George Githinji

Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania.Mziray SR van Zwetselaar M Kayuki CC Mbelele PM Makubi AN Magesa AS Kisonga RM Sonda TB Kibiki GS Githinji G Heysell SK Chilongola JO Mpagama SG
Front Med (Lausanne), (2023). 9:1034682

Global disparities in SARS-CoV-2 genomic surveillance.Brito AF Semenova E Dudas G Hassler GW Kalinich CC Kraemer MUG Ho J Tegally H Githinji G Agoti CN Matkin LE Whittaker C Bulgarian Sars-CoV-sequencing group Communicable Diseases Genomics Network Covid- Impact Project Danish Covid-19 Genome Consortium Fiocruz Covid-Genomic Surveillance Network Gisaid core curation team Network for Genomic Surveillance in South Africa Swiss Sars-CoV-Sequencing Consortium Howden BP Sintchenko V Zuckerman NS Mor O Blankenship HM de Oliveira T Lin RTP Siqueira MM Resende PC Vasconcelos ATR Spilki FR Aguiar RS Alexiev I Ivanov IN Philipova I Carrington CVF Sahadeo NSD Branda B Gurry C Maurer-Stroh S Naidoo D von Eije KJ Perkins MD van Kerkhove M Hill SC Sabino EC Pybus OG Dye C Bhatt S Flaxman S Suchard MA Grubaugh ND Baele G Faria NR
Nat Commun, (2022). 13:7003

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.Tegally H San JE Cotten M Moir M Tegomoh B Mboowa G Martin DP Baxter C Lambisia AW Diallo A Amoako DG Diagne MM Sisay A Zekri AN Gueye AS Sangare AK Ouedraogo AS Sow A Musa AO Sesay AK Abias AG Elzagheid AI Lagare A Kemi AS Abar AE Johnson AA Fowotade A Oluwapelumi AO Amuri AA Juru A Kandeil A Mostafa A Rebai A Sayed A Kazeem A Balde A Christoffels A Trotter AJ Campbell A Keita AK Kone A Bouzid A Souissi A Agweyu A Naguib A Gutierrez AV Nkeshimana A Page AJ Yadouleton A Vinze A Happi AN Chouikha A Iranzadeh A Maharaj A Batchi-Bouyou AL Ismail A Sylverken AA Goba A Femi A Sijuwola AE Marycelin B Salako BL Oderinde BS Bolajoko B Diarra B Herring BL Tsofa B Lekana-Douki B Mvula B Njanpop-Lafourcade BM Marondera BT Khaireh BA Kouriba B Adu B Pool B McInnis B Brook C Williamson C Nduwimana C Anscombe C Pratt CB Scheepers C Akoua-Koffi CG Agoti CN Mapanguy CM Loucoubar C Onwuamah CK Ihekweazu C Malaka CN Peyrefitte C Grace C Omoruyi CE Rafai CD Morang'a CM Erameh C Lule DB Bridges DJ Mukadi-Bamuleka D Park D Rasmussen DA Baker D Nokes DJ Ssemwanga D Tshiabuila D Amuzu DSY Goedhals D Grant DS Omuoyo DO Maruapula D Wanjohi DW Foster-Nyarko E Lusamaki EK Simulundu E Ong'era EM Ngabana EN Abworo EO Otieno E Shumba E Barasa E Ahmed EB Ahmed EA Lokilo E Mukantwari E Philomena E Belarbi E Simon-Loriere E Anoh EA Manuel E Leendertz F Taweh FM Wasfi F Abdelmoula F Takawira FT Derrar F Ajogbasile FV Treurnicht F Onikepe F Ntoumi F Muyembe FM Ragomzingba FEZ Dratibi FA Iyanu FA Mbunsu GK Thilliez G Kay GL Akpede GO van Zyl GU Awandare GA Kpeli GS Schubert G Maphalala GP Ranaivoson HC Omunakwe HE Onywera H Abe H Karray H Nansumba H Triki H Kadjo HAA Elgahzaly H Gumbo H Mathieu H Kavunga-Membo H Smeti I Olawoye IB Adetifa IMO Odia I Ben Boubaker IB Muhammad IA Ssewanyana I Wurie I Konstantinus IS Halatoko JWA Ayei J Sonoo J Makangara JC Tamfum JM Heraud JM Shaffer JG Giandhari J Musyoki J Nkurunziza J Uwanibe JN Bhiman JN Yasuda J Morais J Kiconco J Sandi JD Huddleston J Odoom JK Morobe JM Gyapong JO Kayiwa JT Okolie JC Xavier JS Gyamfi J Wamala JF Bonney JHK Nyandwi J Everatt J Nakaseegu J Ngoi JM Namulondo J Oguzie JU Andeko JC Lutwama JJ Mogga JJH O'Grady J Siddle KJ Victoir K Adeyemi KT Tumedi KA Carvalho KS Mohammed KS Dellagi K Musonda KG Duedu KO Fki-Berrajah L Singh L Kepler LM Biscornet L de Oliveira Martins L Chabuka L Olubayo L Ojok LD Deng LL Ochola-Oyier LI Tyers L Mine M Ramuth M Mastouri M ElHefnawi M Mbanne M Matsheka MI Kebabonye M Diop M Momoh M Lima Mendonca MDL Venter M Paye MF Faye M Nyaga MM Mareka M Damaris MM Mburu MW Mpina MG Owusu M Wiley MR Tatfeng MY Ayekaba MO Abouelhoda M Beloufa MA Seadawy MG Khalifa MK Matobo MM Kane M Salou M Mbulawa MB Mwenda M Allam M Phan MVT Abid N Rujeni N Abuzaid N Ismael N Elguindy N Top NM Dia N Mabunda N Hsiao NY Silochi NB Francisco NM Saasa N Bbosa N Murunga N Gumede N Wolter N Sitharam N Ndodo N Ajayi NA Tordo N Mbhele N Razanajatovo NH Iguosadolo N Mba N Kingsley OC Sylvanus O Femi O Adewumi OM Testimony O Ogunsanya OA Fakayode O Ogah OE Oludayo OE Faye O Smith-Lawrence P Ondoa P Combe P Nabisubi P Semanda P Oluniyi PE Arnaldo P Quashie PK Okokhere PO Bejon P Dussart P Bester PA Mbala PK Kaleebu P Abechi P El-Shesheny R Joseph R Aziz RK Essomba RG Ayivor-Djanie R Njouom R Phillips RO Gorman R Kingsley RA Neto Rodrigues Rmdesa Audu RA Carr RAA Gargouri S Masmoudi S Bootsma S Sankhe S Mohamed SI Femi S Mhalla S Hosch S Kassim SK Metha S Trabelsi S Agwa SH Mwangi SW Doumbia S Makiala-Mandanda S Aryeetey S Ahmed SS Ahmed SM Elhamoumi S Moyo S Lutucuta S Gaseitsiwe S Jalloh S Andriamandimby SF Oguntope S Grayo S Lekana-Douki S Prosolek S Ouangraoua S van Wyk S Schaffner SF Kanyerezi S Ahuka-Mundeke S Rudder S Pillay S Nabadda S Behillil S Budiaki SL van der Werf S Mashe T Mohale T Le-Viet T Velavan TP Schindler T Maponga TG Bedford T Anyaneji UJ Chinedu U Ramphal U George UE Enouf V Nene V Gorova V Roshdy WH Karim WA Ampofo WK Preiser W Choga WT Ahmed YA Ramphal Y Bediako Y Naidoo Y Butera Y de Laurent ZR Africa Pathogen Genomics Initiative double dagger Ouma AEO von Gottberg A Githinji G Moeti M Tomori O Sabeti PC Sall AA Oyola SO Tebeje YK Tessema SK de Oliveira T Happi C Lessells R Nkengasong J Wilkinson E
Science, (2022). 378:eabq5358

Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021.Morobe JM Pool B Marie L Didon D Lambisia AW Makori T Mohammed KS de Laurent ZR Ndwiga L Mburu MW Moraa E Murunga N Musyoki J Mwacharo J Nyamako L Riako D Ephnatus P Gambo F Naimani J Namulondo J Tembo SZ Ogendi E Balde T Dratibi FA Yahaya AA Gumede N Achilla RA Borus PK Wanjohi DW Tessema SK Mwangangi J Bejon P Nokes DJ Ochola-Oyier LI Githinji G Biscornet L Agoti CN
Viruses, (2022). 14:

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study.Agoti CN Ochola-Oyier LI Dellicour S Mohammed KS Lambisia AW de Laurent ZR Morobe JM Mburu MW Omuoyo DO Ongera EM Ndwiga L Maitha E Kitole B Suleiman T Mwakinangu M Nyambu JK Otieno J Salim B Musyoki J Murunga N Otieno E Kiiru JN Kasera K Amoth P Mwangangi M Aman R Kinyanjui S Warimwe G Phan M Agweyu A Cotten M Barasa E Tsofa B Nokes DJ Bejon P Githinji G
Elife, (2022). 11:

Incidence of chikungunya virus infections among Kenyan children with neurological disease, 2014-2018: A cohort study.Nyamwaya DK Otiende M Mwango L Kariuki SM Otieno B Omuoyo DO Githinji G Kitsao BS Karanja HK Gitonga JN de Laurent ZR Davies A Mwarumba S Agoti CN Thumbi SM Hamaluba MM Newton CR Bejon P Warimwe GM
PLoS Med, (2022). 19:e1003994

Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya.Nyagwange J Ndwiga L Muteru K Wamae K Tuju J Testing Team C Kutima B Gitonga J Karanja H Mugo D Kasera K Amoth P Murunga N Babu L Otieno E Githinji G Nokes DJ Tsofa B Orindi B Barasa E Warimwe G Agoti CN Bejon P Ochola-Oyier LI
Wellcome Open Res, (2022). 7:69

Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol.Lambisia AW Mohammed KS Makori TO Ndwiga L Mburu MW Morobe JM Moraa EO Musyoki J Murunga N Mwangi JN Nokes DJ Agoti CN Ochola-Oyier LI Githinji G
Front Med (Lausanne), (2022). 9:836728

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

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

The Plasmodium falciparum Rh5 invasion protein complex reveals an excess of rare variant mutations.Ndwiga L Osoti V Ochwedo KO Wamae K Bejon P Rayner JC Githinji G Ochola-Oyier LI
Malar J, (2021). 20:278

Endemic chikungunya fever in Kenyan children: a prospective cohort study.Nyamwaya DK Otiende M Omuoyo DO Githinji G Karanja HK Gitonga JN Rde Laurent Z Otieno JR Sang R Kamau E Cheruiyot S Otieno E Agoti CN Bejon P Thumbi SM Warimwe GM
BMC Infect Dis, (2021). 21:186

The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing.Nowicki S deLaurent ZR de Villiers EP Githinji G Charles KJ
PLoS One, (2021). 16:e0245910

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

Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy.Kivisi CA Muthui M Hunt M Fegan G Otto TD Githinji G Warimwe GM Rance R Marsh K Bull PC Abdi AI
Front Immunol, (2019). 10:2328

Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.Agoti CN Phan MVT Munywoki PK Githinji G Medley GF Cane PA Kellam P Cotten M Nokes DJ
Sci Rep, (2019). 9:10076

Scalable Workflows and Reproducible Data Analysis for Genomics.Strozzi F Janssen R Wurmus R Crusoe MR Githinji G Di Tommaso P Belhachemi D Moller S Smant G de Ligt J Prins P
Methods Mol Biol, (2019). 1910:723-745