Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Scheepers, Cathrine; Everatt, Josie; Amoako, Daniel G.; Tegally, Houriiyah; Wibmer, Constantinos Kurt; Mnguni, Anele; Ismail, Arshad; Mahlangu, Boitshoko; Lambson, Bronwen E.; Martin, Darren P.; Wilkinson, Eduan; San, James Emmanuel; Giandhari, Jennifer; Manamela, Nelia; Ntuli, Noxolo; Kgagudi, Prudence; Cele, Sandile; Richardson, Simone I.; Pillay, Sureshnee; Mohale, Thabo; Ramphal, Upasana; Naidoo, Yeshnee; Khumalo, Zamantungwa Thobeka Happiness; Kwatra, Gaurav; Gray, Glenda; Bekker, Linda‑Gail; Madhi, Shabir A.; Baillie, Vicky; Van Voorhis, Wesley C.; Treurnicht, Florette K.; Venter, Marietjie; Mlisana, Koleka; Wolter, Nicole; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; Msomi, Nokukhanya; Maponga, Tongai; Preiser, Wolfgang; Makatini, Zinhle; Lessells, Richard; Moore, Penny L.; De Oliveira, Tulio; Von Gottberg, Anne; Bhiman, Jinal N.

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Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Scheepers, Cathrine; Everatt, Josie; Amoako, Daniel G.; Tegally, Houriiyah; Wibmer, Constantinos Kurt; Mnguni, Anele; Ismail, Arshad; Mahlangu, Boitshoko; Lambson, Bronwen E.; Martin, Darren P.; Wilkinson, Eduan; San, James Emmanuel; Giandhari, Jennifer; Manamela, Nelia; Ntuli, Noxolo; Kgagudi, Prudence; Cele, Sandile; Richardson, Simone I.; Pillay, Sureshnee; Mohale, Thabo; Ramphal, Upasana; Naidoo, Yeshnee; Khumalo, Zamantungwa Thobeka Happiness; Kwatra, Gaurav; Gray, Glenda; Bekker, Linda‑Gail; Madhi, Shabir A.; Baillie, Vicky; Van Voorhis, Wesley C.; Treurnicht, Florette K.; Venter, Marietjie; Mlisana, Koleka; Wolter, Nicole; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; Msomi, Nokukhanya; Maponga, Tongai; Preiser, Wolfgang; Makatini, Zinhle; Lessells, Richard; Moore, Penny L.; De Oliveira, Tulio; Von Gottberg, Anne; Bhiman, Jinal N.

URI: http://hdl.handle.net/2263/93366

Date: 2022-04-08

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.

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