Consultant IHP- Sequencing

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Application deadline 1 month ago: Thursday 17 Jun 2021 at 21:59 UTC

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.1. Purpose of the Consultancy

The WHO Eastern Mediterranean Regional Office supports and coordinates closely with 22 countries and territories in the Region to reduce the burden of seasonal influenza, SARS-CoV-2 and other emerging respiratory pathogens nationally and regionally by promoting research and innovation, strengthening influenza and SARS-CoV-2 surveillance, monitoring and utilizing data and expanding seasonal influenza and SARS-CoV-2 prevention and control policies and programs to protect the vulnerable. Technical assistance is also being provided to countries to prioritize the improvement of the regional genome surveillance and building the national capacity for Next Generation Sequencing (NGS) that is critical for the identification and monitoring of new variants in the region.. As requested by the member states, WHO is scaling up the technical assistance to enhance the sequencing capacity through training, mentoring and provision of supplies. As such, Infectious Hazard Preparedness unit, is seeking a consultant to support the rapidly growing start-up that is developing new genomics technologies and help the countries of the Region in leveraging from the Next Generation Sequencing (NGS) technologies.

  1. Background

In the last decade, countries in the Eastern Mediterranean Region (EMR) have invested in the establishment and strengthening of epidemiological and virological surveillance of influenza for determining the seasonality, severity and characteristics of virus circulation in the countries. With the support of WHO/EMRO, some countries in the region conducted studies that document the disease burden of annual influenza epidemics, while calculating the baseline/threshold values to aid in early detection of pandemic influenza. It is expected that the findings and recommendations from these studies will support the development and implementation of seasonal influenza introduction policies and programmes within the context of national health priorities in EMR countries.

In view of this, the WHO Eastern Mediterranean Regional Office (EMRO) and the countries of the Region have been working collaboratively to improve the capacity for detection and response to seasonal and pandemic influenza. WHO/EMRO has supported the expansion of seasonal influenza surveillance and sustainability of the existing surveillance and response for seasonal influenza through different activities focusing on: ensuring the early detection of influenza epidemics through improving the capacities of influenza laboratory for virological surveillance; determining the seasonality and risk factors and disease burden for influenza-associated illness; strengthening multi-sectoral rapid response capacities for early detection and effective response to outbreaks of novel influenza viruses with pandemic potential; enhancing pandemic influenza preparedness; and assisting the development of seasonal influenza vaccine policies that will promote the introduction and increased use of influenza vaccines in high-risk groups in the Region.

As part of the Global Influenza Surveillance System, the IHP unit has been working collaboratively with the Member states in the Region on strengthening the national virological surveillance system for the member states in the region. In this connection and as IHP is committed to provide the continuous support to the member states in any newly applied method, the unit is requesting the recruitment of an international consultant to provide the aimed support for member states on strengthening laboratory capacities for influenza surveillance, preparedness. The consultant will work under the direct supervision of the responsible officer on all the required functions including target identification and validation, as well as the establishment of cellular models, protein reagents, and assays to help advance early detection programmes.

Planned timelines (subject to confirmation)

Start date: 20/06/2021

End date: 19/12/2021

  1. Work to be performed

Output 1: Support the strengthening of sequencing capacities through the implementation of next generation sequencing (NGS) including the Whole Genome Sequencing (WGS) of Influenza and COVID-19 and genetic data management:

Deliverable1.1: Analyse and document results, placing data in proper scientific context through review of relevant literature and report findings at team meetings

Deliverable 1.2: Help to identify, evaluate, new methods or technologies that would enhance workflow efficiency and quality

Deliverable 1.3: work across multiple projects and relevant NGS platform/s

Output 2: Provide technical expertise for setting up and running an NGS facility

Deliverable 2.1: Conduct all aspects of a typical NGS workflow from sample preparation, through to preparation and sequencing of NGS libraries, followed by data analysis.

Deliverable 2.2: Ensure successful understanding of NGS (Next Generation Sequencing), execution and analysis in collaboration with team members.

Deliverable 2.3: Provide technical support to existing methods and analysis solutions

Deliverable 2.4: Produce reports summarizing findings from utilizing available information to use Next Generation Sequencing, documenting, and communicating results and progress

Output 3: Contribute in strengthening the national sequencing capacity at the national laboratories; assess training needs and provide training for laboratory personnel on: Next-generation sequencing: from library preparation to data analysis Sequence analysis (alignment, phylogenetic analysis, evolutionary models.

Deliverable 3.1: design and conduct cross- hands-on-trainings and national workshops in selected countries in the sequence analysis including: Influenza virology and genome composition.

Deliverable 3.2: Provide lectures covering all aspects on Next-generation sequencing: from library preparation to data analysis Sequence analysis (alignment, phylogenetic analysis, evolutionary models

Output 4: Provide technical assistance and expertise on influenza, SARS-CoV2 and other high threat pathogens' laboratory surveillance and laboratory quality management, including during outbreaks

Deliverable 4.1: Providing technical report that document to identify key interventions and findings as well as providing internal reports and presentations as required .

  1. Technical Supervision

The selected Consultant will work on the supervision of:

Amal Barakat (First level)

Technical Officer (Lab) Infectious Hazard Preparedness Unit, Health Emergencies Department

Wasiq Khan (Second level)

Team Lead Influenza and Other Emerging res Diseases, Infectious Hazard Preparedness Unit, Health Emergencies Department

  1. Specific requirements

- Qualifications required:

Essential: Advanced degree in Virology and Molecular biology with Master's degree in public health, epidemiology or related discipline

Desirable: Training in communicable diseases or health policy, systems

- Experience required:

Essential: At least 7 years of progressive experience in public health, influenza lab/National influenza centres. at national and international level with experience in molecular biology techniques including PCR, Strong background on genome alignment, mapping, variant calling, and annotation, molecular phylogeny and evolution as well as Familiarity with public sequence databases

- Skills / Technical skills and knowledge:

  • Theoretical and practical knowledge of the principles and application of international standards applied to virology and laboratory quality
  • Strong efficiency and execution skills, including biosafety operational activities
  • Strong technical, analytical and conceptual skills; demonstrated ability to assess, analyze, synthesize and provide recommendation on key technical issues.
  • Experience designing assays (NGS or PCR), data analysis and interpretation
  • Advance understanding of conventional influenza detection and subtyping

- Language requirements:

English expert level required, intermediate level of French or Arabic is desired.

  1. Place of assignment

Cairo, Egypt

  1. Medical clearance

The selected Consultant will be expected to provide a medical certificate of fitness for work.

  1. Travel

The selected Consultant may be expected to travel to countries of the Region upon request.

All travel arrangements will be made by WHO – WHO will not be responsible for tickets purchased by the Consultant without the express, prior authorization of WHO. While on mission under the terms of this consultancy, the Consultant will receive subsistence allowance.

Visas requirements: it is the consultant’s responsibility to fulfil visa requirements and ask for visa support letter(s) if needed.

Additional Information

This vacancy notice may be used to identify candidates for other similar consultancies at the same level.

Only candidates under serious consideration will be contacted.

A written test may be used as a form of screening.

If your candidature is retained for interview, you will be required to provide, in advance, a scanned copy of the degree(s)/diploma(s)/certificate(s) required for this position. WHO only considers higher educational qualifications obtained from an institution accredited/recognized in the World Higher Education Database (WHED), a list updated by the International Association of Universities (IAU)/United Nations Educational, Scientific and Cultural Organization (UNESCO). The list can be accessed through the link: Some professional certificates may not appear in the WHED and will require individual review.

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Applications from women and from nationals of non and underrepresented Member States are particularly encouraged.

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Consultants shall perform the work as independent contractors in a personal capacity, and not as a representative of any entity or authority. The execution of the work under a consultant contract does not create an employer/employee relationship between WHO and the Consultant.

WHO shall have no responsibility whatsoever for any taxes, duties, social security contributions or other contributions payable by the Consultant. The Consultant shall be solely responsible for withholding and paying any taxes, duties, social security contributions and any other contributions which are applicable to the Consultant in in each location/jurisdiction in which the work hereunder is performed, and the Consultant shall not be entitled to any reimbursement thereof by WHO.

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