Agoti CN

Genomic and clinical epidemiology of SARS-CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave.Lambisia AW, Katama EN, Moraa E, Mwita JM, Gallagher K, Mutunga M, Nyale E, Omungala J, Mwanga M, Murunga N, Nyiro J, Nyagwange J, Sande C, Bejon P, Githinji G, Dellicour S, Phan MVT, Cotten M, Ochola-Oyier LI, Holmes EC, Agoti CN
BMC Glob Public Health, (2025). 3:80

Cryptosporidium parvum virus 1 genome sequences from pediatric diarrhea cases in coastal Kenya.Agoti CN, Njeru R, Mwanga M, Mutunga M, Shah SP, Chu TY, Nokes DJ, Cotten M, Phan MVT
Microbiol Resour Announc, (2025). :e0034925

Epidemiological dynamics of influenza B virus across multiple seasons in Kenya and Uganda inferred from sequence data, 2010-2021.Nyarango BK, Owuor DC, Isoe E, Mutunga M, Cheruiyot R, Katama EN, Makori T, Lambisia A, Nyiro J, Githinji G, Kiguli S, Olupot-Olupot P, Maitland K, Agoti CN
BMC Infect Dis, (2025). 25:1080

External validation of paediatric pneumonia and bronchiolitis risk scores to predict mortality in children hospitalised in Kenya: a retrospective cohort study.Gordon B, Nyiro JU, Nair H, Sheikh Z, Katama E, Agoti CN, Pei R, Zar H, Shi T
J Infect Dis, (2025). :

Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya.Musundi S, Mwanga M, Lambisia A, Morobe JM, Murunga N, Moraa E, Ndwiga L, Cheruiyot R, Musyoki J, Mutunga M, Guzman-Rincon LM, Sande C, Mwangangi J, Bejon P, Ochola-Oyier LI, Nokes DJ, Agoti CN, Nyiro J, Githinji G
Virus Evol, (2025). 11:veaf035

The genome sequence of varicella-zoster virus (Varicellovirus humanalpha3) obtained by metagenomics from a patient presenting with an exanthem rash.Musundi S, Okanda D, Lambisia A, Morobe JM, Muthanje E, Ochola-Oyier LI, Carter DP, Agoti CN, Kiiru J, Githinji G
Microbiol Resour Announc, (2025). :e0024825

Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.Lambisia AW, Mwita Morobe J, Moraa E, Mwarumba S, Korir FKN, Seif Athman R, Kiptui R, Mbee M, Mugo N, Amoth P, Muange P, Houldcroft JC, Barasa E, Mwangangi J, Githinji G, Holmes CE, Ochola-Oyier LI, Agoti CN
Wellcome Open Res, (2025). 10:28

Adenovirus-Specific T Cells in Adults Are Frequent, Cross-Reactive to Common Childhood Adenovirus Infections and Boosted by Adenovirus-Vectored Vaccines.Mukhopadhyay R, Lambisia AW, Hoang JP, Ravenhill BJ, Agoti CN, Krishna BA, Houldcroft CJ
J Med Virol, (2025). 97:e70222

Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, JN.1.4, and KP.3.1.1 using samples from two health demographic surveillance systems in Kenya.Lugano D, Kutima B, Kimani M, Sigilai A, Gitonga J, Karani A, Akech D, Karia B, Ziraba AK, Maina A, Lambisia A, Omuoyo D, Mugo D, Lucinde R, Owuor S, Konyino G, Newman J, Bailey D, Nduati E, Githinji G, Agoti CN, Bejon P, Scott JAG, Agweyu A, Kagucia W, Warimwe GM, Sande C, Ochola-Oyier LI, Nyagwange J
BMC Infect Dis, (2024). 24:1474

Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data.Owuor DC, Ngoi JM, Nyasimi FM, Murunga N, Nyiro JU, Chaves SS, Nokes DJ, Agoti CN
Sci Rep, (2024). 14:23426

Spatio-temporal distribution of rhinovirus types in Kenya: a retrospective analysis, 2014.Morobe JM, Kamau E, Luka MM, Murunga N, Lewa C, Mutunga M, Bigogo G, Otieno N, Nyawanda B, Onyango C, Nokes DJ, Agoti CN, Munywoki PK
Sci Rep, (2024). 14:22298

Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa.Owuor DC, de Laurent ZR, Oketch JW, Murunga N, Otieno JR, Nabakooza G, Chaves SS, Nokes DJ, Agoti CN
Sci Rep, (2024). 14:18987

Age-dependent acquisition of IgG antibodies to Shigella serotypes-a retrospective analysis of seroprevalence in Kenyan children with implications for infant vaccination.Kapulu MC, Muthumbi E, Otieno E, Rossi O, Ferruzzi P, Necchi F, Acquaviva A, Martin LB, Orindi B, Mwai K, Kibet H, Mwanzu A, Bigogo GM, Verani JR, Mbae C, Nyundo C, Agoti CN, Nakakana UN, Conti V, Bejon P, Kariuki S, Scott JAG, Micoli F, Podda A
Front Immunol, (2024). 15:1340425

Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, during the COVID-19 pandemic, 2019-2022.Lambisia AW, Murunga N, Mutunga M, Cheruiyot R, Maina G, Makori TO, Nokes DJ, Agoti CN
Gut Pathog, (2024). 16:2

Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons.Owuor DC, de Laurent ZR, Nyawanda BO, Emukule GO, Kondor R, Barnes JR, Nokes DJ, Agoti CN, Chaves SS
Sci Rep, (2023). 13:22342

Symptom prevalence and secondary attack rate of SARS-CoV-2 in rural Kenyan households: A prospective cohort study.Gallagher KE, Nyiro J, Agoti CN, Maitha E, Nyagwange J, Karani A, Bottomley C, Murunga N, Githinji G, Mutunga M, Ochola-Oyier LI, Kombe I, Nyaguara A, Kagucia EW, Warimwe G, Agweyu A, Tsofa B, Bejon P, Scott JAG, Nokes DJ
Influenza Other Respir Viruses, (2023). 17:e13185

New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023.Mwanga MJ, Lambisia AW, Morobe JM, Murunga N, Moraa E, Ndwiga L, Cheruiyot R, Musyoki J, Mutunga M, Guzman-Rincon LM, Sande C, Mwangangi J, Bejon P, Ochola-Oyier LI, Nokes DJ, Agoti CN, Nyiro J, Githinji G
Emerg Infect Dis, (2023). 29:

Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8.Makori TO, Bargul JL, Lambisia AW, Mwanga MJ, Murunga N, de Laurent ZR, Lewa CS, Mutunga M, Kellam P, Cotten M, Nokes DJ, Phan M, Agoti CN
Virus Evol, (2023). 9:vead025

Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013-2022).Lambisia AW, Makori TO, Mutunga M, Cheruiyot R, Murunga N, Quick J, Githinji G, Nokes DJ, Houldcroft CJ, Agoti CN
Virus Evol, (2023). 9:vead023

Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains.Nabakooza G, Owuor DC, de Laurent ZR, Galiwango R, Owor N, Kayiwa JT, Jjingo D, Agoti CN, Nokes DJ, Kateete DP, Kitayimbwa JM, Frost SDW, Lutwama JJ
Sci Rep, (2023). 13:5516