What are SARS-CoV-2 genomes from the WHO Africa region member states telling us?

### Summary box Pathogen genome sequencing can inform control measures including diagnosis, identifying infection sources and patterns of infection and disease prognosis. The first case of SARS-CoV-2 was reported on 31 December 2019, and on 10 January 2020 the first sequences of the virus were made publicly available allowing the development and standardisation of the real-time PCR diagnostics for the virus. The reagents for the PCR diagnostic test were designed using the full spectrum of the SARS-CoV-2 reference genome collected on 5 January 2020, in Wuhan.1 A recent analysis has shown that the majority of current PCR diagnostic targets have undergone mutations with the nucleocapsid (N) gene primers and probes having undergone the most mutations.2 In Africa, analysing virus genome sequences revealed transmission patterns within individual countries. For example, analyses of sequences in Kenya during the early phase of the epidemic identified both imported and local community transmission, demonstrating transmission from Nairobi to the coastal regions.3 Similarly, South Africa was able to identify nosocomial transmission using genome sequencing.4 The course of infection and disease prognosis can vary depending on the virulence of the pathogen. In addition, viruses may be able to adapt to the environment and evade recognition by the immune system, so it is …