Brazil's Ministry of Health has launched an investigation into the cluster of babies born with brain defects linked to the Zika virus, after an expected "explosion" of cases across the country did not occur.

The bulk of the cases of congenital Zika syndrome – fetal brain defects that sometimes cause microcephaly, or abnormally small skulls – remain clustered in the northeast region of the country where the phenomenon was first identified last October, the ministry says.

And that has epidemiologists and infectious disease experts asking what is going on: Is it Zika and another virus working together that damages the fetal brains? Is it Zika and an environmental factor? Or something about the women themselves whose fetuses are affected?

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The research in Brazil won't have conclusions for months, but will have implications across the Americas, where the Brazilian experience and the rapid spread of Zika has caused governments to take protective measures and even warn women to delay getting pregnant.

"We can see there is a kind of cluster in [part of] the northeast region with high prevalence and high severity, of miscarriage and congenital malformation that is really severe," said Fatima Marinho, co-ordinator of epidemiological analysis and information at the ministry.

"But we didn't find this in other states – even the [adjacent] states didn't see the same situation as in the epicentre.… We were preparing for an explosion and it didn't come.

"So we started to think that in this central area maybe more than Zika is causing this intensity and severity."

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A central theory the ministry is now exploring is whether co-infection with other viruses, such as dengue or chikungunya, is the factor. For example, does a mother's previous (or simultaneous) infection with dengue, which is also ubiquitous in Brazil, mean that the Zika virus affects a fetus differently? Or is it other viruses?

"This is an area that was under attack by viruses: Some parts even had measles," during the period when the bulk of the congenital Zika babies were conceived, Dr. Marinho said.

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The ministry is also looking at social determinants, she said, because initial analysis makes it clear the women with affected fetuses have a clear "profile." Some 77 per cent of them are black or mixed-race (the national figure is 52 per cent), and the great majority are poor. That's surprising, she said, given that dengue, for example, carried by the same mosquito, infects people across social classes. Most of the mothers are young (between 14 and 24) whereas typically birth defects affect older women.

The World Health Organization is supporting research into co-factors. "Even though a causal link between Zika virus and congenital malformations has been conclusively demonstrated as published in international peer-reviewed scientific publications, other factors that may aggravate these conditions also require investigation," said Sylvain Aldighieri, incident manager for Zika with the Pan American branch of the WHO.

"I totally agree some co-factors are likely involved," said Ernesto Marques, a professor of infectious disease and microbiology at the University of Pittsburgh and scientific director of a program called Cura Zika. But it isn't the cluster that convinces him: "It's because not every woman exposed during pregnancy has a baby with the congenital effects."

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But not all epidemiologists concur: "I think it's too early to say there is a disparity in the rate of microcephaly," said Laura Rodrigues, a professor of infectious disease epidemiology at the London School of Hygiene and Tropical Medicine, who has been working on Brazil's Zika epidemic since it was first identified. The epidemic is nearly a year behind in its spread in some other countries and perhaps other parts of Brazil, she said. "So maybe haven't got to the peak. But that's not to say we shouldn't think about co-factors."

Because the virus produces no symptoms in up to 80 per cent of people who get it, and only mild symptoms in many others, few people confirm Zika infection with laboratory tests, and so statistics of Zika cases are always estimates. The virus currently infecting Brazilians is a new, Asian strain of Zika, which was identified more than 60 years ago but never associated with congenital problems, or known to be sexually transmissible, as this strain is.

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After Brazil, the next country that was expected to see the wave of congenital Zika was Colombia, which has the second-largest number of reported Zika cases. But of more than 12,000 pregnant Colombian women with Zika, only 21 have had fetuses or babies with the brain defects.

Dr. Marinho, with the ministry, said this reinforces her suspicions about the role of co-infection or other factors in Brazil. Dr. Marques said Colombia is only seeing the babies of women who were infected late in their pregnancies so far (because the virus season is about six months behind, further to the north) and the evidence is that the likelihood of damage by Zika is higher earlier in gestation – so those babies may yet come.

But Dr. Rodrigues had another explanation. "Now we know that in places where Zika comes the rate of abortion shoots up," she said. "The feminist groups that will send pills by post to women … as a way of making up for the unfairness of the restrictive abortion laws, report an enormous increase in requests from Brazil and Latin America. I wouldn't be surprised if when we look at cohorts in other counties, pregnancies disappear, and we can't say if it was spontaneous or medical abortion."

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Researchers reported in the New England Journal of Medicine on July 28 that in Latin American countries where the new strain of Zika is spreading and abortion is illegal, there has been a huge spike in the number of requests to Women on Web, a Dutch-based organization which proves women with online consultations and then mails the drugs to induce a medical abortion. The increase over the rate of requests last year ranges from 38 per cent to 108 per cent in Brazil. (Brazilian authorities are now intercepting all deliveries to Brazilian women, the group said.)

On July 15, Adriana Melo, a fetal medicine specialist in the state of Paraiba who was the first to find Zika in the brains of affected babies, released research in which she and her co-authors report finding proteins of bovine viral diarrhea virus (BVDV), a cattle disease, in the brains of three fetuses with microcephaly from Paraiba whose brains also tested positive for RNA from the Zika virus. BVDV is known to cause serious birth defects in cows, but not to infect people. The findings were posted on BioArchive, a U.S.-based website for scientists to quickly share research findings on urgent matters, before peer review and publication. Their hypothesis is that Zika infection may weaken physiological barriers, so the cow virus that would not normally affect a human fetus can cause damage.

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However other researchers are expressing skepticism of this theory – and Dr. Melo and her colleagues acknowledged the possibility that the BVDV they found was the result of sample contamination, because the virus is often found in fetal bovine serum, which is a reagent (a substance used in chemical analysis) frequently used in laboratories.

Dr. Marinho is at pains to make clear that the health ministry does not doubt that Zika is the primary cause of the fetal brain damage. (Brazilian doctors were quick to persuade the ministry of the link last year, but had a much longer job to convince the World Health Organization, which declared an emergency over microcephaly only in February.) Then conspiracy theories tore through the public in Brazil and beyond – that microcephaly was actually caused by a pesticide, or vaccines, or genetically modified mosquitoes – and she does not want to revive that debate.

"We know here Zika caused neurological damage – we have no doubt – but the question is how can we explain this situation in the epicentre that was not reproduced in other areas – in Colombia, and in other states in Brazil. A lot of pregnant women were infected and there were few cases of microcephaly or congenital malformation – it must be more than Zika itself," she said. "We could be wrong of course but it is the responsibility of the Ministry of Health to investigate all possibilities."

Beneath all of these theories lies a fundamental problem with data. Until this crisis, Brazil had very weak reporting of microcephaly, with rates in some areas reported as 1,000 times lower than in Europe even though researchers have every reason to believe that it occurred at roughly the same rates.

With the emergency declared, health workers suddenly erred in the wrong direction, overreporting microcephaly. Almost none of the women with affected babies had a serologically confirmed Zika diagnosis. Beyond that, Dr. Melo and her colleagues realized many of the worst-affected babies had completely normal looking skulls, and it was not until they showed neurological problems that they were reported as Zika-affected. She told The Globe in February that it was impossible to know how many had slipped through the net and were as yet undiagnosed. In addition, an unknown number of affected pregnancies ended in miscarriage.

"The current epidemiological info is very fragile, so how do we know, for example, that we didn't have an explosion of cases in Rio in 2014 and we didn't pick it up?" asked Dr. Marques.

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The Asian strain of Zika hit French Polynesia in 2013 and researchers have gone back to retrospectively diagnose 17 cases of babies born with microcephaly in a total population of 275,000 people – but researchers hotly debate how useful that information is for indicating the likelihood of co-factors, since it's retrospective and based on modelling. In addition, while Zika was not known to be related to fetal development problems at the time, abortion is legal in French Polynesia and women who were told their babies had brain defects could have terminated their pregnancies.

Brazil has 1,749 cases of confirmed congenital Zika syndrome so far, with 106 stillbirths and deaths. Dr. Marinho said it will be months before the ministry has solid data to confirm that the cases are clustered and there are co-factors involved, let alone what they are, and meanwhile congenital Zika remains a real threat: Paraiba is now seeing a second wave of cases. "But this could be good news, for other areas of Brazil, and other countries," she said.

Editor's note: An earlier version of this story incorrectly referred to Eduardo Marques, a professor of infectious disease and microbiologist. In fact, his name is Ernesto Marques. This is a corrected version.