Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species

Evaluation of immunohistochemical expression of bile transporter proteins in hepatocellular carcinoma and in cholangiocarcinoma

A análise das proteínas transportadoras de compostos biliares, antes restrita à fisiologia e à fisiopatologia de colestases, recentemente passou a incluir neoplasias hepato-biliares. O presente estudo teve como objetivo caracterizar a expressão das proteínas ABC de transporte biliar BSEP, MDR3, MRP2 e MRP3 em amostras retrospectivamente colecionadas de 80 casos de autópsias de carcinoma hepatocelular (CHC) e 56 casos de ressecção cirúrgica de colangiocarcinoma (CC). Áreas representativas das neoplasias foram organizadas em tissue microarrays e submetidas à pesquisa imuno-histoquímica (IHQ) com o anticorpo policlonal anti-BSEP (HPA019035) e os anticorpos monoclonais anti-BSEP (F6), anti-MDR3 (P3 II-26), anti-MRP2 (M2 III-6) e anti-MRP3 (DTX-1) com amplificação de sinal mediante uso de sistema de polímeros curtos conjugados à peroxidase. A comparação entre a positividade das reações imuno-histoquímicas para cada anticorpo e as variáveis anatomopatológicas foi realizada através dos testes de qui-quadrado de Pearson ou Exato de Fisher. A positividade das reações IHQ cujos anticorpos propiciaram melhor distinção do sinal positivo vs coloração inespecífica de fundo e detecção de casos positivos e/ou melhor capacidade de discriminar as duas neoplasias hepáticas foi comparada com a positividade observada para as reações IHQ com os anticorpos anti-CEA policlonal, anti-Hep-par-1 e anti-Arginase-1. A expressão canalicular de BSEP nos CHC foi observada em 77,3% (58/75) com o anticorpo monoclonal e 75,9% (60/79) com o anticorpo policlonal. Não foi detectada associação significativa da expressão de BSEP em relação ao tamanho, número dos nódulos e grau de diferenciação de CHC, tendo apenas sido significativamente reduzida (P 0,05). As reações IHQ para detecção de MRP2 exibiram positividade canalicular em 92,3% dos casos de CHC e em 96,3% nos casos de CC. A detecção da alta expressão de MRP2 no CHC foi constante (P > 0,05) em comparação ao tamanho, número dos nódulos, padrão arquitetural e grau histológico de diferenciação de CHC assim como, também não apresentou associação (P > 0,05) com a localização, padrão de crescimento e grau de diferenciação do CC. A reação IHQ para MRP3 resultou positiva em 15/80 casos de CH (18,8%). A reatividade IHQ para MRP foi detectada em 24/54 (44,5%) de CC. Diferente dos transportadores descritos acima, a expressão de MRP3 foi preferencialmente basolateral. A positividade para MRP3 não variou (P > 0,05) em relação ao número, tamanho dos nódulos, padrão arquitetural (inclusive os sólidos), e grau de diferenciação (inclusive os menos diferenciados). A proteína MRP3 esteve expressa regularmente (P > 0,05) em todos os casos de CC, apresentando-se reduzida apenas no subtipo histológico ductular (P=0,023). Em conclusão, o excelente contraste de reação, a frequência razoavelmente alta de positividade de CHC e a plena negatividade de CC para BSEP levam-nos a recomendar a introdução do anticorpo monoclonal anti-BSEP no painel adotado para o diagnóstico diferencial dessas duas neoplasias. A alta expressão de MRP2 no CHC e no CC é conservada independentemente dos parâmetros anatomopatológicos avaliados. A expressão do transportador MRP3 mostrou variação dentre os subtipos histológicos de CC, aspecto que torna promissoras pesquisas futuras para avaliação mais detalhada da expressão deste marcador nos colangiocarcinomasThe assessment of biliary transporters, previously restricted to the physiology and pathophysiology of cholestasis, has recently included hepato-biliary neoplasms. The present study aimed to characterize the expression of BSEP, MDR3, MRP2 and MRP3 biliary transport proteins in retrospectively collected samples from 80 cases of autopsy of hepatocellular carcinoma (HCC) and 56 cases of surgical resection of cholangiocarcinoma (CC). Representative areas of the neoplasms were organized into tissue microarrays and submitted to immunohistochemical (IHC) reaction with polyclonal antibody anti-BSEP (HPA019035) and monoclonal antibodies anti-BSEP (F6), MDR3 (P3 II-26), MRP2 (M2 III-6) and MRP3 (DTX-1). Signal amplification was achieved with a short polymer system conjugated to peroxidase. The comparison between the positivity of the immunohistochemical reactions for each antibody and the pathological variables was performed using the Pearson chi-square test or the Fisher\'s exact test. The performance of antibodies which provided a better distinction of the positive signal vs nonspecific background staining and yield better discrimination between the two hepatic neoplasms was compared with that achieved with the already accepted HCC markers polyclonal anti-CEA, Hep-par-1 and Arginase-1. The canalicular expression of BSEP in HCC was observed in 77.3% (58/75) with the monoclonal antibody and 75.9% (60/79) with the polyclonal antibody. BSEP expression levels were not significantly different according to tumor size, number of nodules and degree of differentiation. The frequency of positive reaction of HCC cases with the monoclonal anti-BSEP was apparently lower than that achieved with the canalicular expression of CEA, Hep-par-1 and Arginase-1, but these values did not reach statistical significance. All cases of cholangiocarcinoma were negative for IHC reactions to BSEP, which was significantly different (P=0.0001) from the results obtained with polyclonal anti-CEA (circumferential pattern) and Hep-par-1, but not from the resultas achieved with Arginase-1 (P=0.222). The canalicular expression of MDR3 was observed in 56.4% (44/78) of HCC cases. Among histological variables, only the finding of more complex architecture (P=0.009) and higher histological grade (P=0.005) of HCC yielded, significantly lower expression of MDR3. The expression of MDR3 in HCC was significantly lower than that of CEA, Hep-par-1 and Arginase-1 (P 0.05). The IHC reactions with the MRP2 antibody exhibited canalicular positivity in 92.3% of HCC cases and 96.3% in CC cases. High expression of MRP2 in HCC was constant (P > 0.05) despite changes in size, number of nodules, architectural pattern and histological degree of HCC differentiation, as well as no association (P > 0.05) with the location, pattern of growth and degree of differentiation of CC. The IHC reaction for MRP3 was positive in 15/80 cases of HCC (18.8%) and in 24/54 (44.5%) of CC. Unlike the carriers described above, the hepatocellular expression of MRP3 was preferentially basolateral. Positivity for MRP3 did not vary (P > 0.05) in relation to number, nodule size, architectural standard (including solids), and degree of differentiation. The MRP3 protein was expressed regularly (P > 0.05) in different presentations of CC, but significant lower frequency of positivity was found in the ductular histological subtype (P=0.023). In conclusion, the excellent signal-to-noise ratio, reasonably high frequency of HCC positivity and full negativity of CC to BSEP lead us to recommend the introduction of the anti-BSEP monoclonal antibody in the panel adopted for the differential diagnosis of these two neoplasms. The high expression of MRP2 in HCC and in CC is conserved independently of the pathological parameters evaluated herein. The frequency of expression of the MRP3 transporter varied among the histological subtypes of CC, which makes promising future research for a more detailed assessment of the expression of this marker in the cholangiocarcinoma

Adenovirus surveillance in wild carnivores from Brazil

Landscape transformation favors the spread of new pathogens that can be shared between domestic and wild animals. Certain adenoviruses (e.g., canine adenovirus 1 and 2, family Adenoviridae) can infect domestic and wild carnivores. In domestic canids, these viruses are associated with hepatic and respiratory diseases (among others). Nevertheless, information regarding adenovirus pathogenicity and molecular features in wild carnivores is still limited. Herein we surveyed adenovirus in free-ranging carnivores from Brazil. Total DNA was extracted from and subsequently tested by a nested panPCR in spleen and/or lung of 52 carnivores, representing species of the following families: Canidae (n = 4), Felidae (n = 3), Mustelidae (n = 2) and Procyonidae (n = 2). The obtained sequences were compared to others available at GenBank. Available tissue samples from the positive cases were evaluated histopathologically. One out of 52 (1.9%, CI 95%, 0.0–5.7%) carnivores was positive; a roadkilled ocelot (Leopardus pardalis). The obtained sequence presented a low deduced amino acid (78.1%) similarity with the closest adenovirus, identified in a pinniped from the United States of America. This fact and its detection in a novel host suggest it may be representative of a novel species and denominated ocelot adenovirus 1. None of the gross and microscopic findings of the positive case were associated with adenovirus. To the authors' knowledge, this is the first report of adenovirus in wild felids of South America and the second worldwide. Further studies are necessary to assess the epidemiology and potential pathogenicity of this agent in wild carnivores.This study was funded by the Coordination for the Improvement of Higher Education Personnel (CAPES) and the São Paulo Research Foundation (FAPESP). Ana Carolina Ewbank and Carlos Sacristán are recipients of PhD and postdoctoral fellowships by the FAPESP (FAPESP grant #2016/20956–0 and grant #FAPESP 2018/25069–7, respectively). José Luiz Catão-Dias is the recipient of a professorship from CNPq (304999–18).Peer reviewe

Outbreak of Yellow Fever among Nonhuman Primates, Espirito Santo, Brazil, 2017

In January 2017, a yellow fever outbreak occurred in Espirito Santo, Brazil, where human immunization coverage is low. Histologic, immunohistologic, and PCR examinations were performed for 22 deceased nonhuman New World primates; typical yellow fever features were found in 21. Diagnosis in nonhuman primates prompted early public health response

Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples

Abstract New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype

A retrospective pathology study of two Neotropical deer species (1995-2015), Brazil: Marsh deer (<i>Blastocerus dichotomus</i>) and brown brocket deer (<i>Mazama gouazoubira</i>)

<div><p>This retrospective study describes the biological and epidemiological aspects, gross and microscopical findings, and most likely causes of death (CD) in two species of Neotropical deer in Brazil. The animals were collected between 1995 and 2015 and represented 75 marsh deer (MD) and 136 brown brocket deer (BBD). Summarized, pneumonia was diagnosed microscopically in 48 MD and 52 BBD; 76 deer suffered trauma, involving dog attack (14 BBD) and vehicle-collision (14 BBD). Pulmonary edema (50 MD; 55 BBD) and congestion (57 MD; 78 BBD) were the most common findings for both species. Additionally, we diagnosed ruminal and myocardial mycosis in MD and BBD, respectively; ovarian dysgerminoma and pancreatic trematodiasis in BBD; and lesions suggestive of malignant catarrhal fever and orbiviral hemorrhagic disease in both species. The main CD in MD was: respiratory (41/75), alimentary, nutritional, trauma and euthanasia (3/75 each). Correspondingly, in BBD were: trauma (34/131), respiratory (30/131) and euthanasia (9/131). Respiratory disease was often defined by pulmonary edema and pneumonia. We provide evidence that respiratory disease, mainly pneumonia, is a critical pathological process in these Neotropical deer species. Although no etiological agents were identified, there is evidence of bacterial and viral involvement. Our results show trauma, mainly anthropogenic, as a common ailment in BBD. We propose to prioritize respiratory disease in future research focused on South American deer health aspects. We believe anthropogenic trauma may be a primary threat for populations of BBD.</p></div