Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Githinji, George; Laurent, Zaydah R. de; Mohammed, Khadija Said; Omuoyo, Donwilliams O.; Macharia, Peter M.; Morobe, John M.; Otieno, Edward; Kinyanjui, Samson; Agweyu, Ambrose; Maitha, Eric; Kitole, Ben; Suleiman, Thani; Mwakinangu, Mohamed; Nyambu, John; Otieno, John; Salim, Barke; Kasera, Kadondi; Kiiru, John; Aman, Rashid; Barasa, Edwine; Warimwe, George M.; Bejon, Philip; Tsofa, Benjamin; Ochola‐Oyier, Lynette Isabella; Nokes, D. James; Agoti, Charles N.

doi:10.1101/2020.10.05.20206730

Cited by 8 publications

(9 citation statements)

References 11 publications

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“…2), suggesting the importance of this route in the introduction and spread of the virus into Uganda. Most of the genomes from truck drivers sampled at ports of entry (POEs) bordering Kenya belonged to lineage B.1 and B.1.393, which is consistent with the pattern reported in Kenya 10 . However, genomes identified from truck drivers from Tanzania and from the Elegu POE bordering South Sudan, albeit small numbers, belonged to both the A and B.1 lineages.…”

Section: Virus Sequence Diversitysupporting

confidence: 81%

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Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Bugembe

Phan

Ssewanyana³

et al. 2021

Nat Microbiol

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Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.

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Section: Virus Sequence Diversitysupporting

confidence: 81%

“…June to August 2020, the lineage B.1 and B.1.393 strains were abundant, similar to patterns observed in Kenya 10 (Fig. 1b) although lineage A viruses did not decline as seen in US and Europe.…”

supporting

confidence: 79%

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Bugembe

Phan

Ssewanyana³

et al. 2021

Nat Microbiol

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“…The relatively low frequency of P.1 and high frequency of P.2 in our sample from the south of the state of Bahia, a region distant from large airports, may shed light on a much more complex relation between traveling and viral dynamics rather than guilt by association (i.e., mere vicinity). Indeed, previous works suggest that viral spread in smaller or distant cities may happen in a first-come-first-get dynamic, with one lineage overtaking the population [25–27]. Beyond south Bahia cities, this can be seen on Amazonas samples, where all four samples were from P.1 lineage.…”

Section: Discussionmentioning

confidence: 89%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Lamarca

Almeida

Francisco

et al. 2021

Preprint

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. Novel SARS-CoV-2 lineages P.1 and P.2, first identified respectively in Manaus and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed a whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraiba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) aiming to identify SARS-CoV-2 mutations that could be involved in the surge of COVID19 cases in Brazil. Here, we showed a widespread dispersion of P.1 and P.2 across Brazilian regions. Except for Manaus, P.2 was the predominant lineage identified country-wise. P.2 lineage was estimated to have originated in February, 2020 and has diverged into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December. P.1 origin was inferred to have happened in August 2020. We also confirmed the presence of the variant under investigation (VUI) NP13L recently described in the southernmost region of Brazil to have spread across the Northeastern states. P.1, P.2 and NP13L are descended from the ancient B.1.1.28 strain, although during the first phase of the pandemic in Brazil presence of B.1.1.33 strain was also reported. Here, for the first time, we investigate the possible occurrence of a new variant of concern descending from B.1.1.33 that also carries the E484K mutation. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to early identify novel variants of concern and to monitor for vaccine effectiveness.

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“…The relatively low frequency of P.1 and high frequency of P.2 in our sample from the south of the state of Bahia, a region distant from large airports, may shed light on a much more complex relation between traveling and viral dynamics rather than guilt by association (i.e., mere vicinity). Indeed, previous works suggest that viral spread in smaller or distant cities may happen in a first-come-first-get dynamic, with one lineage overtaking the population [ 44 – 46 ]. Beyond south Bahia cities, this can be seen on Amazonas, where all four samples were from P.1 lineage.…”

Section: Discussionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

et al. 2021

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.

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Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Cited by 8 publications

References 11 publications

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

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