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PARTNER N° |
18 / NIPH / 999478883 |
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NAME OF INSTITUTION |
Norwegian Institute of Public Health |
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BRIEF DESCRIPTION OF THE TEAM |
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The NIPH-team is utilizing their recently established genome sequencing facility to study outbreaks and evolution of bacterial and viral pathogens. On-going large-scale projects focus on DNA- and RNA viruses, such as TBEV, ZIKV, DENV, Mycobacterium tuberculosis, Neisseriae meningitides, Escherichia coli as well as various metagenomic datasets. The team is actively working on applying phylodynamic methods as well as novel epidemiological methods to reconstruct outbreaks and transmission events. The team-members is also involved in a number of projects in Africa and South America, including, but not limited to, Neisseriae meningitides epidemiology in Burkina Faso and Ethiopia, Ebola vaccination in Guinea, HCV prevalence and spread in Nepal, the evolution of drug resistant tuberculosis in South America and has recently started working on recovering whole genome viral sequences from human serum samples from Colombia. |
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KEY CONTACT PERSON(S) |
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Key scientific contact person 1 (Team leader) |
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Name |
John H.–O. Pettersson |
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Photo |
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Position in the Institution |
Researcher |
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Email address |
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Phone number
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(+47) 2107 6895 |
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Mobile phone number |
(+46) 732 612 611 |
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Postal address |
Norwegian Institute of Public Health Dept of infectious disease epidemiology and modelling PO box 4404, N-0403 Oslo Norway
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Role in the Consortium |
WP: WP3 – Virology and Antivirals |
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Task: Task 3.2 : Comparative genomics |
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Sub-task: 3.2.2: Virus genetic diversity and genetic epidemiology (virulence/emergence) (Theys) 3.2.3: Molecular epidemiology & phylogeography (Abecasis) |
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Role: Subtask 3.2.2: Virus genetic diversity and genetic epidemiology (virulence/emergence) (Theys) Various genetic regions will be analyzed (based on conservation, phylogenetic signal, function, etc). Assessing genetic drift, selective pressure, immunogenicity and glycosylation sites, examining epidemic fitness and population dynamics will be performed by Cuypers, Theys, Pettersson, Eldholm, Andreassen, Bello, Ribeiro de Vasconcelos, Abecasis, Alcantara, Giovanetti and Goes de Jesus, each focussing on their own speciality. Datamining to assess the potential association between particular variants with epidemic potential, immune response, clinical outcome, vector range, and human‐to human transmission will be done by Theys, Vandamme and Abecasis. The combined results of this population level analysis and the within‐patient results from WP2 will be communicated to other tasks of this WP3 to inform which variants need special attention.
Subtask 3.2.3: Molecular epidemiology & phylogeography (Abecasis) Prior to phylogeographic analysis, detailed recombination analysis will be done, an agreement on nomenclature will be reached and this will be implemented in the ZIKV typing tool (Alcantara, Giovanetti, Abecasis, Theys, Vandamme, de Lamballerie). Phylogeography and molecular clock analyses, on human and mosquito strains separately and combined, will assess the origin and spread of the current ZIKV outbreak and other potential relevant infectious agents (Abecasis, Parreira, Salgueiro, Pettersson and Lemey). As much metadata as available will be included (e.g. vector species, climate, exposure behaviour, connectivity between geographic regions such as flight traffic, etc), to quantify and model parameters predictive of virus transmission and spread. Worrisome variants will be analyzed in more detail. Epidemic spread of clades will inform diagnostic, vaccine and public health prevention efforts. At NIPH we have also very recently established methods for bait-enrichment of flavi viruses from crude samples (blood, insect vectors) for whole genome sequencing. These methods can be used to detect co-infection of zika, dengue and chikungunya virus and could be utilized for the project if needed.
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