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. 2023 May 18;15(5):1194.
doi: 10.3390/v15051194.

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

Kathleen Subramoney  1   2   3 , Nkhensani Mtileni  2 , Jennifer Giandhari  4 , Yeshnee Naidoo  5 , Yajna Ramphal  4 , Sureshnee Pillay  4 , Upasana Ramphal  4 , Akhil Maharaj  4 , Derek Tshiabuila  5 , Houriiyah Tegally  4 , Eduan Wilkinson  5 , Tulio de Oliveira  4   5 , Burtram C Fielding  6 , Florette K Treurnicht  1   2
Affiliations

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

Kathleen Subramoney et al. Viruses. .

Erratum in

Abstract

SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral & Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8/278), B.1.1 (16%; 45/278), B.1.1.348 (3%; 8/278), B.1.1.52 (5%; 13/278), C.1 (13%; 37/278) and C.2 (2%; 6/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.

Keywords: SARS-CoV-2; lineages; low frequency; molecular epidemiology.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Prevalence of SARS-CoV-2 lineages over time from 2020 to 2022 by epiweek. The bar graph represents the SAR-CoV-2 lineages and VOCs identified in our study cohort. The black line graph represents the total number of samples that were sequenced during each epiweek. (A) Distribution of SARS-CoV-2 lineages in 2020, (B) Distribution of SARS-CoV-2 lineages in 2021, and (C) Distribution of SARS-CoV-2 lineages in 2022.
Figure 2
Figure 2
Phylogenetic analysis of SARS-CoV-2 lineages and VOCs detected in South Africa from 2020 to 2022. (A) Radial phylogenetic tree display of the lineages identified in South Africa. Tree rooted with the Wuhan-Hu1 strain. Our dataset was compared to the global database embedded in Nextstrain. (B) Nextclade custom time-tree displaying the increase in the number of mutations observed for each SARS-CoV-2 clade observed as time progressed.
Figure 3
Figure 3
SARS-CoV-2 low-frequency lineages identified in this study. The blue-shaded circles represent the samples designated as low-frequency lineages from our study cohort. The horizontal clusters in the background represent the additional lineages and VOCs identified globally.
Figure 4
Figure 4
SARS-CoV-2 low-frequency lineages identified over time. (A) The bars represent the SAR-CoV-2 lineages, and the line graph represents the total number of samples that were successfully sequenced during each month from 2020 to 2022. (B) The shaded dots represent the samples designated as low-frequency lineages. The x-axis represents the total number of mutations identified in each lineage across the whole genome. The y-axis represents the date during which the lineages were observed.
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References

    1. Carabelli A.M., Peacock T.P., Thorne L.G., Harvey W.T., Hughes J., de Silva T.I., Peacock S.J., Barclay W.S., de Silva T.I., Towers G.J., et al. SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat. Rev. Microbiol. 2023 doi: 10.1038/s41579-022-00841-7. - DOI - PMC - PubMed
    1. Tegally H., Wilkinson E., Giovanetti M., Iranzadeh A., Fonseca V., Giandhari J., Doolabh D., Pillay S., San E.J., Msomi N., et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592:438–443. doi: 10.1038/s41586-021-03402-9. - DOI - PubMed
    1. Wilkinson E., Giovanetti M., Tegally H., San J., Lessels R., Cuadros D., Martin D., Zekri A.-R., Sangare A., Ouedraogo A.-S., et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. 2021;431:423–431. doi: 10.1126/science.abj4336. - DOI - PMC - PubMed
    1. Dhar M.S., Marwal R., Radhakrishnan V.S., Ponnusamy K., Jolly B., Bhoyar R.C., Sardana V., Naushin S., Rophina M., Mellan T.A., et al. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science. 2021;374:995–999. doi: 10.1126/science.abj9932. - DOI - PMC - PubMed
    1. Tegally H., Moir M., Everatt J., Giovanetti M., Scheepers C., Wilkinson E., Subramoney K., Moyo S., Amoako D.G., Althaus C.L. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat. Med. 2022;28:1785–1789. doi: 10.1038/s41591-022-01911-2. - DOI - PMC - PubMed

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