Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1030438 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26454800_1.fastq.gz | Fastqsanger.gz | |||
| SRR26454800_2.fastq.gz | Fastqsanger.gz | |||
| SRR26454801_1.fastq.gz | Fastqsanger.gz | |||
| SRR26454801_2.fastq.gz | Fastqsanger.gz | |||
| SRR26454802_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered. Genome DNA from Peruvian Isolates vs. Reference 3D7
2010-08-04 | E-GEOD-22861 | biostudies-arrayexpress
Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered.
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Project description:Peruvian Native American individuals were genotyped as part of the Peruvian Genome Project (PGP). This data was used to infer population structure, demographic history and natural selection. We addressed question about gene flow across the Andes and Natural Selection in Andes and Amazon
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Project description:Arthropod-borne viruses (arboviruses) represent a threat to global public health, especially in the tropical and subtropical regions of the world. More than 150 arboviruses can infect humans; they cause mainly febrile illness, although hemorrhagic complications and diseases affecting the central nervous system (SNC) can also be observed. Arboviruses represent a threat to Brazil and, therefore, a permanent surveillance of these viruses is required to timely reduce the risk of epidemic outbreaks. The Brazilian Amazon region is where the highest number of arboviruses has been detected in the world. Besides, malaria is also endemic in the Amazon region, with a significant predominance of Plasmodium vivax. It is often difficult to differentiate between malaria and arboviral diseases, as they share similar clinical features and laboratory findings, mainly undifferentiated fever. This study aimed to estimate possible viral etiology in patients with febrile syndrome negative for Plasmodium infection, in the Brazilian Amazon. We initially analyzed serum samples of 124 participants with a DNA microarray platform designed for the detection of arboviruses and viruses transmitted by small mammals, but no virus was detected. Then, the serum samples of 76 participants were analyzed with a deep New Generation Sequencing, which showed evidence of the presence of only one arbovirus, the Zika virus in only one pool of 9 serum samples. This result is in contrast with our hypothesis, showing that arboviruses are not frequent in suspected malaria cases in Manaus, Brazil. Other viruses instead of arboviruses were found in this study. Primate erythrovirus 1 was the virus most frequently found virus in the suspected malaria patients, followed by Enterobacteria phage lambda. Besides, we detected, in a lower frequency, the Pegivirus C. In addition to the exogenous viruses, we also detected human endogenous retrovirus in all pools. Due to the high number of viruses that are important in the differential diagnosis of malaria, cost-effective and simple high throughput methods are required, helping molecular surveillance of misdiagnosed viral infections. Further studies with more robust sample sizes in other areas in the Amazon are needed.
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