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

Abstract

Background: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-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 metadata.

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: Amino acid change; COVID-19; Genetic diversity; Lineage; SARS-COV-2 variants; Waves.

Fig. 1

Distribution of COVID-19 confirmed cases in 2021 and the SARS-COV-2 lineage composition of different COVID-19 waves. This bar plot shows the number of laboratory-confirmed COVID-19 cases documented in Burundi during the present study period and the SARS-COV-2 lineages involved in specific COVID-19 waves. B.1.1.7 = Alpha variant, B.1.351 = Beta variant, B.1.617.2 = Delta variant, B.1.1.529 = Omicron variant, BA.1 and BA.1.1 are Omicron sublineages, AY. 122 & AY.46 are Delta sublineages

Fig. 2

Distribution of different SARS-COV-2 lineages involved in COVID-19 infections in Burundi from May to December 2021. This graph captures the monthly proportions of different SARS-COV-2 lineages identified in Burundi from May to December 2021

Fig. 3

Maximum Likelihood phylogenetic tree of the nucleotide sequences of SARS-COV-2 genomes detected in Burundi in 2021. The B.1.351 genomes (n = 5) are indicated in pink, Delta (B.1.617.2) and its sublineages (n = 109) in orange, the Omicron (B.1.1.529) and its sublineages BA.1 and BA.1.1 genomes (n = 57) in green, and the only one B.1.1.7 genome was not colored. The reference SARS-COV-2 genome used was the SARS-CoV-2 isolate Wuhan-Hu-1, accession number NC_45512.2, retrieved from the GenBank database