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Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda.
Bugembe, Daniel Lule; Phan, My V T; Ssewanyana, Isaac; Semanda, Patrick; Nansumba, Hellen; Dhaala, Beatrice; Nabadda, Susan; O'Toole, Áine Niamh; Rambaut, Andrew; Kaleebu, Pontiano; Cotten, Matthew.
  • Bugembe DL; Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
  • Phan MVT; Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
  • Ssewanyana I; Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda.
  • Semanda P; Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda.
  • Nansumba H; Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda.
  • Dhaala B; Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
  • Nabadda S; Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda.
  • O'Toole ÁN; Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Rambaut A; Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Kaleebu P; Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
  • Cotten M; Uganda Virus Research Institute, Entebbe, Uganda.
Nat Microbiol ; 6(8): 1094-1101, 2021 08.
Article in English | MEDLINE | ID: covidwho-1294473
ABSTRACT
Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Nat Microbiol Year: 2021 Document Type: Article Affiliation country: S41564-021-00933-9

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Nat Microbiol Year: 2021 Document Type: Article Affiliation country: S41564-021-00933-9