Stats Chat

Team Ratings for Round 3

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 14 matches played, 9 of which were correctly predicted, a success rate of 64.3%.
Here are the predictions for last week’s games.

Predictions for Round 3

Here are the predictions for Round 3. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for Finals Week 2

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 196 matches played, 142 of which were correctly predicted, a success rate of 72.4%.
Here are the predictions for last week’s games.

Predictions for Finals Week 2

Here are the predictions for Finals Week 2. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

• Good Herald piece on the Covid network contagion model 
• Andrew Chen organised a bunch of people to write a letter about privacy for Covid location data. He’s also been saying the same things to journalists.  It’s not that we think the government has any intention of misusing the data or letting the private sector misuse it, but the protections aren’t all that strong, the data collection is not voluntary, and having high-quality data is very important.
• There’s an interesting poll on US vaccine attitudes from the Washington Post and ABC News. Highlights: 82% of unvaccinated people said the FDA full approval for the Pfizer vaccine won’t make any difference to their decision. Crosstabulations (don’t you love polls with actual detail) showed 18% of unvaccinated respondents were in favour of requiring vaccination for school teachers and staff, and 15% requiring vaccination for students when a vaccine is approved at their age.  72% of those employed by someone else and not vaccinated said they would resign if required by their employer to be vaccinated. Politics site The Hill headlined this as Over 70 percent of unvaccinated Americans in survey would quit their job if vaccines are mandated, which is unlikely to be true — it’s a lot easier to claim to a poller you’d quit than to actually do it.
• Derek Lowe writes about bad clinical trials in Covid “I’m all for trying out new ideas – that’s essential, in fact. But try them out for real. … If you’re going to do research on human beings, you owe it to the subjects of your trial and to the rest of the medical community – and to the rest of the world, in this case – to do it right. To ask solid questions and get solid data on them that will allow you to make a real decision at the end of it.”
• Animation of vaccination progress in NZ (from Jonathan Marshall)
  

There are different ways of testing for the SARS-Cov-2 virus that causes Covid-19.  Broadly speaking, there are three approaches to the actual measurement: amplifying and testing for the viral RNA, testing for viral proteins, and testing for antibodies against the virus.  On top of that, samples can be be taken in different places: way up in the back of your nose, less far up, saliva samples, blood.

These tests are useful for different purposes because they have different characteristics.  The viral RNA tests using a deep swab and PCR have essentially zero false positives if you can avoid contamination.  That’s important in New Zealand because we use positive PCR tests to lock down the whole country, at nine-digit costs, and because we use them to put people in non-voluntary medical isolation.

The swab/PCR tests also have reasonably low false negatives. Nowhere near as low as the false positives — the lab assay is incredibly sensitive, but sometimes the swab just doesn’t pick up virus.  Again, we know this from NZ data. We currently have tests as soon after exposure as possible, again at five days, and again at twelve days, and people do test positive at five days or twelve days for the first time.  The false negative rate is important in New Zealand because we don’t want to miss even one case and allow an outbreak to expand.

For the places where we use swab/PCR testing now, we don’t want to substitute anything else. It’s the best technology available. But there are limits. The swab is a bit uncomfortable and the PCR process is slow and requires lab equipment in limited supply. We couldn’t, for example, do daily testing of all customer-facing essential workers with swab/PCR: they’d hate it and the labs would struggle to keep up.

In other countries, it’s much more valuable to have easy, rapid, and inexpensive tests even at a slight cost in sensitivity. There’s some risk of infection all the time; the consequences of a false positive or false negative are lower; there isn’t the same need to make sure all positive tests get reported. There’s a lot more scope for other tests to be helpful.

Even in NZ, though, there are gaps where other tests could be useful.  The obvious one is frequent testing of high-risk people. In normal times that would be people at the border; during an outbreak it might be essential workers whose job involves being exposed to customers or crossing the alert-level boundaries.  If we compare to swab/PCR the rapid antigen tests are not as good; but that’s not the right comparison. The rapid tests would be useful in settings where there isn’t going to be a swab/PCR. In those settings, the chance of detecting a case with swab/PCR is obviously zero, and the chance of detection with another test is actually pretty fair.

There’s a theoretical downside that negative rapid tests might slow someone with symptoms from getting a swab/PCR test until they get a positive.  If we were getting nearly 100% testing among people with symptoms, this would be a big concern. We probably aren’t anywhere near that; but it would need monitoring. There’s also a theoretical downside that false positive rapid tests might make people take positive results less seriously. I don’t think that’s plausible during lockdown, but again it would need monitoring. Somewhat more likely, it might turn out that there’s nothing actually wrong with the tests but that they don’t detect enough additional cases to be worth the cost and hassle. But that’s worth investigating, and where the realistic options are additional rapid tests or just the status quo, the effectiveness comparison should be between additional rapid tests and just the status quo.

Team Ratings for Round 2

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 7 matches played, 3 of which were correctly predicted, a success rate of 42.9%.
Here are the predictions for last week’s games.

Predictions for Round 2

Here are the predictions for Round 2. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for Round 1

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Predictions for Round 1

Here are the predictions for Round 1. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for Finals Week 1

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 192 matches played, 139 of which were correctly predicted, a success rate of 72.4%.
Here are the predictions for last week’s games.

Predictions for Finals Week 1

Here are the predictions for Finals Week 1. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for the Currie Cup Final

The basic method is described on my Department home page.
Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 37 matches played, 23 of which were correctly predicted, a success rate of 62.2%.
Here are the predictions for last week’s games.

Predictions for the Currie Cup Final

Here are the predictions for the Currie Cup Final. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

The world’s Covid response has benefited from the twenty-odd years of large-scale genetics research that preceded it: inexpensive, widely-available PCR and sequencing; mRNA synthesis and delivery.  None of that was the plan, though.  Genomics was supposed to produce widely-applicable treatments for diverse medical problems, and revolutionise medical diagnosis and treatment. It didn’t: there have been genuine breakthroughs, but mostly in the  form of expensive treatments for rare diseases.

Today in Britain, there was definite progress.   NICE, who make recommendations for medication subsidy decisions, have pushed for the funding of inclisiran in people who have high cholesterol and who’ve already had a stroke or heart attack.  Inclisiran lowers LDL (‘bad’) cholesterol a long way, by a different mechanism from the current ‘statin’ drugs, and it can be given by twice-yearly injection at a GP’s office. The drug would usually cost more than it’s worth, but the NHS has a Pharmac-like secret deal to pay less than the £2,000 sticker price.

I’m not sure this is huge news from a public health point of view, but it’s interesting to someone who has worked in genetic epidemiology.  Inclisiran inhibits a gene called PCSK9.  The function of PCSK9 was originally fairly obscure; mutations in it were found by genetic linkage analysis to be related to familial high cholesterol in a group of families who didn’t have mutations in the known high-cholesterol genes.  Research in the Dallas Heart Study, a cohort study of risks for heart disease, found that several people with unusually low cholesterol also had mutations in PCSK9, suggesting that blocking the gene’s action would lower cholesterol.  Now, we actually need some cholesterol, so you’d worry that blocking the gene could be dangerous — but the Dallas Heart Study also found one woman who had natural mutations in both her copies of the gene, and who had extraordinarily low LDL cholesterol and no apparent adverse health effects.  All this came from largely correlational research that relied on inexpensive, large-scale gene sequencing — exactly what genomics had promised.

The other genetic aspect of the new treatment is that it works by silencing the gene, rather than the more-usual approach of blocking the activity of the enzyme after it has been produced.  Inclisiran is a ‘small interfering RNA’ molecule that binds to messenger RNA from the PCSK9 gene and triggers the cell’s recycling mechanisms to chop it up. The protein never gets produced.  This idea has been through hype and disappointment cycles — a small piece of RNA injected into the body looks remarkably like a virus, and the immune system tends to disapprove — but this time it seems to work, and to work on a common risk fact for a common disease.

The return on genetic ‘precision medicine’ has still been rather disappointing compared to the hype, but it’s nice to have the occasional example where it does basically work as promised.

Newshub has a commendably restrained story about some biochemical research into possible starting points for Covid treatment

Brazilian researchers have found that a molecule in the venom of a type of snake inhibited coronavirus reproduction in monkey cells, a possible first step toward a drug to combat the virus causing COVID-19.

Not everyone is so calm about it: The Hill says Brazilian viper venom shows promise as drug to combat COVID-19, the Daily Express says Covid breakthrough as deadly Brazilian snake venom 75% effective in stopping virus, and Indian site Zee News says Jararacussu pit viper, found in Brazil, can be the answer to Coronavirus, says study.

The research paper is here.

Researchers in Brazil were already studying the properties of a fragment of a protein from the venom of the jararacussu, a South American pit viper. This fragment blocks a protease, a protein-snipping enzyme, that is needed by the SARS-Cov-2 virus.  The protein fragment isn’t a drug on its own — and the protein it comes from definitely isn’t; it’s in the snake venom for a reason, and that reason isn’t to benefit animals that get bitten. However, this genuinely is one of the ways we get new drugs. A protein fragment from the venom of a related South America pit viper, which blocked a human protease enzyme,  was the starting point for developing ACE inhibitors, an important class of medications for high blood pressure and heart failure.

A few more things to  point out, though. First, the research paper is studying the ability of the SARS-Cov-2 virus to infect lab-grown hamster kidney cells in a Petri dish. These aren’t particularly realistic targets; they’re just convenient. The paper describes the use of a ‘positive control’, a chemical that they know is effective at stopping infection of these hamster cells under lab conditions. You might have heard of this chemical; it’s called chloroquine.  And finally, the tweet from The Hill that pushed me to write this post has a picture of a pretty green snake. It’s not the jararacussu. It’s an African snake that’s not especially closely related and whose venom hasn’t been studied all that much. They have the picture handy because a snake of that species bit a handler at the San Diego zoo in April. Zee News also use a pretty green snake picture, and it’s even less closely related.