virus detector | Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study.

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study.

Calvet G1, Aguiar RS2, Melo ASO3, Sampaio SA4, Filippis I5, Fabri A4, Araujo ESM4, Sequeira PC4, Mendonça MCL4, Oliveira L2, Tschoeke DA6, Schrago CG2, Thompson FL7, Brazil P1, Dos Santos FB4, Nogueira RMR4, Tanuri A2, by Filippis AMB8.
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Abstract
BACKGROUND:
The incidence of microcephaly in Brazil in 2015 was 20 times higher than in previous years. Congenital microcephaly is associated with genetic factors and several causative agents. Epidemiological data suggest that microcephaly in Brazil might be associated with the introduction of Zika virus. We aimed to detect and sequence the Zika virus genome in amniotic fluid samples of two pregnant women in Brazil whose fetuses were diagnosed with microcephaly.

METHODS:
In this case study, amniotic fluid samples from two pregnant women from the state of Paraíba in Brazil whose fetuses had been diagnosed with microcephaly were obtained, on the recommendation of the Brazilian health authorities, by ultrasound-guided transabdominal amniocentesis at 28 weeks' gestation. The women had presented at 18 weeks 'and 10 weeks' gestation, respectively, with clinical manifestations that could have been symptoms of Zika virus infection, including fever, myalgia, and rash. After the amniotic fluid samples were centrifuged, DNA and RNA were extracted from the purified virus particles before the viral genome was identified by quantitative reverse transcription PCR and viral metagenomic next-generation sequencing. Phylogenetic reconstruction and investigation of recombination events were done by comparing the Brazilian Zika virus genome with sequences from other Zika strains and from flaviviruses that occur in similar regions in Brazil.

FINDINGS:
We detected the Zika virus genome in the amniotic fluid of both pregnant women. The virus was not detected in their urine or serum. Tests for dengue virus, chikungunya virus, Toxoplasma gondii, rubella virus, cytomegalovirus, herpes simplex virus, HIV, Treponema pallidum, and parvovirus B19 were all negative. After sequencing of the complete genome of the Brazilian Zika virus isolated from patient 1, phylogenetic analyzes showed that the virus shares 97-100% of its genomic identity with lineages isolated during an outbreak in French Polynesia in 2013, and that in both envelope and NS5 genomic regions, it is clustered with sequences from North and South America, southeast Asia, and the Pacific. After assaying the possibility of recombination events between the Zika virus and other flaviviruses, we ruled out the hypothesis that the Brazilian Zika virus genome is a recombinant strain with other mosquito-borne flaviviruses.

INTERPRETATION:
These findings reinforce the putative association between Zika virus and cases of microcephaly in neonates in Brazil. Moreover, our results suggest that the virus crosses the placental barrier. As a result, Zika virus should be considered as a potential infectious agent for human fetuses. Pathogenesis studies that confirm the tropism of Zika virus for neuronal cells are warranted.

FUNDING:
National Consortium of Development and Research (CNPq), Foundation for Research Support of the State of Rio de Janeiro (FAPERJ).

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