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Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari, Jennifer; Pillay, Sureshnee; Wilkinson, Eduan; Tegally, Houriiyah; Sinayskiy, Ilya; Schuld, Maria; Lourenço, José; Chimukangara, Benjamin; Lessells, Richard; Moosa, Yunus; Gazy, Inbal; Fish, Maryam; Singh, Lavanya; Sedwell Khanyile, Khulekani; Fonseca, Vagner; Giovanetti, Marta; Carlos Junior Alcantara, Luiz; Petruccione, Francesco; de Oliveira, Tulio.
  • Giandhari J; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Pillay S; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Wilkinson E; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Sinayskiy I; Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa.
  • Schuld M; Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa.
  • Lourenço J; Department of Zoology, University of Oxford, Oxford, UK.
  • Chimukangara B; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Lessells R; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Zoology, University of Oxford, Oxford, UK.
  • Moosa Y; Department of Zoology, University of Oxford, Oxford, UK.
  • Gazy I; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Fish M; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Singh L; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Sedwell Khanyile K; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Fonseca V; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; La
  • Giovanetti M; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil.
  • Carlos Junior Alcantara L; Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil.
  • Petruccione F; Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa.
  • de Oliveira T; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa; Department of Global Health, University o
Int J Infect Dis ; 103: 234-241, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-919645
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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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Africa Language: English Journal: Int J Infect Dis Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: J.ijid.2020.11.128

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Africa Language: English Journal: Int J Infect Dis Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: J.ijid.2020.11.128