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

Abstract

Background: The emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network for Genomics Surveillance of COVID (SANGS_COVID), a network of ten government and university laboratories. Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one 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), we aim to shed light on the patterns of infections that define the epidemic in South Africa. Methods: R was calculated using positive cases and deaths from reports provided by the four major provinces. Molecular epidemiology investigation involved sequencing viral genomes from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations. Findings: The epidemic in South Africa has been very heterogeneous. Two of the largest provinces, Gauteng, home of the two large metropolis Johannesburg and Pretoria, and KwaZulu-Natal, home of the third largest city in the country Durban, had a slow growth rate on the number of detected cases. Whereas, Western Cape, home of Cape Town, and the Eastern Cape provinces the epidemic is spreading fast. Our estimates of transmission potential for South Africa suggest a decreasing transmission potential towards R=1 since the first cases and deaths have been reported. However, between 06 May and 18 May 2020, we estimate that R was on average 1.39 (1.04 - 2.15, 95% CI). We also demonstrate that early transmission in KZN, and most probably in all main regions of SA, was associated with multiple international introductions and dominated by lineages B1 and B. The study also provides evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic, which inflated early mortality in KZN. Interpretation: This first report of SANGS_COVID consortium focuses on understanding the epidemic heterogeneity and introduction of SARS-CoV-2 strains in the first month of the epidemic in South Africa. The early introduction of SARS-CoV-2 in KZN included caused a localized outbreak in a hospital, provides potential explanations for the initially high death rates in the province. The current high rate of transmission of COVID-19 in the Western Cape and Eastern Cape highlights the crucial need to strength local genomic surveillance in South Africa.

Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama

“…As of July 21, SARS-CoV-2 has spread to 188 countries with around 14 763 911 confirmed cases and 611 322 fatalities 9 . To characterize SARS-CoV-2 local transmission across the globe 10 , the few mutations accumulated to date in the viral genome [11][12][13] have allowed the characterization of different lineages or clades (A and B) 14 .…”

Late incidence of SARS-CoV-2 infection in a highly-endemic remote rural village. A prospective population-based cohort study

“…Indeed, we conducted a comprehensive literature search for publications on community-based epidemiological studies of SARS-Cov2 in developing countries (using relevant keywords), and identified no high-quality published population-based study assessing the incidence of SARS-CoV-2 infection in community-based settings in developing countries. We only found four preprints on serological surveys in Iran, South Africa and Brazil, all taking probabilistic samples in small fractions of the studied populations [20,21,22,23]. However, the design of those studies does not allow to ascertain the incidence of this infection.…”

First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region

“…Up to now, only limited sequencing data of Northern Africa and the Sahel region is available compared to other regions of the world like America, Asia or Europe. Viral genomes spreading on the African continent are mainly accessible from states like South Africa [24], the Democratic Republic of Congo (DRC) and Kenya [25]. For the Sahel region, genomic information of SARS-CoV-2 is only provided by Nigeria [26] and Senegal [5,27], while data from countries like Mauritania, Niger, Burkina Faso, Chad, Eritrea and Sudan is still missing.…”

“…In contrast, the B.1 lineage comprises sequences associated with the large Italian outbreak in February 2020 and represents to date (date 21.07.2020), together with its sublineage B.1.1, the worldwide prevalent virus clade [19]. The African continent, especially South Africa is dominated by lineage B (its origin still lying in Asia) and B.1 [24]. In Mali, only ⅓ of the patient samples were assigned to lineage B.1, thus giving rise to speculation that this and Sahelian G5 partner countries.…”