The timing could hardly have been worse. As our 23-month-old son was being driven to hospital to be introduced to his new-born brother, he vomited violently in the car and had to be taken home. He was sick for the next 24 hours and then appeared better, albeit a little pale and cranky. We knew there was a bug doing the rounds at his nursery, so thought no more of it.

But within 10 days, the stomach virus that had spoiled the brothers’ introduction had almost certainly travelled up to our toddler’s brain, where it caused inflammation - encephalitis - that could easily have killed him or resulted in brain damage.

It was a glorious Saturday morning last May and the four of us were enjoying the first weekend on our own as a family. On returning from a walk in the park and a trip to the ice-cream van, our son ran into our garden to eat his lollipop. Suddenly we heard a cry as he collapsed, hit his head on the patio and had a convulsion. We called an ambulance.

At first we were not too worried; he had had two febrile (fever) convulsions the year before, both brought on by ear infections. Such convulsions are thought to affect around one in 25 children and generally have no long-term effects, so when yet another ear infection was diagnosed we were reassured and came home from hospital with antibiotics and Calpol.

But the infection had masked the real cause of the seizure. That night he had three more convulsions in bed, despite our desperate efforts to keep him cool, and three more at the Whittington hospital’s A&E department.

I lay on the bed with him as hospital staff wheeled us up from casualty to the children’s ward. From that point he had convulsions about every two hours, day and night. The Whittington gave us a room to ourselves so that the four of us could stay together, and his dad and I took turns to sleep on a camp bed while the other lay next to our son, ready to press the call button as soon as we heard the high-pitched cry that signalled the start of another seizure.

The doctors, unsure of the cause of the seizures, started him on a series of anti-convulsant drugs along with antibiotics and an anti-viral drug. Our new-born slept on a cot in the corner and his four grandparents, who had driven down from Lancashire as soon as they heard the news, took him out for the walks and attention we could not provide.

After four days the seizures stopped and our toddler appeared to be on the mend. We were sent home after three more convulsion-free days with him weak and wobbly on his feet. But at 6am the next day the convulsions started again.

This time they occurred every 90 minutes or so and his condition quickly worsened. Between seizures he was no longer his charming, cheeky self - he mainly cried hysterically or dozed. Several times the doctors had to sedate him to stop cycles of seizures that were coming close together. Even worse, in addition to the two- to three-minute generalised seizures, he started having “drop” seizures, involving a momentary loss of consciousness, for which there were no warnings.

The doctors, who were still not sure whether he was suffering from epilepsy or encephalitis, warned us that conditions where patients had different kinds of seizures were potentially more difficult to control.

Our once active toddler could no longer even hold his head up, let alone walk, and his hands were so shaky that he could barely hold a toy. One thing gave us some reassurance: nearly every time he came round after a seizure he managed to open and shut his mouth like a fish to signal that he wanted to be carried into the playroom, where there was a fishtank. It was a sign that he was still with us.

Meanwhile, the Whittington was still searching for the cause of his illness. He had two lumbar punctures, innumerable blood tests, an MRI scan and several EEGs - brainwave tests. We were told that it was often difficult to find veins in the chubby arms of toddlers and his joints soon became covered in needle marks and bruises like those of a drug addict.

The doctors, who were rushing his results to Great Ormond Street children’s hospital to ensure that everything was being done to diagnose and treat him, were unable to reassure us - but they did their best.

Meanwhile, all the staff in the children’s ward at the Whittington were committed to the idea of family-centred care, making the obvious link between the parents’ state of mind and that of their child.

The nurses made sure we all had enough to eat, chatted to us as they went about their work as if we were the only patients in the busy ward, and helped to take care of our baby. The doctors made sure we were fully informed, taking us and a grandparent to another room away from the hospital bed so we felt free to ask all our dreaded questions, and sending a psychotherapist to talk to us when the strain became too much.

After a fortnight, the seizures stopped and we all held our breath. On our son’s second birthday Clare, one of the ward’s play specialists, helped to decorate his room, and the playroom and medical staff clubbed together to buy him presents. Later in the morning they crowded round to sing happy birthday as we blew out the candles on his Bob the Builder cake.

That afternoon we were transferred to the neurology department of Great Ormond Street for a diagnosis, and a day later we got the news we had not dared hope for. Despite being unable to find a source - as is, apparently, often the case, the specialists were convinced that our son had viral encephalitis and were confident that he would make a full recovery.

Seven months on, his course of anti-convulsant medication has finished. In the first few weeks he slowly grew less shaky, and steadier on his feet, and he has not suffered any more seizures, although he does have a higher than average risk of developing epilepsy. We’re still holding our breath and finding it hard not to panic every time he so much as sneezes, but all in all we are hoping he had a very lucky escape.

According to the specialists at Great Ormond Street, viral encephalitis - which can follow measles - kills around 15% of sufferers and causes brain damage to about 25%. I don’t know about the possible link between autism and the MMR triple vaccine, but I do know about the definite connection between measles and encephalitis. Around one in 1,000 children with measles develops encephalitis; during an outbreak of measles affecting 2,500 people in the Netherlands in 1999, 55 developed pneumonia, five had encephalitis and a further three died.

Each parent has to make his or her own decision on MMR but our son has been vaccinated and we will be doing the same for his brother.

• This article was amended on 18 October 2016 to remove some personal details.