ArticleNature communications2022
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.
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Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19citing papers in PubMed
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19 citing papers in PubMed, 38 citations in OpenAlex.
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- The Omicron variant BA.2.86.1 of SARS- CoV-2 demonstrates an altered interaction network and dynamic features to enhance the interaction with the hACE2.Scientific reports · 2025Article
- Population shift in antibody immunity following the emergence of a SARS-CoV-2 variant of concern.Scientific reports · 2025Article
- SeqAfrica: empowering Africa's fight against antimicrobial resistance through genomics.Frontiers in public health · 2025Article
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- Estimation of vaccine effectiveness against SARS-CoV-2-associated hospitalization using sentinel surveillance in South Africa.International journal of epidemiology · 2024Article
- The COVID-19 experience in Africa and the Middle East.Annals of medicine · 2023Review
- Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.Viruses · 2023Article
- Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike.PLoS pathogens · 2023Article
- mRNA-based COVID-19 booster vaccination is highly effective and cost-effective in Australia.Vaccine · 2023Article
- Variable neutralizing antibody responses to 10 SARS-CoV-2 variants in natural infection with wild- type (B.1) virus, Kappa (B.1.617.1), and Delta (B.1.617.2) variants and COVISHIELD vaccine immunization in India: utility of the MSD platform.Frontiers in immunology · 2023Article
- The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study.JMIRx med · 2023Article
- Risk Factors for Severe Coronavirus Disease 2019 Among Human Immunodeficiency Virus-Infected and -Uninfected Individuals in South Africa, April 2020-March 2022: Data From Sentinel Surveillance.Open forum infectious diseases · 2022Article
- The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.Science (New York, N.Y.) · 2022Article
- Leveraging South African HIV research to define SARS-CoV-2 immunity triggered by sequential variants of concern.Immunological reviews · 2022Review
- Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2.Nature microbiology · 2022Article
- Alum/CpG Adjuvanted Inactivated COVID-19 Vaccine with Protective Efficacy against SARS-CoV-2 and Variants.Vaccines · 2022Article
- Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.Science (New York, N.Y.) · 2022Article
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Authors and funding
45 authors at 10 institutions in 4 countries.
Cathrine Scheepers *National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0002-1683-0282
Josie Everatt *National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0002-0373-2093
Daniel G AmoakoNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0003-3551-3458
Houriiyah TegallyKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.
Constantinos Kurt WibmerNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Anele MnguniNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0002-1854-5573
Arshad IsmailNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0003-4672-5915
Boitshoko MahlanguNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Bronwen E LambsonNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Darren P MartinInstitute of Infectious Disease and Molecular Medicine, University of Cape Town, 7925, Cape Town, South Africa.
Eduan WilkinsonKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.ORCID 0000-0002-2503-9441
James Emmanuel SanKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.ORCID 0000-0002-5736-664X
Jennifer GiandhariKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.
Nelia ManamelaNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Noxolo NtuliNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Prudence KgagudiNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Sandile CeleAfrica Health Research Institute, 4001, Durban, South Africa.
Simone I RichardsonNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0001-7678-2609
Sureshnee PillayKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.
Thabo MohaleNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Upasana RamphalKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.ORCID 0000-0002-2441-3868
Yeshnee NaidooKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.
Zamantungwa T KhumaloNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Gaurav KwatraSouth African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, 2000, Johannesburg, South Africa.
Glenda GraySouth African Medical Research Council, 7505, Cape Town, South Africa.
Linda-Gail BekkerDesmond Tutu HIV Centre, 7925, Cape Town, South Africa.
Shabir A MadhiSouth African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, 2000, Johannesburg, South Africa.
Vicky BaillieSouth African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, 2000, Johannesburg, South Africa.
Wesley C Van VoorhisCenter for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Washington, 98195, USA.ORCID 0000-0001-6141-2015
Florette K TreurnichtNational Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Marietjie VenterZoonotic Arbo and Respiratory Virus Research Programme, Department of Medical Virology, Faculty of Health, University of Pretoria, 0031, Gezina, South Africa.ORCID 0000-0003-2696-824X
Koleka MlisanaSchool of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 4041, Durban, South Africa.
Nicole WolterNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Alex SigalAfrica Health Research Institute, 4001, Durban, South Africa.ORCID 0000-0001-8571-2004
Carolyn WilliamsonInstitute of Infectious Disease and Molecular Medicine, University of Cape Town, 7925, Cape Town, South Africa.ORCID 0000-0003-0125-1226
Nei-Yuan HsiaoInstitute of Infectious Disease and Molecular Medicine, University of Cape Town, 7925, Cape Town, South Africa.ORCID 0000-0003-4926-6216
Nokukhanya MsomiNational Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Tongai MapongaDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7602, Cape Town, South Africa.ORCID 0000-0002-6876-3712
Wolfgang PreiserNational Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0002-0254-7910
Zinhle MakatiniNational Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.
Richard LessellsKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.ORCID 0000-0003-0926-710X
Penny L MooreNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0001-8719-4028
Tulio de OliveiraKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa.ORCID 0000-0002-3027-5254
Anne von GottbergNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa.ORCID 0000-0002-0243-7455
Jinal N BhimanNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), 2131, Johannesburg, South Africa. jinalb@nicd.ac.za.ORCID 0000-0001-6354-4003
National Health Laboratory Service · ZAStellenbosch University · ZASouth African Medical Research Council · ZAUniversity of KwaZulu-Natal · ZAAfrica Health Research Institute · ZADesmond Tutu HIV Foundation · ZAMax Planck Institute for Infection Biology · DEUniversity of Cape Town · ZAUniversity of Pretoria · ZAUniversity of Washington · US
Funding
Research on the Epidemiology,Prevention,Vaccine Effectiveness and Treatment of Influenza and Other Respiratory Viruses in South Africa.09U01IP001048 · IP · NATIONAL HEALTH LABORATORY SERVICE · PI COHEN, CHERYL · 2016 to 2020
$19.9MUniversity of Washington Arboviral Research Network (UWARN)U01AI151698 · NIAID · UNIVERSITY OF WASHINGTON · PI Michael Gale, PETER MACGARR RABINOWITZ · 2020 to 2026
$13.3MIdentification of the HIV Reservoir in Lymph Nodes Using Single Cell RNA-SeqR01AI138546 · NIAID · KWAZULU-NATAL RESEARCH INSTITUTE TB-HIV · PI SIGAL, ALEXANDER · 2018 to 2022
$721kACL HHS U01IP001048Department of HealthGates Foundation INV-018944Gates Foundation INV-018978NCIRD CDC HHS U01 IP001048NIAID NIH HHS R01 AI138546NIAID NIH HHS U01 AI151698Wellcome TrustWellcome Trust 221003/Z/20/ZWellcome Trust 222574/Z/21/Z
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.
Indexed as
COVID-19SARS-CoV-2Antibodies, NeutralizingAntibodies, ViralHumansNeutralization TestsSpike Glycoprotein, CoronavirusAntibodies, NeutralizingAntibodies, ViralSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2
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