The call that would change Celina Maria Turchi Martelli’s life came out of the blue one day last September. It was a friend from the ministry of health in central Brazil. Turchi is well known there; it was where she grew up and spent most of her career as a doctor in infectious diseases and then epidemiology before moving 10 years ago to Recife, more than a thousand miles away in the north-eastern state of Pernambuco. The ministry was hearing reports of surprising numbers of babies born in Recife with small heads – a condition called microcephaly. Would Turchi mind taking a look?

Happy to help, Turchi set off. What she found was devastating.

“I went to three hospitals and a lab and as soon as I saw them, I couldn’t stop thinking about them,” she says. “I had not seen anything like it. And they all looked alike.”

The brain damage these babies had suffered was obvious at a glance. “My grandma could diagnose it,” Turchi says. Conventional microcephaly babies have a small head relative to their body. These had a head that was squashed and deformed at the crown, as if part of it was missing. “It’s as if the cortex of the brain is so seriously damaged that the brain shrinks very quickly,” says Jailson de Barros Correia, paediatrician, professor of infectious diseases and health chief of Recife. “It seems to occur in a very fast way. These children have redundant skin – small heads with redundant skin.”

It is distressing, Correia says. And it is only when you see these babies that you understand why the surge in such births caused real alarm in Pernambuco, and the neighbouring states of Bahia and Paraíba. There was consternation among the obstetricians, paediatricians and neurologists – among all those who deal with babies and brain damage. Anxious WhatsApp messages began to circulate about cases and numbers. In any year there might be four or five microcephaly cases in Recife. By October, they were seeing that many brain-damaged babies in a week. Microcephaly cases may well have been missed in the past – but it is unlikely babies with this distinctive pattern of deformity would have been overlooked.

A baby with microcephaly in Recife earlier this year. Photograph: Barcroft Media/Clara Gouvêa

“We were astonished,” Turchi says. “I heard the same thing from all the doctors: ‘I have never seen anything like this.’” Oddly, the babies in Recife were of normal weight and most had good Apgar scores, measuring heart rate, breathing, muscle tone, reflexes and skin colour at birth. They were able to breastfeed. But their chances of normal development with the sort of calcifications of the brain that were seen on CT scans were zero. Some had spasticity. Many were irritable. “From the beginning, the children would scream and scream and scream. It is very hard for families coping with that,” Turchi says.

The Brazilian doctors quickly understood they were on the frontline of a potential global health crisis. “It is a threat to everybody. It is a societal threat,” Turchi says. “Every time I would go to a hospital or lab, I would see people working to exhaustion. Young people and very senior doctors. They were really marvellous in trying to understand the problem and be collaborative.” She has similar praise for the health authority in Recife and the ministry of health in Brasilia.

As for Turchi herself, she says that for months she could hardly breathe.

More damaged babies were being picked up during routine scans of pregnant women. It was Dr Adriana Melo, a researcher in foetal medicine in Campina Grande, capital of the next state, Paraíba, who drew off amniotic fluid from the wombs of two of these women and sent it for testing in Rio de Janeiro. The lab found Zika – a virus new to Latin America, which had been sweeping through the north-east region. It had crossed the placenta, which protects the baby from most infections, including HIV. Later, others found Zika could destroy brain tissue in the lab. Then there was evidence it could be sexually transmitted.

“If I was a film-maker offering a scenario like this, people would say I was mad – a congenital disease transmitted by a vector that is everywhere and could also be sexually transmitted?” Turchi says. “From the first moment, I had this feeling of being in a horror movie and having no cure for it.”

The armed forces have been deployed under a national mobilisation against the Aedes aegypti mosquito. Photograph: Evaristo Sa/AFP/Getty Images

The World Health Organisation now says it is “highly likely” that Zika virus is causing microcephaly in babies. José Paulo Pereiro Jr, head of obstetrics at the Instituto Fernandes Figueira Fiocruz in Rio de Janeiro, thinks the time for any doubt is over. “I don’t know what people are waiting for,” he says. “What more evidence do we need?”

His own study, carried out with the University of California, Los Angeles, and published recently by the New England Journal of Medicine, suggests what is happening to Zika-infected pregnant women is even worse than was first feared. From mid-December he has been recruiting, testing and monitoring pregnant women in Rio with the rash typical of Zika infection. The numbers are still small, but out of 42 willing to have an ultrasound (28 refused), 12 were carrying babies with a range of abnormalities. More common than a small head was poor growth in the womb and a serious reduction in the amount of amniotic fluid around the baby. Two women have had stillbirths since and six of the babies have been born – three were normal, one had severe brain injuries and the other two were underweight.

“Microcephaly is an important abnormality but not the only one,” Pereiro says. “If you don’t see microcephaly in the foetus [during a scan], you can have other problems such as placental insufficiency in the second or third trimester.” That can mean the baby is not getting all the nutrients or oxygen it needs.

He does not know how many pregnant women with Zika are going to have brain-damaged babies. The study is as yet too small. “When we have 100 or 200, we can maybe answer the question,” he says. But among the 42 women – infected at various stages of pregnancy – they found seven foetuses with serious brain injuries caused by calcifications or microcephaly. “That is 18%. This is near the real number today,” he says. “I don’t believe it will increase. Maybe it will decrease.” But if the true figure turns out to be 10% or even 1%, as a study from French Polynesia of pregnant women with Zika in the first three months or pregnancy suggested, many thousands of babies could be damaged in Brazil, which has 3 million births a year.

Linha do Tiro favela lacks proper sanitation. Photograph: Sarah Boseley/The Guardian

Scientists have not yet declared Zika the cause of microcephaly only because they can’t find the virus in the babies when they are born, says Laura Rodrigues, professor of infectious disease epidemiology at the London School of Hygiene and Tropical Medicine, who now is spending a lot of time in Recife. “The reason people are hesitant is because you don’t find lots of Zika virus in the babies with microcephaly – it is very rare to find. In rubella, for example, the babies are still excreting the virus when they are born, but not in Zika.

“I think it is very likely that the infection doesn’t last until birth. I think they have an infection, the brain gets damaged, the cortex gets damaged by the infection, and then the infection dies out.”

She has no doubt. The study she is working on with Turchi and others, following 200 babies with microcephaly and 400 others without, will prove it, she believes. “The answer is going to be yes – a very big yes.”

Zika is also linked to small numbers of adult cases of Guillain-Barré syndrome, a muscle-weakening disease of the nervous system that has occurred in every country the virus has hit. If this is part of a pattern, the Guillan-Barré cases that have been seen in Colombia, Venezuela and other Latin American nations could be followed by the births of many brain-damaged babies.

“It is very, very serious,” says Paulo Gadelha, director of Fiocruz (the Oswaldo Cruz Foundation) in Rio, which is Brazil’s main state-funded scientific institution. “This is a global threat in terms of public health.”

Zika is still a big enigma, he says, but “I think it is very clearly established that it causes not only microcephaly but also damage in terms of [other] congenital abnormalities.” And if – as is suspected – it is transmitted by the Aedes aegypti mosquito, Zika could spread into the southern states of the US, and Europe.

Two thirds of the 6,906 suspect Brazilian cases reported between 22 October and 2 April this year have yet to be fully investigated, but more than a third (36%) are confirmed as linked to Zika. And yet in Brazil by far the largest number are still in the north-east – 303 in Pernambuco, 194 in Bahia and many in neighbouring states, out of the 1,046 in total linked to infection in the womb across Brazil. Scientists warn that the arrival of the virus was first identified in the north-east, so the rest of the country is yet to catch up.

Graffiti in Recife reads: ‘We all have a right to live’. Photograph: Ueslei Marcelino/Reuters

But nobody is ruling out co-factors – something else about the poorest region of Brazil that might cause it to be especially hard-hit. It is possible that previous infection with another virus is involved – more than 90% of the women with microcephaly babies have had dengue. Most live without a proper water supply or sanitation.

In a favela in Linha do Tiro, like so many other slums that have crept up the hillsides on the edge of the official city of Recife, the more sturdily built houses at the bottom of the valley give way to one-room shacks with crumbling walls and tin roofs higher up. Up steep rubble tracks, past black plastic sacking pinning the hillside in place against landslides when it rains, is the dilapidated habitation that 16-year-old Bruna Figueiredo shares with three siblings, her mum and occasionally her mum’s boyfriend and his son.

They know about Zika because the city has sent health officials to every home warning families to protect themselves against the Aedes aegypti mosquito that spreads not only Zika but also dengue and chikungunya in the area. Everyone has had dengue, which has been endemic for the past 30 years. Chikungunya, a very painful disease attacking the joints, has now taken off. Recife had 30 cases notified in 2015 but nearly 2,000 so far this year. Figueiredo spent a day in hospital with chikungunya two months ago.

“I am worried about Zika,” she says. “People talk about it. I know if you are pregnant and get Zika you can have a baby with microcephaly.” But outside, although the big water storage container is covered, water pools in the bottom of open plastic bowls and buckets where mosquitoes can breed. “We have one day with water [piped to the favela] and four days without,” says Figueiredo. So they have to store it in anything they can.

She says she uses mosquito repellent, as the health officials advise. Ademilson Barros, who runs the Centro de Atendimento a Meninos e Meninas [Centre for Helping Boys and Girls] at the foot of the hill, which gives the local children a safe place to go for education and support, snorts at this. “She doesn’t have repellent,” he says. “She doesn’t have food.”

Further down, Marli Amara, 50, and her sister, Lenira Amara Luna, 56, live in adjacent houses and keep the dry taps turned full on. “The water starts at 2am and has run out by morning,” says Marli Amara. When they hear water gushing in the middle of the night, they get out of bed and fill every container they possess.

Marli Amara outside her home in Linha do Tiro. Photograph: Sarah Boseley/The Guardian

Every 15 days, somebody from the city comes to put larvicide in their main water tank, which they are happy with, they say. Rumours that it may be a factor in the microcephaly cases, strongly denied by Fiocruz scientists and the WHO, have not reached the Amara sisters.

“They tell us to turn bottles upside down and cover the water tank and use repellent,” says Lenira. “We can’t afford to buy repellent. They say to use it but they don’t give it to us.”

What about advice to wear long sleeves? Marli Amara, wearing a yellow vest and orange shorts, laughs as if the suggestion is ridiculous. “It’s too hot,” she says.

Barros founded the children’s centre 35 years ago with his wife, who was born in the favela. More than 5,000 children are registered. It is not possible to control the mosquitoes, he says, pointing to rubbish on the ground where rainwater collects and the lack of sanitation. Dirty water runs in a slow trickle from the top of the favela to the bottom.

Telling people to cover their water tanks is not enough, he says. “It is a matter of education.” He does not mean schooling. “In these houses, families don’t have a meal together, they don’t talk or discuss or have a garden. Children arrive here and are told how to take care of their teeth and their health, but when they go home they don’t have food or family. The mothers are working and they are by themselves. And some of them go home to a dad who is abusive or drug trafficking.”

Rodrigues and Turchi’s study will be an important piece in the jigsaw puzzle. With colleagues, they are recruiting 200 of the microcephaly babies and their mothers and 400 unaffected babies from the same backgrounds from eight hospitals in Recife. As well as finally settling the Zika/microcephaly link and following the development of the babies, they are on the hunt for co-factors. “We are looking for other exposures, such as vaccines and drugs taken in pregnancy or earlier in the mother’s life and for other congenital abnormalities in the families,” Turchi says. There is no evidence that vaccines are linked to microcephaly, according to the WHO, but the study needs to look at everything the women and their babies have been exposed to.

Correia, Recife’s health chief, continues to mastermind the battle against mosquitoes, pleased that the numbers of breeding grounds his teams are finding in homes have been dropping. However two attempts in the past to eradicate Aedes aegypti because of dengue have failed. The numbers came down, then soared again. Meanwhile some other scientists have raised the possibility that the wrong mosquito is being blamed. Dr Constancia Ayres in Fiocruz Recife has shown that a far more common mosquito, Culex quinquefasciatus, which breeds in dirty water (Aedes aegypti mostly breeds in clean water), can be infected with Zika virus in the lab.

In a few months it will be clear whether Colombia and other countries are also going to see unprecedented numbers of brain-damaged babies, when women who were infected with Zika virus in pregnancy give birth. If so, there will be new fears over the epidemic’s potential spread to the US and southern Europe. It will take years, however, for scientists to be sure of what is happening and to find ways – most likely a vaccine – to stop it. In the meantime, the women of the favelas, whose lives are already limited by poverty and sometimes violence, are facing yet another desperate threat, this time to their unborn children.