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Sudanese people who fled the conflict in Sudan's Darfur region and were previously internally displaced in Sudan set up makeshift shelters near the border between Sudan and Chad, in Borota, Chad, on May 13.ZOHRA BENSEMRA/Reuters

Fighters and smugglers are preying on the nearly half-million refugees who have fled from Sudan’s conflict, perpetrating horrific acts of sexual violence on a growing number of women and children before they can reach safety, the United Nations refugee agency says.

More than 470,000 people have crossed from Sudan into neighbouring countries in the two months since the battles erupted, and many have been raped or sexually exploited along the way, often at checkpoints or on human trafficking routes, the UNHCR said in a report on Thursday.

In total, more than 2.1 million people have been forced to abandon their homes and seek shelter inside or outside Sudan as a result of the daily fighting between the Sudanese military and the paramilitary Rapid Support Forces, and the number of refugees is increasing daily. Thousands of Sudanese have been killed or injured.

The sexual attacks are being reported to UN protection teams by refugees arriving in Egypt, Chad, South Sudan and Central African Republic.

“In addition to lasting physical, sexual, reproductive and mental-health consequences, some survivors have now arrived in neighbouring countries pregnant as a result of rape,” UNHCR assistant high commissioner for protection Gillian Triggs said in a statement.

Although women and girls are disproportionally affected, boys and men are also reported to be among the survivors, she said. “Adolescent girls are facing an increased risk of child marriage as some families are forced to resort to this harmful practice – reportedly in an attempt to ‘shield’ them from further risks of sexual violence, assault or exploitation.”

Smuggling networks existed before the latest conflict, but human trafficking risks are “clearly on the rise” and some smugglers are extorting huge fees from the desperate refugees on often dangerous routes, Ms. Triggs said.

For those left behind, there is a constant threat of death or injury from the fighting, which includes artillery shelling, air strikes and gun battles. At just one hospital, Bashair Teaching Hospital in Khartoum, nearly 1,170 patients have needed emergency treatment in the past five weeks, including 906 victims of violent trauma, according to the humanitarian group Médecins sans frontières (Doctors Without Borders).

Gunshot wounds and blast wounds from shelling or air strikes are among the most common injuries at the hospital, and a growing number of the victims are children, it said in a report on Thursday.

“This is a profoundly chaotic and violent situation that almost defies comparison,” MSF emergency co-ordinator Raphael Veicht said in the report. “I cannot recall any time in recent years when MSF has treated anything like the number of trauma cases or done as many major surgeries as we have done in Khartoum.”

In addition to the injuries caused by fighting, the agency reported a rise in violence from crime and lawlessness in Khartoum. The Sudanese capital, a city of five million people, had been stable and densely populated before the clashes erupted. But in recent weeks, Bashair hospital treated 183 people for stab wounds and another 62 for assault injuries, MSF said.

The agency said it urgently needs to bring more staff into Sudan because the fighting and violence are showing no signs of ending.

Repeated attempts at negotiating ceasefires in recent weeks have all failed, and mediators have suspended talks between the two sides in Jeddah, Saudi Arabia.

Much of the worst fighting is in Darfur, the western region of Sudan where the Rapid Support Forces had its origins in Arab militias that began fighting against Darfuri rebels in 2003. At the time, the RSF was known as the Janjaweed and was supplied with weapons by the Sudanese government. The violence killed an estimated 300,000 people and led to an investigation by the International Criminal Court, which filed charges of genocide and other war crimes against Omar al-Bashir, president of Sudan at the time.

In the latest fighting, activists say that about 1,100 people have been killed in the city of El Geneina, the capital of West Darfur. Videos on social media showed thousands of civilians on foot as they fled El Geneina and headed to the border of neighbouring Chad. Nearly nine million people are in urgent need of protection and humanitarian aid in Darfur, the UN says.

One of the latest victims is West Darfur state governor Khamis Abbaker, who was killed on Wednesday, just hours after giving a television interview in which he accused the RSF and its militia allies of committing genocide in the region.

The UN transition assistance mission in Sudan condemned the killing of the governor as a “heinous act.” It cited “compelling eyewitness accounts” that blamed the RSF and Arab militias for the killing, although the RSF denied it.

The UN emergency relief co-ordinator, Martin Griffiths, said the people of Darfur are trapped in a living nightmare. “Babies dying in hospitals where they were being treated; children and mothers suffering from severe malnutrition; camps for displaced persons burned to the ground; girls raped; schools closed; and families eating leaves to survive,” he said in a statement on Thursday, recounting the reports he has received.

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