James Nokes

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