Forster P, Forster L, Renfrew C, Forster M. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci U S A. 2020;117:9241–3.
Article
CAS
Google Scholar
Acera Mateos P, Balboa RF, Easteal S, Eyras E, Patel HR. PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. Sci Rep. 2021;11:3209.
Article
CAS
Google Scholar
Khan M, Adil SF, Alkhathlan HZ, Tahir MN, Saif S, Khan M, et al. COVID-19: a global challenge with old history, Epidemiology and Progress So Far. Molecules. 2020;26:39.
Article
Google Scholar
Salyer SJ, Maeda J, Sembuche S, Kebede Y, Tshangela A, Moussif M, et al. The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study. Lancet. 2021;397:1265–75.
Article
CAS
Google Scholar
Oluwagbemi OO, Oladipo EK, Dairo EO, Ayeni AE, Irewolede BA, Jimah EM, et al. Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new south-African SARS-CoV-2 virus strains. Inform Med Unlocked. 2022;28:100845.
Article
Google Scholar
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, et al. Early transmission of SARS-CoV-2 in South Africa: an epidemiological and phylogenetic report. Int J Infect Dis. 2021;103:234–41.
Article
CAS
Google Scholar
Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. 2021;374:423–31.
Article
CAS
Google Scholar
Ministry of Health, Kenya. Ministry of Health, Kenya COVID-19 Immunization Status Report. https://www.health.go.ke/wp-content/uploads/2022/02/MINISTRY-OF-HEALTH-KENYA-COVID-19-IMMUNIZATION-STATUS-REPORT-1ST-FEBRUARY-2022.pdf. Accessed 1 May 2022.
Ministry of Health, Kenya. Ministry of Health. https://www.health.go.ke/. Accessed 1 May 2022.
Brand SPC, Aziza R, Kombe IK, Agoti CN, Hilton J, Rock KS, et al. Forecasting the scale of the COVID-19 epidemic in Kenya. MedRxiv. 2020.
Adetifa IMO, Uyoga S, Gitonga JN, Mugo D, Otiende M, Nyagwange J, et al. Temporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya. Nat Commun. 2021;12:3966.
Article
CAS
Google Scholar
Brand SPC, Ojal J, Aziza R, Were V, Okiro EA, Kombe IK, et al. COVID-19 transmission dynamics underlying epidemic waves in Kenya. Science. 2021;374:989–94.
Article
CAS
Google Scholar
Githinji G, de Laurent ZR, Mohammed KS, Omuoyo DO, Macharia PM, Morobe JM, et al. Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nat Commun. 2021;12:4809.
Article
CAS
Google Scholar
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020;182:812–27 e19.
Article
CAS
Google Scholar
Barasa E, Kazungu J, Orangi S, Kabia E, Ogero M, Kasera K. Indirect health effects of the COVID-19 pandemic in Kenya: a mixed methods assessment. BMC Health Serv Res. 2021;21:740.
Article
Google Scholar
Sevinsky J, Nassiri A, Young E, Blankenship H. SARS-CoV-2 sequencing on Illumina MiSeq using ARTIC protocol: part 1–tiling PCR V. 1. Protocols. 2020. https://doi.org/10.17504/protocols.io.bfefjjbn.
Kalantar KL, Carvalho T, De Bourcy CFA, Dimitrov B, Dingle G, Egger R, et al. IDseq: an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience. 2020;9:giaa111.
Article
Google Scholar
O’Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7:veab064.
Article
Google Scholar
Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, et al. Ultrafast sample placement on existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nat Genet. 2021;53:809–16.
Article
CAS
Google Scholar
Aksamentov I, Roemer C, Hodcroft E, Neher R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773.
Article
Google Scholar
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.
Article
CAS
Google Scholar
Stang A, Robers J, Schonert B, Jöckel K-H, Spelsberg A, Keil U, et al. The performance of the SARS-CoV-2 RT-PCR test as a tool for detecting SARS-CoV-2 infection in the population. J Inf Secur. 2021;83:237–79.
Google Scholar
Kahle D, Wickham H. ggmap: Spatial Visualization with ggplot2. The R Journal. 2013;5:144–61.
Article
Google Scholar
Rastogi M, Pandey N, Shukla A, Singh SK. SARS coronavirus 2: from genome to infectome. Respir Res. 2020;21:318.
Article
CAS
Google Scholar
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, et al. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. 2022.
Google Scholar
Ade C, Pum J, Abele I, Raggub L, Bockmühl D, Zöllner B. Analysis of cycle threshold values in SARS-CoV-2-PCR in a long-term study. J Clin Virol. 2021;138:104791.
Article
CAS
Google Scholar
Robert Koch Institut. Covid-19 Entlassungskriterien aus der Isolierung; 2022. https://doi.org/10.25646/6957.3. https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Entlassmanagement-Infografik.pdf?_blob=publicationFile. Accessed 1 May 2022
Book
Google Scholar
Racaniello VR. Emerging infectious diseases. J Clin Invest. 2004;113:796–8.
Article
CAS
Google Scholar
Munene II. Multicampus University systems: Africa and the Kenyan experience. New York: Routledge; 2014. https://www.taylorfrancis.com/books/mono/10.4324/9780203659847/multicampus-university-systems-ishmael-munene.
Petersen E, Ntoumi F, Hui DS, Abubakar A, Kramer LD, Obiero C, et al. Emergence of new SARS-CoV-2 variant of concern omicron (B.1.1.529) - highlights Africa’s research capabilities, but exposes major knowledge gaps, inequities of vaccine distribution, inadequacies in global COVID-19 response and control efforts. Int J Infect Dis. 2022;114:268–72.
Article
CAS
Google Scholar