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Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Subramoney, Kathleen; Mtileni, Nkhensani; Bharuthram, Avani; Davis, Ashlyn; Kalenga, Beauty; Rikhotso, Mikateko; Maphahlele, Mpho; Giandhari, Jennifer; Naidoo, Yeshnee; Pillay, Sureshnee; Ramphal, Upasana; Ramphal, Yajna; Tegally, Houriiyah; Wilkinson, Eduan; Mohale, Thabo; Ismail, Arshad; Mashishi, Bonolo; Mbenenge, Nonhlanhla; de Oliveira, Tulio; Makatini, Zinhle; Fielding, Burtram C; Treurnicht, Florette K.
  • Subramoney K; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Mtileni N; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
  • Bharuthram A; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Davis A; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Kalenga B; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
  • Rikhotso M; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Maphahlele M; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Giandhari J; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Naidoo Y; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Pillay S; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Ramphal U; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Ramphal Y; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Wilkinson E; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Mohale T; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Ismail A; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
  • Mashishi B; Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa.
  • Mbenenge N; Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa.
  • de Oliveira T; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Makatini Z; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
  • Fielding BC; Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
  • Treurnicht FK; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
J Med Virol ; 94(8): 3676-3684, 2022 08.
Article Dans Anglais | MEDLINE | ID: covidwho-1849500
ABSTRACT
The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS-CoV-2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID-19 real-time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS-CoV-2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole-genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9% (173/175) of samples, of which 88.0% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS-CoV-2 will be beneficial in limited-resource settings.
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Texte intégral: Disponible Collection: Bases de données internationales Base de données: MEDLINE Sujet Principal: SARS-CoV-2 / COVID-19 Type d'étude: Étude diagnostique / Études expérimentales / Essai contrôlé randomisé Les sujets: Variantes Limites du sujet: Humains Pays comme sujet: Afrique langue: Anglais Revue: J Med Virol Année: 2022 Type de document: Article Pays d'affiliation: JMV.27797

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Texte intégral: Disponible Collection: Bases de données internationales Base de données: MEDLINE Sujet Principal: SARS-CoV-2 / COVID-19 Type d'étude: Étude diagnostique / Études expérimentales / Essai contrôlé randomisé Les sujets: Variantes Limites du sujet: Humains Pays comme sujet: Afrique langue: Anglais Revue: J Med Virol Année: 2022 Type de document: Article Pays d'affiliation: JMV.27797