Dataset Information

Complete Genome Sequences of Dengue Virus Type 2 Epidemic Strains from Reunion Island and the Seychelles.

ABSTRACT: Dengue virus has recently reemerged in the southern Indian Ocean islands, causing outbreaks in Reunion Island and the Seychelles. In the present study, we determined the complete genome sequences of closely related clinical isolates of dengue virus type 2 circulating in the Seychelles in 2016 and Reunion Island in 2018.

SUBMITTER: Pascalis H

PROVIDER: S-EPMC6979306 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Complete Genome Sequences of Dengue Virus Type 2 Epidemic Strains from Reunion Island and the Seychelles.

Pascalis Hervé H Biscornet Leon L Toty Céline C Hafsia Sarah S Roche Marjolaine M Desprès Philippe P Atyame Nten Célestine C Bibi Jastin J Louange Meggy M Gedeon Jude J Mavingui Patrick P

Microbiology resource announcements 20200123 4

Dengue virus has recently reemerged in the southern Indian Ocean islands, causing outbreaks in Reunion Island and the Seychelles. In the present study, we determined the complete genome sequences of closely related clinical isolates of dengue virus type 2 circulating in the Seychelles in 2016 and Reunion Island in 2018. ...[more]

PMID: 31974157

Similar Datasets

Project description:BackgroundAn unprecedent increase in the number of cases and deaths reported from dengue virus (DENV) infection has occurred in the southwestern Indian ocean in recent years. From 2017 to mid-2021 more than 70,000 confirmed dengue cases were reported in Reunion Island, and 1967 cases were recorded in the Seychelles from 2015 to 2016. Both these outbreaks displayed similar trends, with the initial circulation of DENV-2 which was replaced by DENV-1. Here, we aim to determine the origin of the DENV-1 epidemic strains and to explore their genetic characteristics along the uninterrupted circulation, particularly in Reunion.MethodsNucleic acids were extracted from blood samples collected from dengue positive patients; DENV-1 was identified by RT-qPCR. Positive samples were used to infect VERO cells. Genome sequences were obtained from either blood samples or infected-cell supernatants through a combination of both Illumina or MinION technologies.ResultsPhylogenetic analyses of partial or whole genome sequences revealed that all DENV-1 sequences from Reunion formed a monophyletic cluster that belonged to genotype I and were closely related to one isolate from Sri Lanka (OL752439.1, 2020). Sequences from the Seychelles belonged to the same major phylogenetic branch of genotype V, but fell into two paraphyletic clusters, with greatest similarity for one cluster to 2016-2017 isolate from Bangladesh, Singapore and China, and for the other cluster to ancestral isolates from Singapore, dating back to 2012. Compared to publicly available DENV-1 genotype I sequences, fifteen non-synonymous mutations were identified in the Reunion strains, including one in the capsid and the others in nonstructural proteins (NS) (three in NS1, two in NS2B, one in NS3, one in NS4B, and seven in NS5).ConclusionIn contrast to what was seen in previous outbreaks, recent DENV-1 outbreaks in Reunion and the Seychelles were caused by distinct genotypes, all likely originating from Asia where dengue is (hyper)endemic in many countries. Epidemic DENV-1 strains from Reunion harbored specific non-synonymous mutations whose biological significance needs to be further investigated.

Project description:Depredation in marine ecosystems is defined as the damage or removal of fish or bait from fishing gear by predators. Depredation raises concerns about the conservation of species involved, fisheries yield and profitability, and reference points based on stock assessment of depredated species. Therefore, the development of accurate indicators to assess the impact of depredation is needed. Both the Reunion Island and the Seychelles archipelago pelagic longline fisheries targeting swordfish (Xiphias gladius) and tuna (Thunnus spp.) are affected by depredation from toothed whales and pelagic sharks. In this study, we used fishery data collected between 2004 and 2015 to propose depredation indicators and to assess depredation levels in both fisheries. For both fisheries, the interaction rate (depredation occurrence) was significantly higher for shark compared to toothed whale depredation. However, when depredation occurred, toothed whale depredation impact was significantly higher than shark depredation impact, with higher depredation per unit effort (number of fish depredated per 1000 hooks) and damage rate (proportion of fish depredated per depredated set). The gross depredation rate in the Seychelles was 18.3%. A slight increase of the gross depredation rate was observed for the Reunion Island longline fleet from 2011 (4.1% in 2007-2010 and 4.4% in 2011-2015). Economic losses due to depredation were estimated by using these indicators and published official statistics. A loss of 0.09 EUR/hook due to depredation was estimated for the Reunion Island longline fleet, and 0.86 EUR/hook for the Seychelles. These results suggest a southward decreasing toothed whale and shark depredation gradient in the southwest Indian Ocean. Seychelles depredation levels are among the highest observed in the world revealing this area as a "hotspot" of interaction between pelagic longline fisheries and toothed whales. This study also highlights the need for a set of depredation indicators to allow for a global comparison of depredation rates among various fishing grounds worldwide.

Dataset Information

Complete Genome Sequences of Dengue Virus Type 2 Epidemic Strains from Reunion Island and the Seychelles.

Publications

Complete Genome Sequences of Dengue Virus Type 2 Epidemic Strains from Reunion Island and the Seychelles.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets