Below is a brief description of the Zika virus and it’s origins taken from Wikipedia:
Zika virus (ZIKV) is a member of the virus family Flaviviridae and the genus Flavivirus, transmitted by daytime-active Aedes mosquitoes, such as A. aegypti.
In humans, the virus causes a mild illness known as Zika fever, Zika, or Zika disease, which since the 1950s has been known to occur within a narrow equatorial belt from Africa to Asia.
In 2014, the virus spread eastward across the Pacific Ocean to French Polynesia, then to Easter Island and in 2015 to Mexico, Central America, the Caribbean, and South America, where the Zika outbreak has reached pandemic levels.
Here is a brief description of the rare birth defect known as Microcephaly taken from Wikipedia:
Microcephaly is a neurodevelopmental disorder. It serves as an important neurological indication or warning sign, but no uniformity exists in its definition.
It is usually defined as a head circumference (HC) more than two standard deviations below the mean for age and sex.[Some academics advocate defining it as head circumference more than three standard deviations below the mean for the age and sex.
Microcephaly may be congenital or it may develop in the first few years of life.
The disorder may stem from a wide variety of conditions that cause abnormal growth of the brain, or from syndromes associated with chromosomal abnormalities. Ahomozygousmutation in one of the microcephalin genes causes primary microcephaly.
Until just recently the link between the Zika Virus and Microcephaly has never been in place – searching google for documents pre-2015 comes up with no definite data connecting the two.
The ‘European Centre for Disease & Control’ own risk assessments on the Zika Virus only begin to warn of a connection between Microcephaly and the Zika Virus from their November 2015 
There are also multiple articles on the CDC’s own website regarding the Zika Virus with no mention of any link between the virus and Microcephaly, in fact before late 2015 there are no articles connecting the two that we could find. Here are a couple of examples of articles found on the CDC website pre-dating 2015:
The current CDC page with advisory notes for pregnant women states:
‘This notice follows reports in Brazil of microcephaly and other poor pregnancy outcomes in babies of mothers who were infected with Zika virus while pregnant.
However, additional studies are needed to further characterize this relationship. More studies are planned to learn more about the risks of Zika virus infection during pregnancy.'
The connection is purely circumstantial and no scientific evidence what so ever is in place to prove a link.
We also now know that the original statement that there were over 4180 cases in Brazil of Microcephaly caused by the Zika virus is false:
Health Ministry officials said they had done a more intense analysis of more than 700 of those cases, confirming 270 cases and ruling out 462 others.[ 5]
So the actual number of confirmed cases of Microcephaly could be as much as half the original 4180 stated. There is also the question of how many of the confirmed cases of Microcephaly actually had the Zika Virus detected in their body – this data is still unavailable as far as we are aware.
Another consideration is whether this increased number of cases of Microcephaly in Brazil are purely down to an alert to look for cases of microcephaly and report all potential cases to authorities ?
First, historical birth prevalence of microcephaly in Brazil, approximately 0.5 cases per 10,000 live births, calculated from birth certificates, was lower than expected estimates of 1–2 cases per 10,000 live births (9), which might indicate general underascertainment of microcephaly in Brazil.
However, during the second half of 2015 alone, >3,000 suspected cases of microcephaly (approximately 20 cases per 10,000 live births) were reported to the MoH through the special notification protocol, suggesting a sharp increase in birth prevalence, although the special notification protocol might have also increased case reporting.
The above statement was taken from the CDC website and they themselves even suggest the increase could be due to a ‘special notification protocol’, bare in mind also that the 3000 cases they mention which increased to 4180 by january 2016 may actually be half that bringing the cases down to 10 in 10,000 births, which although still considerably higher than historical statistics is much lower than what the mainstream media are telling us.
With no evidence what so ever linking the Zika virus with Microcephaly it would be prudent to check other potential links, now in late 2014 the Brazilian Government recommended that all Children and Pregnant women should have the Tdap/DTwP vaccination :
DTwP (Butantan) are recommended at 15 months of age and 4 years of age (Sanofi Pasteur). The country will recommend Tdap in the routine immunization programme for pregnant women from 2014 onwards. 
There are many other countries which have also recommended the TDaP vaccine for children and pregnant women including the US and the UK, but what is unclear is the uptake of the vaccine in pregnant women, what is also important to consider is which Vaccine was used in Brazil, as there is not just one TDaP vaccine on the market.
The UK’s uptake for the vaccine in pregnant women in 2014 was around 60%, whereas in the US it was just shy of 20% – I would estimate the uptake in Brazil for the vaccine would be extremely high, somewhere in the >90% region but we have yet to source the data for this.
So there is a potential connection between Microcephaly and the TDaP vaccine, although due to lack of data it is as circumstantial as the Zika-Microcephaly link.
Finally, there is the case of the GM Mosquitos introduced into Brazil in late 2014, although trials have been done now by the UK company Oxitec in various countries the version of GM Mosquito used is different.
The mosquitoes, which Oxitec has dubbed OX513A, have been bred to carry a sort of genetic self-destruct mechanism that causes their offspring to die before they reach sexual maturity, preventing them from reproducing. Currently this version of Mosquito has only been trialed in Grand Cayman and Malaysia prior to Brazil.
With Brazil it was the OX513A Mosquito that was used, the idea is the male genetically modified Mosquito’s are released into the wild; they mate with the existing female population and any offspring dies off as their modified genetics intended.
The males are only released because they do not bite, whereas females bite, however, concerns have been raised over the accidental release of female GM Mosquitoes into the wild as these will bite humans, even Oxitec themselves have admitted this is possible:
Oxitec, itself, admits that as well as GM male mosquitoes, GM females may be released accidentally, and these are the biting form of the insect which passes on disease. The company has still not dealt convincingly with the medical consequences of a GM female mosquito biting people .
There is huge concerns over the affects of Tetracycline an anti-biotic commonly and excessively used in farming in Brazil. Small amounts of this ant-biotic be ingested by the modified mosquito represses the modified gene development and increased the life span of the modified mosquito allowing them to reproduce further.
Brazil is third in the World for using tetracycline with farmed animals. This is not well absorbed and over 75% is excreted into the soil. GM mosquitos looking for food can ingest this tetracycline as part of their blood meal. Even small amounts will suppress the modified development, allowing the altered mosquitoes to survive.
Another piece of good circumstantial evidence supporting this theory is the release location of the mosquitoes and the epicentre for the Zika outbreak:
The Zika outbreak in Brazil followed shortly after Oxitec’s release of it’s GM mosquitos.
The release location is the epicenter of the outbreak where a surge in babies with microcephaly was noted.
There is also speculation about whether the commonly used pesticides in Brazil are the cause of the rapid increase in birth defects, Atrazine (ATR), one of the most widely used herbicides in the world has already been proven to cause Microcephaly among various other defects and Brazil is third in the World for usage of the herbicide:
The main effects were delayed development, reduced body size, microcephaly, axial flexures, wavy tail and edema. In addition, delayed development, reduced development of forelimbs, and edema were recorded at metamorphosis stages.
Finally, behind both the GM Mosquitoes and the TDaP vaccine is the Bill and Melinda Gates foundation who have both financially supported the Company responsible for the GM Mosquito Oxitec and the research company Vanderbilt who performed a study into immune responses of pregnant women in Brazil after having the TDaP Vaccine.
At the moment we still have no definitive conclusions to make, but it’s clear there are many unanswered questions as well as questionable assumptions being portrayed by the mainstream media.
From everything we do know the best ‘circumstantial evidence’ we have is the link between GM Mosquitoes and the rise in birth defects, however with incorrect statistics on Zika contraction rates and cases of Microcephaly it is difficult to determine whether all three are interconnected or not.
 European Centre for Disease Prevention & Control: Risk Assessments
 CDC: Q&A
 Associated Press
 The World Health Organisation
 Gene Watch
 Pub Med