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. 2022 Sep:122:136-143.
doi: 10.1016/j.ijid.2022.05.041. Epub 2022 May 20.

Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo

Patrick Bisimwa Ntagereka  1 , Samuel O Oyola  2 , Simon Patrick Baenyi  3 , Gilbert Kibet Rono  2 , Ahadi Bwihangane Birindwa  3 , Dieudonné Wasso Shukuru  3 , Tshass Chasinga Baharanyi  4 , Théophile Mitima Kashosi  3 , Jean-Paul Cikwanine Buhendwa  4 , Parvine Basimane Bisimwa  4 , Aline Byabene Kusinza  4 , Rodrigue Ayagirwe Basengere  3 , Denis Mukwege  5
Affiliations

Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo

Patrick Bisimwa Ntagereka et al. Int J Infect Dis. 2022 Sep.

Abstract

Objectives: We used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies.

Methods: A total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature.

Results: Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences.

Conclusion: Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control.

Keywords: COVID-19; Genetic evolution; Pandemic; SARS-CoV-2; South Kivu; Variants.

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Figures

Figure 1
Figure 1
Phylogenetic tree comparing the 74 Congolese SARS-CoV-2 sequences with 399 previously published whole-genome sequences. Sequences are represented as rectangular tips, with genomes generated from this study in dark-green color and reference genomes in dark blue. The internal nodes display bootstrap values generated in IQ-TREE v2. 2.0 based on ultra-fast bootstrapping (UFBoot 10,000 replicates) and single-branch support (SH-aLRT): (UFBoot%/SH-aLRT%). The phylogenetic tree was generated with Wuhan/WH01 as the root sequence. The lineages (variants) A.23.1, B.1.1.7, B.1.214.*, B.1.617.2, B.1.351, C.16, and P.1 are labeled. Delta sublineages are highlighted with light-brown background, the Gamma in yellow background, and the Beta sublineages are highlighted with a pink background. Branch length indicates the number of mutations in reference to Wuhan-Hu-1/2019 genome. DRC, Democratic Republic of the Congo.
Figure 2
Figure 2
Frequency of Pangolin lineages between May 2020 and August 2021 in eastern Democratic Republic of the Congo.
See this image and copyright information in PMC

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Supplementary concepts