We present JUNIPER, our outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets to achieve state-of-the-art performance. Led by @ivan_specht et al. @sabeti_lab. 1/12 🧵medrxiv.org/content/10.110… Outbreak reconstruction, the inference of who infects whom in disease outbreaks, offers critical insights into pathogen spread and helps inform our response efforts. But major methodological and computational breakthroughs are needed for its wide use. 2/12

As I kick off the #BlackHistoryMonth celebrations of @sabeti_lab members who made an extraordinary impact on our lab history, I am grateful to Harlisa Minaya, our Human Resources partner for many years for helping to create and nurture that community. 1/4 Harlisa was an incredible thought partner to us as we tried to create a supportive and inclusive environment and navigate many challenging issues, through some of the most difficult of times. 2/4

In answer to a recurring question “When can adults finally stop wearing masks indoors?” I find myself articulating in various ways ‘when our kids can’. Put simply, in my personal view -- We adults don’t have to wear masks when kids don’t have to wear masks. 🧵1/8 It was always bananas to me, that adults made kids miss whole years of school, graduation, sports seasons, prom, to keep adults safe. But the second vaccinations were available for adults, they were out partying in clubs and bars with not a care in the world. 2/8

Over the last 48 hours I have been asked the same question many times in many ways - ‘Is the Provincetown outbreak due to this being a largely LGBTQ+ community?’ It is NOT. A thread on the dangers of #othering in outbreaks. #ptown #delta #covid 1/14 It comes as both direct attacks and in tepid questioning like ‘You know Ptown is well a special community, could this be more about how they socially interact?’ or ‘There is a lot of HIV in the gay comunity, could they just be more immunocompromised?’ 2/14

Altruism is not only good for society––in an outbreak, it can also be self-serving. A thread on our modeling paper medrxiv.org/content/10.110… w/ @ivan_specht @KianSani @codeanticode and thanks @EmilyAnthes piece @NYT nytimes.com/2021/03/24/hea… 1/16 COVID-19 made clear that diagnostic testing is a highly effective tool to curb viral spread. A positive test result informs infectious individuals that they & their close contacts must self-isolate, reducing transmission. #covid19 #testing 2/16

Anyone who was there in the early days of @sabeti_lab knows that Eric Phelan is a man of extraordinary brilliance, talent, & passion. I would need several books to tell the tales of his time in my lab. But here is a brief history @epcphelan #blackhistorymonth 1/14 Eric was one of those superstar Harvard grads in Economics snapped up out of college by Lehman Brothers, only to have them file bankruptcy in 2008. It drove Eric to take a pause where he reconnected with science & we were the very fortunate beneficiaries 2/14

A year into the COVID-19 pandemic, we still lack a testing and surveillance system to stop SARS-CoV-2 or respond to new variants that might emerge. How did we get here and where can we go? A thread based on our @NEJMperspective nejm.org/doi/full/10.10… 1/11 U.S. has 3 core issues: 1. limited bandwidth & support for labs to rapidly stand up new tests 2. over-reliance on commercial manufacturers leading to testing shortages & perverse incentives 3. failure to prioritize symptomatic over asymptomatic testing. Some startling facts: 2/11