Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Abstract

The emergence and rapid spread of SARS-CoV-2 variants of concern (VOC) have been linked to new waves of COVID-19 epidemics occurring in different regions of the world. The VOC have acquired adaptive mutations that have enhanced virus transmissibility, increased virulence, and reduced response to neutralizing antibodies. Kenya has experienced six waves of COVID-19 epidemics. In this study, we analyzed 64 genome sequences of SARS-CoV-2 strains that circulated in Nairobi and neighboring counties, Kenya between March 2021 and July 2021. Viral RNA was extracted from RT-PCR confirmed COVID-19 cases, followed by sequencing using the ARTIC network protocol and Oxford Nanopore Technologies. Analysis of the sequence data was performed using different bioinformatics methods. Our analyses revealed that during the study period, three SARS-CoV-2 variants of concern (VOC) circulated in Nairobi and nearby counties in Kenya. The Alpha (B.1.1.7) lineage predominated (62.7%), followed by Delta (B.1.617.2, 35.8%) and Beta (B.1.351, 1.5%). Notably, the Alpha (B.1.1.7) VOC were most frequent from March 2021 to May 2021, while the Delta (B.1.617.2) dominated beginning June 2021 through July 2021. Sequence comparisons revealed that all the Kenyan viruses were genetically similar to those that circulated in other regions. Although the majority of Kenyan viruses clustered together in their respective phylogenetic lineages/clades, a significant number were interspersed among foreign strains. Between March and July 2021, our study's findings indicate the prevalence of multiple lineages of SAR-CoV-2 VOC in Nairobi and nearby counties in Kenya. The data suggest that the recent increase in SARS-CoV-2 infection, particularly in Nairobi and Kenya as a whole, is attributable to the introduction and community transmission of SARS-CoV-2 VOC among the populace. In conclusion, the findings provide a snapshot of the SARS-CoV-2 variants that circulated in Kenya during the study period.

Keywords: Coronaviruses; Kenya; Lineage; SARS-CoV-2.

Fig. 1

Distribution of SARS-CoV-2 variants and cases detected in Nairobi and Kenya respectively, between March–July 2021. A The bar graph showing frequency of SARS-CoV-2 lineages detected among PCR-confirmed samples sampled in Nairobi County during the study period. The Alpha, Beta, and Delta lineages are shown in blue, orange and grey, respectively. B Graph showing the daily distribution of PCR-confirmed SARS-CoV-2 cases in Kenya between March–July 2021. The y-axis indicates the frequency of detections, while the x-axis represents the time-period of each day of the sampling period

Fig. 2

Maximum-likelihood tree of Kenyan and global strains. Phylogenetic analysis depicting assignment of the genome sequences analyzed in the study to SARS-CoV-2 Alpha, Beta, and Delta genetic clades/lineages, signified by different colours. The Kenyan strains are identified in red. The bootstrap numbers at the nodes denote statistical branch support values. The bar indicates the number of nucleotide substitutions per site