TY - JOUR
T1 - Early transmission of SARS-CoV-2 in South Africa
T2 - an epidemiological and phylogenetic report
AU - Giandhari, Jennifer
AU - Pillay, Sureshnee
AU - Wilkinson, Eduan
AU - Tegally, Houriiyah
AU - Sinayskiy, Ilya
AU - Schuld, Maria
AU - Lourenço, José
AU - Chimukangara, Benjamin
AU - Lessells, Richard
AU - Moosa, Yunus
AU - Gazy, Inbal
AU - Fish, Maryam
AU - Singh, Lavanya
AU - Sedwell Khanyile, Khulekani
AU - Fonseca, Vagner
AU - Giovanetti, Marta
AU - Carlos Junior Alcantara, Luiz
AU - Petruccione, Francesco
AU - de Oliveira, Tulio
N1 - Funding Information:
This work was based upon research supported by the UKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic; by the Saouth African Medical Research Council Self-Initiated Research grant (MRC SIR HIVDR-POC); by a research Flagship grant from the South African Medical Research Council ( MRC-RFA-UFSP-01-2013/UKZN HIVEPI ); by the Technology Innovation Agency and the Department of Science and Innovation ; and by the National Human Genome Research Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa). The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funders.
Funding Information:
This work was based upon research supported by the UKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic; by the Saouth African Medical Research Council Self-Initiated Research grant (MRC SIR HIVDR-POC); by a research Flagship grant from the South African Medical Research Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI); by the Technology Innovation Agency and the Department of Science and Innovation; and by the National Human Genome Research Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa). The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funders.
Publisher Copyright:
© 2020
PY - 2021/2
Y1 - 2021/2
N2 - 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.
AB - 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.
KW - Epidemiology
KW - Next Generation Sequencing
KW - NGS-SA
KW - Phylogenetic
KW - SARS-CoV-2
KW - South Africa
KW - Transmission genomics
UR - http://www.scopus.com/inward/record.url?scp=85098221602&partnerID=8YFLogxK
U2 - 10.1016/j.ijid.2020.11.128
DO - 10.1016/j.ijid.2020.11.128
M3 - Article
C2 - 33189939
AN - SCOPUS:85098221602
SN - 1201-9712
VL - 103
SP - 234
EP - 241
JO - International Journal of Infectious Diseases
JF - International Journal of Infectious Diseases
ER -
