Anne Arundel County, Maryland

The instantaneous reproduction number (R) is estimated using the daily incidence of new cases, while including effects of social distancing, population density, and combined temperature and humidity lagged over the prior 14 days.

This model projects the effect of a theoretical May 15 midway return of normal travel to non-essential businesses. Future cases are estimated from predicted values of R.

SOURCE: COVID-Lab

Density is destiny

There’s no simple, one-size-fits-all protocol for reopening the economy, said David Rubin, director of PolicyLab at Children’s Hospital of Philadelphia. Rubin is developing a model to forecast how reopening 260 large U.S. counties on May 15 would play out if residents maintained only half the social distancing measures now in place.

The good news, Rubin said, is that modest-size, relatively spread-out cities will probably have room to make adjustments. But if restrictions ease too much, New York and similarly dense cities will rapidly see infections spike again.

“It comes back really quick, and the peaks are much higher than what you’re seeing right now,” Rubin said. “It was sobering. I was more optimistic before we did our models.”

This is why epidemiologists are cautioning state leaders to inch toward reopening with tentative, staggered steps.

SOURCE: Washington Post

map of europe

Santa Clara CA

Santa Clara CA. Estimation of R.

The instantaneous reproduction number (R) is estimated using the daily incidence of new cases, while including effects of social distancing, population density, and combined temperature and humidity lagged over the prior 14 days.

Santa Clara CA. Projected cases through August 2020.

This model projects the effect of a theoretical May 15 midway return of normal travel to non-essential businesses. Future cases are estimated from predicted values of R.

SOURCE: COVID-Lab

The effective reproduction number (Rt)

Excerpt

R0 is the basic reproduction number of an epidemic. It’s defined as the number of secondary infections produced by a single infection. If R0 is greater than one, the epidemic spreads through every susceptible individual in a population. If R0 is less than one, the epidemic spreads, but limps along and disappears before everyone becomes infected. The flu has an R0 between one and two while measles sits in the high teens. While R0 is a useful measure, it is flawed in an important way: it’s static.

We’ve all witnessed that humans are adaptable. Our behavior changes, whether mandated or self-prescribed, and that changes the effective R value at any point in time. As we socially distance and isolate, R plummets. Because the value changes so rapidly, Epidemiologists have argued that the only true way to combat COVID19 is to understand and manage by Rt.

I agree, and I’d go further: we not only need to know Rt, we need to know local Rt. New York’s epidemic is vastly different than California’s and using a single number to describe them both is not useful. Knowing the local Rt allows us to manage the pandemic effectively.

SOURCE: Kevin Systrom

DEEP DIVE: Github notebook

States have had a variety of lockdown strategies, but there’s very little understanding of which have worked and which need to go further. Some states like California have been locked down for weeks, while others like Iowa and Nebraska continue to balk at taking action as cases rise. Being able to compare local Rt between different areas and/or watch how Rt changes in one place can help us measure how effective local policies are at slowing the spread of the virus.

Tracking Rt also lets us know when we might loosen restrictions. Any suggestion that we loosen restrictions when Rt > 1.0 is an explicit decision to let the virus proliferate. At the same time, if we are able to reduce Rt to below 1.0, and we can reduce the number of cases overall, the virus becomes manageable. Life can begin to return to ‘normal.’ But without knowing Rt we are simply flying blind.

SOURCE: Kevin Systrom

DEEP DIVE: Github notebook

map of europe

Anchorage

The instantaneous reproduction number (R) is estimated using the daily incidence of new cases, while including effects of social distancing, population density, and combined temperature and humidity lagged over the prior 14 days.

This model projects the effect of a theoretical May 15 midway return of normal travel to non-essential businesses. Future cases are estimated from predicted values of R.

SOURCE: COVID-Lab