Next Generation Sequencing capacity building in Viet Nam

What is the project?

The National Lung Hospital (NLH), a leading hospital in the National TB Program (VNTP) and Pasteur Institute in Nha Trang (PINT), a regional institute in the infectious disease control network, are provided the support via provision of portable, low-cost Oxford Nanopore Technologies (ONT) sequencers and sequencing kits, consumables, technology training and continuous supports through technical assistance, monitoring and evaluation to enable them further transferring the technologies to other facilities in their respective networks, and in conducting SARS-CoV-2 genomic analysis and genomic surveillance in the localities. The project aims to enhance whole genome sequencing (WGS) capacity to study and survey pandemic, epidemic, emerging and re-emerging infectious pathogens. Especially, NLH also receives the support on drug resistant tuberculosis (DR-TB) sequencing with aims to apply sequencing for DR-TB detection in the VNTP network.

Why are we working on it?

Next generation sequencing (NGS) or whole genome sequencing (WGS) offers transformative potential for improving clinical and public health microbiology. By rapidly identifying pathogens and tracing their properties, including antimicrobial resistance, NGS/WGS can enhance outbreak and infectious disease control. NGS/WGS is transforming the public health approach to infectious disease control, as well as the management of patients’ diagnosis and treatment toward more efficiency. Nevertheless, the transition from research to routine use in LMICs faces challenges, such as infrastructure and workforce development. At a broader and systemic level, substantial efforts are needed to develop standard protocols, proficiency-testing programs, professional guidelines, and regulatory policies. Thus, supporting NGS/WGS adoption in LMICs is crucial to accelerate its impact.

WGS of SARS-CoV-2: SARS-CoV-2’s genomic material constantly evolves, influencing transmission, disease severity, vaccine resistance, etc. Although COVID-19 may currently no longer be a global public health emergency, the threat of other virulent variant emerging that causes new surges of disease and death remains. WHO suggested that countries must still strengthen response to the disease and prepare for future pandemics and other threats. NGS/WGS is the most optimal method to investigate viral pathogen genomes and identify new variants/strains. The project enables genomic surveillance to prepare for potential surges and better understand the virus’s behavior.

WGS/NGS for TB-DR detection: The World Health Organization’s End Tuberculosis Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with TB as a key component of integrated, patient-centered TB care. DR-TB poses a dangerous public health threat. NGS/WGS technology demonstrates exceptional potential for reliable and comprehensive drug resistance prediction in Mycobacterium tuberculosis isolates, allowing personalized treatment decisions. The adoption of NGS/WGS in low-income, high TB-burden settings where it is most needed is encouraged. Viet Nam is among the 30 countries with the highest burden of TB and DR-TB, thus urgent action is needed to adopt NGS/WGS technology for the prevention and control the disease.

What are its objectives?

The specific objectives are:

• Support the country’s SARS-CoV-2 NGS/WGS capacity building through training and catalytic support.
• Assess the country’s capacity for DR-TB NGS/WGS and conduct a pilot for DR-TB diagnosis using NGS/WGS.

What does it involve?

The project involves:

• Organizing on-site training programs for the NLH, PINT, and other facilities in VNTP and the infectious disease control network .
• Procuring and distributing procurement devices, test kits, reagent, and consumables.
• Providing technical support, monitoring, and evaluation,
• Implementing the survey to assess the need and capacity for DR-TB NGS/WGS of VNTP.
• Developing of technical procedure for NLH for DR-TB sequencing and conducting performance pilot of the procedure.

What is the expected outcome?

SARS-CoV-2 WGS capacity building through training and catalytic support at NLH and PINT

• On-site trainings and lab setup for ONT WGS techniques for each facility. Similar trainings for personnel from other four provincial lung hospitals and other four provincial for disease control centers (CDCs).
• Further support for bioinformatic analysis through technical training at the sites.
• Provision of Oxford Nano Technology (ONT) sequencers and sequencing kits, consumables and other essential equipment and supplies for conducting SARS-CoV-2 WGS samples taken from COVID-19 positive patients.
• Continued technical support to the sites for conducting genomic analysis to investigate the circulating variants, genomic diversity and evolution of SARS-CoV-2 in the country.
• 500 SARS-CoV-2 genomes sequenced and analyzed.

Assessment of the country capacity for DR-TB NGS and NGS performance pilot for DR-TB diagnosis

• Facility-level survey of needs and existing capacities for DR-TB NGS in VNTP.
• Build up DR-TB NGS capacity at NLH, with a pilot program for DR-TB sequencing of 30 tuberculosis cultures from multi-drug resistant (MDR)-TB patients.
• Completion of operational questionnaires and costing tool implementation for DR-TB sequencing.

What is the time scale?

The project is scheduled to run from Sep 2022 to Dec 2023.

Partners and Funding

The project is jointly undertaken by FIND Viet Nam and National Lung Hospital and Pasteur Institute in Nha Trang, with funding from Canadian Department of Foreign Affairs, Trade and Development (DFATD).