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. 2021 Feb:103:234-241.
doi: 10.1016/j.ijid.2020.11.128. Epub 2020 Nov 12.

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Jennifer Giandhari  1 , Sureshnee Pillay  1 , Eduan Wilkinson  1 , Houriiyah Tegally  1 , Ilya Sinayskiy  2 , Maria Schuld  3 , José Lourenço  4 , Benjamin Chimukangara  1 , Richard Lessells  5 , Yunus Moosa  4 , Inbal Gazy  1 , Maryam Fish  1 , Lavanya Singh  1 , Khulekani Sedwell Khanyile  1 , Vagner Fonseca  6 , Marta Giovanetti  7 , Luiz Carlos Junior Alcantara  8 , Francesco Petruccione  2 , Tulio de Oliveira  9
Affiliations

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Jennifer Giandhari et al. Int J Infect Dis. 2021 Feb.

Abstract

Objectives: The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa.

Design: This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry - KwaZulu-Natal (KZN) - during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa.

Results: Two of the largest provinces - Gauteng and KZN - had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6-18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided.

Conclusion: The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.

Keywords: Epidemiology; NGS-SA; Next Generation Sequencing; Phylogenetic; SARS-CoV-2; South Africa; Transmission genomics.

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Figures

Figure 1
Figure 1
Timeline of measures implemented in South Africa from the first detected COVID-19 case on 05 March to the expansion of the lockdown in April 2020.
Figure 2
Figure 2
Summary of the COVID-19 epidemic in South Africa. A) Numbers of COVID-19 cases and deaths in the Western Cape (WC), Gauteng (GP), KwaZulu-Natal (KZN) and the Eastern Cape (EC). B) Geographic map showing the location of South African provinces.
Figure 3
Figure 3
Phylogenetic analysis. (A) A time-scaled maximum likelihood tree of 1849 sequences, including 21 genotypes from KwaZulu-Natal, South Africa. Major lineages of SARS-CoV-2 are labelled. B) Monophyletic cluster of KZN sequences. (C) Stacked bar plot showing the lineage breakdown of the dataset by region.
Figure 4
Figure 4
Time-stamped phylogenetic trees of the three lineages of SARS-CoV-2 found in KwaZulu-Natal (KZN). The genomes produced in this study are marked with a red triangle, and the NICD genome by a red square. The geographic region of the other sequences is marked with coloured circles.
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