Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
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Date
Authors
Scheepers, Cathrine
Everatt, Josie
Amoako, Daniel G.
Tegally, Houriiyah
Wibmer, Constantinos Kurt
Mnguni, Anele
Ismail, Arshad
Mahlangu, Boitshoko
Lambson, Bronwen E.
Martin, Darren P.
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
Abstract
Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased
transmissibility, neutralization resistance and disease severity. Here we report the emergence
of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other
countries. The initial C.1.2 detection is associated with a high substitution rate, and includes
changes within the spike protein that have been associated with increased transmissibility or
reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest.
Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma
from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent
donors infected with either Beta or Delta show high plasma neutralization against
C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to
Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection
against C.1.2.
Description
CODE AVAILABILITY : The R and python scripts used to generate figures (excluding bar charts) in this paper are available at https://github.com/NICD-CRDM/C.1.2_scripts. The Nextstrain build profile, other scripts required to run the custom pipeline, and GISAID accession identifiers for all sequences in the final tree are available at https://github.com/NICD-CRDM/ C.1.2_scripts/tree/main/Nextstrain_files. The MATLAB scripts used for microscopy are available at https://github.com/NICD-CRDM/C.1.2_scripts/tree/main/microscopy. This code is also available in Supplementary Software 1.
DATA AVAILABILITY : All of the global SARS-CoV-2 genomes generated and presented in this article are publicly accessible through the GISAID9 platform (https://www.gisaid.org/), along with all other SARS-CoV-2 genomes generated by the NGS-SA. The GISAID accession identifiers of the C.1.2 sequences analyzed in this study are provided as part of Supplementary Tables 1 and 2, which also contain the metadata for the sequences. The Nextstrain build of C.1.2 and global sequences is available at https://nextstrain.org/ groups/ngs-sa/COVID19-C.1.2-2022-01-05. The GISAID accession identifiers for the full set of sequences used in this build can be accessed at https://github.com/NICD-CRDM/ C.1.2_scripts/tree/main/Nextstrain_files. The GISAID accession identifiers for the sequences used in Supp. Fig. 2a and temporal analysis can be accessed at https:// github.com/NICD-CRDM/C.1.2_scripts in the files violin_plot_IDs.xlsx and C.1.2_global_tempest.xlsx respectively. The shapefile used for South African maps in Supplementary Fig. 1 was downloaded from https://gadm.org/ (licensed for use in academic publications, see https://gadm.org/license.html) and visualised in R with ggplot2. The global map in Supplementary Fig. 1 was obtained from the rnaturalearth package (public domain, see https://docs.ropensci.org/rnaturalearth/articles/ rnaturalearth.html) and visualised with ggplot2. The data was based on sequences available on GISAID at the time.
DATA AVAILABILITY : All of the global SARS-CoV-2 genomes generated and presented in this article are publicly accessible through the GISAID9 platform (https://www.gisaid.org/), along with all other SARS-CoV-2 genomes generated by the NGS-SA. The GISAID accession identifiers of the C.1.2 sequences analyzed in this study are provided as part of Supplementary Tables 1 and 2, which also contain the metadata for the sequences. The Nextstrain build of C.1.2 and global sequences is available at https://nextstrain.org/ groups/ngs-sa/COVID19-C.1.2-2022-01-05. The GISAID accession identifiers for the full set of sequences used in this build can be accessed at https://github.com/NICD-CRDM/ C.1.2_scripts/tree/main/Nextstrain_files. The GISAID accession identifiers for the sequences used in Supp. Fig. 2a and temporal analysis can be accessed at https:// github.com/NICD-CRDM/C.1.2_scripts in the files violin_plot_IDs.xlsx and C.1.2_global_tempest.xlsx respectively. The shapefile used for South African maps in Supplementary Fig. 1 was downloaded from https://gadm.org/ (licensed for use in academic publications, see https://gadm.org/license.html) and visualised in R with ggplot2. The global map in Supplementary Fig. 1 was obtained from the rnaturalearth package (public domain, see https://docs.ropensci.org/rnaturalearth/articles/ rnaturalearth.html) and visualised with ggplot2. The data was based on sequences available on GISAID at the time.
Keywords
PANGO lineage C.1.2, Variants, Beta or Delta, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SDG-03: Good health and well-being
Sustainable Development Goals
SDG-03:Good heatlh and well-being
Citation
Scheepers, C., Everatt, J., Amoako, D.G. et al. 2022, 'Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage', Nature Communications, vol. 13, no. 1976, pp. 1-9. DOI : 10.1038/s41467-022-29579-9.