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Qatar said it had identified the parents of the boy, who was found in the garbage at Doha airport last month.
The prosecution said that a woman from an “Asian country” fled abroad after disposing of the baby and noted that efforts were being made to extradite her.
It added that a DNA test confirmed that the father was of Asian nationality.
The prosecution said officials have also been charged in connection with forced vaginal examinations carried out by women traveling during the initial search for the mother.
This sparked international outrage after a group of women who had traveled to Sydney, including citizens of Australia, Great Britain and New Zealand, complained that they had been tested for evidence that they had recently given birth.
The Qatari government said the accident began after a newborn girl was found, in a plastic bag in a garbage can, in the departure hall of Hamad International Airport on October 2.
The discovery prompted an immediate search for parents, including aboard 10 aircraft.
Several women said, on board a Qatar Airways plane bound for Sydney, that they were ordered to disembark, taken to ambulances on the airport runway and asked to remove their underwear for an examination.
The women said they did not receive any information from officials and did not have the opportunity to give informed consent.
Australian Prime Minister Scott Morrison described the incident as “horrible” and “unacceptable”.
As for his Qatari counterpart, Khalid bin Khalifa Al Thani, he said that customary procedures had been violated and expressed his “sincere apology for what some of the female travelers have been through.”
And the Qatari Prosecutor’s Office announced, in an official statement on Monday, that it has filed criminal charges against several employees working in the airport’s security department.
A statement said the agents had violated the law by “summoning a medical team of women to carry out checks on some of the passengers,” and face a three-year prison sentence if convicted.
The prosecution said that it accused the girl’s mother, who survived the ordeal, of attempting to murder, and that she “takes the appropriate legal measures within the framework of international judicial cooperation to arrest the fugitive”, who faces up to 15 years imprisonment if extradited and convicted.
The statement said: “Investigations revealed that the mother of the baby, who has the nationality of an Asian country, had a relationship with another person who had the nationality of an Asian country.”
She added: “The baby’s father admitted he was in a relationship with the baby’s mother and that she sent him a message and a photo of the newborn baby immediately after his birth.”
According to the statement, the message “included her saying that (she) abandoned the baby she gave birth and fled to her country.”
The father is known to still be in Qatar. It is unclear if he faces any charges.
The Qatari authorities take care of the girl.