PMID- 33189939
OWN - NLM
STAT- MEDLINE
DCOM- 20210217
LR  - 20231019
IS  - 1878-3511 (Electronic)
IS  - 1201-9712 (Print)
IS  - 1201-9712 (Linking)
VI  - 103
DP  - 2021 Feb
TI  - Early transmission of SARS-CoV-2 in South Africa: An epidemiological and 
      phylogenetic report.
PG  - 234-241
LID - S1201-9712(20)32322-5 [pii]
LID - 10.1016/j.ijid.2020.11.128 [doi]
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.
CI  - Copyright (c) 2020. Published by Elsevier Ltd.
FAU - Giandhari, Jennifer
AU  - Giandhari J
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Pillay, Sureshnee
AU  - Pillay S
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Wilkinson, Eduan
AU  - Wilkinson E
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Tegally, Houriiyah
AU  - Tegally H
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Sinayskiy, Ilya
AU  - Sinayskiy I
AD  - 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.
FAU - Schuld, Maria
AU  - Schuld M
AD  - Quantum Research Group, School of Chemistry and Physics, University of 
      KwaZulu-Natal, Durban, South Africa.
FAU - Lourenco, Jose
AU  - Lourenco J
AD  - Department of Zoology, University of Oxford, Oxford, UK.
FAU - Chimukangara, Benjamin
AU  - Chimukangara B
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Lessells, Richard
AU  - Lessells R
AD  - 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.
FAU - Moosa, Yunus
AU  - Moosa Y
AD  - Department of Zoology, University of Oxford, Oxford, UK.
FAU - Gazy, Inbal
AU  - Gazy I
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Fish, Maryam
AU  - Fish M
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Singh, Lavanya
AU  - Singh L
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Sedwell Khanyile, Khulekani
AU  - Sedwell Khanyile K
AD  - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of 
      Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, 
      South Africa.
FAU - Fonseca, Vagner
AU  - Fonseca V
AD  - 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; Laboratorio de 
      Flavivirus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil.
FAU - Giovanetti, Marta
AU  - Giovanetti M
AD  - Laboratorio de Flavivirus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, 
      Brazil.
FAU - Carlos Junior Alcantara, Luiz
AU  - Carlos Junior Alcantara L
AD  - Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas 
      Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratorio de Flavivirus, 
      Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil.
FAU - Petruccione, Francesco
AU  - Petruccione F
AD  - 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.
FAU - de Oliveira, Tulio
AU  - de Oliveira T
AD  - 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 of Washington, 
      Seattle, Washington, USA. Electronic address: deoliveira@ukzn.ac.za.
LA  - eng
PT  - Journal Article
DEP - 20201112
PL  - Canada
TA  - Int J Infect Dis
JT  - International journal of infectious diseases : IJID : official publication of the 
      International Society for Infectious Diseases
JID - 9610933
SB  - IM
UOF - medRxiv. 2020 May 30;:. PMID: 32511505
MH  - COVID-19/*transmission
MH  - Humans
MH  - *Phylogeny
MH  - SARS-CoV-2/*genetics
MH  - South Africa/epidemiology
PMC - PMC7658561
OTO - NOTNLM
OT  - Epidemiology
OT  - NGS-SA
OT  - Next Generation Sequencing
OT  - Phylogenetic
OT  - SARS-CoV-2
OT  - South Africa
OT  - Transmission genomics
EDAT- 2020/11/16 06:00
MHDA- 2021/02/18 06:00
PMCR- 2020/11/12
CRDT- 2020/11/15 20:26
PHST- 2020/06/18 00:00 [received]
PHST- 2020/11/02 00:00 [revised]
PHST- 2020/11/05 00:00 [accepted]
PHST- 2020/11/16 06:00 [pubmed]
PHST- 2021/02/18 06:00 [medline]
PHST- 2020/11/15 20:26 [entrez]
PHST- 2020/11/12 00:00 [pmc-release]
AID - S1201-9712(20)32322-5 [pii]
AID - 10.1016/j.ijid.2020.11.128 [doi]
PST - ppublish
SO  - Int J Infect Dis. 2021 Feb;103:234-241. doi: 10.1016/j.ijid.2020.11.128. Epub 
      2020 Nov 12.