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Brazil has the highest SARS-CoV-2 case-fatality rate in pregnant women in the Americas. In this study, clinical and virological findings of five mildly symptomatic pregnant women and their infected fetuses/newborns treated at a referral hospital for COVID19-pregnant women in Midwestern Brazil are reported. Mother and fetal samples were tested by RT-qPCR, ECLIA and Illumina MiSeq sequencing. From the five cases, one resulted in spontaneous abortion, one was stillborn, two were preterm births and one full-term birth. Maternal and fetal placenta, newborn and stillborn secretions were SARS-CoV-2+; one neonate developed ground-glass opacities in his lungs. One neonate’s umbilical cord was IgG+ and all were IgM negative upon hospital discharge. Genomes recovered from two placentas belong to the B.1.1.28 and B.1.1.33 lineages and present nonsynonymous mutations associated with virus fitness and infectivity; other not frequently reported mutations (B.1.1.33: NSP3 V2090G, M A2S and ORF3ab S253P and Y264N; B.1.1.28: NSP3 E995D, NSP12 R240K, NSP14 H1897Y and in ORF7b V21F) were found in proteins involved in viral replication, viral induction of apoptosis, viral interference on interferon and on NF-Κβ pathways. Phylogeny indicates the south of Brazil as the possible origin of these lineages circulating in MT. These findings contribute to describe SARS-CoV-2 infection and outcomes in pregnant women and their fetuses, at any stage of gestation and even in mild symptomatic cases.

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