Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa

Abstract

Since November 2021, five genetically distinct SARS-CoV-2 Omicron lineages (BA.1-BA.5) are believed to have emerged in southern Africa, with four (BA.1, BA.2, BA.4, and BA.5) spreading globally and collectively dominating SARS-CoV-2 diversity. In 2023, BA.2.86, a highly divergent BA.2 lineage that rose to prominence worldwide, was first detected in Israel and Denmark, but the subsequent diversity of South African sequences suggests it too emerged in the region. Using Bayesian phylogeographic inference, we reconstruct the origins and dispersal patterns of BA.1-BA.5 and BA.2.86. Our findings suggest that Gauteng province in South Africa likely played a key role in the emergence and/or amplification of multiple Omicron lineages, though regions with limited sampling may have also contributed. The challenge of precisely tracing these origins highlights the need for broader genomic surveillance across the region to strengthen early detection, track viral evolution, and improve preparedness for future threats.

Fig. 1. Inferred global origins and spatio-temporal dispersal patterns of Omicron BA lineages.

The first 100 inferred movements are shown, with dark red lines depicting the earliest movement, following a counter-clockwise trajectory.

Fig. 2. Distribution of Omicron BA lineages identified through genomic surveillance in South Africa.

a The primary axis displays a stacked bar chart of the weekly proportion of lineages from all South African sequences, as assigned by Pangolin and extracted from GISAID, since the initial introduction of Omicron. The secondary axis highlights the weekly count of sequences in the form of a line graph. b Time series maps displaying the prevalence of respective BA lineages at a province level, highlighting their first occurrence and spread thereafter. Colour gradients reflect the maximum prevalence for each lineage, respectively.

Fig. 3. Molecular evolution and profile of Omicron BA lineages.

a Time-Resolved MCC phylogenetic tree with marginal density plots unveiling the temporal dynamics and evolutionary relationships among BA lineages. b Phylogeographic reconstruction of BA lineages depicting the inferred origin and early spatiotemporal dispersal patterns, displayed on a population density basemap (source: https://hub.worldpop.org/). The movement between locations follows a counter-clockwise direction along the arcs.

Fig. 4. Inferred origins of Omicron BA lineages.

Most Recent Common Ancestor (MRCA) inferred locations are represented by points and bounded by corresponding 95% Highest Posterior Density (HPD), indicating the spatial uncertainty associated with each MRCA location estimate.