Reports that Italian PhD student Giulio Regeni was tortured before his death in Cairo stem from a "misunderstanding," the Egyptian prosecutor leading the investigation told Italian newspaper La Repubblica.

Regeni, 28, disappeared on January 25 on the way to meet friends at a restaurant. The date coincided with the fifth anniversary of the 2011 uprising that ousted longtime dictator Hosny Mubarak and was marked by extreme security measures.

His body was found on February 3, and Egyptian authorities initially blamed the death on a road accident. The Italian government later said it showed clear signs of torture, such as missing nails and cut off ears.

"A misunderstanding has arisen about the nails and the damaged ears: it was Egyptian coroners who removed both to carry out in-depth exams," Giza Prosecutor Hassam Nassar said in an interview published Wednesday.

Nassar said nail samples were taken to ascertain whether Regeni fought against his aggressors. The prosecutor acknowledged that there were also burn marks on his left shoulder, but added: "Our doctors could not tell us what may have been their cause."

The prosecutor's account clashed with a statement from Italy's ambassador to Cairo, Maurizio Massari, who said he saw Regeni's body a few hours after news of its discovery, in all likelihood before any autopsy had been carried out.

"Seeing it was devastating for me. It showed clear signs of beatings and torture. I noticed wounds, bruises and burn marks. There is no doubt that the man was severely beaten and tortured," the diplomat said in a February 6 interview with Corriere della Sera.

Nassar described the death of Regeni as "a murder with no motive," and said he had found "not a single lead" that could solve the case. But he added that "there are no reasons whatsoever suggesting that Giulio may have had any problem with the people he knew and met here in Egypt."

Amid suggestions that Regeni got in trouble for having links with trade unions and other opposition groups, his death has attracted renewed scrutiny of Egypt's rights record under President Abdel-Fattah al-Sissi, a former army chief.

The affair has also strained close economic and political ties between Rome and Cairo. Egypt is a key player in the Libyan crisis, which Italy is keen to solve, while Italian energy company Eni last year discovered a huge offshore gas field in Egyptian waters.

In a separate report, a friend of the victim was quoted as saying that Egyptian police had been looking for Regeni since December, after he interviewed some people at a non-governmental organization's meeting on trade union rights.

The friend - who has returned to Italy and is wanted for questioning by Nassar - said Regeni noticed a girl taking pictures of him during the assembly, and speculated about her about being a police informant. "We talked about it a lot," the unnamed witness said.

Arturo Scotto from the opposition Italian Left party reacted to the La Repubblica revelations by calling for the withdrawal of ambassador Massari from Cairo. He described Egypt's apparent reluctance to pursue the case as a "systematic insult."

On Sunday, Eni Chief Executive Claudio Descalzi urged the Egyptian government to "give clarity as soon as possible" about the murder. "It is not our role to investigate, but everybody has a right to know [what happened]," Descalzi said to Il Messaggero newspaper.

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