Pathogen genomic monitoring launch in Lesotho

Specialists from WHO and NICD South Africa arrive in Lesotho to assess the country's readiness for pathogen genomic monitoring. The mission aims to enhance COVID-19 response through laboratory techniques, sampling strategies, and epidemiology reporting. The experts will also advise on data collection tools and assist in the formulation of a national genomic monitoring plan. This initiative is part of WHO's global strategy to expand and expedite genomic monitoring. Genomic sequencing plays a crucial role in identifying outbreaks, understanding transmission dynamics, and developing diagnostics, treatments, and vaccines.

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Four specialists from WHO-AFRO, the South African National Informatics Centre, and the National Academy for Infectious Diseases (NICD South Africa) have arrived in Lesotho on a mission to examine the country's readiness to begin pathogen genomic monitoring, commencing with SARS-CoV 2. This mission follows a previous mission to undertake a countrywide contextual analysis in December 2021.


The mission will assess SARS-CoV-2 genomic monitoring capabilities and offer technical advice based on WHO standards, including laboratory techniques, sampling strategies, and epidemiology reporting on COVID-19 indicators, as well as a collaborative Epi-Lab variant prevalence analysis.

"Pathogen genome sequencing is currently needed in Lesotho since it will be a critical tool in adding to relevant data for the country's strategic response to COVID-19," stated Dr. Maile, the Ministry of Health's Incident Management Systems Manager. "We extend a warm welcome to the team in Lesotho and eagerly await their findings and recommendations."

"This expedition is part of WHO's plan to expand and expedite genomic monitoring in the African region and internationally," says Dr. Richard Banda, WHO Country Director for Lesotho. WHO's Global genome surveillance strategy for diseases with pandemic and pandemic potential 2022–2032, he explained, isn't targeted at a single disease or disease concern. It provides a high-level framework for leveraging current capabilities.


The experts will also offer advice on how to create better data collecting tools that collect the data needed for epidemiological investigations within Lab Information Systems (LIMS) while keeping first-line healthcare practitioners in mind. The group will also assist in the formulation of a national genomic monitoring plan.

"The WHO, in partnership with the Africa CDC, is eager to assist countries in building capacity, and missions like these allow experts to assess the degree of technological and infrastructural capacity required." WHO AFRO Epidemiology Specialist Paul Ouma is the mission's team leader. "This is beneficial to us."

Genomic sequencing has a wide range of applications, including identifying outbreak causes, better understanding transmission dynamics, confirming and validating routine diagnostics, and developing new diagnostics, treatments, and vaccines. The discovery of many SARS-CoV 2 variants across the continent necessitates the use of bioinformatics to track groove within and between countries.

To speed up SARS-CoV-2 sequencing in Africa, WHO and other partners are providing sequencing equipment, reagents, and technical support to member states. About 98 000 genomic sequence from Africa had been submitted to the publicly accessible Global Action plan on Sharing All Flu Data (GISAID) database, which is a repository of genetic and metadata from SARS-CoV 2 genomic monitoring, as of March 28, 2022.

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