Coronavirus cases among migrant children in U.S. government custody have surged in recent days after an outbreak in one Chicago shelter infected more than three dozen minors.

Heartland Alliance, a non-profit that oversees shelters in the Chicago area for unaccompanied migrant children, reported on Tuesday at least 37 confirmed cases of coronavirus among the minors it cares for, according to Mailee Garcia, a spokeswoman for the group. Before the outbreak, the Office of Refugee Resettlement, the government agency with custody of these minors, had confirmed six positive cases among children at three facilities in New York, the epicenter of the pandemic in the U.S.

The 37 infected children at the shelter in Chicago's South Side make up more than half of the 69 minors currently housed at the three facilities Heartland Alliance is currently operating. According to Garcia, 28 of the infected children were asymptomatic at the time of testing. She said the group is "operating under the assumption" that more cases will arise since officials have been working to test all the children in their custody.

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"At the first indication of COVID-19 symptoms in our program, we aggressively moved to obtain testing for all of the children in our care — even those who are asymptomatic — which goes even beyond the CDC recommendations," Garcia said in a statement. "We did this to ensure the highest quality of care to our participants, and to safeguard our staff as well."

Garcia said the prognosis for all the children is "very good." She said Heartland Alliance has instituted "robust policies" to curb the spread of the virus within its facilities, including isolating symptomatic children, expanding social distancing measures, providing protective equipment to staff and rotating employees, who are being screened before their shifts. The group is also hiring more nurses and asking several staff to stay at home.

In this Sept. 24, 2019, photo, a migrant girl in U.S. government custody holds a card. Wilfredo Lee / AP

ProPublica first reported on Monday that at least 19 minors and two staff members at the Heartland Alliance shelter in Chicago's South Side had tested positive for coronavirus. Garcia said Tuesday there has not been an increase in cases among staff.

In a statement on Tuesday, the Office of Refugee Resettlement reported 21 new cases of coronavirus among children housed at two facilities in Texas and one in Illinois, presumably the Chicago shelter with the outbreak. But it's unclear how many minors in the agency's custody have tested positive since the agency has not yet reported all the 37 positive test results announced by Heartland Alliance. An agency official said there could be a delay in headquarters compiling and announcing all cases.

The number of children in the agency's custody had dwindled to 2,500 as releases to sponsors, who tend to be family members in the U.S., have continued during the pandemic.

The refugee agency has also been receiving very few children from Customs and Border Protection officials, who are typically the first to encounter unaccompanied migrant minors at the U.S. southern border. The sharp drop has come as border officials have expelled thousands of unauthorized migrants, including children who arrive at the border alone, by invoking expansive turn-back powers under a public health order they say is designed to curb spread of the coronavirus.

On Monday, the Office of Refugee Resettlement received just one referral of an unaccompanied migrant minor from border agents, an agency official told CBS News.

In addition to the cases among unaccompanied migrant minors in U.S. custody, more than 70 immigrant adults in U.S. Immigration and Customs Enforcement (ICE) custody have also tested positive. ICE oversees the long-term detention of adults and some families with children. The agency has yet to report coronavirus cases at its three family detention centers in Texas and Pennsylvania.

The refugee office also said Tuesday that at least 53 personnel at facilities for minors in the agency's custody across seven states had self-reported testing positive for coronavirus. The agency has said it has taken all the necessary steps to safeguard the health of children and staff. Officials are no longer placing minors in facilities in California, New York and Washington.

To avoid air travel during the pandemic, the refugee agency is prioritizing placing migrant children in local facilities after receiving them from border officials. It has also issued guidance requiring that migrant children in its custody undergo mandatory temperature checks twice day. If a child has a temperature higher than 100 degrees, the shelters have to notify the government.

But advocates have said children in government custody can't properly shield themselves from the virus in congregate settings with other minors. Citing the pandemic, they have been asking a federal judge in California to order the administration to promptly release all migrant children in its custody.