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In kids at low risk of neurodevelopmental problems, deficits emerged in the first year of life without a smaller head circumference.
The virus can have long-lasting consequences for those exposed in utero and will likely strike again, experts say.
The Asian Zika virus strain was found to be the cause, a first for an African country.
The plan focuses on 10 strategic priorities, including combating antimicrobial resistance.
In one group, 35% scored below average for language, 10% for cognitive development, and 16% for motor development.
Zika infection in early pregnancy raise the risk of microcephaly 17 times, the study says.
Partial protection from earlier dengue exposure in the favela population might explain Zika's quick decline there.
Dengue immunity, however, doesn't seem to generally protect against Zika infection, the researchers find.
Sexual partners of case-patients were 2.2 times more likely to contract Zika than other contacts
The data suggest that, for the vast majority of men, Zika RNA is cleared from semen within 4 months.
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