The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya

Githinji, George; Lambisia, Arnold W.; Omah, Ifeanyi; O’Toole, Áine; Mohammed, Khadija Said; Mwanga, Mike J.; Mburu, Maureen W.; Makori, Timothy; Morobe, John M.; Ong’era, Edidah M.; Ndwiga, Leonard; Laurent, Zaydah R. de; Gathii, Kimita; Thiong’o, Kelvin; Omuoyo, Donwilliams O.; Chepkorir, Edith; Musyoki, Jennifer; Kingwara, Leonard; Matoke, Damaris; Oyola, Samuel O.; Onyango, Clayton; Waitumbi, John N.; Bulimo, Wallace; Khamadi, Samoel; Kiiru, John; Kinyanjui, Samson; Cotten, Matthew; Tsofa, Benjamin; Ochola-Oyier, Isabella L.; Rambaut, Andrew; Nokes, D. James; Bejon, Philip; Agoti, Charles N.

doi:10.1101/2022.10.26.22281446

Cited by 9 publications

(9 citation statements)

References 31 publications

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“…However, we note that these sequences conform to molecular clock estimations of the emergence of Delta globally estimated around 19 October 2020 with an earliest possible date estimated as 06 September 2020 [55], Figure S5. A similar pattern of early emergence and slow rise to dominance is observed in several countries across the continent [34] and, in a more detailed study in Neighboring Kenya [56].…”

Section: Discussionsupporting

confidence: 75%

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

Misganaw

Tshiabuila

Tesfaye

et al. 2023

Preprint

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Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499 000 cases, and ~7 500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was out-competed by the Delta variant. Notably, Ethiopia lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

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Section: Discussionsupporting

confidence: 75%

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

Misganaw

Tshiabuila

Tesfaye

et al. 2023

Preprint

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“…In the present study, we document SARS-CoV-2 transmission patterns within households in coastal Kenya by analysing infections identified in a case-ascertained cohort (i.e. households enrolled if a member was confirmed case of SARS-CoV-2 or a contact of one) during successive local waves of infections 28 . We undertook detailed genomic analyses to identify patterns of SARS-CoV-2 introductions into households and to document the frequency and patterns of infection spread within households in coastal Kenya.…”

Section: Introductionmentioning

confidence: 99%

Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study

Agoti

Gallagher

Nyiro

et al. 2022

Preprint

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Background Analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data from household infections should aid its detailed epidemiological understanding. Using viral genomic sequence data, we investigated household SARS-CoV-2 transmission and evolution in coastal Kenya households. Methods We conducted a case-ascertained cohort study between December 2020 and February 2022 whereby 573 members of 158 households were prospectively monitored for SARS-CoV-2 infection. Households were invited to participate if a member tested SARS-CoV-2 positive or was a contact of a confirmed case. Follow-up visits collected a nasopharyngeal/oropharyngeal (NP/OP) swab on days 1, 4 and 7 for RT-PCR diagnosis. If any of these were positive, further swabs were collected on days 10, 14, 21 and 28. Positive samples with an RT-PCR cycle threshold of <33.0 were subjected to whole genome sequencing followed by phylogenetic analysis. Ancestral state reconstruction was used to determine if multiple viruses had entered households. Results Of 2,091 NP/OP swabs that were collected, 375 (17.9%) tested SARS-CoV-2 positive. Viral genome sequences (>80% coverage) were obtained from 208 (55%) positive samples obtained from 61 study households. These genomes fell within 11 Pango lineages and four variants of concern (Alpha, Beta, Delta and Omicron). We estimated 163 putative transmission events involving members of the sequenced households, 40 (25%) of which were intra-household transmission events while 123 (75%) were infections that likely occurred outside the households. Multiple virus introductions (up-to-5) were observed in 28 (47%) households with the 1-month follow-up period. Conclusions We show that a considerable proportion of SARS-CoV-2 infections in coastal Kenya occurred outside the household setting. Multiple virus introductions frequently occurred into households within the same infection wave in contrast to observations from high income settings, where single introduction appears to be the norm. Our findings suggests that control of SARS-CoV-2 transmission by household member isolation may be impractical in this setting.

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“…In the samples analysed from Kenya this study, Alpha was the dominant variant between March 2021-May 2021 and was then replaced by Delta in May 2021, followed by Omicron in mid-December 2021, which is in keeping with epidemiological data from other regions of Kenya (24,25). Other studies have reported the Beta variant co-circulating with the Alpha variant in regions of Kenya (26). The HRM-VOC-2 assay used to screen all 506 samples in this study doesn’t detect the Beta VOC and no samples were identified as Beta in those that were sequenced, so it is unknown whether Beta was present in this sample set.…”

Section: Discussionmentioning

confidence: 88%

“…An HRM panel for detecting Delta, Omicron BA.1, BA. (26,28). This could be due to non-specific binding of the omicron primer sets to the RNA, or alternatively a mutation in one of the primer target sites resulting in a temperature shift of the peak that results in the shift of a peak into the Tm range for Omicron for HRM-VOC-2 resulting in the miscalling of the Omicron variant for these samples.…”

Section: Discussionmentioning

confidence: 99%

Application of a High-Resolution Melt Assay for Monitoring SARS-CoV-2 Variants in Burkina Faso and Kenya

Greenland-Bews,

Shah,

Achieng

et al. 2024

Preprint

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The rapid emergence and global dissemination of SARS-CoV-2 highlighted a need for robust, adaptable surveillance systems. However, financial and infrastructure requirements for whole genome sequencing (WGS) mean most surveillance data have come from higher-resource geographies, despite unprecedented investment in sequencing in low-middle income countries (LMICs) throughout the SARS-CoV-2 pandemic. Consequently, the molecular epidemiology of SARS-CoV-2 in some LMICs is limited, and there is a need for more cost-accessible technologies to help close data gaps for surveillance of SARS-CoV-2 variants. To address this, we have developed two high-resolution melt curve (HRM) assays that target key variant-defining mutations in the SARS-CoV-2 genome, which give unique signature profiles that define different SARS-CoV-2 variants of concern (VOCs). Extracted RNA from SARS-CoV-2 positive samples collected from 205 participants (112 in Burkina Faso, 93 in Kenya) on the day of enrolment in the MALCOV study (Malaria as a Risk Factor for COVID-19) between February 2021 and February 2022 were analysed using our optimised HRM assays and compared to Next Generation Sequencing (NGS) on Oxford Nanopore MinION . With NGS as a reference, two HRM assays, HRM-VOC-1 and HRM-VOC-2, demonstrated sensitivity/specificity of 100%/99.29% and 92.86/99.39%, respectively, for detecting Alpha, 90.08%/100% and 92.31%/100% for Delta and 93.75%/100% and 100%/99.38% for Omicron. The assays described here provide a lower-cost approach (<$1 per sample) to conducting molecular epidemiology, capable of high-throughput testing. We successfully scaled up the HRM-VOC-2 assay to screen a total of 506 samples from which we were able to show the replacement of Alpha with the introduction of Delta and the replacement of Delta by the Omicron variant in this community in Kisumu, Kenya. These assays are readily adaptable and can focus on local epidemiological surveillance questions or be updated quickly to accommodate the emergence of a novel variant or adapt to novel and emerging pathogens

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The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya

Cited by 9 publications

References 31 publications

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study

Application of a High-Resolution Melt Assay for Monitoring SARS-CoV-2 Variants in Burkina Faso and Kenya

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