TY - JOUR
T1 - Sixteen novel lineages of SARS-CoV-2 in South Africa
AU - Tegally, Houriiyah
AU - Wilkinson, Eduan
AU - Lessells, Richard J.
AU - Giandhari, Jennifer
AU - Pillay, Sureshnee
AU - Msomi, Nokukhanya
AU - Mlisana, Koleka
AU - Bhiman, Jinal N.
AU - von Gottberg, Anne
AU - Walaza, Sibongile
AU - Fonseca, Vagner
AU - Allam, Mushal
AU - Ismail, Arshad
AU - Glass, Allison J.
AU - Engelbrecht, Susan
AU - Van Zyl, Gert
AU - Preiser, Wolfgang
AU - Williamson, Carolyn
AU - Petruccione, Francesco
AU - Sigal, Alex
AU - Gazy, Inbal
AU - Hardie, Diana
AU - Hsiao, Nei yuan
AU - Martin, Darren
AU - York, Denis
AU - Goedhals, Dominique
AU - San, Emmanuel James
AU - Giovanetti, Marta
AU - Lourenço, José
AU - Alcantara, Luiz Carlos Junior
AU - de Oliveira, Tulio
N1 - Funding Information:
This research was funded by the South African Medical Research Council, MRC SHIP and the Department of Science and Innovation of South Africa. The KwaZulu-Natal Research Innovation and Sequencing Platform is funded by a core award of the South African Technology Innovation Agency. We thank A. Rambaut and Á. O’Toole for scientific discussion on how to include the South African lineages on PANGOLIN dynamic classification. We also thank all NGS-SA laboratories in South Africa that were responsible for producing the SARS-CoV-2 genomes that were the focus of the analysis in this paper. A full list of originating laboratories and authors is provided in Supplementary Table 2. Finally, we thank all other global laboratories for generating and making public the SARS-CoV-2 sequences (through GISAID) that were used as the reference dataset in this study. A complete list of individual contributors of sequences is provided in the Supplementary Information.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2021/3
Y1 - 2021/3
N2 - The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).
AB - The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).
UR - http://www.scopus.com/inward/record.url?scp=85100288723&partnerID=8YFLogxK
U2 - 10.1038/s41591-021-01255-3
DO - 10.1038/s41591-021-01255-3
M3 - Article
C2 - 33531709
AN - SCOPUS:85100288723
SN - 1078-8956
VL - 27
SP - 440
EP - 446
JO - Nature Medicine
JF - Nature Medicine
IS - 3
ER -
