Background
Declared a public health emergency and pandemic in March 2021, COVID-19 has since affected over 184 million people worldwide and caused nearly 4 million deaths so far. This number is in addition to the annual worldwide mortality of more than 8 million people due to existing infectious diseases, including 1.2 million deaths from TB, a quarter of which due to drug-resistant TB. Mortality from infectious diseases, especially TB, is particularly high in developing countries. Most deaths from infectious diseases can be prevented with effective early diagnosis followed by appropriate treatment and infection control.

DNA sequencing enables simultaneous detection of specific microbes, their epidemiological markers and drug resistance testing in a single assay. In the past decades this technique has been used mainly in large institutes for research and surveillance purposes. Nanopore DNA sequencing with hand-held (MinION) devices, in principle, enables application of DNA sequencing for diagnostic purposes at laboratories close to the patient. Implementation of this technique will facilitate early and accurate diagnosis and, thus, reduction in infectious diseases morbidity and mortality. In addition, it will contribute to surveillance.

KNCV is currently recruiting a PhD candidate for a study on the use of DNA sequencing using MinION devices for the diagnosis of TB, COVID-19, and WHO AMR priority pathogens. This position is part of a larger project in which the technique will be implemented in decentralized routine diagnostics in Kyrgyzstan, Tanzania, and Vietnam. PhD candidates in these countries will perform local validation studies and document the acceptability, feasibility, and cost-effectiveness of the technique.

The PhD candidate of this position will be based in the Netherlands and work on the development and optimization of protocols for DNA sequencing on MinION devices directly on clinical material and carry out data analysis regarding the detection of microbial pathogens. Bioinformatic algorithms will be developed to extract and interpret the necessary information from the DNA sequence data. Validation and evaluation studies will be conducted to determine the utility of various laboratory and bioinformatics methods, including e.g. analytical sensitivity and specificity.
The project also has a capacity building component, as the newly generated knowledge should be exchanged with the colleagues in the other project countries.
This work will be conducted in collaboration with the TB reference laboratory at the National Institute for Public Health and the Environment (RIVM) in Bilthoven, where the PhD candidate will be based, and the medical microbiology laboratory Twente Achterhoek (LabMicTA) in Hengelo. 

Purpose of the position and organizational position
KNCV aims to generate evidence on the use of DNA sequencing for diagnosis of infectious diseases and AMR during the implementation of the MinION devices. As a PhD candidate, your work will focus on the day-to-day technical coordination of diverse laboratory research activities. You will carry out laboratory experiments, bioinformatics data analysis and operational research. In addition, you may conduct surveys and perform data analysis. The PhD candidate reports to the manager of the Technical Division  at KNCV with functional lines to the Director of the Technical Division.  The PhD candidate  is supervised daily by the project technical lead at KNCV (Dr. Kristin Kremer),  Em. Prof. Dick van Soolingen and Dr. Richard Anthony at RIVM, in close collaboration with Dr. Adri van der Zanden at LabMicTA.

Duties and responsibilities

• Support the development of research protocols;
• Facilitate local ethics and administrative approvals;
• Contribute to the development and optimization of standard operating procedures;
• Develop a project plan for the implementation of the research protocols;
• Carry out laboratory and bioinformatics analysis;
• Based on the approved research protocol train research assistants on appropriate standard operating procedures;
• Organize and support data collection;
• Validate data received from studies;
• Collaborate with project research teams in The Netherlands, Kyrgyzstan, Tanzania, and Vietnam;
• Participate in scheduled results dissemination activities;
• Contribute to reports and scientific articles writing and publishing;
• Other related necessary duties per request of the line manager.

Who are we looking for?

• Masters or corresponding degree in molecular biology and/or bioinformatics; preference shall be given to candidates with experience in both fields;
• Knowledge on epidemiological and statistical analysis in the field of public health;
• Skills in statistical/programming software for data validation and data analysis (e.g. R-studio, STATA, SPSS);
• Ability to work as part of a team and independently;
• Ability to cope with stress and to organize and prioritize workload;
• Affinity for working in an international team;
• Willingness to work at various institutes (KNCV, RIVM, and LabMicTA) and to travel to one of the project countries, if needed;
• Excellent oral and writing skills in English.
• Proficiency in Dutch, Russian and/or Vietnamese is an asset.

Fixed-term contract: 4 years.

What does KNCV Tuberculosis Foundation offer?

• A full time (38 hours) fixed-term 4-year contract;
• An informal work atmosphere in an international environment where initiative is appreciated;
• A highly motivated team of experienced, self-driven colleagues;
• A link to a Dutch university, where you can attend courses of the Graduate School;
• The salary is dependent upon education and relevant working experience;
• KNCV Tuberculosis Foundation has its own Employment Conditions Scheme;
• Duty station is The Hague but most of the duties will be done at affiliated laboratories in Bilthoven (RIVM) and Hengelo (LabMicTa).

KNCV Tuberculosis Foundation

KNCV Tuberculosis Foundation is an international non-profit organization dedicated to the fight against tuberculosis (TB), and related health problems like HIV, antimicrobial resistance and COVID-19. Tuberculosis is the deadliest infectious disease in the world after COVID-19. Being an international knowledge center, KNCV promotes effective, efficient, innovative and situation specific strategies and solutions to eliminate TB and related health problems in a national and international context.
Our multidisciplinary team of passionate professionals covers a broad range of expertise such as quantitative and qualitative research; programmatic prevention and management of TB and related health problems; new diagnostics, drugs and regimens; clinical management, patient support and stigma reduction; laboratory technologies and networks; education; mobile and digital health solutions and surveillance; strategic planning and advocacy; communication and project management.
For over a century KNCV worked tirelessly to improve the lives of those affected by TB, with a leading role in the successful fight against TB in the Netherlands, exchanging knowledge and expertise with other countries. KNCV is a global network organization, consisting of our global office in The Hague, the Netherlands, eight branch offices and four country based KNCV entities in East, South and Central Asia and Africa. KNCV raises funds from private, institutional, corporate and government sources.
On the journey towards TB Elimination, in 2020 KNCV has defined nine innovation pathways and pursues the development, demonstration and scale-up of innovations as well as existing strategies that can accelerate elimination of TB and related health problems around the world. To do so, KNCV generates evidence, supports global and in-country policy making as well as strategic planning and supports the development of supportive systems.