What sequence analysis and computation reveal about the deadly spread of the virus

Photo: Isaac Quesada/Unsplash

The first wave of the coronavirus hit Brazil’s Amazonas state very hard. So many people got sick in the capital Manaus that researchers estimated 70% or more of the population had immunity by fall 2020. This level of population immunity is in the ballpark of what would be needed for herd immunity, and people in Manaus began to feel that their previous ordeal meant that they would not face another surge in infection and death.

Unfortunately, they were wrong. In December 2020 a new spike in cases began, and by early January the level of daily hospital admissions was more…

© Tomas Castelazo, www.tomascastelazo.com / Wikimedia Commons / CC BY-SA 4.0

A few months before the pandemic my family stayed at a hotel on Lake Turkana in northern Kenya. The place was run by an expatriate European and had an extremely tolerant attitude toward small animals. Mostly I think this reflected a desire not to be bothered about things.

There were various creepy crawlies on the ground and mosquitos breeding in the hot spring bath, but the most disconcerting animal companions were the bats in the rafters of our room. There were three or four of them, and when they wanted to leave, they flew out through a hole in the…

The region around Lake Turkana in Northern Kenya is a desert landscape. To a Californian, the look of the hills and rocks and washes is familiar even if the vegetation is not. Bumping along in a land cruiser, we must have crossed a half-dozen dry river beds. Their size made it clear that at least some of the time water could be present — and violent.

Satellite image of Lake Turkana from NASA, via Wikimedia Commons.

Like storm water in the desert, time has many ways. In Turkana, my family and I were on vacation time. Two weeks packed with a wedding, a safari, and a fortuitous visit to a…

Eliot Bush

Computational biologist and chair of the Biology Department at Harvey Mudd College. Current research focuses on microbial genome evolution.

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