Mutation Tracking

Interesting article from the New York Times on tracking the spread of C19 by looking at genetic mutations in samples from various places.

That combination of old and new mutations suggested that the student did not acquire the coronavirus from someone who had recently arrived from another country. Instead, the coronavirus was probably circulating undetected in the Seattle area for about five weeks, since mid-January.

Since then, viruses with a genetic link to the Washington cluster have now appeared in at least 14 states and several countries around the world, as well as nine cases on the Grand Princess cruise ship.

Mobile Positioning

With various countries rolling out apps to assist with contact tracing, here’s a look at the various ways to determine position from a mobile phone and why Bluetooth makes the most sense for those apps.

This tells you not much – if anything at all about absolute location, but it does tell you about proximity with high confidence and decent precision and isn’t as creepy as RRLPing the planet. That sounds like what we’re after and there’s a good reason the Singaporean health ministry, NHSX, the Apple/Google joint project, and a bunch of others have converged on solutions that use BLE plus public-key cryptography. It does have some problems – notably, as Ross Anderson points out, it’s still radio and it doesn’t care if you were on opposite sides of double glazing, and there are complicated platform restrictions in Apple iOS to stop you being creepy and weird with it.

Humanity

Finally, Tim Harford has a nice reminder that despite all the stories of bad behaviour, the vast majority of people are actually well-behaved in a crisis

…a mere 3 per cent of shoppers had bought “extraordinary amounts” of pasta. Most of us were merely adjusting our habits to life spent away from restaurants, sandwich bars and offices with their own loo paper. We all went shopping a bit more often, and when we did, spent a little more. No cause for collective shame, but it was enough to strain supermarket supply chains.

What about those who ignore pleas to keep their distance? Again, the misdeeds are exaggerated. Lambeth council grumpily closed Brockwell Park in south London, complaining of 3,000 visitors in a single day — not mentioning that the park might easily see 10 times that number on a normal sunny Saturday, nor that taking exercise in a park is perfectly permissible.

Today’s biology lesson answers the question Why Do We Keep Getting Diseases from Bats? with a look at the differences between our respective immune systems.

…bat cells just continually assume they’re under attack and never stop fighting viruses, regardless of whether they’ve detected any. This is surprising. Interferon is a really powerful molecule, and continually producing it should have the same effect on a cell as continually putting a factory on red alert. It should make the cell run much worse, and cause a lot of collateral damage.

After all, when this sort of immune system overreaction happens in humans, humans get serious disorders, like Multiple Sclerosis and Lupus. Bats do not tend to get these. In fact, many bat species live around 20 years on average, which is not only way longer than it should have with its overactive immune system, but is exceptionally long for such a small animal. To give a comparison, rats live a year or two, as do rabbits.

There’s lots more, explaining how bats can live such relatively long lives with an “always-on” immune system, and also why their immune system evolved to be that way.

As an aside, I wasn’t aware that we had Natural Killer (NK) cells…

NK cells are as heavy duty as their name implies; while their cousins, T cells, kill any cell that displays signs of being infected, NK cells kill any cells that don’t display signs of being not infected. Viruses will frequently prevent cells from indicating that they’re infected, so NK cells just kill any cell that looks like it’s hiding something.

No messing around there!

A complete and callous abdication of responsibility by the Feds. How can Trump survive this? Is it possible to spin this? Are enough Americans that dumb that they will fall for “it’s the states’ problem? From the New Yorker…

For two weeks, Ries and his fellow-volunteers had believed that it was only a matter of time until the federal government came to the rescue. They planned to serve as a bridge for the desperate states and cities that started calling their hotline as soon as it was up and running, but, eventually, the federal government would take care of it, because isn’t that what the federal government is supposed to do?…

What they did not foresee was that the federal government might never come to the rescue. They did not realize this was a government failure by design—not a problem to be fixed but a policy choice by President Trump that either would not or could not be undone.

Meanwhile the NY Intelligencer has a dispatch from Beijing detailing what the crisis looked like from the ground.

The state switched on social distancing. There was no need for weeks of educating people about the need to stay at home — the 2003 SARS epidemic remained in living memory for most people. The authorities didn’t hesitate to shut down movie theaters and attractions like the Forbidden City in late January, a peak consumption period when the country celebrated Lunar New Year. People stayed home: I’ve heard friends say that they’ve not left their apartment for six weeks. Offices set quotas for how many people could be at work.

Mask wearing quickly became universal. In a public park, I furtively took off my mask when I saw no staff around. Speakers on a ranger’s car then came to life, blaring at me to put it back on.

The author also talks about the mistakes made, both by China initially and other countries subsequently.

There’s no getting around the fact that the authorities in charge of Wuhan and Hubei made a disastrous set of decisions that allowed the virus to spread. Local authorities delayed warning the public to ensure the smooth operation of a relatively unimportant political conference. Instead of shutting down large events and ordering social distancing, it congregated people around an enormous potluck. Most egregiously, it silenced early whistle-blowers in the medical community. The best-known case is of Dr. Li Wenliang, whom the policy summoned in and admonished for “spreading rumors.” The doctor subsequently contracted the virus and died in early February. Anger at the news was swift and broad, exacerbated perhaps by the intense restrictions on daily life.

Mistakes, however, weren’t unique to China. Governments all over the world have repeated them, sometimes adding their own twists. The U.S. might never have admonished a whistle-blower. But the political elite, even the White House, downplayed the virus out of electoral concerns. U.S. authorities have hesitated to implement containment measures for fear of hurting the economy, failed to elevate health experts into positions of power, and have still not adequately ramped up testing and containment. Official reluctance to induce panic and hurt the economy has been a universal tendency across governments, and the result was far worse for Hubei having given into it.

The current epidemic is exposing all the weak points in our current society, like this example from the UK.

New deliveries of eggs to British supermarkets are being snapped up as quickly as the shelf stackers can get them onto the shelves. At the same time, tons of eggs are going off in warehouses which currently hold massive stocks of food. The unexpected reason for this situation, we learn from the BBC’s Farming Today programme on Wednesday, is that the UK is currently in the grip of an unanticipated egg carton shortage. The entire of Europe is supplied by just three egg carton manufacturers. None is based in Britain; and the nearest one – in Denmark – is closed for the next fortnight.

An example of Liebig’s Law of the Minimum, which holds that a complex system fails at its weakest point.

It also shows neatly how adjusting to a crisis is far from straighforward, and often has unintended consequences

The initial problem for public transport operators was the severe fall in demand in February as passengers reasoned that trains and buses were incubation chambers for the SARS-CoV-2 virus. While some took to working from home, others walked or dug that old bicycle out from the back of the shed. The result was a collapse in demand which obliged operators to cut back the service. The unfortunate consequence has been that despite the instruction to avoid social contact, the remaining trains and buses are overcrowded at rush hour. The knock-on problem that this has now caused is that public transport staff are now going sick in large numbers.

Which will no doubt further curtail services and continue to increase the infection rate.

Interesting video on Youtube looking at simulating an epidemic and how changing different parameters affects the infection outcomes.

Despite all the COVID news from Europe, and Italy in particular, it would seem that we’re learning nothing here in Australia. Our Government, and by extension the population as a whole, seems to be in reactive rather than proactive mode.

To wit, yesterday Bondi Beach was packed…

… and, in Sydney, 2,700 people were allowed to disembark from a cruise ship while 13 passengers were awaiting results of Covid swabs. Four have since discovered to be positive, so frantic announcements are being made for the other 2,696 passengers to quarantine themselves.

People are still going out to pubs, clubs and bars and our footie codes are one of the few codes globally who are still playing games, albeit behind closed doors. No doubt the Government will shut that all down in the near future, but if they are going to have to do it next week, they should just do it now. Learn from Europe & Asia’s prior experiences.

Australia’s case rate has been increasing at roughly 25% per day for the last ten days, reaching 768 yesterday. Some simplistic maths shows that if we continue on that path, in 4 weeks we’ll have approx. 360,000 cases, whereas if we can drop the rate to 10% daily increase we’ll “only” have 10,000 cases.

This edition of Axios Edge makes some key points.

The spread of the novel coronavirus is similarly a function of decisive action by heads of state, or the lack thereof. Governments alone determine whether the number of new cases increases exponentially, or whether it is brought under control within days.

and

The bottom line: In normal day-to-day life, someone with the novel coronavirus will infect more than 3 other individuals. That’s a simple recipe for exponential growth. Effective heads of state have shown that they have the ability to change individual behavior across their country so that the number gets reduced to less than 1.

When will our Govt. switch to proactive mode?