Project description:The recent reemergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the rapid dissemination of the virus in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil, we generated 18 complete and nearly complete genomes from the peak of the epidemic curve from nonhuman primates (NHPs) and human infected cases across the Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the estimated timing, source, and likely routes of yellow fever virus transmission and dispersion during one of the largest outbreaks ever registered in Brazil. We showed that during the recent epidemic, YFV was reintroduced from Minas Gerais to the Espírito Santo and Rio de Janeiro states multiple times between 2016 and 2019. The analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce the idea that continued genomic surveillance strategies can provide information on virus genetic diversity and transmission dynamics that might assist in understanding arbovirus epidemics.IMPORTANCE Arbovirus infections in Brazil, including yellow fever, dengue, zika, and chikungunya, result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by the limited availability of genomic data. In this study, we investigated the genetic diversity and spatial distribution of YFV during the current outbreak by analyzing genomic data from areas in southeastern Brazil not covered by other previous studies. To gain insights into the routes of YFV introduction and dispersion, we tracked the virus by sequencing YFV genomes sampled from nonhuman primates and infected patients from the southeastern region. Our study provides an understanding of how YFV initiates transmission in new Brazilian regions and illustrates that genomics in the field can augment traditional approaches to infectious disease surveillance and control.

Project description:Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.

Project description:Purpose: In carcinogenesis, the stomach, the MYC gene is frequently amplified and its protein is overexpressed, which contributes to uncontrolled cell proliferation mucosal gástrica.Três cell lines were subjected to sequencing semiconductor Proton Ion before and after the silencing of MYC. These lines were originating from diffuse and intestinal histologic types and the third of a metastasis from a stomach tumor originating in a ascites. Methods: mRNA profiles were generated from three established lines of CG previously characterized by our group. AGP01 (Obtained from ascitic fluid of an intestinal-type GC), ACP02 (diffuse-type GC) and ACP03 (intestinal-type GC). The three cell lines present chromosome 8 trisomy and MYC amplification, reflecting the genetic characteristics found in gastric cancer samples from Northern Brazil. They were generated by sequencing depth in triplicate using the Sequencer ™ Ion Proton. Raw data reads Obtained by primary sequencing Were Submitted to quality control in order to calculate alignment and to assess how the reads behave When Compared to the reference human genome (Hg19 / GRCh37). The aligned reads Were mapped and quantified using TMAP. Gene expression levels Were quantified using Sailfish pack software and the RPKM (Reads Per kilobase per Million mapped reads) method was used to estimate Then expression levels gene. Results: Using analysis of an optimized workflow, we mapped more than 13 million readings sequences between our samples from the human genome. Were mapped a total of 917 up-regulated genes and 1,566 different genes down-regulated Were When comparing the expression of AGP01 non-targeting control (1C) versus AGP01 MYC-silenced (1M), with a total of 2,483 DEGS. The evaluation of ACP02 cells treated with non-targeting control (2C) versus ACP02 MYC-silenced (2M) Showed a total of 5,327 DEGS, with 1,299 up-regulated and 4,098 down-regulated genes. The total of 4,117 were found DEGS When comparing ACP03 control cells (3C) with ACP03 MYC-silenced cells, with 3,274 up-regulated and 843 down-regulated genes. Silencing of the MYC gene, allowed the detection of more than 1,000 DEGS (Differentially Expressed Genes) between the three strains that were considered significant if the False Discovery Rate (FDR) was ≤0.001, P-value <0.05, and the absolute value of the Fold change (FC) was ≥1. The analysis of DEGS showed 22% and 34% were detected with a profile down-regulated in intestinal and diffuse type, respectively. The up-regulated profile was higher in the intestinal type, with 77% of DEGS than the diffuse type with 13% DEGS. Furthermore, the lineage from metastasis showed 33% of DEGS up-regulated and 66% of DEGS down-regulated. Conclusions: Our study is the first to describe bioinformatics methods the effect before and after the silencing of the MYC gene in cell lines of gastric cancer northern people of Brazil. Our results showed that depending on the histological type there are many functional genes between the three strains that were recorded significantly associated with pathways enriched for cancer, metabolism, adhesion, cell cycle, proteolysis and signaling, suggesting the existence of routes of different carcinogenesis that lead normal mucosa to turn into gastric cancer.

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Spread of cantagalo virus to northern Brazil.

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