What a time to be alive! These days, just staying alive feels like an accomplishment. As of late January 2021, at least two million people have died worldwide from COVID-19 (the disease caused by the virus SARS-CoV-2). A little more than a year after it was first recognized in Wuhan, China, we have the first vaccines being distributed; a scientific feat brought to you by the study of evolution. Yes, evolution. If you learned anything during this pandemic, I hope it is a healthy dose of the ‘forbidden science’ (no one calls it that).
‘Herd immunity’, ‘mRNA vaccines’, ‘mutations’, ‘phylogeny’, what a great resource for our evolution lectures! Evolutionary biologists will no longer be relegated to being the bantering wit at cocktail parties (remember those) yapping about birds being dinosaurs, or how extinct Neanderthals live on in our DNA; no, now is a time for us evolutionary biologists to roll up our sleeves and explain to others what the people actually saving humanity are doing. Sure, we weren’t those fabulous front-line workers actually risking their lives for the greater good, or the microbiologists, immuno-engineers, and Faucis heroically working to find an end to the scourge. Instead, we evolutionary biologists worked mostly behind the scenes, but you could say we’ve seen this play before and could help set the stage. Evolutionary biologists include those figuring out what this disease is and where it came from in the first place. We are used to thinking in geological time, so forgive our stumbling acceleration from our typical glacial pace; all this “evolution-in-action” data that came pouring out during this pandemic was hellishly exciting and horrifying at the same time.
Starting in late February and March 2020 many of us were drooling over the data coming off the science website NextStrain (https://nextstrain.org/) which proudly exclaims on its homepage to show ‘real time tracking of pathogen evolution’ (1) (and it doesn’t disappoint). On that site you can actually play (and replay, over and over) a day-by-day phylogeny (an evolutionary diagram depicting relatedness) and a corresponding world map showing the spread and growth of SARS-CoV-2 as it moved and mutated into new forms. Recently we learned of new even more virulent variants of SARS-CoV-2 first appearing in the United Kingdom, Brazil and South Africa (2,3). These variants are a result of mutations; mutations are errors in the copying of the genetic code of the virus as it is replicated, and are the raw material of evolution. Coronaviruses, like SARS-CoV-2, use the host cells to replicate and copying errors arise from this process (4). They are called “coronaviruses” because they look spiky, like an evil monarch’s crown (“corona” means “crown” in Latin); fun fact: several viruses that cause the ‘common cold’ are coronaviruses. The virus uses the crown to latch on to host cells; the vaccines being produced help your immune system recognize the proteins that make the spiky crown (via a messenger(m)RNA, hence ‘mRNA vaccines’), thus priming you to fight off the real virus if you encounter it (5). As the virus mutates into new variants it becomes harder for your immune system to recognize the disease compared to what the vaccine originally primed it to fight. That is why there is evidence that some of the available vaccines may not be so effective against the new strains (6). That genetic variation caused by mutations is also why you need a different flu shot every year; the flu is evolving and changing so a different vaccine is needed each year to keep up. Expect getting updated shots each year for COVID too.
The more people that get the virus the more opportunities it has to reproduce and mutate resulting in new strains and new complications for scientists trying to stop it (which is why avoiding other people is so important right now)(7). Eventually, if enough people do receive protection from the vaccines we will achieve ‘herd immunity’. For the anti-vax crowd, herd immunity is when everyone gets the disease and those that survive will be part of a new immune population. While that is very Darwinian of them, survival of the fittest shouldn’t be used to “trim the herd” of our most vulnerable e.g., the elderly, the immunocompromised, and those exposed to the virus like front-line workers and fast-food employees and others forced to work. Natural selection is brutal, ‘applying’ natural selection to humans is really just eugenics (since you would really just be sparing the privileged who can afford to avoid the virus). It isn’t ‘survival of the richest’ you know.
In the ‘age of COVID’ we also learned about human variation; not all populations are impacted by the virus in the same way, revealing the biased nature of our healthcare system (8). Worse still is that the vaccine may not be as effective on Black and Asian populations due to our different histories and genetic makeup (9,10). We also see big geographic discrepancies in where COVID genetic samples come from (11) which will also hurt our chances for finding new variants before they spread around the globe.
When the virus first emerged we didn’t know what it was until it was included in an evolutionary tree and found to be a SARS (Severe Acute Respiratory Syndrome) coronavirus (12), then with further evolutionary detective work we learned it originated from pangolins or bats (13,14), and definitely was not man-made in a lab as some conspiracy theorist and past-presidents suggested (15). Learning the origin of this disease helped demonstrate another reason why natural history collections should be supported so they can help identify and detect these disease vectors as they emerge (16) (natural history and taxonomy being an important part of the study of evolution). New zoonoses (diseases coming from wild animal populations) can be better tracked if we have a good understanding of what organisms exist out there and what disease they carry (and how they live with those diseases, i.e., after they get herd immunity the hard way) and how those organisms and diseases relate to each other in the evolutionary Tree of Life (17,18).
So as we watch the virus evolve, and the vaccines do their work, let’s keep in mind the evolutionary biology that went into the study of both. And after we’ve thanked the real heroes of this pandemic, remember to keep learning a little bit of that evolutionary biology that can teach us the nature of these pandemics in the past, present and future.
Stay safe and wear a mask or two,
Your friendly neighborhood evolutionary biologist,
Prosanta Chakrabarty
1 Hadfield, J., Megill, C., Bell, S.M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T. and Neher, R.A., 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), pp.4121-4123. https://academic.oup.com/bioinformatics/article/34/23/4121/5001388
2 Baric, R.S., 2020. Emergence of a Highly Fit SARS-CoV-2 Variant. New England Journal of Medicine https://www.nejm.org/doi/full/10.1056/NEJMcibr2032888
3 CDC. Emerging SARS-CoV-2 Variants. January 28 https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html
4 V’kovski, P., Kratzel, A., Steiner, S., Stalder, H. and Thiel, V., 2020. Coronavirus biology and replication: implications for SARS-CoV-2. Nature Reviews Microbiology, pp.1-16. https://www.nature.com/articles/s41579-020-00468-6
5 Zhang, N.N., Li, X.F., Deng, Y.Q., Zhao, H., Huang, Y.J., Yang, G., Huang, W.J., Gao, P., Zhou, C., Zhang, R.R. and Guo, Y., 2020. A thermostable mRNA vaccine against COVID-19. Cell, 182(5), pp.1271-1283. https://pubmed.ncbi.nlm.nih.gov/32795413/
6 Zimmer, C., Weiland, N., LaFraniere, S. 2021. Johnson & Johnson’s Vaccine Offers Strong Protection but Fuels Concern About Variants. New York Times. January 29, 2021 https://www.nytimes.com/2021/01/29/health/covid-vaccine-johnson-and-johnson-variants.html
7 Evolution goes viral. Nat Ecol Evol (2021). https://doi.org/10.1038/s41559-021-01395-2
8 Manning, K.D., 2020. The Art of Medicine: More than Medical Mistrusts. The Lancet, 396: 1481-1482. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32286-8/fulltext
9 Ray, T. 2020. MIT machine learning models find gaps in coverage by Moderna, Pfizer, other Warp Speed COVID-19 vaccines https://www.zdnet.com/article/mit-machine-learning-models-find-gaps-in-coverage-by-moderna-pfizer-other-warp-speed-covid-19-vaccines/
10 Liu, G., Carter, B. and Gifford, D.K., 2020. Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and their Augmentation by Compact Peptide Sets. Cell systems. https://www.sciencedirect.com/science/article/pii/S2405471220304610
11 Centre for Genomic Pathogen Surveillance https://beta.microreact.org/project/pa7U6YScBKgFkEmk1sp1SX-cog-uk-2021-01-25-global-sars-cov-2
12 Eickmann, M., Becker, S., Klenk, H.D., Doerr, H.W., Stadler, K., Censini, S., Guidotti, S., Masignani, V., Scarselli, M., Mora, M. and Donati, C., 2003. Phylogeny of the SARS coronavirus. Science, 302(5650), pp.1504-1506. https://science.sciencemag.org/content/302/5650/1504.2
13 Zhang, T., Wu, Q. and Zhang, Z., 2020. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Current Biology (30) 1346-1351.e2 https://www.sciencedirect.com/science/article/pii/S0960982220303602
14 Flores-Alanis, A., Sandner-Miranda, L., Delgado, G., Cravioto, A. and Morales-Espinosa, R., 2020. The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789. BMC research notes, 13(1), pp.1-6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7450963/
15 Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. 2020. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452. https://doi.org/10.1038/s41591-020-0820-9
16 DiEuliis, D., Johnson, K. R., Morse, S. S., and Schindel, D. E. 2016. Opinion: Specimen collections should have a much bigger role in infectious disease research and response. Proceedings of the National Academy of Sciences, 113(1), 4–7. https://www.pnas.org/content/113/1/4
17 Quammen, D., 2012. Spillover: animal infections and the next human pandemic. WW Norton & Company.
18 Thompson, C.W., Phelps, K.L., Allard, M.W., Cook, J.A., Dunnum, J.L., Ferguson, A.W., Gelang, M., Khan, F.A.A., Paul, D.L., Reeder, D.M. and Simmons, N.B., 2021. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. Mbio, 12(1). https://mbio.asm.org/content/12/1/e02698-20
Thanks to Dr. Vicky Forster (@vickyyyf) for help and discussion about this post.