The research in the journal Cell Host and Microbe was led by scientists at the University of California, Los Angeles and the Chinese Academy of Medical Sciences and Peking Union Medical College in Beijing.
Researchers looked for individual differences between more than 40 strains of Zika virus -- 30 of which came from people, 10 from mosquitoes, and one from a monkey.
They found big differences between the Asian and African lineages of the virus, and "significant changes in both amino acid and nucleotide sequences during the past half-century," said the study.
All of the human strains identified in the 2015-2016 outbreak appear most closely related to the virus identified in 2013 in French Polynesia.
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The team also found that a certain protein, called the pre-membrane precursor or prM, was quite different between the Asian human and the African mosquito subtypes.
"We believe these changes may, at least partially, explain why the virus has demonstrated the capacity to spread exponentially in the human population in the Americas," said senior study author Genhong Cheng, a professor at the University of California, Los Angeles's department of microbiology, immunology and molecular genetics.
More research is needed to uncover the precise reasons for Zika's ability to cause birth defects in some children.
Never before has a mosquito-borne virus shown the potential to cause a condition known as microcephaly in babies born to mothers infected while pregnant, leaving the infants with small heads and deformed brains.
Thousands of babies in Brazil, the epicenter of the latest outbreak, are suspected of being born with microcephaly since last year.
A vaccine against the virus, which can also be sexually transmitted, is years away, US health authorities say.