Nokes DJ

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri AN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang'a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O'Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LO, Tyers L, Ramuth M, Mastouri M, Aouni M, El Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T
Science, (2021). 374:423-431

COVID-19 transmission dynamics underlying epidemic waves in Kenya.Brand SPC, Ojal J, Aziza R, Were V, Okiro EA, Kombe IK, Mburu C, Ogero M, Agweyu A, Warimwe GM, Nyagwange J, Karanja H, Gitonga JN, Mugo D, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Murunga N, Otiende M, Ochola-Oyier LI, Agoti CN, Githinji G, Kasera K, Amoth P, Mwangangi M, Aman R, Ng'ang'a W, Tsofa B, Bejon P, Keeling MJ, Nokes DJ, Barasa E
Science, (2021). 374:989-994

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018.Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN
Wellcome Open Res, (2021). 6:178

The Etiology of Pneumonia in HIV-uninfected Children in Kilifi, Kenya: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study.Awori JO, Kamau A, Morpeth S, Kazungu S, Silaba M, Sande J, Karani A, Nyongesa S, Mwarumba S, Musyimi R, Bett A, Wande S, Shebe M, Ngama M, Munywoki PK, Muturi N, Nokes DJ, Feikin DR, Murdoch DR, Prosperi C, O'Brien KL, Deloria Knoll M, Hammitt LL, Scott JAG
Pediatr Infect Dis J, (2021). 40:S29-S39

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya.Githinji G, de Laurent ZR, Mohammed KS, Omuoyo DO, Macharia PM, Morobe JM, Otieno E, Kinyanjui SM, Agweyu A, Maitha E, Kitole B, Suleiman T, Mwakinangu M, Nyambu J, Otieno J, Salim B, Kasera K, Kiiru J, Aman R, Barasa E, Warimwe G, Bejon P, Tsofa B, Ochola-Oyier LI, Nokes DJ, Agoti CN
Nat Commun, (2021). 12:4809

Spatially resolved simulations of the spread of COVID-19 in three European countries.Parisi A, Brand SPC, Hilton J, Aziza R, Keeling MJ, Nokes DJ
PLoS Comput Biol, (2021). 17:e1009090

Comparative analysis of spatial-temporal patterns of human metapneumovirus and respiratory syncytial virus in Africa using genetic data, 2011-2014.Oketch JW, Kamau E, Otieno JR, Mwema A, Lewa C, Isoe E, Nokes DJ, Agoti CN
Virol J, (2021). 18:104

Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level.Salimi V, Viegas M, Trento A, Agoti CN, Anderson LJ, Avadhanula V, Bahl J, Bont L, Brister JR, Cane PA, Galiano M, Graham BS, Hatcher EL, Hellferscee O, Henke DM, Hirve S, Jackson S, Keyaerts E, Kragten-Tabatabaie L, Lindstrom S, Nauwelaers I, Nokes DJ, Openshaw PJ, Peret TC, Piedra PA, Ramaekers K, Rector A, Trovao NS, von Gottberg A, Zambon M, Zhang W, Williams TC, Barr IG, Buchholz UJ
Emerg Infect Dis, (2021). 27:1-9

Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019.Lambisia AW, Phan MVT, de Laurent ZR, Cotten M, Nokes DJ, Agoti CN
Microbiol Resour Announc, (2021). 10:

The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, Lshtm Cmmid Covid- Working Group, Scott J, Flasche S, Adetifa I
BMC Med, (2021). 19:35

Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission.Kombe IK, Agoti CN, Munywoki PK, Baguelin M, Nokes DJ, Medley GF
Sci Rep, (2021). 11:1463

Respiratory syncytial virus seasonality in three epidemiological zones of Kenya.Rose EB, Nyawanda BO, Munywoki PK, Murunga N, Bigogo GM, Otieno NA, Onyango C, Chaves SS, Verani JR, Emukule GO, Widdowson MA, Nokes DJ, Gerber SI, Langley GE
Influenza Other Respir Viruses, (2021). 15:195-201

Characteristics of SARS-CoV-2 infections in households in rural coastal Kenya: a prospective genomic study..Agoti CN, Nyiro J, Murunga N, Lambisia AW, Mohammed KS, de Laurent ZR, Morobe JM, Mburu MW, Ndwiga L, Ongera EM, Makori T, Musyoki J, Mwangangi J, Tsofa B, Ochola-Oyier LI, Bejon P, Githinji G, Nokes DJ, Gallagher KE
1st International Conference on Public Health in Africa (CPHIA-2021), (2021). :

Genomic surveillance of SARS-CoV-2 in Kenya: March 2020-October 2021..Githinji G, Lambisia WA, Mohamed KS, Morobe MJ, de Laurent ZR, Mburu WM, Ongera ME, Omuoyo OD, Ndwiga L, Otieno E, Murunga N, Musyoki J, KWTRP COVID Testing Team, Kilifi Rapid Response Team, Kiiru J, Kasera K, Amoth P, Mwangangi M, Aman R, Kinyanjui S, Warimwe GM, Agweyu A, Barasa E, Tsofa B, Mwangangi J, Matoke D, Nokes DJ, Bejon P, Ochola-Oyier LI, Agoti CN
1st International Conference on Public Health in Africa (CPHIA-2021), (2021). :

Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season.Nyasimi FM, Owuor DC, Ngoi JM, Mwihuri AG, Otieno GP, Otieno JR, Githinji G, Nyiro JU, Nokes DJ, Agoti CN
Virus Evol, (2020). 6:veaa045

Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on.Kamau E, Otieno JR, Lewa CS, Mwema A, Murunga N, Nokes DJ, Agoti CN
Sci Rep, (2020). 10:21176

Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction.Mwanga MJ, Verani JR, Omore R, Tate JE, Parashar UD, Murunga N, Gicheru E, Breiman RF, Nokes DJ, Agoti CN
Pathogens, (2020). 9:

Implications of gestational age at antenatal care attendance on the successful implementation of a maternal respiratory syncytial virus (RSV) vaccine program in coastal Kenya.Nyiro JU, Bukusi E, Mwaengo D, Walumbe D, Nyaguara A, Nyawanda B, Otieno N, Berkley JA, Munywoki P, Nokes DJ
BMC Public Health, (2020). 20:1723

Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya.Adema IW, Kamau E, Uchi Nyiro J, Otieno GP, Lewa C, Munywoki PK, Nokes DJ
Wellcome Open Res, (2020). 5:63

Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya.Luka MM, Kamau E, Adema I, Munywoki PK, Otieno GP, Gicheru E, Gichuki A, Kibinge N, Agoti CN, Nokes DJ
Open Forum Infect Dis, (2020). 7:ofaa385