This suggests that these babies had recent or current infection by ZIKV.
The authors remind us that IgM does not cross the blood-brain barrier (it's a big molecule) and so its presence in the CSF suggests that the foetus was infected, not the mother.
The absence of RNA could be interpreted as the infection having occurred at least a week ago. But that's hard to know and it is unclear how long IgM lingers for in the foetus and child after ZIKV infection. There is no discussion about the possibility of the BBB being less than perfectly intact or in some other way failing to perform its role as a barrier in these babies.
Unfortunately, as has usually been the case throughout the Brazil microcephaly surge, there is little by way of a denominator to help us understand the scale of the proposed role of ZIKV here. What is happening in the serum and CSF of babies delivered to mothers from the same regions of Brazil who gave birth to babies sampled in the same way, at the same time after delivery, which were not diagnosed with microcephaly or other central nervous system disorders?
We can probably be safe in assuming that not every mother who has been infected with ZIKV delivers a baby with congenital abnormalities but that many mothers have in fact, been infected during this epidemic.
If ZIKV or ZIKV together with something else is the cause of microcephaly, why is it still relatively so rare among so many births?