As molecular diagnostic technologies have expanded across Africa over the past decade, particularly for HIV viral load (VL) and early infant diagnosis (EID) testing, the challenges associated with safely managing and disposing of laboratory waste generated by these platforms have grown as well.

Through support from the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR), the African Society for Laboratory Medicine (ASLM), working with technical partners and multiple African countries, has developed this set of considerations to address the safe handling and treatment of waste streams produced by molecular diagnostic platforms, particularly those containing guanidinium thiocyanate (GTC) and guanidinium isothiocyanate (GITC) chemicals, which are widely used in nucleic acid extraction.

These reagents, while essential for effective diagnostics, pose significant environmental and occupational health risks if improperly managed, including the potential release of toxic gases when mixed with commonly used disinfectants such as bleach. Drawing on implementation experiences from nine collaborating countries—Eswatini, Ethiopia, Kenya, Malawi, Mozambique, Nigeria, Uganda, Zambia, and Zimbabwe—this document provides evidence-based considerations for feasible waste treatment and disposal options for resource-limited settings. It presents a structured disposal options matrix, decision-making tools, and operational work instructions intended to support national authorities, laboratory managers, and waste management personnel in selecting and implementing safe, context-appropriate disposal methods.

By integrating technical considerations with practical tools and country experiences, this document aims to strengthen laboratory biosafety practices, protect healthcare workers and communities, and promote environmentally responsible waste management as diagnostic capacity continues to expand across the continent.