Human Congenital Zika Syndrome whole exome sequencings (affected children and respective mother, infected during pregnancy

Review descriptionEdit DescriptionHuman Congenital Zika Syndrome whole exome sequenceBarreiros, Lucila Akune1; Pontes, Leticia Gomes1; Fialho, Eder Magalhães Silva2; Passos, Saulo Duarte3; Pereira, Paulo Vitor Soeiro2; Condino-Neto, Antonio1Author affiliationsForthcoming on Dryad. https://doi.org/10.5061/dryad.2fqz612zjCite this datasetBarreiros, Lucila Akune et al. (Forthcoming 2024). Human Congenital Zika Syndrome whole exome sequence [Dataset]. Dryad. https://doi.org/10.5061/dryad.2fqz612zjAbstractZika virus is a flavivirus that re-emerged in the Americas in 2015 and has become an international health problem especially due to neurological complications in newborns, known as the Congenital Zika Syndrome (CZS). Despite the severity of certain cases, zika infection presents a broad clinical spectrum, and only 20% of those infected manifest symptoms of the disease. Environmental and viral genetic factors have been linked to CZS, but the host genetic background contribution remains to be elucidated. This work aimed to investigate genetic factors and biological pathways that contribute to the development of CZS in humans, with special focus on the antiviral immune response. Women infected during pregnancy, and their children, with normal development or with CZS were genetically investigated through whole exome sequencing. Human subjects and sample collectionChildren exposed to the Zika virus during the embryonic period (with and without Congenital Zika Syndrome) and their respective mothers were selected for the study during the years of 2017-2019 as described previously (Fialho et al., 2023a; Fialho et al., 2023b); exposure to ZIKV was identified by the detection of neutralizing antibodies through a Plaque Reduction Neutralization Test (PRNT) of 90% or by positive serology, both after the acute phase of the disease. Maternal clinical and demographic data was collected and all infants underwent routine clinical and extensive neurologic evaluation at the time of birth and were tested for TORCH infections (toxoplasmosis, rubeola, Cytomegalovirus, and Herpes Simplex) because positivity was an exclusion criterion. This study was approved by the ethics committee of the Research Ethics Committee of the Federal University of Maranhão Hospital (CAAE 65897317.1.0000.5086) and the Institute of Biomedical Sciences of the University of São Paulo (CAAE 90468518.2.0000.5467). Informed consent was given by either the subject itself, parent, or another legal guardian to allow for sample collection and data publication of all patients. Following informed consent, peripheral blood samples were collected and individual samples were identified by numbers, followed by the letter A for the group of children, or B for the group of mothers. Clinical data were analyzed from 22 children with SCZ and their 22 mothers (cases group), as well as 25 healthy children that were exposed during the embryonic period and their 25 mothers (control group).DNA isolation and whole exome sequencing analysisGenomic DNA (gDNA) was isolated from whole blood using Wizard® Genomic DNA purification extraction kit (Promega Corporation, USA) according to the manufacturers’ instructions. After DNA elution, sample concentration and quality were measured by spectrophotometry using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). gDNA integrity was assessed by gel electrophoresis with 1.5% agarose (SIGMA-ALDRICH, USA) in Tris-Acetate-EDTA stained with SYBR® Green II stain RNA (Thermo Fisher Scientific, USA). For WES, briefly, DNA libraries were quantified and validated by Qbit fluorometer (dsDNA high-sensitivity assay kit, Thermo Fisher Scientific, USA), Illumina Eco Realtime (Illumina, USA). Libraries were dual indexed, pooled, and sequenced using 300 cycles (2 x 151bp) paired-end read v2 chemistry on a standard Miseq flowcell (Illumina, USA), to obtain a mean coverage of at least 100x. Generated fastq files were mapped to GRCh37/hg19 reference sequence, local realigned and variants called using the Low Frequency Variant Detection tool of CLC Genomics Workbench (CLCBio, QIAGEN, the Netherlands). Variants were stored in an in-house SQL database (MariaDB, MariaDB Corporation, Finland).