Congenital Zika syndrome (CZS) causes early brain development impairment by affecting neural progenitor cells (NPCs). Here, we analyze NPCs from three pairs of dizygotic twins discordant for CZS. We compare by RNA-Seq the NPCs derived from CZS-affected and CZS-unaffected twins. Prior to Zika virus (ZIKV) infection the NPCs from CZS babies show a significantly different gene expression signature of mTOR and Wnt pathway regulators, key to a neurodevelopmental program. Following ZIKV in vitro infection, cells from affected individuals have significantly higher ZIKV replication and reduced cell growth. Whole-exome analysis in 18 affected CZS babies as compared to 5 unaffected twins and 609 controls excludes a monogenic model to explain resistance or increased susceptibility to CZS development. Overall, our results indicate that CZS is not a stochastic event and depends on NPC intrinsic susceptibility, possibly related to oligogenic and/or epigenetic mechanisms.

Congenital Zika syndrome (CZS) is a cluster of malformation, and the mechanisms that lead it are still unclear. Using hypothesis-driven candidate genes and their function in viral infections, single-nucleotide polymorphisms (SNPs) were genotyped by quantitative polymerase chain reaction in a sample population from Sergipe State, Brazil. This study shows that rs3775291 SNP at Toll-like receptor 3, which triggers type I interferon antiviral responses in mothers infected by Zika virus during pregnancy, is associated with CZS occurrence (odds ratio [OR], 2.19; 95% confidence interval [CI], 1.158–4.148). Moreover, rs1799964 SNP at tumor necrosis factor-α gene in CZS babies is associated with severe microcephaly (OR, 2.63; 95% CI, 1.13–6.21).

Background: There is an urgent need to understand the complex relationship between cross-reactive anti-viral immunity, disease susceptibility, and severity in the face of differential exposure to related, circulating Flaviviruses. Co-exposure to Dengue virus and Zika virus in Brazil is a case in point. A devastating aspect of the 2015-2016 South American Zika outbreak was the dramatic increase in numbers of infants born with microcephaly to mothers exposed to Zika virus during pregnancy. It has been proposed that this is more likely to ensue from Zika infection in women lacking cross-protective Dengue immunity. In this case series we measure the prevalence of Dengue immunity in a cohort of mothers exposed to Zika virus during pregnancy in the 2015-2016 Zika outbreak that gave birth to an infant affected by microcephaly and explore their adaptive immunity to Zika virus. Results: Fifty women from Sergipe, Brazil who gave birth to infants with microcephaly following Zika virus exposure during the 2015-16 outbreak were tested for serological evidence of Dengue exposure and IFNγ ELISpot spot forming cell (SFC) response to Zika virus. The majority (46/50) demonstrated Dengue immunity. IFNγ ELISpot responses to Zika virus antigens showed the following hierarchy: Env>NS1>NS3>C protein. Twenty T cell epitopes from Zika virus Env were identified. Responses to Zika virus antigens Env and NS1 were polyfunctional with cells making IFNγ, TNFα, IL-4, IL-13, and IL-10. In contrast, responses to NS5 only produced the immune regulatory TGFβ1 cytokine. There were SFC responses against Zika virus Env (1-20) and variant peptide sequences from West Nile virus, Dengue virus 1-4 and Yellow Fever virus. Conclusion: Almost all the women in our study showed serological evidence of Dengue immunity, suggesting that microcephaly can occur in DENV immune mothers. T cell Reynolds et al. CD4 Immunity in ZIKV Infection immunity to Zika virus showed a multifunctional response to the antigens Env and NS1 and immune regulatory responses to NS5 and C protein. Our data support an argument that different viral products may skew the antiviral response to a more pro or anti-inflammatory outcome, with an associated impact on immunopathogenesis.

Visceral leishmaniasis (VL) is a severe, systemic and potentially lethal parasitosis. The lung, like any other organ, can be affected in VL, and interstitial pneumonitis has been described in past decades. This research aimed to bring more recent knowledge about respiratory impairment in VL, characterizing pulmonary involvement through clinical, radiographic and tomographic evaluation. This is an observational, cross-sectional study that underwent clinical evaluation, radiography and high-resolution computed tomography of the chest in patients admitted with the diagnosis of VL in a university service in Northeast Brazil, from January 2015 to July 2018. The sample consisted of 42 patients. Computed tomography was considered abnormal in 59% of patients. Images compatible with pulmonary interstitial involvement were predominant (50%). The most observed respiratory symptom was cough (33.3%), followed by tachypnea (14.1%). Chest radiography was altered in only four patients. VL is a disease characterized by systemic involvement and broad spectrum of clinical manifestations. The respiratory symptoms and tomographic alterations found show that the involvement of respiratory system in VL deserves attention because it is more common than previously thought. Chest X-ray may not reveal this impairment.

28 29 *Denotes equal contribution. 30 31 Corresponding author mailing address: doencasporvetor@ial.sp.gov.br and 32 nuno.faria@zoo.ox.ac.uk 33 34 Article Summary Line: Genomic surveillance of yellow fever in São Paulo during the yellow fever 35 2017-2018 epidemic reveals movement towards Atlantic coast. 36 37 Running title: Phylogeography of yellow fever virus in São Paulo 38 Keywords: Yellow fever, outbreak, Brazil 3 40 Abstract 41 São Paulo (SP), a densely populated state in southeast Brazil that contains one of the world's largest 42 urban regions, has experienced its largest yellow fever virus (YFV) outbreak in decades. 43 Surveillance in non-human primates (NHP) is important in order to detect YFV early during an 44 epidemic or epizootic, to quantify the magnitude of the outbreak in NHP, and to evaluate the risk of 45 YFV spillover infection in human populations. To better understand the genetic diversity and 46 spatial distribution of YFV during the current outbreak in southeast Brazil, we generated 46 new 47 virus genomes from YFV positive cases identified in 18 different municipalities in SP, mostly 48 sampled from non-human primates between April 2017 and February 2018. Our data show that 49 most NHP cases in São Paulo state were likely caused by the introduction of a single YFV lineage 50 from Minas Gerais to São Paulo. Phylogenetic and phylogeographic analyses of these data indicate 51 that YFV spread southwards from Minas Gerais into São Paulo state at a typical rate of <1km per 52 day. These results shed light in the sylvatic transmission of yellow fever in highly fragmented 53 forested regions in São Paulo state and highlight the importance of continued operational research 54 and surveillance of zoonotic pathogens in sentinel populations. 55 4 56 Author´s Summary 57 Since July 2016, the southeast region of Brazil has experienced the largest yellow fever virus (YFV) 58 outbreak in decades. São Paulo is the most densely populated state in southeast Brazil. YFV is not 59 normally present in São Paulo state and therefore a large proportion of the 18 million inhabitants of 60 the state have not been vaccinated against YFV. The presence of YFV in São Paulo state therefore 61 represents a serious threat to public health. In Brazil, YFV typically circulates among non-human 62 primates, with cases in humans representing isolated 'spillover' events from this predominantly 63 sylvatic cycle. Understanding the epidemiological dynamics and spread of YFV in primates is 64 therefore critical for contextualising human cases, and guiding vaccination strategies that can better 65 protect local human populations. Here, we analyse the geographic and temporal distribution of 66 observed cases of YFV in non-human primates in São Paulo state. We generate sequence data from 67 46 YFV positive cases, and perform phylogenetic and phylogeographic analyses aimed at 68 understanding the spatial spread of YFV in São Paulo state. We show that most cases in non-human 69 primates in the São Paulo state were likely caused by a sing...