FREI MIGUELINHO, Brazil — On Tuesdays, 18-month-old Joaquim Santos spends an hour sitting by himself in a corner of a special needs classroom in this small city in northeast Brazil, one of the country’s poorest regions and one hit hard by the Zika virus. Two harried teachers look on as other toddlers play around Joaquim, who has severe developmental delays after being born with a small head.

As limited as Joaquim is in the early education classroom, his family and doctors say he is lucky to be there. “When Joaquim was born, I thought he was going to be in a vegetative state forever,” said his mother, Maria de Fatima Santos, who must take the boy to therapy sessions and medical appointments most other days of the week. “I thought my life was going to be in a hospital.”

Three years ago, an outbreak of the Zika virus in Brazil’s impoverished northeast led to thousands of babies being born with a birth defect called microcephaly.

The virus is spread by mosquito, and scientists determined that it could lead to congenital defects in fetuses of mothers who were infected during pregnancy.

Today, some of the children born during the outbreak are trying school for the first time — in limited capacities — while others have died or are struggling to survive, hindered by health and developmental problems.

Dr. Epitacio Rolim, of the Getulio Vargas Hospital in Recife, where many children with Zika-related birth defects are treated, said there are still myriad unknowns.

“How much they will learn or live, unfortunately, is a huge question mark,” said Rolim, who during a recent afternoon spent hours injecting babies with Botox to ease muscle spasms.

Beyond developmental delays, around 40 percent of the children with microcephaly treated at the hospital started showing new physical problems by the time they reached their first birthdays, including dislocated hips, which needed to be repaired surgically. “I only know of four who are walking,” said Rolim.

Zika began spreading in Latin America’s largest nation in April 2015 and exploded in 2016, with more than 260,000 cases of virus that year, according to the Health Ministry. In 2015, there were 960 confirmed cases of microcephaly and just over 1,800 the next year, the majority in the northeast.

Then, thanks to what scientists call “herd immunity” in hard-hit areas and public awareness campaigns, the number of cases of Zika and microcephaly fell.

In 2017, there were fewer than 18,000 Zika cases and fewer than 300 children born with microcephaly. This year, Brazil has seen 2,200 cases of Zika and 20 cases of microcephaly and other developmental abnormalities.

For doctors, researchers and therapists, the Brazilian toddlers born with microcephaly a few years ago represent by far the largest pool in the world for them to observe and learn from.

Seeing the children in school helps provide a window into the challenges children with microcephaly may face as they grow, but the institutions receiving them are often ill-equipped to meet their needs.