Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022

C. Nduwimana , N. Nzoyikorera, A. Ndihokubwayo, T. Ihorimbere, C. Nibogora, A. Ndoreraho, O. Hajayandi, J. C. Bizimana, I. Diawara, D. Niyonizigiye and J. Nyandwi

BMC Genomics

Background The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARSCOV-
2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that
pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly
understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive
COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic.
We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing.
Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available

Results In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs,
accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its
descendants predominated the peak observed in July–October 2021. It replaced the previously predominant B.1.351
lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino
acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike
proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-
detected cases were genetically closely related.

Conclusion The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied
by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the
virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country.
It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing
the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or
introduction of new SARS-COV-2 VOCs in the country.

Keywords COVID-19, SARS-COV-2 variants, Waves, Genetic diversity, Lineage, Amino acid change

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