Search

The Orthobunyavirus oropoucheense species encompasses a group of arthropod-borne zoonotic viruses transmitted by biting midges to animals including humans. Several large-scale human outbreaks caused by the prototype member of this species, Oropouche virus (OROV) have been documented since the 1970s and were primarily confined to the Amazon basin. However, since 2022, more widespread OROV outbreaks have been unfolding in Brazil and across South America, with cases exported to Cuba, Italy, Spain, USA and Germany. In Brazil, the virus has reached and established communitary transmission in all geographic areas of the country. We isolated, characterized the cytopathic effect and recovered the full genome of two OROV isolates from the 2022-24 outbreak detected in patients from the Pernambuco state. Phylogenetic data supports a direct introduction from the Amazonas state, the epicenter of the epidemics in the country. As case counts accumulate in the state mounting evidence is supporting the establishiment of sustained transmission chains. Continued studies are critical to understand the transmission cycle in this region, including the most important vectors and reservoirs, to appropriately deploy control measures., (© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

Dengue is a global and growing health threat, especially in Southeast Asia, West Pacific and South America. Infection by the dengue virus (DENV) results in dengue fever, which can evolve to severe forms. Cytokines, especially interferons, are involved in the immunopathogenesis of dengue fever, and so may influence the disease outcomes. The aim of this study was to investigate the association between severe forms of dengue and two single nucleotide polymorphisms (SNPs) in the interferon-gamma gene (IFNG): A256G (rs2069716) and A325G (rs2069727). We included 274 patients infected with DENV serotype 3: 119 cases of dengue without warning signs (DWoWS), and 155 with warning signs (DWWS) or severe dengue (SD). DNA was extracted, and genotyped with Illumina Genotyping Kit or real time PCR (TaqMan probes). We estimated the adjusted Odds Ratios (OR) by multivariate logistic regression models. When comparing with the ancestral AA/AA diplotype (A256G/A325G), we found a protective association of the AA/AG against DWWS/SD among patients with secondary dengue (OR 0.51; 95% IC 0.24-1.10, p = 0.085), adjusting for age and sex. The variant genotype at locus A325G of the IFNG, in combination with the ancestral genotype at locus A256G, can protect against severe clinical forms of secondary dengue in Brazilian DENV3-infected patients.

We present a genome polymorphisms/machine learning approach for severe COVID-19 prognosis. Ninety-six Brazilian severe COVID-19 patients and controls were genotyped for 296 innate immunity loci. Our model used a feature selection algorithm, namely recursive feature elimination coupled with a support vector machine, to find the optimal loci classification subset, followed by a support vector machine with the linear kernel (SVM-LK) to classify patients into the severe COVID-19 group. The best features that were selected by the SVM-RFE method included 12 SNPs in 12 genes: PD-L1 , PD-L2 , IL10RA , JAK2 , STAT1 , IFIT1 , IFIH1 , DC-SIGNR , IFNB1 , IRAK4 , IRF1 , and IL10 . During the COVID-19 prognosis step by SVM-LK, the metrics were: 85% accuracy, 80% sensitivity, and 90% specificity. In comparison, univariate analysis under the 12 selected SNPs showed some highlights for individual variant alleles that represented risk ( PD-L1 and IFIT1 ) or protection ( JAK2 and IFIH1 ). Variant genotypes carrying risk effects were represented by PD-L2 and IFIT1 genes. The proposed complex classification method can be used to identify individuals who are at a high risk of developing severe COVID-19 outcomes even in uninfected conditions, which is a disruptive concept in COVID-19 prognosis. Our results suggest that the genetic context is an important factor in the development of severe COVID-19.

This paper examines the predictability of COVID-19 worldwide lethality considering 43 countries. Based on the values inherent to Permutation entropy ( H s ) and Fisher information measure ( F s ), we apply the Shannon-Fisher causality plane (SFCP), which allows us to quantify the disorder an evaluate randomness present in the time series of daily death cases related to COVID-19 in each country. We also use Hs and Fs to rank the COVID-19 lethality in these countries based on the complexity hierarchy. Our results suggest that the most proactive countries implemented measures such as facemasks, social distancing, quarantine, massive population testing, and hygienic (sanitary) orientations to limit the impacts of COVID-19, which implied lower entropy (higher predictability) to the COVID-19 lethality. In contrast, the most reactive countries implementing these measures depicted higher entropy (lower predictability) to the COVID-19 lethality. Given this, our findings shed light that these preventive measures are efficient to combat the COVID-19 lethality., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors. Published by Elsevier B.V.)

Introduction and Objective: Hepatotoxicity during tuberculosis (TB) treatment is frequent and may be related to the Arylamine N-Acetyltransferase (NAT2) acetylator profile, in which allele frequencies differ according to the population. The aim of this study was to investigate functional polymorphisms in NAT2 associated with the development of hepatotoxicity after initiating treatment for TB in people living with HIV/AIDS (PLWHA) in Pernambuco, Northeast Brazil., Material and Methods: This was a prospective cohort study that investigated seven single nucleotide polymorphisms located in the NAT2 coding region in 173 PLWHA undergoing TB treatment. Hepatotoxicity was defined as elevated aminotransferase levels and identified as being three times higher than it was before initiating TB treatment, with associated symptoms of hepatitis. A further 80 healthy subjects, without HIV infection or TB were used as a control group. All individuals were genotyped by direct sequencing., Results: The NAT2*13A and NAT2*6B variant alleles were significantly associated with the development of hepatotoxicity during TB treatment in PLWHA (p<0.05). Individual comparisons between the wild type and each variant genotype revealed that PLWHA with signatures NAT2*13A/NAT2*13A (OR 4.4; CI95% 1.1-18.8; p 0.037) and NAT2*13A/NAT2*6B (OR 4.4; CI95% 1.5-12.7; p 0.005) significantly increased the risk of hepatotoxicity., Conclusion: This study suggests that NAT2*13A and NAT2*6B variant alleles are risk factors for developing hepatotoxicity, and PLWHA with genotypes NAT2*13A/NAT2*13A and NAT2*13A/NAT2*6B should be targeted for specific care to reduce the risk of hepatotoxicity during treatment for tuberculosis., (Copyright © 2019 Fundación Clínica Médica Sur, A.C. Published by Elsevier España, S.L.U. All rights reserved.)

Dengue has become one of the most important worldwide arthropod-borne diseases. Dengue phenotypes are based on laboratorial and clinical exams, which are known to be inaccurate., Objective: We present a machine learning approach for the prediction of dengue fever severity based solely on human genome data., Methods: One hundred and two Brazilian dengue patients and controls were genotyped for 322 innate immunity single nucleotide polymorphisms (SNPs). Our model uses a support vector machine algorithm to find the optimal loci classification subset and then an artificial neural network (ANN) is used to classify patients into dengue fever or severe dengue., Results: The ANN trained on 13 key immune SNPs selected under dominant or recessive models produced median values of accuracy greater than 86%, and sensitivity and specificity over 98% and 51%, respectively., Conclusion: The proposed classification method, using only genome markers, can be used to identify individuals at high risk for developing the severe dengue phenotype even in uninfected conditions., Significance: Our results suggest that the genetic context is a key element in phenotype definition in dengue. The methodology proposed here is extendable to other Mendelian based and genetically influenced diseases.

Dengue is considered one of the most challenging public health threats in the world. Infection may be clinically asymptomatic but can result in severe forms. The indoleamine 2,3 dioxygenase ( IDO ) gene encodes one of first enzymes ( IDO ) of the kynurenine pathway. This study aimed to verify the association between G2431A IDO1 gene single nucleotide polymorphism (SNP) (rs3739319) and dengue fever development. We included 299 dengue-infected individuals in the study and 96 dengue-free controls. We collected clinical and diagnostic test data and divided the patients with dengue infection into three groups, based on World Health Organization (WHO) criteria: 131 Dengue without warning signs (DWOS), 143 Dengue with warning signs (DWS), and 25 severe dengue (SD). We genotyped 193 of the dengue cases using quantitative polymerase chain reaction to the SNP rs3739319. The other 106 dengue cases and 96 dengue-free controls had previously been genotyped using the Illumina Genotyping Kit. Genotyping of the infected patients revealed frequencies of 106 GG (35.4%), 126 GA (42.1%), and 67 AA (22.4%), whereas the nondengue exposed control group showed similar frequencies, 29 GG (30.2%), 52 GA (54.2%), and 15 AA (15.6%). Under risk analysis we found that AA genotype patients had a higher risk of developing SD in a codominant model (AA × GG; odds ratio [OR] = 11.5-fold in comparison to non-SD group -DWOS and -DWS patients; confidence interval [CI] = 0.02-0.32; Yates correction = 1.9e-05) and in a recessive model (AA × AG+GG; OR = 9.41; CI = 3.62-26.7; Yates correction = 4.8e-08). An allelic model reinforced the association between A allele and SD phenotype development that was found in the SD versus DWOS+DWS analysis (OR = 3.59; CI = 1.50-9.56; Yates correction = 0.0033). Our data show an association between the IDO G2431A variant and the risk for SD. This SNP may be relevant for further investigation into disease mechanisms and host factors in future genetic and pathophysiological studies.

Hepatotoxicity is frequently reported as an adverse reaction during the treatment of tuberculosis. The aim of this study was to determine the incidence of hepatotoxicity and to identify predictive factors for developing hepatotoxicity after people living with HIV/AIDS (PLWHA) start treatment for tuberculosis. This was a prospective cohort study with PLWHA who were monitored during the first 60 days of tuberculosis treatment in Pernambuco, Brazil. Hepatotoxicity was considered increased levels of aminotransferase, namely those that rose to three times higher than the level before initiating tuberculosis treatment, these levels being associated with symptoms of hepatitis. We conducted a multivariate logistic regression analysis and the magnitude of the associations was expressed by the odds ratio with a confidence interval of 95%. Hepatotoxicity was observed in 53 (30.6%) of the 173 patients who started tuberculosis treatment. The final multivariate logistic regression model demonstrated that the use of fluconazole, malnutrition and the subject being classified as a phenotypically slow acetylator increased the risk of hepatotoxicity significantly. The incidence of hepatotoxicity during treatment for tuberculosis in PLWHA was high. Those classified as phenotypically slow acetylators and as malnourished should be targeted for specific care to reduce the risk of hepatotoxicity during treatment for tuberculosis. The use of fluconazole should be avoided during tuberculosis treatment in PLWHA.

Four genetic polymorphisms located at the promoter (C-257T) and coding regions of CFH gene (exon 2 G257A, exon 14 A2089G and exon 19 G2881T) were investigated in 121 dengue patients (DENV-3) in order to assess the relationship between allele/haplotypes variants and clinical outcomes. A statistical value was found between the CFH-257T allele (TT/TC genotypes) and reduced susceptibility to severe dengue (SD). Statistical associations indicate that individuals bearing a T allele presented significantly higher protein levels in plasma. The -257T variant is located within a NF-κB binding site, suggesting that this variant might have effect on the ability of the CFH gene to respond to signals via the NF-κB pathway. The G257A allelic variant showed significant protection against severe dengue. When CFH haplotypes effect was considered, the ancestral CG/CG promoter-exon 2 SNP genotype showed significant risk to SD either in a general comparison (ancestral × all variant genotypes), as well as in individual genotypes comparison (ancestral × each variant genotype), where the most prevalent effect was observed in the CG/CG × CA/TG comparison. These findings support the involvement of -257T, 257A allele variants and haplotypes on severe dengue phenotype protection, related with high basal CFH expression., (Copyright © 2013 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.)

The management of acute dengue patients during outbreaks is a challenging problem. Most of the dengue fever cases are benign, but some cases develop into a severe and possibly lethal vasculopathy, known as dengue hemorrhagic fever. Early symptoms of dengue and hemorrhagic fever are very similar. An early differential diagnosis is needed to predict which of these two clinical presentations is crucial to proper patient care and public health management. This study evaluates the predictive potential of specific mRNA expression markers of dengue hemorrhagic fever using quantitative real-time PCR assays. Six candidate 'dengue hemorrhagic fever specific signature genes' were evaluated and all showed good correlation among their transcription levels at early days of infection and the later development of severe vasculopathy. The markers selected were able to indicate, at early stages of infection, the evolution of a dengue-infected patient to the severe form of the illness. Despite the fact that these results grant further validation studies, the panel of candidate prognostic markers obtained demonstrated the potential to be useful for clinical use in the form of a fast assay based in blood samples.

Transcriptional changes in Pisolithus tinctorius leading to ectomycorrhizal formation in P. tinctorius- Castanea sativa were investigated using a 12-h fungal interaction in vitro system. Using a 3107-cDNA clone microarray, 34 unique expressed sequence tags (ESTs) were found to be differentially expressed. These ESTs represent 14 known genes, 5 upregulated and 9 downregulated, and 20 orphan sequences. Some transcripts of upregulated genes (with unknown function) were previously identified in other mycorrhizal Pisolithus spp. associations. ESTs for S-adenosyl-L-homocysteine hydrolase and several orphan sequences were identified in our system. The identified transcript of downregulated genes involved hydrophobins, 5S, 18S, and 28S ribosomal RNA genes, large subunits of ribosomal RNA (mitochondrial gene), and two types of heat shock proteins. This study demonstrates the high complexity of molecular events involved in the preinfection steps and suggests the utilization of different fungal gene repertories before ectomycorrhizal formation. These data constitute a first contribution for the molecular understanding of early signaling events between P. tinctorius and C. sativa roots during ectomycorrhizal formation.

Dengue disease can clinically evolve from an asymptomatic and mild disease, known as dengue fever (DF), to a severe disease known as dengue hemorrhagic fever (DHF). Recent evidence has shown how host genetic factors can be correlated with severe dengue susceptibility or protection. Many of these genes, such as CD209, TNF-a, vitamin D receptor, and FC gamma receptor IIA, are components of the innate immune system, suggesting that innate responses might have a role in dengue pathogenesis. MBL2 gene polymorphisms have been shown to modulate susceptibility or protection in many viral diseases. We investigated the involvement of MBL2 gene in the dengue clinical outcome through the analysis of MBL2 exon 1 polymorphisms (at codons 52, 54, and 57) known to be associated with reduced serum levels of the MBL protein. The genotypes of 110 well-characterized dengue-positive patients were statistically analyzed to establish possible correlations between MBL2 polymorphisms and parameters such as sex, type of infection (primary or secondary response), race/ethnicity, course of infection, and age. We found significant correlations between wild-type AA MBL2 genotype and age as associated risk factors for development of dengue-related thrombocytopenia.