Covid Update 3/31/20

There's some interesting news today, basically encouraging. The news appears to be especially encouraging for California--a matter Bebe and Ray SoCal have raised. In essence, it confirms my cautiously optimistic view--for the West Coast. On the West Coast, at least, Covid has been more of a localized thing, not a community spread thing. That's what I theorized early on--Covid was a bit of a late arrival in the US, compared to the rest of the world, and might be containable with aggressive action. That's not so much the case on the East Coast (NY), where it seems to be more on the loose in the community. And we don't really know about other hot spots like Michigan and Illinois. Here's what I'm talking about.

USAToday has an article--8 strains of the coronavirus are circling the globe. Here's what clues they're giving scientists--that explains what scientists have been able to learn through genomic sequencing. I won't attempt to explain that process, because I'd probably get it wrong, but here are the important points that have been learned. I'll leave out the ellipses, but you can go to the original for more:

While researchers caution they're only seeing the tip of the iceberg, the tiny differences between the virus strains suggest shelter-in-place orders are working in some areas and that no one strain of the virus is more deadly than another. They also say it does not appear the strains will grow more lethal as they evolve.  

... 

The SARS-CoV-2 virus first began causing illness in China sometime between mid-November and mid-December. Its genome is made up of about 30,000 base pairs. Humans, by comparison, have more than 3 billion. So far even in the virus's most divergent strains scientists have found only 11 base pair changes.  

That makes it easy to spot new lineages as they evolve, said Chiu.  

“The outbreaks are trackable. We have the ability to do genomic sequencing almost in real-time to see what strains or lineages are circulating,” he said.  

So far, most cases on the U.S. West Coast are linked to a strain first identified in Washington state. It may have come from a man who had been in Wuhan, China, the virus’ epicenter, and returned home on Jan. 15. It is only three mutations away from the original Wuhan strain, according to work done early in the outbreak by Trevor Bedford, a computational biologist at Fred Hutch, a medical research center in Seattle.  

On the East Coast there are several strains, including the one from Washington and others that appear to have made their way from China to Europe and then to New York and beyond, Chiu said. 

... 

“Remember, we’re seeing a very small glimpse into the much larger pandemic. We have half a million described cases right now but maybe 1,000 genomes sequenced. So there are a lot of lineages we’re missing,” he said.

The California experience is what I was hoping would be true of most of the US. It seems not true in metro New York City--including parts of New Jersey and Connecticut--and maybe some other East Coast areas. Hopefully we'll find out more about Michigan and Illinois soon.

Shelter in place working in California

Chiu’s analysis shows California’s strict shelter in place efforts appear to be working. 

Over half of the 50 SARS-CoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state. Another 30% are associated with health care workers and families of people who have the virus. 

“Only 20% are coming from within the community. It’s not circulating widely,” he said. 

That’s fantastic news, he said, indicating the virus has not been able to gain a serious foothold because of social distancing. 

It's like a wildfire, Chiu said. A few sparks might fly off the fire and land in the grass and start new fires. But if the main fire is doused and its embers stomped out, you can kill off an entire strain. In California, Chiu sees a lot of sparks hitting the ground, most coming from Washington, but they're quickly being put out. 

So, good news for California.