SARS-CoV-2 Family Tree

Environmental & Science Education, STEM, Biodiversity, Nature, Health, Medicine, Biological Evolution, Art & Environment, Nature of Science, History of Science

Goats & Soda (NPR) commissioned an artist to develop a family tree for SARS-CoV-2. The accompanying story by Michaleen Doucleff explains the structure of the tree telling us first why they are so useful in science. They "give biologists insights into how a virus has evolved over time and what changes to expect in the future."

The tree was inspired by the SARS-CoV-2 phylogenetic tree generated by Emma Hodcroft of Nexstrain and the University of Bern. That tree is reproduced within Michaleen Doucleff's story.

Doucleff begins with an observation about the tree's growth. When the tree first took root, "many virologists thought they knew how it would evolve: slowly and minimally." But the virus surprised us with Omicron, variants "BA.1 and its sibling BA.2" The standard understanding was that SARS would mutate slowly and it did. The original structure prevailed early on in the pandemic, resulting in "only about one or two mutations each month." The tree seemed to have a single trunk with "only a few tiny little branches."

In December 2020, "the virus began to change rapidly. ... Two variants of concern: alpha and beta appeared," each having around 20 mutations each."  In addition, branches began to sprout from the main trunk: "gamma, lambda and mu appeared (although none of these variants ended up spreading across the globe) while at"the top of the tree, dozens of delta branches from the delta canopy." The future growth of the tree appeared clear."

Then omnicron. What was so different about it is "it didn't have any close relatives on the tree..."no parents, no grandparents, not even great-great-great-grandparents." Different genes which led to a profound puzzle. Where did it come from? BA.1 went world-wide; BA.2 "is now reported to be taking over South Africa. (A third sibling also appeared, but so far it doesn't seem able to keep up with its glove-trotting siblings.)"

The question of the origin of the omnicron branch's origin has left a "gap in our knowledge" bringing "much uncertainty about the future of the pandemic." Doucliff points to possibilities, e.g., under surveillance "in parts of Africa that scientist weren't watching closely enough..." or omnicron "was evolving inside another animal...and then jumped back to people..." or "was evolving...inside a person who had a chronic infection." At present, these are hypotheses in need of investigation.

About the possibility of invisible variants emerging from the tree, Emma Hodcroft, University of Bern told Doucleff, that "right now, there could be several other long -- and invisible -- branches growing on the SARS-Cov-2 tree. And in the oncoming months one of those branches could sprout off another family of rapidly spread variants, similar to omicron." 

Or, according to Doucleff, one even "more lethal than any previous variant." Commenting on this scenario, infectious disease physician Roby Bhattacharyya (Massachusetts General Hospital and Harvard Medical School.) told her that "'Variants, that transmit better are going to be selected for, and it's kind of the luck of the draw whether that variant is also more severe or less severe.'"

At present there is every reason to cheer loudly for our immune systems which have handled "whatever variant emerges. ...Vaccination or a prior infection has still offered good protection against hospitalization and severe disease."