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The Mystery of Botswana’s Mass Elephant Die-Off

Under the scorching sun, they walk around in circles and then suddenly drop dead. This has happened to at least 350 African Elephants in Botswana since March 2020 and, initially, no one knew why.

What exactly is killing these animals? Is this a new threat to the species that is already vulnerable to extinction?

In this article, I will be discussing the mysterious deaths of these elephants, the hypotheses proposed to be responsible (such as poison or anthrax), and what scientists have identified as the actual cause.

The victim

The African Elephant (Loxodonta africana) is the largest land animal on Earth. It inhabits a wide range of environments across the continent, where it is a keystone species. This means that elephants play an important role in their ecosystem and that many other organisms depend on them.

For example, the elephants shape the habitat by trampling dense vegetation to allow other species to co-exist. In particular, these huge animals dig for water which, in turn, can be used by all animals in the ecosystem - this is really important especially during the periods of drought. Meanwhile, elephant dung spreads seeds across a much greater range than most other animal dispersers, which enables vegetation to continue growing.

Unfortunately, various threats to the survival of these elephants mean they are categorised as ‘threatened with extinction’ on the IUCN (International Union for Conservation of Nature) Red List. These include habitat loss due to urbanisation and agriculture, climate change, and the introduction of invasive species and diseases into their environment. What’s more, one of the most significant pressures facing African Elephants is the ivory trade, whereby around 35,000 elephants are killed every year for their tusks. In fact, this threat is so great that females are evolving to become tuskless. Overall, the pressure that human activity has on these animals is exemplified by the fact that the elephant population is thought to have been as great as 26 million in Africa, until the Europeans colonised and eventually reduced their numbers to around only 400,00 today.

This is a massive problem, as their significance in the ecosystem means that threats to the survival of elephants would also equate to threats to numerous other species.

The deaths

18,000 elephants and 16,000 people live in the Okavango Delta, a region in Northern Botswana (Figure 1). From March 2020, an unusual number of corpses were found in the area. 281 elephants were officially reported to have died by July, and 350 by the end of September, however conservation NGOs (non-governmental organisations) say the number of deaths might be even higher.

Witnesses claim the animals exhibited unusual behaviour before dropping dead, thereby suggesting that the mysterious deaths are caused by a new disease that was not previously associated with these elephants.

The deaths seemed to have stopped as the pans have dried up in the wetlands. However, it is still essential that whatever is responsible for this tragedy is identified in order to prevent future deaths. Given that the African Elephant population is already vulnerable to extinction, events like this could seriously endanger the future of the species.

Figure 1: Illustration showing the Okavango Delta in Northern Botswana, the area where mysterious elephant deaths have been reported. The African Elephant, Loxodonta africana, is also shown.

Various approaches were taken in order to determine which hypothesis was correct. These include post-mortem examinations of the corpses and lab tests of samples from the environment. A significant challenge with studying the bodies is that they may not be found for days – why this matter is because, in the time between death and location of the corpses, the heat accelerates rotting and scavengers eat the organs. This means that there often isn’t much left for scientists to look at.

Now let’s take a look at the main hypotheses proposed, which are summarised in Figure 2, and discuss why they were supported or ruled out.

Figure 2: The various hypotheses proposed as the cause behind the elephant deaths in Botswana. Bacillus anthracis is a species of bacteria that causes anthrax. Encephalomyocarditis virus can infect a range of species and cause inflammation for the heart and brain. But several tests have found that cyanobacteria, present in water holes where the elephants drank from and bathed, were causing the deaths. This figure was produced using BioRender.


Elephant poaching is a huge problem, with tens of thousands of animals being killed each year for their tusks to meet the demand of the illegal ivory trade. Poaching was quickly eliminated as a cause as the corpses were found with their tusks.

Starvation or dehydration

This theory was quickly dismissed as recent heavy rainfall meant that waterholes were full and there was lots of vegetation for elephants to feed on. In contrast, there had been a drought in previous years, so if this was the issue, the deaths would have occurred much earlier.


As mentioned earlier, the elephants exhibited behavioural (neurological) symptoms before they died (for example, walking around in circles).

Anthrax is caused by Bacillus anthracis, a pathogen you may be familiar with because of its potential use in biological warfare. It is a naturally occurring bacteria that causes disease in humans as well as domestic and wild animals. Infected animals often present neurological symptoms, though the disease progresses so quickly that the animal sometimes dies before any symptoms are observed.

This species has the remarkable capability to form spores that can survive in the environment for decades due to their resistance to conditions such as extreme temperature and desiccation. These spores will germinate, like a dormant plant seed, under the right conditions (and this tends to be once they are inside a human or animal). B. anthracis can cause different types of anthrax depending on how the infectious spore gets into an individual. When a spore enters via a break in the skin, the host develops cutaneous anthrax. Meanwhile, the consumption of contaminated meat leads to gastrointestinal anthrax, whilst spore inhalation causes inhalation anthrax.

Given what we know about B. anthracis and that anthrax is endemic throughout Africa, it was proposed as a possible cause of the elephants' deaths. It was deemed quite possible that the elephants could have become infected by breathing in the infectious spores or consuming contaminated vegetation or water. Furthermore, anthrax outbreaks in Botswana and its surrounding countries such as Namibia, Zambia, and Zimbabwe are regularly reported.

Anthrax outbreaks can be difficult to eradicate due to the presence of persistent spores in the environment. It would be important to burn corpses as soon as possible to limit the spread of B. anthracis, but this would obviously pose a significant practical challenge given the size of elephants and the time it takes to recover the dead bodies in the wild. Susceptible livestock is often vaccinated to prevent outbreaks but vaccinating the 18,000 elephants in the Okavango Delta to control anthrax would probably be impossible.

Fortunately, tests were carried out and the Botswana Department of Wildlife was able to disprove the anthrax hypotheses. These tests would most likely have been taking samples of blood from dead elephants and observing them under the microscope to look for their distinctive chains of ‘squared’ cells and presence of spores or endospores (spores developing in cells). Both of these features can be seen in Figure 3.

Figure 3: A microscopic image of chains of Bacillus anthracis, the causative agent of anthrax. Vegetative cells are cells that don’t form spores. Endospores are spores inside a spore-forming cell. This image was retrieved from CDC PHIL.


When people live alongside wildlife, conflict is not uncommon. Elephants in the Okavango Delta could have been eating crops or killing the locals’ livestock, so they may have poisoned waterholes or food in response. Managing these conflicts in communities can be difficult, apparently so much that the president of Botswana lifted the ban on hunting elephants, citing the need to protect people from dangerous encounters with animals.

The clusters of deaths seen in Botswana are characteristic of poisoning, but the theory was ultimately dismissed as scavenger animals who feed on corpses should also have been killed by the poison, but they weren’t.

Encephalomyocarditis virus (ECMV)

This virus, a member of the family Picornaviridae alongside poliovirus, infects animals when they ingest contaminated food or water.

Rats are thought to vector the disease, meaning they can carry the pathogen between organisms. Meanwhile, ECMV has a broad host range (i.e. it can infect numerous species) and, as the name suggests, can cause myocarditis (i.e. inflammation of the heart) and encephalitis (i.e. inflammation of the brain) as well as neurological and reproductive disorders. By seriously impairing heart function, ECMV also induces sudden death of infected organisms.

The virus is known to infect elephants and the symptoms associated with it led people to believe it could be killing the elephants in Botswana. Also, the pathogen has previously been known to cause a cluster of deaths in African elephants. Specifically, in 1993, an outbreak of ECMV in the Kruger National Park (South Africa) killed 64 elephants.

Nevertheless, the virus was ruled out as the cause as post-mortem studies didn’t reveal any signs associated with infection or find the virus itself.

Killer microbes

The origin of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic presented solid evidence that emergent pathogens can evolve and become dangerous in a new host. An emergent pathogen is defined as a pathogen that has recently appeared in the population or was already present but is quickly becoming more prevalent and widespread in its geographic range. Although the occurrence of the elephant deaths coincided with the pandemic, no evidence was found indicating that the coronavirus was killing them.

Past events have shown that sudden environmental changes can trigger pathogens to become more harmful than usual (or even deadly). For example, following an extreme heatwave in Kazakhstan, 200,000 Siaga antelopes were killed after the Pasteurella multocida infection caused fatal blood poisoning in them. Under normal conditions, this bacterium is harmless to the animals. Climate change can also expand the habitat range of arthropods which act as a vector for these viruses, leading to the emergence of SARS-CoV-2 in a new area.

Although an unusually heavy rainfall had recently occurred in Southern Africa, the emergence of a new killer microbe would have led to widespread deaths throughout the population, so this hypothesis was eventually eliminated.

Toxins in the water

So far, you’ve read six theories and you’re probably starting to wonder if anyone ever worked out what killed the elephants, but rest assured because this last theory was confirmed as the cause…

70% of the dead elephants were located near waterholes. Months of testing in labs across the world finally identified cyanobacteria, as well as the neurotoxins produced by them, in samples from these waterholes. To our knowledge, the African Elephants were the only species that fell victim to the bacteria, except for an unfortunate horse, as they drink huge amounts of water from the waterholes and spend lots of time bathing and keeping cool.

The killer

Cyanobacteria is a prokaryotic phylum containing single-celled organisms that have a property which is relatively unique amongst bacteria - they can photosynthesise.

Just like plants, they can convert CO2 into biomass using solar energy, with oxygen as a by-product. Because of this incredible capability, cyanobacteria were responsible for oxidation of the Earth’s atmosphere, one of the major stages in the evolution of our planet.

Confusingly, these bacteria are also known as blue-green algae, but they are not actually algae. The term ‘algae’ (plural of alga) refers to photosynthesising eukaryotes, which are not ‘higher plants’ (embryophytes). Cyanobacteria were initially classified as algae because they photosynthesise and have various lifestyle features resembling those of true algae.

However, in the 1960s, new biochemical, genetic, and microscopic evidence indicated that cyanobacteria are actually bacteria and not algae. For example, unlike actual algae, cyanobacteria are susceptible to the antibiotic penicillin, have bacteria-sized ribosomes, and lack organelles such as chloroplasts (found in photosynthesising eukaryotes) and mitochondria (present in almost all eukaryotes but not prokaryotes). Figure 4 illustrates some of the key differences between eukaryotic algae and cyanobacteria.

Figure 4: Some of the main differences between blue-green and green algae. Blue-green algae is another name for cyanobacteria. On the other hand, green algae refer to photosynthesising eukaryotes which aren’t higher plants (embryophytes). At the bottom of each column are cartoon examples of a cyanobacterium and green alga cell. This figure was adapted from

The ‘blue-green’ part of their name comes from their blue-green appearance (Figure 5a), which is a result of the production of a cyan pigment called phycocyanin. Cyanobacteria also produce a range of other pigments, such as green chlorophyll, red phycoerythrin, and yellow-orange carotenoids, meaning that the bacteria can appear in a range of different colours (Figure 5b and 5c). Conditions such as the level of sunlight influence how much of each pigment is produced and therefore whether the bacteria will be blue-green or another colour.

Figure 5: Cyanobacteria, or blue-green bacteria, can be a variety of different colours, due to the presence of light-harvesting photosynthetic pigments. For example, the main photosynthetic pigment, chlorophyll appears green. Other accessory pigments such as carotenoids, which pass sunlight energy onto chlorophyll, can be many different colours. (a) The blue-green appearance of the cyanobacteria in the flask is due to the production of the pigment phytocyanin. This image was obtained from (b) Cyanobacteria and various other bacteria can accumulate to form coloured rings in hot springs, such as the one seen in this image. (c) The variety and quantity of pigments produced by different species of cyanobacteria mean they can be different colours. Factors such as the level of sunlight the bacteria are exposed to can also influence their colour. This image was obtained from

Cyanobacteria don’t cause illness and death in the same way as most other pathogenic bacteria, like Mycobacterium tuberculosis which infects humans and causes tuberculosis. Instead, they produce cyanobacterial blooms, much like algal blooms. Although these can look quite beautiful, as seen in Figure 5b, the dense populations of cells can cause a number of serious problems. The respiration in the bloom requires lots of oxygen, whilst bloom decomposition (when dead organic matter is broken down by decomposers) also depletes oxygen - these factors create a hypoxic or anoxic (meaning low or no oxygen) aquatic environment which suffocates fish and other animals living there.

Cyanobacteria also degrade water quality and produce cyanotoxins that are capable of causing disease in animals that ingest it (such as the elephants in Botswana). As a matter of fact, for millions of years, these toxic blooms have caused mass mortalities in cave lions, dodos, giant turtles, elephants, horses and various other creatures. Besides that, a cyanobacterial bloom in Lake Bogoria, Kenya, killed around 30,000 flamingos in 1999.

The toxins produced by cyanobacteria are called secondary metabolites, meaning they aren’t needed for growth or reproduction of the organism. The most common toxin example is microcystin - this peptide binds and inhibits protein phosphatases in animals. This is a big problem as phosphatases are very important enzymes that are needed in various processes performed by a huge range of cells. Hence, the presence of this toxin can exert damaging effects all across the body, causing microcystin poisoning in humans and animals. To make matters worse, the toxin is very difficult to remove once it is dissolved in water.

Why is all of this important?

Unusual deaths can be a cause for concern in both animals (particularly for those that are already threatened and vulnerable to extinction) and humans. They could indicate the emergence of a new pathogen in a species or geographical region or be an unfortunate case of unlawful killing. Such deaths could even be a result of extreme weather events, which are becoming increasingly common because of climate change. This means that the cause of deaths must be understood so that, if possible, methods to treat and/or control it can be implemented, as well as measures to prevent re-occurrence. In the case of the elephant deaths in Botswana, even though the deaths have stopped, the risk of cyanobacteria to elephants in the area is now known. Waterholes could be tested regularly for cyanobacteria and, if necessary, treated with chemicals to clear toxic blooms in order to prevent unnecessary deaths in the future.

Author: Ambar Khan, BSc Biological Sciences

Disclaimer: All figures created using BioRender are intended solely for educational purposes and not for profit.


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