Infectious Disease on Big Muddy

How SARS-CoV-2 variants get named on GitHub

Thu, 26 Mar 2026 07:00:00 -0400

Bioinformatics has long been an unusually collaborative and transparent field, with genomes, protein structures, and other complex biological data habitually deposited into open databases during the course of research. The situation was no different at the outset of the COVID-19 pandemic, when a small group of scientists developed the Pango nomenclature for classifying variants of the SARS-CoV-2 virus. Outside of a handful of Greek-letter “variants of concern” names assigned by the World Health Organization, the Pango nomenclature is the standard for tracking the evolution of the SARS-CoV-2 virus. You may recall names such as B.1.1.7 (Alpha or the UK variant), B.1.351 (Beta or the South African variant), and P.1 (Gamma or the Brazilian variant). You can see a complete list of active SARS-CoV-2 lineages using the Pango nomenclature here.

By August 2020, the work of defining new lineages of SARS-CoV-2 had moved to GitHub, where the scientific process could happen in transparent and collaborative way. The definition of new lineages happens on proposals submitted as GitHub issues. In May 2023, a second GitHub repository was opened to move discussions of smaller or less clear lineages out of the main repository. These discussions can be promoted to the main repository, as this issue tracking LP.8.1 sub-lineages was in May 2025.

The work of defining new lineages of SARS-CoV-2 continues to this day on the GitHub repository, as the virus continues to mutate and evolve. And bioinformatics continues to be a shining beacon for open science for the rest of us to learn from.

Properly the work of federal public health agencies

Sun, 22 Mar 2026 23:38:00 -0400

One of the reasons I started this blog was to have a place to put down posts and articles that have lodged themselves in my brain. The wind-down announcement of the COVID Tracking Project, a volunteer-led COVID-19 data tracking collaboration, is one such article.

But the work itself—compiling, cleaning, standardizing, and making sense of COVID-19 data from 56 individual states and territories—is properly the work of federal public health agencies. Not only because these efforts are a governmental responsibility—which they are—but because federal teams have access to far more comprehensive data than we do, and can mandate compliance with at least some standards and requirements.

After one year of work, the COVID Tracking Project decided to quite collecting data on COVID-19 in the United States, because they recognized that the work of collecting a comparable, national-level dataset was the responsibility of federal government agencies.

As someone who co-led the COVID-19 Canada Open Data Working Group, which curated COVID-19 data for Canada until the end of 2023, I think about this article a lot. It’s a good read, and it speaks to how essential open data was to filling in the gaps in the national and international understanding of the COVID-19 pandemic.

Guinea worm one step closer to eradication

Wed, 04 Feb 2026 23:57:00 -0500

Only 10 cases of guinea worm were reported in 2025, down from an estimated 3.5 million cases per year when the elimination campaign began four decades ago. The disease is an ancient one, believed by some to be the “fiery serpents” that beset the ancient Israelites in The Book of Numbers. It is treated by carefully wrapping the parasite around a small stick as it painfully emerges over the course of weeks. This may be the inspiration for the Staff of Asclepius (⚕), the predominant symbol of medicine showing a a serpent wrapped around a rod.

When I was studying mathematical modelling of infectious diseases at the University of Ottawa in the mid 2010s, the question was whether Jimmy Carter would outlive the guinea worm. Tragically, he did not, but his life’s work helped to prevent an estimated 100 million cases of the disabling disease and made him a hero in global health.

While we are within spitting distance of zero cases in humans, true eradication will be more difficult due to significant animal reservoirs of the disease. The press release notes nearly 700 reported cases in animals across six countries (and who knows how many unreported cases). These non-human reservoirs pose a significant barrier to true eradication, since the disease must die out not only in human populations but also in wildlife.