We still don’t know why more than 400 elephants died in Botswana

Just north of Botswana’s world-famous Okavango Delta, it was lush and green as the summer rains tapered off and the air began to cool, but something wasn’t right. Savanna elephants, weighing as much as seven tons each, stumbled and staggered and walked in circles. Their heavy legs weakened as they struggled to take another step. One by one, they collapsed, many falling chest-first.

The first cluster of 44 elephants died in March 2020. By mid-June, conservationists had counted more than 350 carcasses scattered across the remote, roughly 3,000-square-mile region. By the following January, the number of mysterious deaths surpassed 450.

 “There was a very foul smell,” says Davango Martin, the former manager of Kadizora Camp, a tourist lodge in the area. He was driving through the grounds in early May when he first noticed the stench and came across an elephant carcass splayed in a thicket of bush. “It was all rotten and nothing had actually eaten it—only maggots.”

Any loss of African elephants is alarming. Their numbers have plunged from an estimated million in 1979 to approximately 415,000, driven down by decades of ivory poaching, shrinking habitat, and confrontations with humans. Botswana, with some 130,000 elephants, is considered one of their last strongholds, so the mysterious deaths of hundreds made international news. 

In September 2020, under intense international pressure from concerned conservationists, Botswana authorities announced that they’d identified the culprit: cyanobacteria neurotoxins. Poisons released by blue-green algae that bloom in stagnant, nutrient-rich water, cyanobacteria neurotoxins attack the nervous system if ingested. 

However, a 14-month review of documents and interviews with investigators by National Geographic has found that much of the evidence leading to that diagnosis was unreliable—and that the Botswana government missed crucial opportunities to complete a timely and thorough investigation. 

Several outside experts, as well officials at labs that conducted analyses for the government, say tests for various possible causes of death—including cyanobacteria—were inconclusive and the evidence was degraded and mishandled, raising concerns that whatever killed the elephants could emerge as a threat again.

Mystery has shrouded the deaths from the start. The tusks were intact, ruling out poaching. Vultures and other scavengers that fed on some of the carcasses didn’t appear to have died of illness. Nor did the cattle and zebra that drank from the same water holes, making poisoning seem unlikely. And the elephants’ strange behavior didn’t clearly match any known disease. (Read more about the possible causes of death.)

The elephants died in remote areas that were hard to reach, especially during the COVID-19 pandemic, which may partly explain why months passed before Botswana’s Department of Wildlife and National Parks sent a full team to recover tissue samples from the carcasses. But the department ignored or dismissed multiple offers from individuals and organizations to search for fresh carcasses and collect samples quickly, according to experts whose offers for assistance were refused.

“We had the opportunity to thoroughly investigate the cause of these mortalities and manage potential future episodes,” says Erik Verreynne, a wildlife veterinarian and consultant based in Botswana’s capital, Gaborone, who was not involved in the government’s investigation. “But unfortunately we’ve missed it.” 

He and many other veterinarians, scientists, and conservationists have argued that neurotoxins from algal blooms aren’t a logical explanation for elephants’ deaths. The many other animals drinking from the same water holes didn’t die, apart from a single horse. Moreover, the earliest deaths occurred during the rainy season when flowing water usually washes away blue-green algae. And why were some elephants’ bodies found on floodplains, where cyanobacteria typically don’t thrive? 

Mmadi Reuben, the wildlife department’s principal veterinarian, told National Geographic in an email that government investigators didn’t rely solely on tissue samples from the elephants and water samples from water holes; rather, they pieced together information from lab results, symptoms, genetic analysis, environmental factors, the distribution of various diseases, and more. The government also says it was able to reverse the neurological symptoms of one sick elephant using a drug that acts on the nervous system and is commonly used to immobilize animals, suggesting neurotoxicity was involved.  

“Diagnosis of such a complex scenario should never be thought of as something that is always determined by one laboratory scientist using one set of findings,” Reuben said. It requires “investigation where different parts of the jigsaw are put together until a clearer picture emerges.”

While cyanobacteria neurotoxins may have been the cause of death, most outside experts interviewed say the evidence is far from conclusive. “I would consider it possibly consistent with a clinical, but not a confirmed diagnosis,” says Val Beasley, a professor emeritus of veterinary, wildlife, and ecological toxicology at the University of Illinois Urbana-Champaign, who was not involved in the investigation. 

What if the cause was a new cyanobacteria toxin that scientists have not yet identified? Or multiple toxins acting in concert in an unexpected way? What if the killer was an unknown contagious disease? 

In the absence of definitive proof, skeptical scientists say it’s essential to keep looking for answers. Failing to do so could have fatal repercussions—not just for elephants, but for all animal wildlife in and around the region. 

“If they had more knowledge and more awareness, they might be able to prevent it not only in elephants, but in other valued wildlife and in domestic animals and human exposures as well,” Beasley says. 

Collecting and analyzing evidence

Determining the cause of mass animal die-offs is notoriously difficult, says Christine Gosden, a medical geneticist at the University of Liverpool, in the U.K., who was not involved in the Botswana investigation. She noted that it took the United States more than 25 years, huge sums of money, and collaborations with international experts for scientists to conclude that bald eagles were dying from a previously unidentified strain of cyanobacteria neurotoxins.

To establish the cause of the elephants’ death, investigators collected and analyzed evidence, including tissue from the organs of stricken animals, water from nearby sources, and soil at the bottom of water holes, where cyanobacteria can sometimes be found.

Investigators in Botswana—with few financial resources, challenging travel conditions, and limited in-country expertise—were at a disadvantage from the start. By mid-May 2020, the wildlife department’s regional team had surveyed carcasses and taken samples, but the department didn’t send its primary, Gaborone-based team, led by Reuben, until about six weeks later.

By then, many of the bodies were decomposing, and identifying the fresher carcasses from an aircraft was difficult. “The majority of the samples collected in the field were not of the ideal quality—they were old,” Reuben acknowledges, but he says they were of “sufficient quality” to carry out specific tests.

Kabelo Senyatso, the department’s current director, who was not in charge when the die-off occurred, says government veterinarians in the region were monitoring the situation and only called upon the team from the capital when they felt they needed assistance.

But Joseph Okori, who served as the wildlife department’s chief veterinarian between 2005 and 2009, is one of a number of experts who suspects senior officials only started taking the situation seriously after the world’s attention was focused on hundreds of deaths in Botswana.

Offers of help ignored or declined

Elephants Without Borders, a Botswana-based conservation group, sent early reports about the deaths to the wildlife department, including GPS coordinates and photographs of elephant carcasses. The reports show that the organization offered to bring wildlife department staff to the sites, to fund and conduct an aerial survey of the area, and to help remove tusks from the bodies so they wouldn’t fall into the hands of ivory traffickers. But the department didn’t respond, says Keith Lindsay, a researcher at the Amboseli Trust for Elephants, a nonprofit research organization based in Kenya, who collaborates with Elephant Without Borders.

Botswana’s government has a tense relationship with Elephants Without Borders, which critics have accused of releasing exaggerated data about elephant deaths for political ends. But Niall McCann, director of conservation at National Park Rescue, a conservation group working to protect wildlife across Africa's national parks, says secrecy and a reluctance to accept outside assistance have long been hallmarks of the government. Several experts declined to comment on the record for this story out of concern that criticizing the government’s handling of the investigation could result in their research permits being rescinded.

Another offer of help came from the Botswana Wildlife Producers Association, a group representing game farmers and professional hunters. The association proposed sending a team of local veterinarians and ecologists to assist in taking samples and preparing them for testing. The wildlife department declined, saying that things were under control, according to Verreynne, who’s a member of the association. 

Okori, a former chief veterinarian for the wildlife department, says he also offered his help. He contacted Cyril Taolo, then the acting director of the wildlife department, and says he was turned down. Taolo, who is no longer with the department, declined to comment.

“That’s the sad thing,” says Verreynne. “We were never able to actually investigate this properly.”

The wildlife department’s current director, Senyatso, declined to comment on why the department did not accept these offers, but says it did accept others. One came from Ecoexist, a Botswana-based elephant conservation group, which surveyed the region by air throughout July 2020 to look for fresh carcasses. 

Botswana’s environment ministry announced in late July that the survey turned up no new elephant deaths, though the full report was never made public. Ecoexist directed questions to the wildlife department. Senyatso declined to share the report or detail its findings, saying it was confidential. 

Mishaps and miscommunications

Early tests ruled out anthrax, a potentially deadly disease caused by a bacterium that occurs naturally in soil. To test other theories—including viral diseases, bacterial infections, and various kinds of toxins—the government turned to international experts with specialized equipment. (Read about how anthrax may have killed a hundred hippos in 2017.)

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To coordinate the distribution and testing of samples, the wildlife department contacted Kathleen Alexander, a wildlife conservation professor at Virginia Tech in the U.S. Alexander co-founded CARACAL, a research institute in Botswana that has collaborated with the government in the past. She consulted with experts abroad and, through CARACAL, organized how samples would be shipped, tested, and analyzed. 

Alexander supports the government’s investigation and conclusion, saying she hasn’t seen “any other government invest so much in human resources and money, ensuring that a mass mortality event in wildlife is so completely investigated.”

The laboratories involved in the investigation, however, acknowledge that the quality and quantity of the samples they received was low.

Chris Foggin, a veterinarian at the Victoria Falls Wildlife Trust, a Zimbabwe-based conservation group, received tissue for analysis and said some samples were of such poor quality as to be “useless.” Others, from a symptomatic elephant that was euthanized, were better, but he’s uncertain how representative of the overall die-off its samples were. Foggin remains skeptical about the government’s official diagnosis.

Johan Steyl, a veterinary pathologist at the University of Pretoria, in South Africa, also received tissue samples. While he declined to discuss details, citing client confidentiality, the tests ruled out cyanobacteria toxins that affect the liver, according to a scientist with knowledge of his findings who preferred to remain anonymous because they were not involved in the investigation. These tests also ruled out encephalomyocarditis, a viral infection thought to be spread by rodents that killed 64 elephants in South Africa’s Kruger National Park early 1990s, according to Roy Bengis, former chief state veterinarian of the park. 

Neither lab found direct evidence that cyanobacteria neurotoxins affected the elephants. That would require analyzing the dead elephants’ brain tissue for neurological damage, the University of Liverpool’s Gosden says, but “brain turns to liquid in temperatures in Botswana very quickly.” 

Without brain tissue to analyze, testing water and soil for cyanobacteria and the toxins they produce is a logical next step. 

Alexander and CARACAL sent about 40 such samples to Food and Drug Assurance Laboratories, also in Pretoria. But a series of mishaps ensued: A few of the glass containers holding samples broke during transit, and some weren’t properly labeled with the source of each sample, according to Azel Swemmer, the laboratories’ technical director. Furthermore, there was only enough funding to test about a quarter of samples, she says. 

The effort turned out to be largely futile: Alexander’s leading theory was that anatoxin-a, a potent and fast-acting neurotoxin produced by cyanobacteria, was responsible for the deaths, Swemmer says. But FDA Laboratories doesn’t have the ability to test for this type of cyanobacteria neurotoxin, a point that appears to have been lost amid miscommunication, according to emails between CARACAL and the facility reviewed by National Geographic.

Still, some samples indicated the presence of other cyanobacteria toxins. Swemmer didn’t elaborate on specific results, citing client confidentiality. She cautioned, however, that it would be difficult to draw firm conclusions, considering the small number of samples and the lack of rigor with which they were handled.

Alexander disagrees with Swemmer’s assessment. “Samples were transported correctly and shipped as fast as possible, activities that are particularly difficult in remote locations during a pandemic,” she says. 

New evidence, but uncertainty remains

Even without evidence from brain tissue and water samples showing the presence of cyanobacteria neurotoxins, Reuben says officials eliminated other possibilities. He said the elephants’ dizziness, fatigue, and difficulty walking were strong indicators that neurotoxins were the cause of death.

Still, he acknowledges that there are unanswered questions. The government is looking more closely at “many of the questions which were generated during the investigation,” he says, including why it was only elephants that died.

At Queen’s University Belfast, in Northern Ireland, a multidisciplinary team of researchers received a grant in October 2020 to work with the wildlife department and local researchers to try to determine the cause. The project ended last December, and Eric Morgan, a veterinary epidemiologist and leader of the initiative, says the results were inconclusive. 

The fact that elephants stopped dying once water holes dried up suggests a waterborne pathogen. Further support comes from a satellite-based analysis of the region, published in November 2021, showing an unprecedented spike in cyanobacteria blooms in the Okavango region during the months the elephants were dying. 

But the satellite analysis doesn’t show the strain of cyanobacteria present, which toxins—if any—they released, or how much of them elephants may have been exposed to, says Lindsay, the elephant researcher.

Still, it’s some of the most compelling evidence that cyanobacteria likely was involved in the deaths, says Paul Oberholster, a cyanobacteria expert at the University of the Free State, in Bloemfontein, South Africa, who was not involved in the investigation. 

The elephants died after a period of “lake turnover”—the seasonal mixing of water bodies caused by changes in wind and temperature. Winds blowing into Botswana around October must have stirred up water holes loaded with animal waste, creating the perfect environment for blue-green algae to thrive, Oberholster says. As temperatures cooled in March, cyanobacteria started breaking down, releasing toxins, and killing the elephants who drank from these sources.

Elephants may have been uniquely exposed, he says, because broken-down algae may stay suspended in water from mixing or sink to depths where elephants draw water when they drink. This aligns with what Botswana’s wildlife department initially theorized—that elephants, unlike other animals, drink from below the surface, where they can ingest the neurotoxins.

Elephants may occasionally suck up water from deeper areas when they splash and roll around, Lindsey counters, but not when drinking. Besides, he says, water holes don’t typically experience the same type of seasonal mixing that lakes and other larger bodies of water do. 

Early warning

If cyanobacteria are the cause, pinpointing the exact toxin they released isn’t critical for preventing future deaths, Oberholster says. Regardless, cyanobacteria-infested areas should be fenced off and monitored regularly, particularly during periods of lake turnover.

But the huge size of the Okavango Delta makes monitoring every water source exceptionally difficult. It’s hard to prepare for such complex scenarios, but Alexander advises further study to forecast possible sites of algal blooms and training for local experts who could respond more quickly. (Learn about the ambitious mission to save the Okavango Delta.)

Several experts interviewed remain worried that another die-off could happen again at any time, especially if cyanobacteria neurotoxins were the culprit. Warming temperatures, severe droughts, and intensive use of fertilizers have made algal blooms more likely to flourish worldwide. 

Beasley says the government should be prepared, including developing active relationships with several toxicology labs and investing in technologies—including drones, helicopters, and specialized tools, for example, to break into an elephant skull.

Okori and others say that building a multidisciplinary team of experts who can come together quickly during emergencies is crucial too. 

“Especially when you get the one or two deaths—those need to be monitored, because they are indicators of signs of change within the environment,” Okori says. Acting only when the scale of the mortalities is huge, as he suspects happened in this situation, is a dangerous strategy. 

It’s “a message not only for Botswana,” he says. “It’s a message for all of us.”