Closing the barn door after the virus has escaped

When will we learn? For the past two or three weeks, the world has been fretting over a new Covid-19 virus variant, one that UK Prime Minister Boris Johnson announced was significantly more transmissible than other variants.

Johnson’s announcement has led multiple other countries, including the U.S. and France, to temporarily ban travel from the UK. As scientists began testing for the new variant, at least 3 states in the US–California, Colorado, and Florida–have already reported that they are detecting the new variant too. Expect many more states (and other countries) to report finding the variant in the coming days.

In the UK, the new variant was first detected in September, and by November one-fourth of the cases in London were caused by this variant. That does seem worrisome.

My first reaction upon hearing of this new variant was to ask whether it really is more transmissible or not. The evidence is very preliminary, and it’s still not peer-reviewed, but a very new study from a week ago says that yes, the new variant is 56% more transmissible.

Okay then, that’s not great. But there’s no evidence that the new variant (known variously as B117 or VOC 202012/01) is more deadly, or that the vaccine won’t work against it. It just spreads faster.

My second reaction was about these new travel bans. Why would anyone think that the variant was only in the UK, merely because the UK was open about reporting it? Unless we really know that to be a fact, travel bans are a classic case, as the adage goes, of closing the barn door after the horse (the virus) has escaped.

So has the B117 virus has already spread well beyond the UK? Yes, it appears so.

In a new study released just two days ago on medRxiv, scientists at Helix, a company that has tested millions of samples for the presence of the SARS-CoV-2 virus, looked back at their testing data over the past several months. They found that evidence of the B117 virus in the US extends back at least to October. They also found that the variant is now spreading in the eastern US, in Massachusetts, Ohio, and Florida.

An important caveat is that Helix’s tests weren’t specifically looking for the B117 strain. They instead looked at two key deletions in the spike protein (which I’ve discussed before) that the B117 strain contains, and that their tests can also detect. It might be that they found slightly different strains that shared these deletions, but even if the strains they detected weren’t identical to B117, it’s possible they were equally infectious.

So yes, the new strain seems to be in the US already, and it seems that it’s been here since October. And if it’s been in the UK since September, and the US since October, well then it’s a darned good bet that it’s pretty much everywhere. Banning travel from the UK not only punishes the UK for openly sharing its findings, but it also may prevent other countries from sharing information about newer strains of the virus, should those emerge.

What should we do in response to the new strain? The most effective action will be to roll out vaccines even faster, something that public health authorities across the US are trying to do. So far it is not going well, in part because we have no consistent national strategy. It’s not too late to fix that.

But let’s not pretend that travel restrictions now will do anything to keep this new strain locked up. They’re just closing the barn door after the horse has escaped. Or “Vijgen na pasen” as they say in Flemish, or “arriver après la bataille” in French. There’s an idiom for this behavior in every language, it seems.

CRISPR gene editing controversy - does it cause unexpected mutations?

Just over a month ago, a short paper appeared in Nature Methods saying that the gene editing technique known as CRISPR-Cas9 has a big problem: it creates unexpected mutations all over the genome. This was startling news for a technique that has been hailed worldwide as a dramatic breakthrough, not only because it is the easiest gene-editing method yet invented, but also because it is (supposedly) very precise.

This new paper, by Kellie Schaefer and colleagues, found hundreds of mutations (in experimental mice) that weren't supposed to be there. The results contradicted earlier studies that showed CRISPR caused very few of these "off-target" mutations. One of the authors, Stephen Tsang, commented that

"We feel it's critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR."

Not surprising, the resulting news headlines were gloomy. The stock in three companies trying to commercialize gene editing–Editas Medicine, Intellia Therapeutics, and CRISPR Therapeutics–all fell sharply.  (Interestingly, the stocks started falling on May 24, and bottomed out on May 31. The paper appeared online on May 30.) Scientists involved with these companies quickly responded, arguing that the study was flawed, but of course those scientists have a lot of money at stake.

Who was right? Well, a new paper by Caleb Lareau and colleagues, just released in the bioRxiv preprint repository, re-examines the same data and concludes that CRISPR is just fine. I've read both papers so you don't have to. Here's what seems to be going on.

The study by Schaefer et al. used CRISPR-Cas9 to create mutations in two mice (called F03 and F05), and then sequenced their genomes. They also sequenced the genome of a third mouse, called FVB. All three mice were supposed to be genetically identical.

Then they compared all three genomes to a "reference" mouse to find mutations. (Aside: this is something my own lab does all the time, so I know the techniques well.) They found over 1,500 mutations in each mouse (which wasn't surprising, because the reference mouse differs from their 3 lab animals), but they found hundreds more mutations in the two CRISPR-edited mice. That was the main surprise from Schaefer's paper, and it's the basis for their claim that CRISPR causes numerous off-target mutations.

I had a big problem with this claim even before reading Lareau's paper. Just TWO mice? That's a ridiculously tiny sample. But I digress.

Lareau et al. pointed out, correctly, that Schaefer's conclusion depends on the mice being genetically identical. But what if the two CRISPR mice (F03 and F05) were closer to each other than to the third mouse, FVB? (It's analogous to comparing two siblings with a first cousin, although these mice are much more inbred than any humans.) In that case, the result falls apart.

Fortunately, Schaefer et al. made all their data available (props to them for doing that), so Lareau could answer this question quite precisely.

It turns out that F03 and F05 are much closer to each other than either one is to FVB.  Lareau discovered that the two CRISPR mice share thousands of mutations that FVB doesn't have.

What does this mean? Lareau and colleagues conclude that the "unexpected" mutations in the CRISPR-edited mice were already there before the experiment began, and were not caused by gene editing. As they put it,

"the CRISPR-treated embryos most likely already harbored these private SNPs and indels prior to nuclease treatment whereas the control mouse did not."

In other words, it seems highly unlikely that CRISPR gene editing caused hundreds of unexpected mutations in these mice.

Even though CRISPR is being over-hyped right now, it is nonetheless genuinely exciting technology. Nature Methods was probably too eager to publish a controversial result, an all-too-common problem with big-name journals, and they seem to have done a poor job managing peer review. (Aside: I'd love to see what the reviewers said. Did they miss the obvious problems, or did the journal editors ignore the reviewers? I doubt we'll ever know.)

A final note: this kerfuffle illustrates the tremendous value of rapid publication through pre-print archives. Lareau et al.'s paper appeared a few days ago (July 5) on bioRxiv, along with all the data they used to support their arguments. We'll probably see a journal version too, but that will take months. Getting this paper out faster was a win for science.

(Postscript: two of the authors on the bioRxiv paper have financial interests in CRISPR technology companies, which they disclosed in the paper. I have no financial interests in any of these companies.)

Massive genetic sharing effort shows power but also shows how little we know

Your genes are not your fate. 

Nonetheless, genes can tell us a lot about our risk for disease, and sometimes they can tell us how to lead healthier lives.

The landscape of the human genome is vast and mostly unexplored. There is far, far more that we don’t know than we do know. This is why it’s so important that as we test people for genetic mutations, we share information as much as possible. Genes have different effects on different people, and a mutation that is harmful in one group might be harmless in another. If we’re ever to fill in all the gaps in our knowledge, we have to pool our resources by sharing data.

This is the goal of ClinGen, a new project described in this week’s New England Journal of Medicine. ClinGen relies on a public database called ClinVar, where researchers, clinical labs, clinicians, and patients can deposit information about genetic variants and their effect on disease. 

What makes this effort so complex is that many disease-causing mutations are quite rare. If two patients share the same disease and the same genetic mutation, and if we’ve never seen that mutation before, can we claim that the mutation cause the disease? Not really: we might have to wait until we’ve seen many more patients before we can have any confidence in the cause-and-effect relationship. This is why sharing data is so important: more data means more power to discriminate between real effects and coincidences.

ClinGen has already shown us that our knowledge has flaws: perhaps 17% of the disease associations that clinicians have reported might be incorrect. More precisely, the NEJM paper reports that out of more than 118,000 mutations that have a clinical affect, almost 13,000 were reported by more than one lab. Of those, 17% were interpreted inconsistently, with some labs calling mutations "pathogenic" while other labs calling them benign.

I disagree with the headline of an AP report headlined “flaws in gene testing,” which reported that 

“The first report from a big public-private project to improve genetic testing reveals it is not as rock solid as many people believe.”

This is a straw man argument: experts in the field don't think genetic testing is “rock solid”, and the 17% rate of disagreement in disease-mutation association is not that surprising. What's more, these conflicts don’t always represent flaws, but rather holes in our knowledge that we just haven’t filled yet. 

Disagreements over the effects of a genetic mutation represent opportunities to clarify and improve our genetic knowledge base. And as the ClinGen authors emphasize, it’s only by sharing our findings that we can discover and correct these flaws. This is why clinicians, scientists, and labs need to adopt a culture of sharing results, as the ClinGen project has emphasized (see their “Wall of Fame” of labs and institutions that have shared data).

All of us have mutations in our DNA; geneticists estimate that each of us carries perhaps 30 new mutations that even our own parents don’t share. The vast majority of these, fortunately, are harmless. Even mutations that do affect our health usually only have a small influence, changing our risk for disease but not actually causing it.

I'd be remiss if I didn't point out that sometimes, your genes are your fate. If you have certain mutations in the CFTR gene, you will have cystic fibrosis, and some mutations in the HTT gene will inevitably cause Huntington’s disease. 

As geneticist Luke Jostins cogently wrote, identical twins usually don’t die from the same thing. So even though genes may influence our fate, we still have control over it. Knowing your genetic risks can be valuable, but we have a lot more to learn about how our genes influence our health.