How did we get where we are today with cases surging all over the country?

Well it’s a combination of bad luck and less than laser-like concentration on details. And there’s a lot of politics mixed up in it as well. What happened in New York was bad luck. New York got lots more importations than California or Seattle did. There was at least one giant super spreader event in New York with 132 people who got infected in a synagogue in New Rochelle. It’s largely the Center for Disease Control’s fault in that there were not enough test kits available and they were heavily restricted to people who’d been in China.

Why has it continued to spread across the South, East, and the upper Midwest? It’s simple: People aren’t taking precautions. The New York Times had a map of mask-wearing by county in the United States. The whole southeast outside of Miami was light [indicating less mask-wearing], and the West is all dark [indicating more], except for a few places here and there. Part of that is a less than robust embrace of shelter in place. A lot of it is economic concerns about bringing the economy back up to speed more rapidly than it should have been. And part of it is encouraged by people like the governor of Georgia who won’t [mandate that] people wear masks.

How can we provide targeted support to the communities that need it most?

This is becoming a disease of poor immigrant, Latino communities. Essential workers can’t work from their homes. They’re insufficiently protected, [not because they’re] not wearing masks. They’ll come home to very dense housing and it gets spread around the house. That’s both an urban pattern and a rural pattern.

On top of that, there’s this whole issue of institutional outbreaks, which includes nursing homes and long-term care facilities. We’re also seeing outbreaks in factories. There’s one right now in South Central Los Angeles at Los Angeles Apparel, a sewing factory. There’s been one in a fish-packing plant in Contra Costa County. We’ve seen outbreaks in homeless shelters, especially early on in Los Angeles, Sacramento, and San Francisco. And then finally we have prisons. San Quentin now has almost 60 percent of its inmate population infected. That’s maybe the first place in the world where we’ll see herd immunity.

So that’s the epidemiology we’ve had. The essential worker dynamic needs to be somehow brought under control. The only way it’s going to be brought under control is with a lot of testing, and a lot of isolation, and a lot of quarantine. In order to do that you have to have some place to physically have people isolate and quarantine. You have to remove disincentive by replacing the wages they would have earned. If it’s the main wage earner who has to go into isolation, you have to provide food for the family, rent support, and make sure the guy has a job when he comes back.

Why is aerosol spread less important than respiratory droplet spread?

Aerosols below a certain size — like five microns — they’ll remain at your breathing level. But we think droplet spread is the predominant mode of transmission. The basic reproductive rate of coronavirus, the CDC is saying it’s two, maybe it’s three, maybe it’s three and a half. For measles, a predominantly aerosol-transmitted disease, it’s somewhere between 12 and 18.

In the 14 and a half million cases that have been reported worldwide, there’s one cluster that may be an aerosol transmission at a restaurant in China. If this were really an aerosol disease and transmitted by droplets that remain in suspension, you’d see lots more cases. Outside of hospitals, masks are what work, and that’s not going to be much different if you have aerosols versus droplet spread in the community.

What exactly is going on during incubation?

It’s just like any other incubation period. You get infected. The virus attaches to your respiratory epithelium through these ACE2 receptors. The virus takes over the machinery of the cells and starts making baby viruses. About three days later you have enough of these virions that when you excrete them, you can infect people. About two days after that, your immune system kicks in, which is what causes symptoms.

Is incubation a one-way street at a variety of speeds, but the end result is infection (the speed being determined by viral dose and host factors)?

Leaving aside host factors, we know from influenza and from a variety of other respiratory diseases, that the more you get, the more likely you are to have severe symptoms. So it stands to reason that a bigger inoculum — how many millions of particles you inhale — leads to more symptomatic disease. One of the interesting things about masks is that because they cut down viruses, the people who are getting infected are probably getting infected at lower inoculum sizes. And so that may be one of the reasons we’re seeing less severe disease.

For host factors, it depends on what the host factor is. If they have HIV infection and zero CD4 cells, that’s probably a bad sign. Or if they’re 95 years old and debilitated and lying in bed in a nursing home, they’re more likely to get severe disease. Within reasonable parameters at the population level, host factors may differentiate five percent of people.