CDC stepped up sequencing, but the data haven’t kept pace

The CDC has stepped up its sequencing efforts in a big way over the past few months, going from 3,000 a week in early January to 10,000 a week by the end of March. But data on the results of these efforts are scarce and uneven, with some states doing far more sequencing than others. And the CDC itself publishes data with gaping holes and lags that make the numbers difficult to interpret.

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National numbers, April 4

The pandemic’s current state puts public health leaders like Dr. Walensky in a challenging position. New cases continue to rise, with states like Michigan, New York, New Jersey, and other parts of the northeast seeing more concerning spikes. While a 60,000-cases-per-day average may seem small compared to the numbers we saw this winter, it’s comparable to the summer surge that devastated much of the country. And our still-improving genomic surveillance system is finding more and more cases caused by variants.

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COVID Source callout: Federal Bureau of Prisons

For the past year, nonprofit news organization The Marshall Project has tracked COVID-19 cases in prisons, in collaboration with The Associated Press. The tracking effort has primarily focused on compiling numbers from state and federal prison bureaus, through a weekly tally that compares total cases reported by these agencies to their previous totals. This week, though, the Federal Bureau of Prisons started excluding a lot of prisoners from their count, making it impossible for the Marshall Project to compile accurate numbers.

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New, more local data from the CDC

The CDC made two major updates to its COVID-19 data this week. First: On Tuesday, the agency published a new dataset with more granular information on COVID-19 cases. Second: Vaccination data at the county level are now available on the CDC’s COVID Data Tracker.

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Privacy-first from the start: The backstory behind your exposure notification app

Since last fall, I’ve been fascinated by exposure notification apps. These phone applications use Bluetooth to track people’s close contacts and inform them when a contact has tested positive for COVID-19. As I wrote back in October, though, data on the apps are few and far between, leaving me with a lot of questions about how many people actually have these apps on their phones—and how well they’re working at preventing COVID-19 spread. This week, I put those questions to Jenny Wanger, co-founder of the TCN Coalition and Director of Programs at the Linux Foundation of Public Health.

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National Numbers, March 28

After several weeks of declines, our national count of new cases has started creeping up: the current 7-day average is 57,000, after 53,000 last week and 55,000 the week before. Michigan continues to see concerning numbers, as do New York, New Jersey, Florida, Texas, and California—all states with higher counts of reported variant cases.

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COVID source shout-out: Hawaii

Hawaii is the latest state to add vaccinations by race to its dashboard. I am a fan of both the state’s green-and-orange color choices and its handy finger-pointing icon, instructing users to hover over each bar in order to compare vaccination numbers to Hawaii’s demographics.

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