When the link between Zika virus and birth abnormalities in Brazil first made headlines at the end of last year, many immediately worried about how this might affect the Rio de Janeiro Olympics. Now they are worrying more.

This week Brazil released its first nationwide statistical sweep of the mosquito-borne disease that shows that more than one in four of the 90,000 suspected cases in the first quarter of this year were in the state hosting the 2016 Games in less than 100 days.

The report puts the estimated rate of virus infections in Rio at 157 per 100,000 inhabitants, more than triple the national average.

Up until now, the focus had been on the tropical north-east of the country, in Pernambuco, where the disease was first spotted and linked to a spike in cases of newborns with unusually small heads, or microcephaly, because of restricted fetal brain development. But the release of the first figures since it became a notifiable disease and a public emergency in February suggest the virus has hit other parts of Brazil very badly as well — including the Olympic state.

The revelation comes at a time when the Games are already having to cope with growing allegations of corruption. They are also taking place in the context of a major political crisis, including the seemingly imminent impeachment of President Dilma Rousseff, and in the midst of an economic meltdown.

Claudio Maierovitch, director of the ministry of health's transmittable diseases department, told VICE News that it was all completely predictable, because the disease is carried by the Aedes aegypti mosquito that also transmits Dengue fever. Dengue affects Rio in high numbers every year, particular in March, April, and May.

"The expansion of virus circulation to other states infested by mosquitoes was expected since last year," he said. "Rio de Janeiro is a populous state and has faced some of the biggest Dengue epidemics in Brazil, so the large number of cases at this time of year is not surprising."

Dr Maierovitch added that the real number was likely to be much higher than reported with four or five asymptomatic patients for every probable case.

Zika was first identified in Brazil last May and was declared a health emergency by the World Health Organisation earlier this year. Since then the virus has spread through most of Latin America, with cases of transmission also documented in parts of Asia and Africa and the US. As well as the traditional route of infection via mosquito bites, there is also evidence of some sexual transmission.

The association of Zika to microcephaly prompted authorities to recommend pregnant women avoid travel to affected countries, though Brazil's tourism minister, Alessandro Teixeira insisted there were no restrictions in place in Rio.

Also, while there were almost 26,000 reported cases of Zika in Rio in the first three months of the year, the number of microcephaly cases has remained comparatively low. According to the latest health ministry bulletin, there were 42 confirmed cases of microcephaly compared to 334 in Pernambuco.

"It is not yet possible to have an idea of the proportion of pregnant women, infected by Zika virus who will have babies with microcephaly," Dr Maierovitch said.

Given that the highest number of cases of newborns with Zika-linked microcephaly have appeared associated with infections in the first trimester, it could take a few more months before this is statistically reflected in Rio.

"In relation to microcephaly, we have to wait a little bit more because in the same way microcephaly followed the Zika outbreak in the northeast, it could follow here," said Alberto Chebabo, a Rio-based doctor with the Brazilian Society of Infectology. "It's possible we will see an increase in microcephaly in the coming weeks after it peaked in March."

Meanwhile, the Rio health ministry has sought to explain the high rates of infection in the state by claiming it is due to more efficient reporting than elsewhere in the country.

Alexandre Chieppe, subsecretary for health surveillance, also insisted that the Zika epidemic in the state peaked in mid-February and has been on the decline since then.

"We are coming out of the period of the greatest risk of transmission for Zika," Chieppe said, stressing that the Olympics are taking place during Rio's winter when mosquitos are less active and there is a bigger risk of contracting flu. "It's very early to reach any conclusions based on this first bulletin from the ministry of health."

The World Health Organisation said in its situation report on Thursday that cases of Zika infection had started to drop off but "vigilance needs to remain high" as the organization did not see an overall decline in the outbreak.