Anti-vaxers and Freedom(23/08/2021)

Anti-vaxers

A few weeks ago I was talking to a couple of ant-vaxers (I'm going to them a-vers) at table tennis. One of their points was this: USA has one of the most unhealthy populations in the world and USA has the largest number of vaccinations (different types eg measles, smallpox...) in the world - therefore vaccinations are bad for your health.
Sounds reasonable, but you can't reach this type of conclussion by analysing one data point - for example, of the 30 odd people I've had conversations with at table tennis, at least 3 are a-vers. So it could be estimated that 10% of people are a-vers. I hope this is lower, and making this analysis based on a survey of 30 people from a limited demographic is unlikely to be accuate.
When I got home I tried to research the health and vaccination numbers of various countries. Easy enough to find a health index, but I couldn't find the vaccination numbers for any countries. Since I'd suggested to the a-vers that obesity was likely to be a major factor in health, I looked up that info - and a comparison between countries health index and obesity showed no corrolation. More analysis is needed, but I suspect there is a corrolation between a countries obesity and its 'wealth', and also between its health and its 'wealth' which cancel each other out when comparing health and obesity.
My basic argument against a-vers: Last week NSW reported that 10% of fatalities in its Delta outbreak were fully vaccinated while 24% of its total population has been fully vaccinated. Even considering the 7 vaccination-related deaths Australia-wide (you need to calculate the number for just NSW and 4 weeks ago if you want to do a fair analysis) its hard to deny that vaccinations are a good thing.

Freedom

I imagine everyone wants their freedom back, but I suspect most are not in favour of the protests that are happening recently. I support the vaccination strategy - lets get there as soon as possible,
Come the new year, I hope we have the freedom to go flying. We should be at the government's 80% vaccination level by then, but will the restrictions (that prevent flying) be gone? I expect there will be some states with relatively high numbers of cases (NSW and possibly Vic) and some states with much lower numbers. We can expect border restrictions between these states, hopefully restrictions will be reduced for those us that are fully vaccinated. I have mixed feelings about 'vaccination passports' - there is no legal requirement to get vaccinated in Australia so discirminating against the un-vaccinated seems wrong...

Herd Immunity :: Can we get there? (06/07/2021)

Herd immunity is calculated using 1 - 1 / R⁰...

With the new delta variant having a R⁰ of 6, this means that herd immunity is now acheived at 83%. To get this level using vaccines we would need to get 83% of the population vaccinated with a vaccine that is 100% effective in preventing transmission (we don't have a vaccine this good), or get 100% of the population vaccinated (not likely) with a vaccine that is 83% effective in preventing transmission. Maybe we could get 90% of the population vaccinated with a vaccine that is 90% effective in preventing transmission. That would give us 81%, still not quite there.

So we can expect to have Quarantine/Testing/Tracing in some form with the current vaccine and covid variant mix - but what will it look like? You could cut out the Quarantine component if you maintained a large Testing/Tracing operation (there will be cases and without herd immunity they need to be controlled), or you could continue with the current Quarantine/Testing/Tracing operation. With Quarantine costs being passed on to the traveller, maintaining the current operation is probably going to be the way our government will go. Vaccine passports with self-isolation? - when checking people who are meant to be isolating during our outbreaks, significant numbers have been ignoring the isolation requirements, I would expect the same to happen with returned travellers. Not an option without herd immunity.

Epidemiology vs Maths :: COVID-19 one year on (01/03/2021)

We first heard about Covid back in Jan 2020. I'm not sure I'd heard of epidemiology before that, but I have now

The first reports indicated that it had a R⁰ of 2. Now R⁰ is an epidiological term which indicates how many people are infected by each infecious person. Assuming a cycle of 10 days, the mathematically inclined would quickly realise that each infected person on day 0 would result in 1000 infected people by day 100, 1 million infected people by day 200 and 1 billion infected people by day 300 (that initial estimate takes less than 1 minute to calculate). Of course there are "herd imunity" effects which would come into play and reduce that number, but with no attempts to control the virus we still would have excedded 1 billion by the end of 2020. So why did it take governments so long to stop international travel? Who did they (the govenment) listen to, the epidemiologists or the mathematicians? Or was it the government didn't believe either of them?

Australia goes into lockdown

By the time Australia closed its international borders, we already had significant community spread, and testing and tracing was not able to cope - a lockdown was innevitable. We cancelled the Birchip comp (Easter FTTF Hang Gliding Championships) before lockdown was announced. We didn't think the locals would want us there, with the risk of bringing the virus with to their community.

Modelling the virus

We've heard of governments using supercomputers to model the virus, but the maths is really not that hard. What we want to calculate is the effect on the R⁰ of whatever measures we are taking to slow the spread of the virus.
Imagine a lockdown - if the measures involved reduce interaction between people by 75%, then the R⁰ would also be reduced by 75%. So a R⁰ of 2.8 would become an effective R⁰ of 0.7 - this is less than 1 so the virus would slowly disappear without any additional measures. Simple maths, and lockdowns have been used widely and effectively around the world. (Note: I'll use a R⁰ of 2.8 in my claculations, estimates suggest it is somewhere between 2.5 and 2.8.)
But Australia has mostly been using 3 other measures to control the virus: Quarantine, Test and Trace (QT&T).
By quarantining people coming to Auatralia we keep the number of cases in the community low and this prevents testing and tracing from becoming ovewhelmed.
Tracing identifies people who may have the virus and isolates them before they become contagious, making the effective R⁰ for those individuals 0.
Testing picks up infectious people that were not identified by tracing.
Done properly, these three measures keep the effective R⁰ of the virus at around 0.5 (see notes)
What about state border closures, localised lockdowns, masks, etc?
Well, QT&T already has the effective R⁰ at 0.5. Any other measures will reduce the R⁰ more, but it's not neccessary to control the virus.

The Victorian lockdown
Did I say that Quarantine, Testing and Tracing was all that was needed to control the virus? Yes, but I did qualify that with "done properly". So what went wrong in Victoria?
For starters, Quarantine was NOT done properly - Private security was used and the security companies employed people with no experience, gave them a token day of training and sent them to work. There was an inquiry. No-one in government could remember who decided to use private security, so the inquiry was unable to ask the question of why it was decided to use private security. One government employee resigned, 800 people died of COVID.
So it got past Quarantine, shouldn't Testing and Tracing controlled it still? Yes, if it was done properly. But the turnaround for testing and tracing was 7 days each - by the time a test came back and tracing was done, all the close contacts had already continued to spread the virus. It was not working. One government minister resigned, and as I've already mentioned, 800 people died.

Here come the vaccines
There was a lot of excitement as the vaccines started to roll out, and they will save a lot of lives around the world. But how will they impact Australia?
Not a lot. QT&T seems to be working here and will keep COVID out of Australia. What we need to be able to do is open our international borders to get things back to normal. And this is where the vaccines may not be so good - you see, they were NOT tested to determine if they stopped the spread of the virus. So even if someone is vacinated, they could still be infectious and spread the virus. We don't want them coming here until we have at least herd immunity, so 70% immunuty in our population. The vaccines appear to offer around 90% efficacy, but if they offer less than 70% immunity then they will not allow us to open the borders without risking the virus being spread - if we get too many cases there is then a risk our QT&T systems would be overwhelmed and we would be forced into another lockdown.

Mutations!
The vaccines were good news, but now we're hearing about mutations. Parts of Brisbane had a snap lockdown when a COVID case with the UK mutation got through quarantine. The Qld government and its health experts all proclaimed it as 70% more infectious - well, it does add 0.7 to the R⁰, but that makes it 0.7 / 2.8 = 25% more infectious. And it's more infectious because it lasts longer, so with effective QT&T it poses no additional threat.
More concerning are the Sth African and Brazilian mutations - reports indicate the some vaccines might be less effective against these mutations, and previous COVID cases may also be re-infected. These types of mutations might see us dealing with a flu-like cycle of mutation and annual vacination. And its possible some vaccines might not be as effective when re-engineered for a mutation (eg AstraZeneca is built on a chimp/flu virus and we may see immunities formed to this virus rather than COVID with repeated use)

Note: The maths behind COVID doesn't need to be that complicated.
Cases can be placed into two groups - those identified as a close contact during tracing, and those not identified as a close contact during tracing.
The first group will be isolating by the time they become contagious and will not spread the virus.
The second group will spread the virus. Some of them will test positive and go into isolation. If the second group represents 20% of the cases and are detected by testing 2/3 of the way through the contagious period (on average), then the effective R⁰ becomes 2.8 x 0.2 x 2/3 = 0.37