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.
Coronaviruses
Kenya
Lineage
SARS-CoV-2
Journal
Virology journal
ISSN: 1743-422X
Titre abrégé: Virol J
Pays: England
ID NLM: 101231645
Informations de publication
Date de publication:
08 11 2022
08 11 2022
Historique:
received:
27
10
2021
accepted:
05
10
2022
entrez:
8
11
2022
pubmed:
9
11
2022
medline:
11
11
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36348341
doi: 10.1186/s12985-022-01895-y
pii: 10.1186/s12985-022-01895-y
pmc: PMC9640859
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
178Informations de copyright
© 2022. The Author(s).
Références
Nat Med. 2021 May;27(5):744-745
pubmed: 33828291
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
Biol Methods Protoc. 2020 Jul 18;5(1):bpaa014
pubmed: 33029559
Viruses. 2022 Mar 06;14(3):
pubmed: 35336952
Euro Surveill. 2021 Jan;26(3):
pubmed: 33478621
Microorganisms. 2021 May 12;9(5):
pubmed: 34065789
PLoS One. 2023 Apr 13;18(4):e0284187
pubmed: 37053201
J Biosci. 2021;46:
pubmed: 33737495
BMJ Glob Health. 2021 Aug;6(8):
pubmed: 34385165
Int J Infect Dis. 2021 Apr;105:735-738
pubmed: 33737129
Immunity. 2021 Jul 13;54(7):1611-1621.e5
pubmed: 34166623
Nat Commun. 2020 Nov 26;11(1):6013
pubmed: 33243994
Bull World Health Organ. 2020 Jul 01;98(7):495-504
pubmed: 32742035
J Infect Dev Ctries. 2021 Apr 30;15(4):470-477
pubmed: 33956645
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Euro Surveill. 2021 Jan;26(3):
pubmed: 33478625
Nature. 2022 Mar;603(7902):679-686
pubmed: 35042229
Med Sci Monit. 2021 Jun 21;27:e933622
pubmed: 34149046
J Med Virol. 2022 May;94(5):1825-1832
pubmed: 35023191
Bioinformatics. 2012 Apr 15;28(8):1166-7
pubmed: 22368248
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
Lancet. 2022 Jan 29;399(10323):437-446
pubmed: 35065011
bioRxiv. 2020 Jul 22;:
pubmed: 32743569
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Science. 2021 May 21;372(6544):815-821
pubmed: 33853970
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Nat Microbiol. 2021 Jul;6(7):821-823
pubmed: 34108654
Nature. 2021 Jan;589(7842):337-338
pubmed: 33452508
Cell Host Microbe. 2021 Jan 13;29(1):44-57.e9
pubmed: 33259788
Nucleic Acids Res. 2016 Jul 8;44(W1):W232-5
pubmed: 27084950
Science. 2021 Nov 19;374(6570):989-994
pubmed: 34618602
Nat Commun. 2021 Aug 10;12(1):4809
pubmed: 34376689
Cell. 2022 Feb 3;185(3):457-466.e4
pubmed: 34995482
Nat Commun. 2020 Mar 27;11(1):1620
pubmed: 32221306
Nature. 2021 Apr;592(7853):277-282
pubmed: 33545711
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Ther Adv Infect Dis. 2021 Jun 18;8:20499361211024372
pubmed: 34211709
Nature. 2021 Nov;599(7883):114-119
pubmed: 34488225
Lancet Glob Health. 2021 Sep;9(9):e1177-e1178
pubmed: 34252380
Science. 2021 Mar 12;371(6534):1139-1142
pubmed: 33536258
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681