Sub-Saharan SeqNet

Sub-Saharan African Network for Genomic Diagnostics and Surveillance of Lung Pathogens


Lung diseases are an increasing cause of morbidity and mortality worldwide. Every year, approximately 10 million new cases of tuberculosis (TB) are recorded, resulting in approx.1.5 million deaths. (Multi-) drug-resistant strains further complicate global TB control and challenge the WHO’s goal to end the TB epidemic by 2030. Moreover, the COVID-19 pandemic caused millions of deaths and resulted in an unprecedented global scale of severe acute respiratory syndrome and post-COVID sequelae. Strengthening molecular diagnostics (including genome sequencing approaches), surveillance and the translation of these approaches into clinical and public health practice have emerged as promising tools for combating lung diseases. Next generation sequencing (NGS) technologies are a unique tool for improving diagnostics and integrated molecular surveillance. Building on experiences from previous projects – in which modern sequencing technologies for rapid TB resistance diagnostics and surveillance were established, the project continues to implement and anchor genome sequencing for pathogen diagnostics and surveillance in partner countries. Predominantly, it targets National Reference Laboratories as well as the relevant laboratories working in pathogen diagnostics and surveillance in Eswatini, Mozambique, and Namibia by training their staff to carry out genome sequencing. Moreover, public health officials are trained to trace chains of infection and clinicians are enabled to understand molecular resistance profiles and develop and apply individualised therapeutic regimens based on international guidelines. This enables more efficient therapy concepts and contributes to the well-being of patients by shortening their treatment times and improving treatment outcomes.


Implementing and anchoring state-of-the-art sequencing technologies – such as next generation sequencing – for the diagnosis and surveillance of drug-resistant or multidrug-resistant pulmonary pathogens (especially tuberculosis and SARS-CoV-2).

In Cooperation with

  • Ospedale San Raffaele (OSR), Italy
  • Inselspital Bern (ISB), Switzerland
  • Ministry of Health (MoH Eswatini), Eswatini
  • National TB Reference Laboratory (NTRL Eswatini), Eswatini
  • COVID-19 National Laboratory (COVIDLab Eswatini), Eswatini
  • National TB Control Programme (NTCP Eswatini), Eswatini
  • Baylor College of Medicine (BCM Eswatini), Eswatini
  • Baylor College of Medicine Houston (BCM Houston), USA
  • Instituto Nacional de Saúde (INS), Mozambique
  • University of Namibia School of Medicine (UNAM), Namibia

Thematic priorities

  • Clinical management
  • Infection prevention and control
  • Laboratory diagnostics
  • Outbreak management
  • Strengthening of public health systems
  • Surveillance and reporting



01.01.2023 - 31.12.2025


ca. 2,300,000 Euro

Partner Countries

  • Eswatini
  • Mozambique
  • Namibia


Prof. Stefan Niemann
Research Center Borstel, Leibniz Lung Center
Parkallee 1-40, 23845 Borstel, Germany


  • Staff deployment and exchange

    Training laboratory staff in the partner institutions in genome sequencing and data analysis.

  • Networking and cooperation

    Strengthening established networks through scientific events in Africa and Europe; establishing clinical advisory committees to support translation into the clinic.

  • Capacity development

    Establishing workflows for prospective pathogen surveillance; supporting and implementing sequencing technologies as well as integration of these technologies into diagnostic workflows.



de Araujo L, Cabibbe AM, Mhuulu L, Ruswa N, Dreyer V, Diergaardt A, Günther G, Claassens M, Gerlach C, Utpatel C, Cirillo DM, Nepolo E and Niemann S (2023) Implementation of targeted next-generation sequencing for the diagnosis of drug-resistant tuberculosis in low-resource settings: a programmatic model, challenges, and initial outcomes. Front. Public Health. 11:1204064. doi: 10.3389/fpubh.2023.1204064