Lipidomic Analysis Reveals Serum Alteration of Plasmalogens in Patients Infected With ZIKA Virus

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) in the Flavivirus genus of the Flaviviridae family. Since the large outbreaks in French Polynesia in 2013–2014 and in Brazil in 2015, ZIKV has been considered a new public health threat. Similar to other related flavivirus, ZIKV is associated with mild and self-limiting symptoms such as rash, pruritus, prostration, headache, arthralgia, myalgia, conjunctivitis, lower back pain and, when present, a short-term low grade fever. In addition, ZIKV has been implicated in neurological complications such as neonatal microcephaly and Guillain–Barré syndrome in adults. Herein, serum lipidomic analysis was used to identify possible alterations in lipid metabolism triggered by ZIKV infection. Patients who presented virus-like symptoms such as fever, arthralgia, headache, exanthema, myalgia and pruritus were selected as the control group. Our study reveals increased levels of several phosphatidylethanolamine (PE) lipid species in the serum of ZIKV patients, the majority of them plasmenyl-phosphatidylethanolamine (pPE) (or plasmalogens) linked to polyunsaturated fatty acids. Constituting up to 20% of total phospholipids in humans, plasmalogens linked to polyunsaturated fatty acids are particularly enriched in neural membranes of the brain. The biosynthesis of plasmalogens requires functional peroxisomes, which are important sites for viral replication, including ZIKV. Thus, increased levels of plasmalogens in serum of ZIKV infected subjects suggest a link between ZIKV life cycle and peroxisomes. Our data provide important insights into specific host cellular lipids that are likely associated with ZIKV replication and may serve as platform for antiviral strategy against ZIKV

Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses

Zika infectio

Estudo in silico para a utilização do HTLV-2 atenuado como vetor vacinal contra a infecção pelo HTLV-1

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2013-10-14T17:28:38Z No. of bitstreams: 1 Fernanda Khouri. Estudo in silico....pdf: 3863859 bytes, checksum: 34a7b6c0bc315b65207169652027de26 (MD5)Made available in DSpace on 2013-10-14T17:28:38Z (GMT). No. of bitstreams: 1 Fernanda Khouri. Estudo in silico....pdf: 3863859 bytes, checksum: 34a7b6c0bc315b65207169652027de26 (MD5) Previous issue date: 2013Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilO HTLV-1 foi o primeiro retrovírus descrito associado a doenças humanas, tais como leucemia de célula T do adulto (ATLL), paraparesia espástica tropical/mielopatia associada ao HTLV (TSP/HAM), dermatite infecciosa, entre outras. Esse retrovírus possui um genoma de RNA de fita simples, com os genes gag (grupo antigênico), env (envelope), pol (polimerase), e uma região próxima à extremidade 3' conhecida como pX. Em cada extremidade do genoma existem sequências de repetições terminais longas (LTR – long terminal repeat), que são essenciais na integração do DNA proviral ao DNA do hospedeiro, e também para a regulação transcricional do genoma do vírus. Estima-se que cerca de 5-10 milhões de pessoas estejam infectadas pelo HTLV-1 no mundo. No Brasil, presume-se que 2,5 milhões de pessoas estejam infectadas. Apesar da infecção pelo HTLV-1 ser endêmica em diferentes regiões geográficas do mundo, ainda permanece sem um método de profilaxia eficaz. Pesquisas realizadas em macacos-esquilos no Instituto Pasteur da França e no Instituto Nacional do Câncer nos EUA avaliaram a imunogenicidade e a eficácia de uma vacina contendo o gene env ou env e gag do HTLV-1. Após a vacinação e transfusão de células infectadas com o HTLV-1 todos os animais mostraram-se protegidos. Anteriormente a este estudo, pesquisadores do Instituto Nacional do Câncer, NIH-EUA, avaliaram a eficácia de um vetor vacinal derivado do vírus da varíola atenuado contendo o gene env do HTLV-1 (R-ALVAC), e após o desafio vacinal todos os animais mostraram-se protegidos. Porém, a proteção destes dois estudos não foi permanente. Entretanto, esses resultados sugerem que uma vacina anti-HTLV-1 pode ser viável e, acreditamos que a produção dessa vacina tendo como vetor um vírus persistente como o HTLV-2 pode proteger contra a infecção pelo HTLV-1. Assim, desenvolvemos em colaboração com o NIH, um vetor vacinal contendo as duas regiões LTR do HTLV-2, para serem inseridos os genes gag e env do HTLV-1 sob o controle da região 3’LTR deste vetor. Para a utilização desse vetor recombinante faz-se necessário caracterizar a região promotora do HTLV-2, avaliando assinaturas nucleotídicas presentes em diferentes subtipos, bem como a presença de motifs importantes para a expressão do vetor vacinal. Pelo exposto, o objetivo principal desse trabalho foi avaliar in silico a habilidade do vetor recombinante do HTLV-2 poder ser utilizado como vetor vacinal anti-HTLV-1. Nossos resultados revelaram que existem pequenas diferenças na região promotora dos subtipos HTLV-2a, HTLV-2b, HTLV-2c e HTLV-2d. Algumas alterações resultam em ganho ou perda de motifs importante para a regulação da transcrição gênica, como o motif E Box, presente nas sequências dos diferentes subtipos do HTLV-2 e ausente na região promotora do vetor. Entretanto, estudos sugerem que esse motif pode ser responsável pela repressão da transcrição gênica e, portanto, essa diferença encontrada entre o vetor recombinante do HTLV-2 e as diferentes sequências analisadas sugere que a transcrição gênica do vetor vacinal sem esse motif pode ser mais eficiente. Logo, o vetor recombinante do HTLV-2 pode ser utilizado como vetor vacinal anti-HTLV-1 em ensaios pré-clínicos.The HTLV-1 was first described retroviruses associated with human diseases, such as leukemia adult T cell (ATLL), tropical spastic paraparesis / HTLV-associated myelopathy (TSP / HAM), infective dermatitis, among others. This retrovirus has a genome of single-stranded RNA, with the genes gag (group antigen), env (envelope), pol (polymerase), and a region near the 3 'end known as pX. At each end of the genome are sequences of long terminal repeat (LTR) that are essential for the integration of the proviral DNA in the host DNA and also for the transcriptional regulation of the virus genome. It is estimated that about 5-10 million people are infected with HTLV-1 worldwide. In Brazil, it is assumed that 2.5 million people are infected. Despite the HTLV-1 is endemic in different geographic regions of the world still remains without an effective method of prophylaxis. Research conducted in squirrel monkeys at the Pasteur Institute in France and the National Cancer Institute in the USA evaluated the immunogenicity and efficacy of a vaccine containing the env gene or env and gag of HTLV-1. After vaccination and transfusion of infected cells with HTLV-1 all animals were shown to be protected. Prior to this study, researchers from the National Cancer Institute, NIH, USA, evaluated the efficacy of a vector vaccine derived from attenuated smallpox virus containing the env gene of HTLV-1 (R-ALVAC) and after challenge all animals were shown to be protected. However, the protection of these two studies was not permanent. At the same time, these results suggest that a vaccine anti-HTLV-1 may be feasible and we believe that the production of this vaccine as a vector having one persistent virus as HTLV-2 can protect against HTLV-1 infection. Thus, we developed in collaboration with the NIH, a vector vaccine containing the two LTR of HTLV-2, that will be inserted the env and gag genes of HTLV-1. To use this recombinant vector is necessary characterize the promoter region of HTLV-2, evaluating nucleotide signatures present in different subtypes, as well as the presence of motifs important for the expression vector vaccine. For these reasons, the aim of this study was to evaluate in silico the ability of recombinant vector of HTLV-2 be able to be used as a vector vaccine anti-HTLV-1. Our results reveal that there are small differences in the promoter region of HTLV-2a, HTLV-2b, HTLV-2c and HTLV-2d. Some changes results in loss or gain of motifs important for regulation of gene transcription, such as the E box motif present in the sequences of the different subtypes of HTLV-2 and absent in the promoter region of the vector. However, studies suggest that this motif can be responsible for the repression of gene transcription, and therefore this difference found between the recombinant vector of HTLV-2 and different sequences suggested that the analyzed gene transcription vector vaccine without this motif can be more efficient . Therefore, the recombinant vector HTLV-2 can be used in preclinical trials as a vaccine vector for HTLV- 1

Caracterização molecular da ORF-I do HTLV-1 proveniente de pacientes com diferentes perfis clínicos

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2017-09-01T13:51:39Z No. of bitstreams: 1 Fernanda Khouri Barreto Caracterização molecular....pdf: 4750353 bytes, checksum: 2edf02fe401ffec8ea79b2086d2127ff (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2017-09-01T13:59:39Z (GMT) No. of bitstreams: 1 Fernanda Khouri Barreto Caracterização molecular....pdf: 4750353 bytes, checksum: 2edf02fe401ffec8ea79b2086d2127ff (MD5)Made available in DSpace on 2017-09-01T13:59:39Z (GMT). No. of bitstreams: 1 Fernanda Khouri Barreto Caracterização molecular....pdf: 4750353 bytes, checksum: 2edf02fe401ffec8ea79b2086d2127ff (MD5) Previous issue date: 2017-07-27(PROEP-CNPq/FIOCRUZ-BA) (MEC/MCTI/CAPES/CNPq/FAPs) (FIOCRUZ-IGM)Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrasilINTRODUÇÃO: O HTLV-1 é o agente etiológico de doenças humanas, tais como leucemia/linfoma de célula T do adulto (ATLL), paraparesia espástica tropical/mielopatia associada ao HTLV (HAM/TSP), dermatite infectiva associada ao HTLV-1 (DIH), entre outras. Estima-se que cerca de 5-10 milhões de pessoas estejam infectadas pelo HTLV-1 no mundo e apesar dessa infecção ser endêmica em diferentes regiões geográficas, ainda permanece sem métodos terapêuticos eficazes. O genoma desse retrovírus é composto por duas fitas simples de RNA, com os genes gag, pol, env e uma região próxima à extremidade 3' conhecida como pX. A região pX contém quatro quadros abertos de leitura (ORFs) que codificam proteínas regulatórias específicas. A ORF-I codifica as proteínas p12 e p8, que quando expressas em quantidades equivalentes favorecem a infectividade e persistência viral. Mutações gênicas específicas na ORF-I do HTLV-1 podem alterar o padrão de expressão e, consequentemente, a concentração relativa destas proteínas, implicando na alteração da persistência viral e no desfecho da infecção. OBJETIVO: Caracterizar a ORF-I do HTLV-1 de pacientes com diferentes perfis clínicos. MATERIAL E MÉTODOS: Inicialmente foi realizada a anotação completa do principal genoma do HTLV-1 (ATK1), utilizado como sequência referência para a caracterização molecular da ORF-I. Em seguida, 1530 sequências da ORF-I provenientes de indivíduos assintomáticos e com HAM/TSP foram submetidas a análise de dataming para busca de associações entre mutações, carga proviral e sintomatologia. Para avaliar o grau de conservação genética da ORF-I em outros perfis clínicos, amostras de 23 pacientes assintomáticos, 11 pacientes com DIH, 13 com ATLL e 16 com HAM/TSP foram coletadas e submetidas à amplificação e sequenciamento. As sequências foram analisadas in silico utilizando programas de bioinformática para caracterização molecular. RESULTADOS: No primeiro trabalho foram compiladas as informações sobre a posição nucleotídica inicial e final dos genes do HTLV-1 e seus respectivos produtos. Em seguida, as análises das ORF-I demonstraram que apesar da baixa diversidade genética dessa região, alterações nucleotídicas específicas quando combinadas com alta carga proviral podem estar associadas ao desenvolvimento de HAM/TSP. Os dados da análise da ORFI proveniente de pacientes com diferentes perfis clínicos demonstraram a baixa diversidade genética desta região, corroborando com o fato de que o genoma do HTLV- 1 é geneticamente estável e, portanto, o desenvolvimento de uma vacina terapêutica é viável. CONCLUSÃO: Esse trabalho possibilitou a disponibilização no GenBank de sequências da ORF-I do HTLV-1 provenientes de pacientes com DIH, ATLL, HAM/TSP e pacientes assintomáticos. A partir desses dados foi possível identificar a ORF-I do HTLV-1 como um possível alvo para uma vacina terapêutica baseada na capacidade de influenciar a expressão de p12 e p8.adult T-cell leukaemia/lymphoma (ATLL), HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), infective dermatitis associated to HTLV-1 (IDH), among others. It is estimated that approximately 5-10 million people are infected with HTLV-1 in the world and although this infection is endemic in different geographic regions, it still remains without effective therapeutic methods. The genome of this retrovirus is composed of two single strands of RNA, with the genes gag, pol, env and a region near the 3' end, known as pX. The pX region contains four open reading frames (ORFs) that encode specific regulatory proteins. The ORF-I encodes the p12 and p8 proteins, which when expressed in equivalent concentrations favor infectivity and viral persistence. Specific mutations in HTLV-1 ORF-I may alter the expression and, consequently, the relative concentration of these proteins, implying in viral persistence alteration and outcome of infection. OBJECTIVE: Characterize the HTLV-1 ORF-I from patients with different clinical profiles. MATERIAL AND METHODS: First, the complete annotation of the main genome of HTLV-1 (ATK1), used as a reference sequence for the molecular characterization of ORF-I, was initially performed. Then, 1530 ORF-I sequences from asymptomatic and HAM/TSP individuals were submitted to dataming analysis to search associations. To assess the ORF-I genetic conservation status in other clinical profiles, samples from 23 asymptomatic patients, 11 patients with IDH, 13 with ATLL and 16 with HAM/TSP were collected and submitted to amplification and sequencing. These sequences were analyzed in silico using bioinformatics programs for molecular characterization. between mutations, proviral load and symptomatology. RESULTS: In the first work, the information about the initial and final nucleotide position of the HTLV-1 genes and their respective products was compiled. Then, the ORF-I analyses demonstrated that despite the low genetic diversity of this region, specific nucleotide changes when combined with high proviral load may be associated with the development of HAM/TSP. The data of ORF-I analyses from patients with different clinical profiles demonstrated the low genetic diversity of this region, corroborating the fact that the HTLV-1 genome is genetically stable and the development of a therapeutic vaccine is viable. CONCLUSION: Through this work was possible provide to GenBank HTLV-1 ORF-I sequences from patients with IDH, ATLL, HAM/TSP and asymptomatic patients. From these data, it was possible to identify HTLV-1 ORF-I as a possible target for a therapeutic vaccine based on the ability to influence p12 and p8 expression

A Fully Annotated Genome Sequence of Human T-Cell Lymphotropic Virus Type 1 (HTLV-1)

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2017-09-25T18:10:38Z No. of bitstreams: 1 Barreto FK A fully annotated....pdf: 472001 bytes, checksum: 7713907ae6e4a766b43c82e6e14974c5 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2017-09-25T18:22:35Z (GMT) No. of bitstreams: 1 Barreto FK A fully annotated....pdf: 472001 bytes, checksum: 7713907ae6e4a766b43c82e6e14974c5 (MD5)Made available in DSpace on 2017-09-25T18:22:35Z (GMT). No. of bitstreams: 1 Barreto FK A fully annotated....pdf: 472001 bytes, checksum: 7713907ae6e4a766b43c82e6e14974c5 (MD5) Previous issue date: 2017Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Bahian School of Medicine and Public Health. Salvador, BA, BrazilCatholic University of Salvador. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrasilIn the next generation of genome sequencing, sequence annotation plays an important role with respect to genome evaluation. The aim of annotation is to identify key features in the genome, such as genes and their products. Although annotation tools are available and some sequence features have been published, annotation information for many complete and partial genomes of Human T-Cell Lymphotropic Virus Type 1 (HTLV-1) remains unavailable from GenBank. Sequence analysis is critical to the understanding of the pathogenesis of HTLV-1, and a well-annotated reference sequence is an essential component in this analysis. More accurate and complete information about the HTLV-1 genome can assist the scientific community in investigations on possible therapeutic and prophylactic vaccines, as well as aid studies on the pathogenesis of HTLV-1-associated diseases. Here we describe for the first time the complete nucleotide position annotation of the frequently used HTLV-1 reference sequence, ATK1 (accession number: J02029.1)

Inferences about the global scenario of human T-cell lymphotropic virus type 1 infection using data mining of viral sequences

Human T-cell lymphotropic virus type 1 (HTLV-1) is mainly associated with two diseases: tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM) and adult T-cell leukaemia/lymphoma. This retrovirus infects five-10 million individuals throughout the world. Previously, we developed a database that annotates sequence data from GenBank and the present study aimed to describe the clinical, molecular and epidemiological scenarios of HTLV-1 infection through the stored sequences in this database. A total of 2,545 registered complete and partial sequences of HTLV-1 were collected and 1,967 (77.3%) of those sequences represented unique isolates. Among these isolates, 93% contained geographic origin information and only 39% were related to any clinical status. A total of 1,091 sequences contained information about the geographic origin and viral subtype and 93% of these sequences were identified as subtype “a”. Ethnicity data are very scarce. Regarding clinical status data, 29% of the sequences were generated from TSP/HAM and 67.8% from healthy carrier individuals. Although the data mining enabled some inferences about specific aspects of HTLV-1 infection to be made, due to the relative scarcity of data of available sequences, it was not possible to delineate a global scenario of HTLV-1 infection

Inferences about the global scenario of human T-cell lymphotropic virus type 1 infection using data mining of viral sequences

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2014-06-04T17:50:24Z No. of bitstreams: 1 Araujo TH Inferences about....pdf: 432396 bytes, checksum: 7e7a0ebdfa463339e9afa88c8c9f9e45 (MD5)Made available in DSpace on 2014-06-04T17:50:24Z (GMT). No. of bitstreams: 1 Araujo TH Inferences about....pdf: 432396 bytes, checksum: 7e7a0ebdfa463339e9afa88c8c9f9e45 (MD5) Previous issue date: 2014Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, BrasilUniversidade Federal da Bahia. Instituto de Ciências da Saúde. Salvador, BA, BrasilHuman T-cell lymphotropic virus type 1 (HTLV-1) is mainly associated with two diseases: tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM) and adult T-cell leukaemia/lymphoma. This retrovirus infects five-10 million individuals throughout the world. Previously, we developed a database that annotates sequence data from GenBank and the present study aimed to describe the clinical, molecular and epidemiological scenarios of HTLV-1 infection through the stored sequences in this database. A total of 2,545 registered complete and partial sequences of HTLV-1 were collected and 1,967 (77.3%) of those sequences represented unique isolates. Among these isolates, 93% contained geographic origin information and only 39% were related to any clinical status. A total of 1,091 sequences contained information about the geographic origin and viral subtype and 93% of these sequences were identified as subtype “a”. Ethnicity data are very scarce. Regarding clinical status data, 29% of the sequences were generated from TSP/HAM and 67.8% from healthy carrier individuals. Although the data mining enabled some inferences about specific aspects of HTLV-1 infection to be made, due to the relative scarcity of data of available sequences, it was not possible to delineate a global scenario of HTLV-1 infection