Viral immunogenic footprints conferring T cell cross-protection to SARS-CoV-2 and its variants

COVID-19 brought scenes from sci-fi movies into real life. Infected individuals include asymptomatic cases to severe disease leading to death, suggesting the involvement of the genetic constitution of populations and pathogens contributing to differential individuals’ outcomes. To investigate shared immunogenic features between SARS-CoV-2 targets and other coronaviruses, we modeled their peptides in 3D structures of HLA-A*02:01 (pMHC), comparing their molecular surfaces These structures were also compared with a panel of epitopes from unrelated viruses, looking for potential triggers conferring cross-protection in uninfected individuals. As expected, SARS-CoV 1 and 2 peptides share molecular and physicochemical features, providing an explanation for the verified experimental immunogenicity among them. Surprisingly, even discordant sequences from human coronaviruses 229E, OC43 and epitopes from unrelated viruses involved in endemic human infections exhibit similar fingerprints of immunogenicity with SARS-CoV-2 peptides. The same approach indicates a conserved CD8+ T cell recognition between Wuhan SARS-CoV-2 sequences and altered peptides from Variants of Concern. Examination of structural data over epitope sequence analysis here could explain how previous infections may produce a heterologous immunity response in a global scale against emergent diseases such as Covid-19, mitigating its full lethal potential, and paves the way for the development of wide spectrum vaccine development

SARS-CoV-2’s Variants of Concern: A Brief Characterization

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disclose the variants of concern (VOC) including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and Omicron (B.1.1.529). Its spike protein (S) present on the surface of the virus is recognized by the host cell receptor, the angiotensin-2 converting enzyme (ACE2) which promotes their entry into the cell. The mutations presented by VOCs are found in RBD and the N-terminal region of S protein. Therefore, mutations occurring in RBD can modify the biological and immunogenic characteristics of the virus, such as modifying the spike affinity for ACE2, increasing the virus transmissibility, or conferring the ability to escape the immune responses. The raise of a potential new SARS-CoV-2 variant capable of evading the host defenses at the same time maintaining its fitness justifies the importance of continued genetic monitoring of the pandemic coronavirus

Synthesizing the connections between environmental disturbances and zoonotic spillover

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identifi cation, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region

Peptídeos virais imunogênicos como determinantes de reatividade cruzada no sistema imune

A identificação de epitopos e motivos virais para serem utilizados na imunização de humanos e animais é um objetivo importante e essencial em pesquisa imunológica. No momento, com novas ferramentas de bioinformática, diferentes abordagens são possíveis. A importância da bioinformática reside na possibilidade de trabalhar com grandes quantidades de dados de forma que, várias etapas experimentais do desenvolvimento de vacinas podem ser abreviadas. Quando buscamos por motivos virais (objetivando a vacinação) é necessário estar ciente de todos os passos envolvidos na seleção e apresentação de peptídeos ao sistema imune. Devemos considerar que muitos peptídeos podem ser gerados a partir de uma única proteína, mas apenas uma fração destes peptídeos é realmente apresentada ao sistema imune, pois os peptídeos devem ser capazes de atravessar diferentes “bottlenecks” e apenas aqueles apresentando características específicas serão capazes de estimular o sistema imune. As abordagens apresentadas nesta tese incluem o estabelecimento de um banco de dados de epitopos virais descritos na literatura e a comparação desses epitopos buscando identificar características similares entre eles. Os epitopos selecionados foram classificados de acordo com suas propriedades físico-químicas (polaridade e carga dos grupos R de seus aminoácidos). Das 69 sequências de epitopos incluídas em nossa base de dados, 31 (44,93%) apresentaram, em sítios potenciais de ancoragem ao MHC, aminoácidos com resíduos não-polares. A partir desses resultados é possível inferir o seguinte motivo consenso: X [AGPVLIM] X(6) [AGPVLIM] para epitopos virais. As sequências virais foram então comparadas àquelas de outras proteínas buscando verificar se elas são exclusivamente representadas em vírus: 1) primeiro os epitopos foram comparados a todas as sequências depositadas no GenBank (independente da origem); 2) a seguir, as comparações foram direcionadas a sequências de origem humana. A segunda abordagem foi usada para verificar o potencial de indução de reações autoimunes. As sequências de saída foram classificadas de acordo com seu organismo de origem. Das 31 sequências alinhadas de acordo com a similaridade dos resíduos de ancoragem, 29 (93,54%) apresentaram similaridade significante (estabelecida como 80% ou mais) com outras sequências virais. Destas, 12 (38,71%) apresentavam similaridade apenas com outras sequências de origem viral, nove (29,03%) apresentavam similaridade com sequências de origem bacteriana e duas (6,45%) apresentavam similaridade com sequências humanas, sugerindo que a grande maioria dos epitopos virais pode ser utilizada no desenvolvimento de vacinas. A habilidade dos epitopos serem gerados pela via de processamento de antígenos foi também testada. Uma parte das proteínas citosólicas sofre o processo de ubiquitinação que as dirige para o complexo enzimático proteolítico, denominado proteossomo. Do total de epitopos, cinquenta (73,53%) apresentaram uma sequência que permitia um corte exato na extremidade carbóxi terminal. Este número alcançou 86,67% (26 epitopos), quando restringimos a análise aos epitopos apresentando os resíduos de ancoragem compartilhados, sugerindo que a maioria dos epitopos apresentava os requerimentos clássicos para o processamento antigênico. Das estruturas do Protein Data Bank e de dados de modelagem, foi possível observar que os sítios de clivagem preditos na região amino terminal dos epitopos eram estruturalmente relacionados a alças na estrutura da proteína original (66,7%). Estes dados sugerem que há uma clivagem preferencial em alças (χ2=6.09 p=0.047). O banco de dados de ligantes peptídicos do EpiJen foi utilizado para avaliar a capacidade dos epitopos em serem carreados pelo complexo da TAP. A partir dessa comparação observamos que o motivo predito estava mais representado do que todas outras possíveis sequências entre as saídas, sugerindo novamente que estas características são necessárias à seleção e apresentação de epitopos. Concluindo, sugerimos que é possível identificar padrões entre epitopos derivados de virus e que a predição de motivos virais conservados pode ser aplicada ao desenvolvimento de vacinas. Além disso, considerando a existência de reatividade cruzada, sugerimos que é possível imunizar contra uma quantidade consideravelmente grande de alvos virais utilizando um número de epitopos reduzido. Estudos sobre os aspectos e características dos epitopos virais são o primeiro passo rumo a uma nova geração de vacinas.The identification of epitopes and viral motifs to be used in the immunization of both humans and other animals is an important and essential objective in immunology research. At present, with the new tools of the bioinformatics different approaches are possible. The importance of the bioinformatics is exemplified by its capacity to handle a large amount of data in order to bypass several methodological steps in vaccine development. When searching for conserved viral motifs it is necessary to be aware of all the steps involved in peptide selection and presentation. In this way, we should consider that many different peptides can be generated from a given protein, but only a fraction of these peptides will actually be presented to the immune system. The approaches presented in this thesis include the establishment of a viral epitope databank from sequences described in the literature and the comparison of these epitopes in order to identify similar features among then. The selected epitopes were classified according to their physicochemical properties (i.e. polarity and charge of their amino acid–R groups). From the 69 sequences of epitopes included in our database, 31 (44.93%) presented, in potential MHC anchor sites, amino acids whit non-polar residues. From this, it is possible to infer the following consensus motif: X [AGPVLIM] X(6) [AGPVLIM]. The viral sequences were then compared to those of other proteins in order to verify if they are exclusively represented in viruses: 1) first, the epitopes were compared to all sequences stored in GenBank (disregarding their origin); 2) then, the comparisons were directed to the sequences from human origin. The output sequences were classified according to the organism of origin. From the 31 sequences aligned according to their anchor residues, 29 (93.54%) presented significant similarity (established as 80% or above) with other viral sequences. From these, 12 (38.71%) presented similarity only with other sequences from viral origin, nine (29.03%) presented similarity with sequences from bacterial origin and two (6.45%) presented significant similarity to human sequences, suggesting that a great majority of these viral epitopes could be used in vaccine development. The hability of the epitopes to be generated by antigen processing pathway was also tested. A fraction of all cytosolic proteins suffers the ubiquitination process that directs them to the proteolytic enzymatic complex, called proteasome. From the whole databank, fifty epitopes (73.53%) presented a sequence that allowed a precise cut at the carboxy terminal region. This number reached 86.67% (26 epitopes) when we restricted this analysis to the epitopes presenting the shared anchor residues, suggesting that the majority of the epitopes presented the classical requirements to antigenic processing. From the Protein Data Bank structures and from the modelling data, we could observe that the predicted cleavage sites on the amino-terminal region of the epitopes were structurally related to loops on the structure of the original protein (66.7%), suggesting a preferential cleavage at loops (χ2=6.09 p=0.047). The TAP ligands peptide database of EpiJen was used in order to evaluate the epitopes capacity to be carried by the TAP complex. We were able to observe that our predicted motif was present more frequently than every other possible sequence among the outputs, again suggesting that this feature is necessary to epitope selection and presentation. In conclusion, we suggest that it is possible to identify patterns among virus-derived epitopes and that the prediction of viral conserved motifs would allow the development of vaccines. Also, considering the existence of cross reactivity, we suggest that it will be possible to cover a considerably large amount of targets using a limited number of viral peptides. Equally important is the immunogenicity of viral peptides, since only a fragment and not the whole viral particle will challenge the immune system, therefore reducing risks of undesired immune responses. Studies on viral epitopes features and characteristics are the first step towards a new generation of vaccines

Pesquisa do fator V Leiden e da mutação 20210A no gene da protrombina (fator II) em pacientes com lúpus eritematoso sistêmico

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Pesquisa do fator V Leiden e da mutação 20210A no gene da protrombina (fator II) em pacientes com lúpus eritematoso sistêmico

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Uso de bioinformática para simulação proteolítica de proteínas virais e análise estrutural de epitopos imunodominantes

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