Usually there are nine cases of microcephaly, the condition linked to the virus, in Brazil's Pernambuco state each year. When Dr Vanessa van der Linden examined five cases in two weeks at the end of August last year, her concerns were raised.
Brazil is at the centre of the Zika outbreak and has reported around 4,000 suspected cases of microcephaly since last October alone.
Here are some of the questions you have been asking Dr van der Linden on the BBC News Facebook page.
"It was strange to see such a high number of babies with small heads being born all of a sudden," Dr van der Linden says.
Within a few weeks in August and September last year there were 20 cases in two of the state's hospitals, she says.
That is more than twice the number usually reported in a whole year.
"We tried to explore what happened to the babies. The patterns of our tests pointed to a congenital infection, one that we had not seen before."
Dr van der Linden says that microcephaly is often misunderstood as disease.
"Microcephaly is only a symptom, it is not the disease. The disease is what causes damage to babies' brains and results in small heads," she says.
Microcephaly can have different causes, including genetic disorders and infections like syphilis or toxoplasmosis, Dr van der Linden says.
"When we examine a baby with microcephaly, we analyse their brain scans. Some malformations, such as scars in the brain, point us towards congenital infections."
The link between microcephaly and the Zika virus has not been confirmed.
Doctors also found that some babies who died had the virus in their brain and it has been detected in placenta and amniotic fluid too.
According to Dr van der Linden, there are still more questions than answers about the Zika virus.
But she says that future pregnancies are probably not affected by having contracted the virus previously.
At present, doctors estimate that the virus only stays in the body for two weeks.
"After a Zika infection, it is likely that women will develop immunity to the virus. That would mean that there is no risk of contracting Zika during a future pregnancy," Dr van der Linden says.
Several Latin American and Caribbean governments have advised women to delay pregnancies for up to two years.
The WHO has not recommended travel bans with affected countries, but says it is drawing up advice for pregnant women.
The symptoms of microcephaly depend on the severity of the condition, Dr van der Linden explains.
"There are some babies with a mild form of microcephaly who develop normally."
The most severe cases cry a lot, are very agitated and barely sleep, she says.
"The virus causes the damage during the pregnancy. The baby is born with the consequences and we cannot reverse those," Dr van der Linden says.
There is no cure for microcephaly, she explains, and what can be achieved in terms of treatment depends on the severity of the condition.
"For some babies, rehabilitation can only improve the quality of their lives. Others can learn to walk and communicate via eye contact and smiling."
Babies' heads continue to grow but at a slower rate than normal, she says.
Compiled by Michael Ertl

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His Popular Party (PP) lost its absolute majority in December's election but remains the biggest party.
Most parties have declared they will not back him, including the Socialists under leader Pedro Sanchez.
"We want to change Rajoy's government and this is why we will vote 'no' in a confidence vote," Mr Sanchez said.
Mr Rajoy needs to form a minority or coalition government which must pass a vote of confidence in parliament.
Spain's political turmoil began after the election on 20 December when voters, frustrated with economic crisis and austerity measures, broke the country's traditional two-party dominance.
After the parties filed to agree on a new government, a new election was held on 26 June where, for a second time, no party won an absolute majority.
One of the first doctors who identified the likely link between the Zika virus and thousands of babies being born with underdeveloped brains has been answering your questions.
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The King of Spain has asked acting Prime Minister Mariano Rajoy to try to form a  government after the second inconclusive election in six months.