With rubber gloves, a plastic container full of larvicide and the official badge of Rio de Janeiro’s epidemic control department, Gilberto de Souza gains permission to enter the home of a stranger in the Vila Canoas favela, in one of the latest missions against the Zika virus.

As the bemused residents look on, he goes room to room inspecting every sink, flower vase and empty bottle, shining his torch behind fridges and washing machines, checking every corner for possible mosquito breeding areas.

Satisfied, he then goes out to check the street, nodding approvingly when he sees a crate full of empty bottles that have been diligently placed upside down so they cannot hold even the thimbleful of rainwater that might allow virus-carrying insects to spawn.

But, just when it seems his job is complete, he spots another stack of beer bottles that have been discarded carelessly, with their mouths open to the heavens.

“In a favela, it’s complicated,” he says with a shrug that speaks volumes about the largely unspoken challenge of inequality that could undermine Brazil’s efforts to minimise the fallout from the Zika epidemic.

Although Zika is new in the country, having been first identified here less than a year ago, there are a number of old social problems that have allowed it to proliferate to around 1.5 million cases.

Poverty, inadequate water supplies and weak public health systems are major factors in the spread of other mosquito-borne diseases, such as dengue and Chinkungunya, which tend to cluster in low-income communities. Epidemiologists believe the same is likely to be true of Zika, which has so far been concentrated in the north-east, traditionally one of the poorest regions in Brazil. “Because Zika is carried by the same mosquitoes [as dengue] and influenced by the same sanitary conditions that are more common in poor neighbourhoods, I would predict that the same relationship between poverty and disease will be found to exist,” said Wilson Savino, director of the Oswaldo Cruz Institute, Brazil’s leading centre of health studies.

Many other factors are involved, including climate change and increased global mobility. Savino stressed that there is not yet sufficient data to prove a correlation between income and vulnerability to Zika. But senior government officials say anecdotal evidence so far suggests the virus is hitting the economically weak members of society hardest.

“Most mothers with children with microcephaly have come from poor communities,” said Claudio Maierovitch, director of the Communicable Disease Surveillance Department at the health ministry. “We don’t know the reason yet but it has been an observation noted by the people working on the ground. We hypothesise that this could be because they live in places with less regular water access and less trash collection.”

On door-to-door anti-Zika missions, local government officials prefer to emphasise the equitable aspects of the disease.

“The mosquitoes are very democratic. They will bite anyone, rich or poor,” said a doctor with the public health team visiting Vila Canoas. “It’s not just favelas where they breed. The swimming pools of the rich are also a problem.”

But many favela residents accept they are more vulnerable because their neighbourhoods have more potential breeding areas and locals can afford fewer protections. The price of insect repellent, which is something of a luxury for poor families, has surged in the worst-affected areas. Closing windows and using air-conditioners is expensive. Covering up is more difficult for those who do manual labour outdoors.

Poor sanitation is often cited as a cause for disease transmission, but this is unlikely to be the case for Zika, which is carried by a species of mosquito – Aedes aegypti – that requires clean water to breed. A more significant factor, according to hydrologist Paulo Carneiro of the Federal University of Rio de Janeiro, is the reliability of water supply.

“In places where the supply is precarious, the population invents other ways to store water. People use tanks and containers, often carelessly without proper covers. That allows the mosquito to use them as a repository for its eggs,” he said.

Mario Moscatelli, a conservationist and biologist, agreed. But he said poor public attitudes towards rubbish disposal – particularly near favelas and on disused land – are exacerbating the problem. Ultimately, he argues, this is the consequence of poor urban planning and irresponsible public attitudes.

“If you have a filthy river, you will not find mosquitoes there. But if you use it to discard things, especially plastic containers, you may accumulate the fresh water that generates favourable conditions for the mosquito,” he said.

Those who live nearby face a higher risk of disease and uncertainty about what it means for future generations.

Thaís Cavalcante, a resident of the Maré favela complex, was diagnosed with Zika last October. When she sought help at an emergency clinic, there were five other suspected cases. In her opinion, favelas are more at risk because they are often flooded, leaving puddles of standing water. She soon recovered from the rashes, fever and fatigue, but she is anxious about the long-term effects. “I do not intend to get pregnant now, but if it happens one day I will doubt whether my baby will be healthy or not,” she said.

The government believes Zika is linked to a surge in reported birth defects, particularly microcephaly, but this is not scientifically proven. Infants with microcephaly have abnormally small heads and their brains do not develop properly. The defect has also been linked to environmental conditions associated with poverty, such as severe malnutrition. Alcohol use, exposure to toxic chemicals and drugs, and other kinds of infections (such as toxoplasmosis) may also be a factor. Epidemiologists believe a combination of elements may be behind the rise in the number of cases in Brazil.

“It could be that Zika is causing [microcephaly] with another factor, which is definitely possible. There could be other environmental factors, there could be co-infections that cause the unfortunate microcephaly, and at this point there is just not enough evidence to say it is causing it,” said Kristin Bernard, a mosquito-borne virus researcher at the University of Wisconsin-Madison.

Regardless of the cause, those on lower incomes have fewer choices when deciding how to deal with the risks. Some wealthy pregnant women are quitting their jobs and taking refuge overseas until their babies are born. Others are having illegal pre-emptive abortions at private clinics rather than take the risk of their foetus being diagnosed with microcephaly closer to term.

Poorer women cannot afford to run anywhere that would make a difference and are less likely to be able to pay for a termination.

Whether these assumptions prove correct will not be known for several years. In the meantime, it seems more than plausible that thousands of children, disproportionately concentrated in poor communities, could grow up with small heads and possibly brain defects. During a televised address last week, President Dilma Rousseff vowed that any family affected by such a birth would receive the full support of the state and called on the nation to join the armed forces and public officials in a “mega-operation” on 13 February to stamp out Aedes aegypti.

But many are sceptical, noting that previous mosquito destruction campaigns had only a short-lived effect in the face of bigger trends.

“We are reaping what we sowed,” Moscatelli said. “The mosquito is taking its revenge after decades of uncontrolled growth of urban space and uncoordinated land use. The Zika epidemic is a consequence.”