In March 2016, U.N. officials estimated that the conflict had killed about 50,000 people, and for years, a more accurate death count has been missing as a metric to measure the bloodshed, even as the conflict raged on. Experts say an accurate death toll can be a critical tool for policymakers.

But counting the dead is a challenge in war zones, where many people are displaced and crucial data is hard to come by.

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By comparison, the new estimate puts the death toll from the violence in South Sudan on par with the impact of conflicts such as the war in Syria, where upward of 510,000 people are believed to have died in a significantly larger population.

Gordon Buay, deputy chief of mission at the South Sudanese Embassy in Washington, said he thinks the estimate is “not accurate.” He said he would put the death toll at fewer than 20,000 people.

"If you included disease and everything, it would be less than 20,000," Buay said.

But Francesco Checchi, the lead epidemiologist who worked on the study, said his team’s estimate is conservative. He and other researchers at the London school statistically analyzed mortality data in the country to estimate conflict-related deaths between December 2013 and April 2018.

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They compiled data from humanitarian agencies and media reports, piecing together factors including food security, presence of humanitarian groups and intensity of armed conflict to create a statistical model that predicts mortality by county. At the center of their research were around 200 surveys conducted by humanitarian groups across South Sudan.

Checchi called the process “painstaking.”

In South Sudan, a number of factors, including the dangerous nature of the conflict, have made calculating a death toll through a national survey and interviews with families nearly impossible.

The country broke away from Sudan seven years ago, after decades of deadly conflict that eventually led to shaky independence. But South Sudan soon fell back into war, after a rivalry between President Salva Kiir, from the Dinka ethnic group, and then-Vice President Riek Machar, a Nuer, turned violent.

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The conflict started in Juba, the capital, and spread across the country. Journalists, human rights researchers and humanitarian workers have collected evidence of mass atrocities committed by both sides in the conflict, but rights groups say most attacks on civilians have been carried out by government troops. In some areas, entire villages were said to have been razed. Women were allegedly raped and children burned alive, and some families even reported forced cannibalism.

Checchi’s team took into account assumptions about what the death rate would have been without civil war to find how many excess deaths the conflict has caused. The researchers factored in the reality that many people have fled or were killed in circumstances that might have been exacerbated by the conflict, such as outbreak of disease or malnutrition, he said. South Sudan experienced a man-made famine last year.

A State Department official said the study helps fill a gap in knowledge about the scope of the war in South Sudan.

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“Having good numbers and seeing exactly what the human cost was was an important factual need for us,” the official said.

A U.N. spokesman in New York said in a statement that “the U.N. cannot accurately record the conflict related death toll for a variety of reasons, including a severely curtailed access to conflict areas and hence does not have an official casualty figure for South Sudan.”

More than 14,500 U.N. peacekeepers are deployed to the country, and the mission there cost the United Nations just over $1.1 billion in the last fiscal year.

Yet the violence continues. There have been a number of failed peace agreements since the war began, and another deal was signed this month. But government and rebel forces have clashed since then. There is little hope among observers that the accord will result in tangible change.

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The conflict has prompted a refugee crisis in the region: More than 1 million South Sudanese have fled to neighboring Uganda, and many others crossed into Sudan and Kenya. About two million are displaced within the country.

This refugee exodus became a useful indicator in Checchi’s death toll analysis because, in his experience, he said, “the extent of displacement is a good correlate of how violent things are.”

“People probably will tolerate some violence and will try to stick it out,” he said. But when mass displacement begins to occur, “it usually indicates very severe threats to life.”

Klem Ryan, a former official with the U.N. Mission in South Sudan who later served as the coordinator of the U.N. Panel of Experts on South Sudan, said in an interview that this calculation seems plausible.