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What are SARS-CoV-2 genomes from the WHO Africa region member states telling us?
  1. Lu Lu1,
  2. Samantha Lycett2,
  3. Jordan Ashworth1,
  4. Francisca Mutapi3,4,
  5. Mark Woolhouse1,4
  1. 1Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK
  2. 2The University of Edinburgh The Roslin Institute, Roslin, Midlothian, UK
  3. 3Institute of Immunology & Infection Research, The University of Edinburgh School of Biological Sciences, Edinburgh, UK
  4. 4NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), The University of Edinburgh, Edinburgh, UK
  1. Correspondence to Francisca Mutapi; f.mutapi{at}ed.ac.uk

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Summary box

  • To date, 23 countries from the WHO Africa region have deposited a total of 3995 SARS-CoV-2 sequences to publicly available databases, with the majority of the genomes being from South Africa (56%).

  • Eight-four different lineages have been identified from these countries with 86% genomes belonging to the B.1 sublineage and its descendants.

  • There have been multiple separate introductions of SARS-CoV-2 infections into Africa, with approximately 43% of these coming from Europe.

  • 95% of African SARS-CoV-2 genomes have the D614G mutation in spike protein thought to be associated with higher infectivity but lower disease severity.

Introduction

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 …

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