Latest news with #genomicSurveillance
Zawya
08-07-2025
- Health
- Zawya
Malawi Launches Second Edition of Pathogen Genomic Surveillance Strategy and Implementation Plan
The Malawi Ministry of Health, launched its updated plan for the implementation of its Genomic Surveillance Strategy that was produced with technical support from the Africa Centres for Disease Control and Prevention – Africa Pathogen Genomics Initiative (Africa PGI) on 3 July. As pathogen genomics provides a powerful approach towards the investigation, management, and surveillance of infectious diseases, the plan is geared to include integration of multi-pathogen genomic surveillance into existing public health systems, research and development. The second version of the plan is aligned to Africa CDC Pathogen Genomics Surveillance Policy Framework and identified priority list of pathogens and use cases for genomic surveillance in Malawi and the region. The strategy has a robust, comprehensive, fully integrated, harmonized and well-coordinated mechanisms to guide monitoring of the implementation of the plan and evaluate impact. The improved plan has a National Genomics Committee comprising of a steering committee, advisory group and laboratories from public, private and academia. The first genomic strategy was launched in 2023 and runs to 2030 In his opening remarks, Secretary for Health Dr. Samsom Kwazirira Mndolo emphasized the critical role of genomics in monitoring antimicrobial resistance, disease outbreak detection, response and prevention as well in precision medicine. He underscored the role of the plan as a roadmap for implementing a robust one health genomic surveillance system across the country with different multi stakeholders, ministries and partners. 'We have been front runners in genomics, but we lost the opportunity to learn from others, so we decided to revisit and update the 2023 plan,' said Dr Mndolo. 'This moment marks the dawn of a new era, where science, innovation, and determination converge to build a stronger, more resilient health system for all starting from Malawi by leveraging genomic sequencing power to identify and track pathogens enabling early detection, tracking and characterization of pathogens,' said Dr Lul Riek, Director for the Southern Africa Regional Coordinating Centre. Dr Riek said by integrating pathogen genomic sequencing into its healthcare infrastructure, it aims to enhance its health security and swiftly respond to emerging and reemerging threats effectively. 'This makes Malawi one step ahead of other countries in disease detection and response,' he said. 'In the face of several emerging and reemerging health threats including Disease X ' a hypothetical emerging pathogen, from the COVID-19 pandemic to the resurgence of Mpox, Marburg, Cholera and other epidemics, we have witnessed firsthand the urgent need for resilient public health surveillance systems that can provide timely and actionable data,' said Dr Francis Chikuse, Senior Technical Officer for Public Health at Africa CDC. 'The National Multi Pathogen Genomic Surveillance Strategy is not just a response to these challenges but a proactive step toward building a robust system that leverages the power of molecular diagnostics and sequencing to safeguard the health of the of Malawians and beyond,' said Dr Chikuse. He said, Africa CDC in partnership with public, private and philanthropic sectors is enhancing continent-wide sample referral and data sharing strategy, systems, and governance to promote trusted, quality assured and timely data sharing as well as support the design and pilot implementation of high-impact public health priority genomic surveillance and use-cases and facilitate the utility of genomics data for policy, decision making, research and development of pandemic materials. In 2025, the World Health Assembly adopted the historic Pandemic Agreement to enhance global collaboration and to create a more equitable response to future pandemics. Africa CDC is working with 16 Member States including the Democratic Republic of Congo, Uganda, Mozambique, Ethiopia, Cameroon, Malawi, Zambia, Republic of Congo, Zimbabwe, Ghana, Morocco, Togo, South Africa, Tanzania, Rwanda, Namibia, to develop their national pathogen genomics strategies. Through this collaboration, Malawi becomes the second country after Zambia to launch their genomic strategy. Distributed by APO Group on behalf of Africa Centres for Disease Control and Prevention (Africa CDC).
Zawya
01-07-2025
- Health
- Zawya
Sierra Leone bolters mpox response: World Health Organization (WHO) leads groundbreaking genomic surveillance and bioinformatics training
In a strategic initiative aimed at enhancing mpox outbreak response and genomic surveillance capacity, the Central Public Health Reference Laboratory (CPHRL) in Freetown hosted the mpox Genomics and Bioinformatics training workshop from 23rd – 27th June 2025. The event was organized under the theme: 'Strengthening Genomic Surveillance Capacity for mpox Response in Sierra Leone,' with technical and financial support from the World Health Organization (WHO AFRO and WHO Sierra Leone). The training program targeted 15 participants, including laboratory scientists, public health professionals, and epidemiologists from across Sierra Leone. Despite reporting over 4,400 confirmed cases of mpox as of 27th June 2025, Sierra Leone has performed genomic characterization on only approximately 2.5% of these cases (108 sequences), representing a significant limitation in understanding viral evolution and informing targeted public health interventions. Currently, these genomic data are deposited in international repositories such as Pathoplexus, GISAID, and NCBI Virus; however, the disparity between outbreak detection and genomic data generation hampers real-time surveillance efforts. The Ministry of Health and Sanitation (MoHS) and the Sierra Leone National Public Health Agency (SLNPHA) of Sierra Leone have prioritized strengthening genomic surveillance to enable rapid outbreak detection, track viral transmission, and inform policy decisions. Allan Campbell, Laboratory Lead at CPHRL, emphasized the significance of this training, stating, 'This marks a pivotal moment in Sierra Leone's national response to mpox. The initiative addresses the substantial bioinformatics capacity gap and establishes a foundation for sustainable genomic surveillance that can directly inform public health actions.' The workshop aligns with the objectives outlined in the WHO African Region (AFRO) Joint Continental mpox Response Plan 2.0, focusing on intensification, integration, and establishing a sustainable legacy in genomic epidemiology. The week-long workshop employed a multidisciplinary, hands-on approach combining didactic instruction, practical exercises, and group data analysis. The curriculum included: Day 1: Introduction to genomic surveillance principles, sequencing technologies, and foundational bioinformatics tools such as Linux and Conda environments. Day 2: Emphasis on sequencing data quality control (FastQC, MultiQC), read trimming (Fastp, Hostile), and genome assembly techniques utilizing reference-based (BWA, Cutadapt) and de novo (SPAdes) approaches. Day 3: Variant detection and analysis (SAMtools, FreeBayes, Snippy), consensus sequence generation (Bcftools), and genome annotation (SnpEff, VEP). Day 4: Phylogenetic analysis, clade classification (Nextclade, Nextstrain), and visualization using platforms such as GISAID, Pathoplexus, NCBI Virus, Microreact, iTOL, and Galaxy. Day 5: Integration of all components through a case study simulating mpox outbreak response, culminating in data interpretation and strategic planning. Walter Oguta, WHO AFRO EPI Analytics Specialist and the Lead Bioinformatics Trainer, underscored the practical value of the training, stating, 'Translating genomic data into actionable public health strategies is the ultimate goal. Our aim was to equip participants with both technical proficiency and confidence to utilize these tools effectively.' Doris Harding, Laboratory Pillar Lead at the SLNPHA, highlighted the broader implications: 'Strengthening our capacity for genomic surveillance is no longer optional—it is essential. This initiative empowers our scientists to respond more effectively to mpox and other emerging pathogens.' Similarly, Jonathan Greene, WHO Sierra Leone Laboratory Lead, articulated the importance of workforce development, asserting, 'Building a skilled, locally capable workforce is central to WHO's strategy for resilient health systems. The use of genomics is transforming outbreak intelligence, enabling a shift from reactive to proactive responses.' Dr. Ameh George, WHO Representative in Sierra Leone, emphasized the strategic importance of institutionalizing genomic surveillance: 'Genomics is redefining outbreak science. Sierra Leone must lead in generating and utilizing genomic data to inform policy and strengthen global health security. WHO remains committed to supporting this transformation.' Participants and stakeholders concurred that this training initiative constitutes a long-term investment in Sierra Leone's epidemic preparedness, response and resilience. By decentralizing sequencing capabilities and integrating genomic data into national decision-making processes, the program aspires to support regional efforts for early detection and rapid response to outbreaks. The workshop concluded with the issuance of certificates of completion and a networking session aimed at fostering collaboration and innovation in public health genomics. As Sierra Leone advances its surveillance infrastructure, the overarching goal remains to elevate genomic data from an underutilized resource to a central element of outbreak response and epidemic intelligence, thereby strengthening national and regional health security. Distributed by APO Group on behalf of World Health Organization - Sierra Leone.
