A four-year survey of more than 100,000 newborn babies in north-eastern Brazil has uncovered hitherto unrecognised patterns of microcephaly.

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The discovery suggests microcephaly is not necessarily a new phenomenon, and questions whether Zika virus is even the cause.

Zika virus has been occupying the global media for weeks now, prompted by what appears to be a huge spike in the number of babies born with abnormally small heads.

The scramble in Brazil to discover the cause led paediatric cardiologist Dr Sandra Mattos to realise she was sitting on a database which could provide some answers.

Over four years, she and her colleagues surveyed more than 100,000 newborns for congenital heart disease in the Brazilian state of Paraiba.

But importantly, in just over 16,000 of these babies, the nurses also collected other information, such as length, weight, and head circumference — the indictor for microcephaly.

"We tried to establish the pattern of microcephaly over the last four years," Dr Mattos said.

Dr Mattos and her colleagues were surprised by the numbers.

"What we expected was that we would have something like three to four cases a year of microcephaly — that is what has been documented in the official sites.

"But we then noticed that we had much, much higher numbers."

As part of the survey, Dr Mattos' team assessed head size in three ways to ensure it was as accurate as possible.

"Independent of what criteria we used, we had between 2–8 per cent of babies that would fall into the criteria of microcephaly," she said.

This represents between 2,000 and 4,000 babies per year in the state of Paraíba — about 1,000 times more than the team expected.

Microcephaly usually linked to other defects

The survey goes back to 2012 and 2013 and shows a spike each spring and summer, and while the headlines are all recent, the biggest peak in north-eastern Brazil was actually in 2014.

But Dr Mattos said there was something different and potentially very worrying about the 2015 spring–summer spike in microcephaly, relating to how small the babies' heads were.

"In the most severe cases of microcephaly, that group which are the very severe cases, they are definitely increasing from the last part of 2015," she said.

International publicity about microcephaly has focused on babies with small heads, but it is unusual for microcephaly to present by itself.

It is usually part of a syndrome where there are heart defects, limb defects are other congenital defects.

Dr Mattos said these cases of microcephaly were not coupled with a rise in heart defects in the same babies.

"That's what's really unusual about this outbreak," she said.

"Most of the microcephaly cases that are being reported now are primarily very severe microcephaly without anything else."

The survey calls into question whether these microcephaly cases are caused by Zika virus or something else.

If it is Zika virus, it has been in Brazil for a lot longer than people have thought, but that does not explain why after 50 years Zika has only now been linked to microcephaly.