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Evolution of an outbreak

March 2020

Genomic epidemiology of novel coronavirus (HCoV-19)

Genomic epidemiology of novel coronavirus (HCoV-19). Click on image for larger view. Credit: Nextstrain.org

For the past month, each day has brought worrisome news: more cases of the new coronavirus popping up around the world. This virus was first identified in Wuhan China, just two months ago. Since then it has spread to Southeast Asia, Australia, Europe, and North America. While the virus is no Ebola — its symptoms are much like those of the flu — it is much more transmissible than Ebola and still deadly, killing around 3% of those sickened. New diseases, like this coronavirus, Ebola, SARS, and MERS, might seem to appear out of nowhere. But in fact, these diseases are merely new to us humans. They have all been infecting other species for a long time and only recently made the evolutionary leap to humans.

Where's the evolution?

Because the outbreak of the “new” coronavirus is both caused by an evolving entity (a virus) and is occurring in an evolving entity (humans), looking at this scary situation through an evolutionary lens can help us answer a variety of important questions:

1. Where did the new coronavirus come from?

To answer this, scientists sequenced the genetic material of many different samples of the coronavirus from humans. They compared these sequences to those from coronaviruses infecting other animals and used this information to construct an evolutionary tree (i.e., a phylogeny) of all those viruses. The tree shows that the new human coronavirus is most closely related to a coronavirus found in bats, suggesting that this virus's original host was bats. However, the next closest relatives of the new coronavirus are found in pangolins (scaly anteaters). While scientists are still actively investigating the source of the virus, based on the available evidence, one plausible hypothesis is that a bat passed a coronavirus on to pangolins, where it multiplied and spread, and ultimately jumped into humans.

Genomic epidemiology of novel coronavirus (HCoV-19)

2. How is the new coronavirus spreading?

When the outbreak began, doctors weren't certain if the victims were all infected through contact with another species (e.g., a pangolin) or if the virus made the leap to humans only once and was spreading from human to human. Again, examining the evolutionary relationships of the new coronavirus and its close relatives reveals the answer. If the virus made multiple leaps from another species to ours, we'd expect to see some human coronaviruses more closely related to viruses from other animals. Instead the human viruses all cluster together on the evolutionary tree: they are most closely related to each other. This suggests that the new virus jumped from another species to a human just once, and since then has been diversifying as it spreads from one human to another.

3. When did the new coronavirus start infecting humans?

While the first definitive cases of the new coronavirus in humans were identified in December of 2019, some scientists have wondered if the virus might have been stealthily infecting people for much longer but gone unnoticed. HIV, after all, was first recognized as a distinct viral disease in 1981; however, research has since shown that the virus has been infecting humans since the early 1900s. Could something similar be going on with the new coronavirus? Again, evolution reveals the answer. In general, the longer a lineage has been evolving on its own, the more genetic differences it will accumulate distinguishing it from its close relatives. All of the samples of the new coronavirus from different people are extremely similar to one another genetically, suggesting that they share a very recent common ancestor, and hence, jumped to humans recently. In fact, based on what we know about the rates at which viruses evolve, the new coronavirus probably started infecting people sometime in November of 2019. It didn't go undetected for long!

4. Why coronavirus?

The world is full of viruses. They infect plants, animals, fungi, and bacteria. We encounter them constantly through our homes, pets, and even foods — not just in doctors' waiting rooms and far flung locales. But the vast majority of these viruses are not causing border shut downs or a run on surgical masks. Only a tiny percentage of the viruses that infect other species have made the leap to infecting humans; among these, coronaviruses (a group of viruses that infects mammals and birds and uses RNA, not DNA, as its genetic material) seem to be particularly good at making this switch. They are responsible for the current outbreak, as well as the SARS and MERS outbreaks over the past two decades.

To understand “why coronavirus,” it helps to view the virus like any other species that finds itself in a new environment (only in this case, the new environment is its potential new host, us). For example, imagine a group of lizards that wind up floating to a new island on a raft of debris after a storm. Will they die out or survive? Of course, they are more likely to survive if the new island is similar to the old one because some of their adaptations would still be functional. And if the castaway group includes lizards with lots of different traits, the more likely it is that some individuals have the right combination of traits (e.g., long toes and speckled skin) to survive and establish a lineage on the new island.

The same is true of a virus infecting a new species. If the new host has similar cellular machinery to the old host, the more likely the virus will be able to infect the new host. And if the virus is quite variable genetically, the more likely some individuals will be able to survive to reproduce — and hence, infect the new host. Both of these factors seem to help explain why coronaviruses are poised to jump species barriers to infect humans. First, coronaviruses infect mammals. We humans are mammals. Though we may seem very different from mammals like bats, they are relatively close evolutionary relatives, and our physiology and cellular machinery have much in common. Viruses that normally infect plants, for example, are much less likely to spark a human pandemic. Second, coronaviruses use RNA as their genetic material, and the process of copying RNA is highly error prone. While “error-prone” sounds bad, it is a good thing for generating genetic variation. Most of these copying mistakes will be bad or neutral for the bearer, but a few will be just the thing the virus needs to make it in new host. And as the few viable viruses are copied in the new host, additional mutations keep occurring, providing more variations for natural selection to act upon and allowing the viral lineage to adapt to its new host relatively rapidly.

Unfamiliar infectious diseases are, of course, frightening. But they are not a new phenomenon. Throughout our evolutionary history, disease-causing pathogens have repeatedly made their way from other species into humans.  And we can only expect this pattern to intensify as we spread around the Earth, invading the habitats of other animals and then moving again, carrying new pathogens with us as we travel. Given that such outbreaks will be a predictable part of our future, we need to be prepared to fight them using all the scientific tools and knowledge at our disposal — knowledge that includes evolutionary theory as a critical framework.

Read more about it

Primary literature:

  • Zhou, P., Yang, X., Wang, X., Hu, B., Zhang, L., Zhang, W., ... Shi, Z. (2020). Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. bioRxiv preprint. DOI: https://doi.org/10.1101/2020.01.22.914952. read it
News articles:

Understanding Evolution resources:

Discussion and extension questions

  1. In your own words, describe how scientists figured out the source of the new coronavirus.
  2. In your own words, describe the evolutionary evidence that suggests that the new coronavirus is now spreading directly from human to human.
  3. What factors seem to make coronaviruses particularly good at jumping species barriers to infect human populations?
  4. In your own words, describe why having a high mutation rate allows a virus to quickly adapt to a new host.
  5. Imagine that scientists are studying a new infectious disease. They study the genomes of virus samples taken from different patients and build an evolutionary tree. The tree shows that the samples from humans are all closely related to viruses from mice. They are more distantly related to viruses found in possums. However, the human samples do not form a cluster, or clade. Instead they are spread out over the tree, and some are most closely related to other human viruses, but others are more closely related to mouse viruses than they are to other human samples.
    1. Based on this evidence, what do you think the source of the new disease is? Explain your reasoning.
    2. Based on this evidence, how many times do you think the virus jumped to humans from another species?  Explain your reasoning.
    3. Based on this evidence, do you think the virus is spreading from human to human? Explain your reasoning.
Related lessons and teaching resources

  • Teach about evolutionary trees: This lab for grades 9-12 has two main parts. In the first, students build phylogenetic trees themed around the evidence of evolution, including fossils, biogeography, and similarities in DNA. In the second, students explore an interactive tree of life and trace the shared ancestry of numerous species.
  • Teach about evolution and medicine: In this activity for undergraduates, students use what they know about evolution and medicine to review an article written for a school publication. The task is to identify errors, explain the incorrect statements, and correct the information. They then explain the process of natural selection by creating a labeled illustration using one of the examples from an earlier lesson.
  • Teach about emerging infectious diseases: This article, for grades 9-12, explains how diseases like SARS, HIV, and West Nile Virus are new to humans, but are old news to other species. These and other emerging infectious diseases have recently added humans to the list of hosts they infect. An evolutionary perspective can help us better understand and, we hope, control this problem.


  • Bedford, T. (Feb 18, 2020). Phylogeny of SARS-like betacoronaviruses including novel coronavirus SARS-CoV-2. NextStrain.org. Retrieved February 27, 2020 from https://nextstrain.org/groups/blab/sars-like-cov?c=host
  • Begley, S.. (Jan 24, 2020). DNA sleuths read the coronavirus genome, tracing its origins and looking for dangerous mutations. STAT. Retrieved February 27, 2020 from https://www.statnews.com/2020/01/24/dna-sleuths-read-coronavirus-genome-tracing-origins-and-mutations/
  • Cohen, J. (Jan 31, 2020). Mining coronavirus genomes for clues to the outbreak’s origins. Science. Retrieved February 27, 2020 from https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins
  • Zhou, P., Yang, X., Wang, X., Hu, B., Zhang, L., Zhang, W., ... Shi, Z. (2020). Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. bioRxiv preprint. DOI:  https://doi.org/10.1101/2020.01.22.914952.