduce how well our antibodies bind to the virus (though this is also based on preprint data awaiting peer review).

But there’s no evidence yet to suggest the South African variant is more deadly than the original variants.

The ‘Brazilian variant’ — P.1

This variant was first detected in Japan in a group of Brazilian travellers in January 2021.

It’s now highly prevalent in the Brazilian state of Amazonas, and has been detected in countries including South Korea and the United States.

Like the South African variant, the Brazilian variant has the spike protein mutations N501Y, E484K and K417N (as well as numerous other mutations).

While there’s no evidence this variant causes more severe disease, there’s concern it has facilitated a wave of reinfections in Manaus, the largest city in Amazonas, which was thought to have reached “herd immunity” in October last year.

What does this mean for vaccines?

Major vaccine developers are testing the efficacy of their vaccines against these and other variants. Generally, the currently licensed vaccines protect relatively well against the UK variant.

But recent phase 2/3 data from both Novavax and Johnson & Johnson suggest reduced protection against the South African variant. The Oxford/AstraZeneca vaccine group also released data over the weekend suggesting its vaccine offers only minimal protection against mild-moderate disease caused by this variant.




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However, it’s important to recognise reduced protection doesn’t mean no protection at all, and that data are still emerging.

What’s more, numerous vaccine manufacturers are now investigating whether tweaks to the vaccines can improve their performance against the emerging variants.

The take-home message is that variants will emerge, and we need to closely monitor their spread. However, there’s every indication we’ll be able to adapt our vaccine strategies to protect against these and future variants.The Conversation

Kirsty Short, Senior Lecturer, The University of Queensland

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

Is Sky News shifting Australian politics to the right? Not yet, but there is cause for alarm



Wes Mountain/The Conversation, CC BY-ND

Denis Muller, The University of Melbourne

In his submission to the current Senate inquiry into media diversity in Australia, former prime minister Kevin Rudd warns that Rupert Murdoch’s Sky News Australia is following the template laid down by Murdoch’s Fox News in the United States to radicalise Australian politics. In a decade’s time, Rudd argues, we will see its full impact.

Given the destructive effect of Fox News on the functioning of American democracy, Rudd’s is an alarming prediction.

Whether it comes to pass, however, is another matter. Certainly there are several danger signs that it might, but there are also a few factors pointing the other way.




Read more:
Can Fox News survive without Trump in the White House?


There are three big danger signs.

One is the unconstrained peddling of extreme right-wing propaganda, lies, disinformation, crude distortion of fact and baseless assertions that occurs each night on Sky News.

Here is a brief sample: Rowan Dean’s and Alan Jones’s repeated ravings about the “stolen” US election; Peta Credlin’s false claim that Rudd’s petition for a Murdoch royal commission was an exercise in data-harvesting, for which she had to apologise as part of a confidential defamation settlement; Jones’s disinformation about mask-wearing; James Morrow calling the Trump impeachment trial a “sinister plot by Democrats against the American people”.

Former PM Kevin Rudd is calling for a royal commission into the Murdoch media empire.
Glenn Hunt/AAP

The second big danger sign is the way Sky News has been able to extend its reach from a niche pay-TV base to free-to-air television via 30 WIN regional stations across Australia, and then through social media to the world.

After seeing its audience grow in the first half of 2020, Sky’s pay-TV audience ended the year shrinking. But being on free-to-air TV in regional Australia represents an opportunity for growth.

Data on current regional viewing levels are patchy and incomplete. However, prime-time viewing is reported to have grown 36% in 2020, and is claimed to reach 2.9 million unique viewers.

Sky’s non-TV platform is social media. YouTube, owned by Google, is a very important social media outlet for Sky, and that is where the viewer data reported here come from.

Facebook is also an important outlet. When Facebook blacked out Australian news on February 18, there were roughly 260,000 views of Sky’s announcement of its last appearance there.

If Facebook persists in its blackout, it will clearly damage Sky’s online reach.

The patterns of Sky News viewership on YouTube are revealing.

The big picture is that Sky’s Australian stories get tiny audiences, but stories about the United States get vastly bigger ones, suggesting Sky has developed a following in the US.

For instance, an Alan Jones piece, “Trump’s impeachment charge is ‘more Pelosi rubbish’ ” got 130,000 views.

And the right-wing US journalist Megyn Kelly’s piece, “Trump exposed hidden media bias”, got 467,926 views.




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Courting the chameleon: how the US election reveals Rupert Murdoch’s political colours


Contrast these with Paul Murray’s local story, “Daniel Andrews still playing us v them with quarantine”: about 30,000 views, and Peta Credlin’s “Net zero by 2050 is the ‘economic suicide note for workers’”: about 2000 views.

This tells us Sky is not only playing to a US as well as Australian audience, but is tailoring its programming in ways that have worked for Fox News. At the same time, it is siphoning into Australia the kind of content that has been so divisive in the US.

The growth profile of Fox News shows Murdoch plays a long game.

Fox News started in 1996. Pew Research Center data show it straight-lined near the bottom of the cable ratings in the US for five years, took a jump at about the time of the September 11 attacks, another at the time of the Iraq war in 2003 and thereafter cleared away from its main cable news rivals, CNN and MSNBC.

Rupert Murdoch, owner of Sky News and Fox News, plays a long game.
Dan Himbrechts/AAP

Until the end of the Trump presidency, Fox News was never headed – then after Trump lost, it took a dive. In January 2021, it suffered its worst ratings in 20 years, coming third behind CNN and MSNBC.

This symbiotic connection between an incumbent government and the Murdoch organisation brings us to the third big danger: the relationship between News Corporation in Australia and the Morrison government.

Morrison is not Trump. Yes, he swaggered around in a baseball cap during the 2019 election campaign and, yes, he talks in slogans and sound bites. However, the danger comes not from Morrison’s political persona but from the relationship he and his government have built with News Corporation.

On one reading, it has become a commercial relationship between the government as client and News Corporation as provider of publicity services for a fee.

The fee has taken the form of two payments to Foxtel, one of A$30 million in 2017 and one of A$10 million in 2020, ostensibly for TV coverage of under-represented women’s sport.

No tender process, no publicly available information about the terms, no way of knowing how this public money is being spent. Then recent technical glitches in the televising of W League matches prompted the Greens to ask the auditor-general to investigate.

Against these dangers are some mitigating factors.

One is that Australia’s compulsory voting system makes it very difficult for anyone to win an election with a primary vote that is not at least near the 40th percentile. A Trump-like “base” of 32% or so will not cut it here.

A second is that the religious right in Australia does not have the political clout it does in the US. Issues that excite the religious right, such as abortion, have been long settled here by the courts. The strong vote for marriage equality was another example of the broadly secular nature of our politics.

A third is that the Australian temperament is not, on the whole, excitable. While this means Australians are often excoriated as apathetic, it also means they are not easily outraged.

A fourth is that Australia’s conservatism is of a largely materialistic kind. Franking credits matter. It is also a conservatism that does not like extremism. Morrison seems at last to have realised that outside their Facebook echo chambers, the likes of Craig Kelly and George Christensen may be liabilities.

This pragmatic outlook among voters may prove to be a psychological bulwark against the firebrand reactionary politics promoted by Fox and Sky.

Having said that, there are plenty of emotion-charged issues that give Sky the opportunity to drive wedges into the Australian body politic: asylum-seekers, Muslims, Aboriginal recognition, African gangs, Asians, white supremacy, the pandemic and above all climate change. Sky is into them all.

If anything concrete is to be done to head off the threat seen by Rudd, it is going to involve public policy concerning media accountability, of which a fit-and-proper-person test for television licensees would be an essential part.

However, every attempt so far to exert meaningful accountability on the Australian media has come to nothing in the face of threats from the big media companies, including News Corporation.

Rudd and Malcolm Turnbull, as prime ministers, were in a position to do something about this. Instead, Rudd developed a friendship with the then editor-in-chief of The Australian, and Turnbull made changes to the media ownership laws that empowered Murdoch even more.

It is futile to hope that the Morrison government, engaged as it is in a highly questionable relationship with News Corporation, will do anything about it. As for Labor leader Anthony Albanese, when asked about a Murdoch royal commission, he reached for the barge pole.

If this form of politics-as-usual persists, then Rudd’s prediction cannot be discounted.

Then the nation would be relying on those qualities of the Australian character already mentioned. The question will be whether it will be enough.


Correction: this article originally stated “In February 2021, it suffered its worst ratings in 20 years…”. The month has been corrected to January.The Conversation

Denis Muller, Senior Research Fellow, Centre for Advancing Journalism, The University of Melbourne

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

Morrison takes the shot to promote vaccine confidence, as government and opposition stay tied in Newspoll


Michelle Grattan, University of Canberra

Australia’s COVID vaccination program has begun with Scott Morrison joining a small group of recipients in a carefully orchestrated event, aimed at boosting confidence as the general rollout begins on Monday.

The first recipient was aged care resident Jane Malysiak, 84, from Marayong New South Wales, who was born in Poland and came to Australia soon after the second world war.

Sunday’s line up for the Pfizer shots included, apart from aged care and disability residents, workers in these sectors, and quarantine and border workers. These are the priority recipients for the first round of vaccination.

Chief Medical Officer Paul Kelly and Chief Nursing and Midwifery Officer Alison McMillan also got their shots, with McMillan assuring “it really doesn’t hurt at all”.

Morrison, decked out in an Australian flag mask, sat beside Malysiak, and encouraged her to follow his “V for Vaccine” sign – this went slightly awry when Malysiak’s fingers inadvertently turned in an “up yours” direction.

Morrison averted his eyes from the needle as he received his shot.

The Prime Minister called on the community to follow his and the other recipients’ example to “join us on this Australian path that sees us come out of the COVID-19 pandemic.”

He said he wanted Sunday’s pre-rollout vaccinations to give confidence. “Tens of thousands of people will be coming in tomorrow and I wanted them to know as they went to bed tonight that we have been able to demonstrate our confidence in the health and safety of this vaccination,” he said.

“Today is the beginning of a big game changer.”

Sunday’s figures recorded no community transmission anywhere in the country.

As the rollout starts, Newspoll showed government and opposition remained deadlocked on 50-50 on the two-party vote, but Scott Morrison extended his lead over Anthony Albanese as “better prime minister” to 61-26% (previously 57-29%). The poll is published in Monday’s Australian, and was taken Wednesday to Saturday.

Labor’s primary vote rose one point to 37% since the previous poll three weeks ago; the Coalition was steady on 42%.

Albanese’s net approval is minus 7, following a 3 point fall in his satisfaction level to 38% and a 2 point rise in dissatisfaction to 45%.

Morrison’s net satisfaction is plus 32 – his satisfaction rating increased a point to 64% and his dissatisfaction rating fell a point to 32%.

Although it has not hit his Newspoll numbers, Morrison will continue under pressure in parliament this week over who knew what in his office about the alleged rape of Brittany Higgins.

The Weekend Australian reported a second former Liberal staffer who alleges she was raped last year by the man named by Higgins.

Higgins has alleged she was raped in 2019 by a colleague in the Parliament House office of the then defence industry minister. Linda Reynolds, for whom both she and the man then worked.

Asked about the second allegation, Morrison said at the weekend:“I’m very upset about those circumstances”. He said he did not know who the woman was.

Late Sunday night, The Australian reported a third woman – a Coalition volunteer during the 2016 election campaign – has alleged she was sexually assaulted by the same Liberal staffer days before the election.

Higgins will lay a formal complaint to the police on Wednesday, which will start an investigation.

The Prime Minister said the inquiry by his departmental secretary Phil Gaetjens into who in the Prime Minister’s office knew about the Higgins rape allegation was to be finished “as soon as possible”.

Morrison has said he first knew of this allegation on Monday of last week, when the story was published, and his staff only knew the Friday before that, which was when journalist Samantha Maiden asked his office questions.

He made it clear he was angry he wasn’t alerted to Maiden’s inquiries. “I’ve expressed my view to my staff about that very candidly on Monday.”

The Special Minister of State, Simon Birmingham, indicated at the weekend that Higgins would be able to contribute to the terms of reference for the independent inquiry Morrison has announced into the workplaces of parliamentarians and their staff.

Higgins said in her Friday statement she had “advised the Prime Minister’s Office that I expect a voice in framing the scope and terms of reference for a new and significant review into the conditions for all ministerial and parliamentary staff”.

Birmingham said: “All past and present staff, including Brittany Higgins, will be able to participate in the review.

“I also welcome the input of past and present staff on the terms of the independent review and will be engaging accordingly.”The Conversation

Michelle Grattan, Professorial Fellow, University of Canberra

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