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

Cathrine Scheepers, Josie Everatt, Daniel G. Amoako, Houriiyah Tegally, Constantinos Kurt Wibmer, Anele Mnguni, Arshad Ismail, Boitshoko Mahlangu, Bronwen E. Lambson, Darren P. Martin, Eduan Wilkinson, James Emmanuel San, Jennifer Giandhari, Nelia Manamela, Noxolo Ntuli, Prudence Kgagudi, Sandile Cele, Simone I. Richardson, Sureshnee Pillay, Thabo Mohale, Upasana Ramphal, Yeshnee Naidoo, Zamantungwa T. Khumalo, Gaurav Kwatra, Glenda Gray, Linda-Gail Bekker, Shabir A. Madhi, Vicky Baillie, Wesley C. Voorhis, Florette K. Treurnicht, Marietjie Venter, Koleka Mlisana, Nicole Wolter, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Nokukhanya Msomi, Tongai Maponga, Wolfgang Preiser, Zinhle Makatini, Richard Lessells, Penny L. Moore, Tulio Oliveira, Anne Gottberg and Jinal N. Bhiman ()
Additional contact information
Cathrine Scheepers: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Josie Everatt: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Daniel G. Amoako: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Houriiyah Tegally: University of KwaZulu-Natal
Constantinos Kurt Wibmer: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Anele Mnguni: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Arshad Ismail: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Boitshoko Mahlangu: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Bronwen E. Lambson: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Darren P. Martin: University of Cape Town
Eduan Wilkinson: University of KwaZulu-Natal
James Emmanuel San: University of KwaZulu-Natal
Jennifer Giandhari: University of KwaZulu-Natal
Nelia Manamela: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Noxolo Ntuli: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Prudence Kgagudi: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Sandile Cele: Africa Health Research Institute
Simone I. Richardson: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Sureshnee Pillay: University of KwaZulu-Natal
Thabo Mohale: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Upasana Ramphal: University of KwaZulu-Natal
Yeshnee Naidoo: University of KwaZulu-Natal
Zamantungwa T. Khumalo: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Gaurav Kwatra: University of the Witwatersrand
Glenda Gray: South African Medical Research Council
Linda-Gail Bekker: Desmond Tutu HIV Centre
Shabir A. Madhi: University of the Witwatersrand
Vicky Baillie: University of the Witwatersrand
Wesley C. Voorhis: University of Washington
Florette K. Treurnicht: National Health Laboratory Service (NHLS)
Marietjie Venter: University of Pretoria
Koleka Mlisana: University of KwaZulu-Natal
Nicole Wolter: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Alex Sigal: Africa Health Research Institute
Carolyn Williamson: University of Cape Town
Nei-yuan Hsiao: University of Cape Town
Nokukhanya Msomi: National Health Laboratory Service (NHLS)
Tongai Maponga: Stellenbosch University
Wolfgang Preiser: National Health Laboratory Service (NHLS)
Zinhle Makatini: National Health Laboratory Service (NHLS)
Richard Lessells: University of KwaZulu-Natal
Penny L. Moore: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Tulio Oliveira: University of KwaZulu-Natal
Anne Gottberg: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Jinal N. Bhiman: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)

Nature Communications, 2022, vol. 13, issue 1, 1-9

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-29579-9

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