Abdullah Hassan died Friday in UCSF Benioff Children's Hospital in Oakland, where his father Ali Hassan brought him in the fall to get treatment for a genetic brain disorder.
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Ali Hassan is a U.S. citizen who lives in Stockton, California. He and his wife Shaima Swileh moved to Egypt after marrying in war-torn Yemen in 2016. Swileh is not an American citizen and remained in Egypt while fighting for a visa.
"We are heartbroken. We had to say goodbye to our baby, the light of our lives," Ali Hassan was quoted as saying in the statement published by the council.
Swileh held her son for the first time in the hospital 10 days ago.
A funeral is scheduled for Saturday.
Swileh had been trying to get a visa since 2017, so the family could move to the United States.
Citizens from Yemen and four other mostly Muslim countries, along with North Korea and Venezuela, are restricted from coming to the United States under President Donald Trump' s travel ban.
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When the boy's health worsened, the father went ahead to California in October to get their son help, and Swileh remained in Egypt hoping for a visa. As the couple fought for a waiver, doctors put Abdullah on life support.
"My wife is calling me every day wanting to kiss and hold her son for the one last time," said Ali Hassan, choking up at a news conference earlier this month.
He started losing hope and was considering pulling his son off life support to end his suffering. But then a hospital social worker reached out to the Council on American-Islamic Relations, which sued on Dec. 16, said Basim Elkarra, executive director of the group in Sacramento.
The State Department granted Swileh a waiver the next day.
"With their courage, this family has inspired our nation to confront the realities of Donald Trump's Muslim Ban," said Saad Sweilem, a lawyer with the council who represents the family. "In his short life, Abdullah has been a guiding light for all of us in the fight against xenophobia and family separation."