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We propose a novel, non-discriminatory classification of monkeypox virus. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomics surveillance.Monkeypox is a disease caused by the monkeypox virus (MPXV) from the Orthopoxvirus genus in the family Poxviridae [1,2]. Since the first report of monkeypox virus infection in humans in the 1970s [3], repeated outbreaks have been reported periodically in Western and

The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics. Genomics use cases for improving public health surveillance in Africa Pathogen genomics has the potential to transform public health surveillance by improving outbreak detection and investigation, tracking transmission routes and networks, monitoring genetic changes that impact pathogenicity, diagnostics, therapeutics, and vaccines, and assessing the effectiveness of policies and interventions. 13 Recommended and well established genomics use cases WHO guidance for global surveillance of HIV drug resistance, 21 tuberculosis drug resistance, 22 malaria, 23 antimicrobial resistance, 24 vaccine-preventable diseases, 25 and food borne pathogens 26 already recommend or

COVID-19 testing in Africa: lessons learntLaboratory testing is a pillar of the COVID-19 outbreak response. Unlike the 2014 Ebola epidemic, Africa has reacted early and collectively to the COVID-19 pandemic, ramping up severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity from two to 43 countries between February and April, 2020.The Africa Centres for Disease Control and Prevention (Africa CDC)-led African Task Force for Coronavirus Preparedness and Response (AFTCOR)-a coalition between the African Union (AU), AU member states, the WHO Regional Office for Africa, and other stakeholdershas been instrumental in this impressive achievement, promoting coordination and alignment for evidencebased public health action. AFTCOR has led COVID-19 testing capacity scale-up as one of the key objectives under the Africa joint continental strategy for COVID-19 outbreak. 1 AFTCOR collaborated with the South African National Institute for Infectious Diseases, the Senegalese Institute Pasteur of Dakar, and the West African Health Organization to train expert staff from reference laboratories for molecular detection of SARS-CoV-2. To date, 1•6 million tests donated by the Jack Ma Foundation (Hangzou, China), and more than 1 million tests procured by Africa CDC have been distributed across the 55 AU member states. By May 21, 2020, Africa had reported more than 95 000 confirmed cases of COVID-19.

Medical laboratory services are an essential, yet often neglected, component of health systems in developing countries. Their central role in public health, disease control and surveillance, and patient management is often poorly recognized by governments and donors. However, medical laboratory services in developing countries can be strengthened by leveraging funding from other sources of HIV/AIDS prevention, care, surveillance, and treatment programs. Strengthening these services will require coordinated efforts by national governments and partners and can be achieved by establishing and implementing national laboratory strategic plans and policies that integrate laboratory systems to combat major infectious diseases. These plans should take into account policy, legal, and regulatory frameworks; the administrative and technical management structure of the laboratories; human resources and retention strategies; laboratory quality management systems; monitoring and evaluation systems; procurement and maintenance of equipment; and laboratory infrastructure enhancement. Several countries have developed or are in the process of developing their laboratory plans, and others, such as Ethiopia, have implemented and evaluated their plan.