2020

Nyiro, Joyce U., Bukusi, Elizabeth, Mwaengo, Dufton, Walumbe, David, Nyaguara, Amek, Nyawanda, Bryan, Otieno, Nancy, Berkley, James A., Munywoki, Patrick and Nokes, D. James (2020) Implications of gestational age at antenatal care attendance on the successful implementation of a maternal respiratory syncytial virus (RSV) vaccine program in coastal Kenya. BMC Public Health, 20 (1). 1723. doi:10.1186/s12889-020-09841-9

Luka, Martha M., Kamau, Everlyn, Adema, Irene, Munywoki, Patrick K., Otieno, Grieven P., Gicheru, Elijah, Gichuki, Alex, Kibinge, Nelson, Agoti, Charles N. and Nokes, D. James (2020) Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya. Open Forum Infectious Diseases, 7 (10). ofaa385. doi:10.1093/ofid/ofaa385

Mweu, Marshal M., Murunga, Nickson, Otieno, Juliet W. and Nokes, D. James (2020) Accuracy of diagnostic tests for respiratory syncytial virus infection within a paediatric hospital population in Kilifi County, Kenya. Wellcome Open Research, 5 . 155. doi:10.12688/wellcomeopenres.16067.1

Adema, Irene Wangwa, Kamau, Everlyn, Uchi Nyiro, Joyce, Otieno, Grieven P., Lewa, Clement, Munywoki, Patrick K. and Nokes, D. James (2020) Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya. Wellcome Open Research, 5 . 63. doi:10.12688/wellcomeopenres.15703.2

Otieno, Grieven P., Murunga, Nickson, Agoti, Charles N., Gallagher, Katherine E., Awori, Juliet O. and Nokes, D. James (2020) Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya. Wellcome Open Research, 5 . 150. doi:10.12688/wellcomeopenres.16037.2

RSV GOLD Study Group (Including: Löwensteyn, Yvette N., Phijffer, Emily W. E. M., Simons, Juliette V. L., Scheltema, Nienke M., Mazur, Natalie I., Nair, Harish and Bont, Louis J.). (2020) Respiratory syncytial virus-related death in children with Down Syndrome. Pediatric Infectious Disease Journal, 39 (8). pp. 665-670. doi:10.1097/INF.0000000000002666

(2020) Rotavirus group : a genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018. BMC Infectious Diseases, 20 . 504. doi:10.1186/s12879-020-05230-0

Nyasimi, Festus M., Owuor, D. Collins, Ngoi, Joyce M., Mwihuri, Alexander G., Otieno, Grieven P., Otieno, James R., Githinji, George, Nyiro, Joyce U., Nokes, D. James and Agoti, Charles N. (2020) Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season. Virus Evolution . doi:10.1093/ve/veaa045 (In Press)

Owuor, D. Collins, Ngoi, Joyce M., Otieno, James R., Otieno, Grieven P., Nyasimi, Festus M., Nyiro, Joyce U., Agoti, Charles N., Chaves, Sandra S. and Nokes, D. James (2020) Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017. Influenza and Other Respiratory Viruses, 14 (3). pp. 320-330. doi:10.1111/irv.12717

Brand, Samuel, Munywoki, Patrick, Walumbe, David, Keeling, Matthew James and Nokes, D. James (2020) Reducing RSV hospitalisation in a lower-income country by vaccinating mothers-to-be and their households. eLife, 9 . e47003. doi:10.7554/eLife.47003

Kinyanjui, Timothy, Pan-Ngum, Wirichada, Saralamba, Sompob, Taylor, Sylvia, White, Lisa J. and Nokes, D. James (2020) Model evaluation of target product profiles of an infant vaccine against respiratory syncytial virus (RSV) in a developed country setting. Vaccine: X . 100055. doi:10.1016/j.jvacx.2020.100055 (In Press)

Kamau, Everlyn, Oketch, John W., de Laurent, Zaydah R., Phan, My V. T., Agoti, Charles N., Nokes, D. James and Cotton, Matthew (2020) Whole genome sequencing and phylogenetic analysis of Human metapneumovirus strains from Kenya and Zambia. BMC Genomics, 21 (5). doi:10.1186/s12864-019-6400-z

Abidha, C., Nyiro, J., Kamau, E., Abdullahi, O., Nokes, D. James and Agoti, C. N. (2020) Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-2016. Virus Evolution, 6 (1). veaa031. doi:10.1093/ve/veaa031

Kamau, Everlyn , Otienoa, James R, Lewa, Clement S., Mwema , Anthony , Murunga, Nickson , Nokes, D. James and Agoti , Charles N. (2020) Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on. Scientific Reports . (In Press)

Kamau, Everlyn, Otieno, James R., Murunga, Nickson, Oketch, John W., Ngoi, Joyce M., de Laurent, Zaydah R., Mwema, Anthony, Nyiro, Joyce U., Agoti, Charles N. and Nokes, D. James (2020) Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. Virus Evolution . veaa050. doi:10.1093/ve/veaa050 (In Press)

Nokes, D. James (2020) Global burden of acute lower respiratory infection associated with human metapneumovirus in children under five years for 2018 : a systematic review and modelling study. Lancet Global Health . (In Press)

Mwanga, Mike J., Verani, Jennifer R., Omore, Richard, Tate, Jacqueline E., Parashar, Umesh D., Murunga, Nickson, Gicheru, Elijah, Breiman, Robert F., Nokes, D. James and Agoti, Charles N. (2020) Multiple introductions and predominance of 3 rotavirus group A genotype G3P[8] in Kilifi, coastal Kenya, 4 years after nationwide vaccine introduction. Pathogens . (In Press)

2019

Kamau, Everlyn, Luka, Martha M., de Laurent, Zaydah R., Adema, Irene, Agoti, Charles N. and Nokes, D. James (2019) Genome sequences of human coronavirus OC43 and NL63, associated with respiratory infections in Kilifi, Kenya. Microbiology Resource Announcements, 8 (46). e00730-19. doi:10.1128/MRA.00730-19

(2019) Impact of the introduction of rotavirus vaccine on hospital admissions for diarrhoea among children in Kenya : a controlled interrupted time series analysis. Clinical Infectious Diseases . doi:10.1093/cid/ciz912 (In Press)

Oketch, John W., Kamau, Everlyn, Otieno, Grieven P., Otieno, James R., Agoti, Charles N. and Nokes, D. James (2019) Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007–2016. BMC Infectious Diseases, 19 (1). 757. doi:10.1186/s12879-019-4381-9

Kiti, Moses Chapa, Melegaro, Alessia, Cattuto, Ciro and Nokes, D. James (2019) Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors. Wellcome Open Research, 4 . p. 84. doi:10.12688/wellcomeopenres.15268.2

(2019) Global patterns in monthly activity of influenza virus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus : a systematic analysis. The Lancet Global Health, 7 (8). e1031-e1045. doi:10.1016/S2214-109X(19)30264-5

(2019) Effectiveness of monovalent rotavirus vaccine against hospitalization with acute rotavirus gastroenteritis in Kenyan children. Clinical Infectious Diseases . ciz664. doi:10.1093/cid/ciz664 (In Press)

Agoti, Charles N., Phan, My V. T., Munywoki, Patrick K., Githinji, George, Medley, Graham, Cane, Patricia A., Kellam, Paul, Cotton, Matthew and Nokes, D. James (2019) Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. Scientific Reports, 9 . 10076. doi:10.1038/s41598-019-46509-w

Sand, Charles, Njunge, James, Mwongeli, Joyce, Mutunga, Martin, Chege, Timothy, Gicheru, Elijah, Gardiner, Elizabeth, Gwela, Agnes, Drysdale, Simon, Green, Christopher, Berkley, James, Nokes, D. James and Pollard, Andrew J. (2019) Airway response to respiratory syncytial virus has incidental antibacterial effects. Nature Communications, 10 (1). 2218. doi:10.1038/s41467-019-10222-z

Brand, Samuel, Munywoki, Patrick K., Walumbe, David, Keeling, Matthew James and Nokes, D. James (2019) Data for Reducing RSV hospitalisation in a lower-income country by vaccinating mothers-to-be and their households. [Dataset]

Kamau, E., Onyango, C. O., Otieno, G. P., Kiyuka, P. K., Agoti, C. N., Medley, G. F., Cane, P. A., Nokes, D. James and Munywoki, P. K. (2019) An intensive, active surveillance reveals continuous invasion and high diversity of rhinovirus in households. Journal of Infectious Diseases, 219 (7). pp. 1049-1057. doi:10.1093/infdis/jiy621

Nyiro, Joyce, Kiyuka, Patience K., Mutunga, Martin N., Sande, Charles J., Munywoki, Patrick K., Scott, J. Anthony G. and Nokes, D. James (2019) Agreement between ELISA and plaque reduction neutralisation assay in detection of respiratory syncytial virus specific antibodies in a birth Cohort from Kilifi, coastal Kenya. Wellcome Open Research, 4 . 33. doi:doi:10.12688/wellcomeopenres.15108.1

Kamau, Everlyn, Agoti, Charles N., Ngoi, Joyce M., de Laurent, Zaydah R., Gitonga, John, Cotten, Matthew, Phan, My V. T., Nokes, D. James, Delwart, Eric, Sanders, Eduard, Warimwe, George M. and Dunning Hotopp, Julie C. (2019) Complete genome sequences of dengue virus type 2 strains from Kilifi, Kenya. Microbiology Resource Announcements, 8 (4). e01566-18. doi:10.1128/MRA.01566-18

2018

Kombe, Ivy K., Munywoki, Patrick K., Baguelin, Marc, Nokes, D. James and Medley, Graham (2018) Model-based estimates of transmission of respiratory syncytial virus within households. Epidemics . doi:10.1016/j.epidem.2018.12.001 (In Press)

UNSPECIFIED (2018) Stakeholder’s technical meeting report : epidemiology and control options of respiratory syncytial virus (RSV) in the Kenyan context. KEMRI HQ / National Influenza Centre / KEMRI-Wellcome Trust Programme / KEMRI-CDC.

Morobe, John Mwita, Nyiro, Joyce, Brand, Samuel, Kamau, Everlyn, Gicheru, Elijah, Eyase, Fredrick, Otieno, Grieven, Munywoki, Patrick, Agoti, Charles and Nokes, D. James (2018) Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Research, 3 . 128. doi:doi:10.12688/wellcomeopenres.14836.1

Morobe, John Mwita, Nyiro, Joyce U., Brand, Samuel, Kamau, Everlyn, Munywoki, Patrick K., Agoti, Charles N. and Nokes, D. James (2018) Data for Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. [Dataset]

Sande, Charles J., Mutunga, Martin, Muteti, Jacqueline, Berkley, James A., Nokes, D. James and Njunge, James (2018) Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics. Scientific Reports, 8 (1). 13814 . doi:10.1038/s41598-018-32072-3

Nyiro, Joyce Uchi, Munywoki, Patrick, Kamau, Everlyn, Agoti, Charles, Gichuki, Alex, Etyang, Timothy, Otieno, Grieven and Nokes, D. James (2018) Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations. Wellcome Open Research, 3 . 89. doi:10.12688/wellcomeopenres.14662.1

Morpeth, Susan C., Munywoki, Patrick, Hammitt, Laura L., Bett, Anne, Bottomley, Christian, Onyango, Clayton O., Murdoch, David R., Nokes, D. James and Scott, J. Anthony G. (2018) Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children. Scientific Reports, 8 (1). 11030. doi:10.1038/s41598-018-29119-w

Nyiro, Joyce U., Otieno, Grieven P. and Nokes, D. James (2018) Data for Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations. [Dataset]

Otieno, J. R., Kamau, E. M., Oketch, J. W., Ngoi, J. M., Gichuki, A. M., Binter, Š., Otieno, G. P., Ngama, M., Agoti, C. N., Cane, P. A., Kellam, P., Cotten, M., Lemey, P. and Nokes, D. James (2018) Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains. Virus Evolution, 4 (2). vey027. doi:10.1093/ve/vey027

Kiyuka, Patience K, Agoti, Charles N, Munywoki, Patrick K, Njeru, Regina, Bett, Anne, Otieno, James R, Otieno, Grieven P, Kamau, Everlyn, Clark, Taane G, van der Hoek, Lia, Kellam, Paul, Nokes, D. James and Cotten, Matthew (2018) Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya. The Journal of Infectious Diseases, 217 (11). pp. 1728-1739. doi:10.1093/infdis/jiy098

Munywoki, Patrick K., Koech, Dorothy C, Agoti, Charles N., Cane, Patricia A., Medley, Graham and Nokes, D. James (2018) Continuous invasion by respiratory viruses observed in rural households during a respiratory syncytial virus seasonal outbreak in coastal Kenya. Clinical Infectious Diseases, 67 (10). pp. 1559-1567. doi:10.1093/cid/ciy313

Mohammed, Khadija Said, Kibinge, Nelson, Prins, Pjotr, Agoti, Charles N., Cotten, Matthew, Nokes, D. James, Brand, Samuel and Githinji, George (2018) Evaluating the performance of tools used to call minority variants from whole genome short-read data. Wellcome Open Research, 3 . 21. doi:10.12688/wellcomeopenres.13538.2

Agoti, Charles N., Munywoki, Patrick K., Cotten, Matthew and Nokes, D. James (2018) Data for Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. [Dataset]

Nyiro, Joyce U., Munywoki, Patrick K. and Nokes, D. James (2018) Data for Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya. [Dataset]

Owor, Betty E., Mwanga, Mike J., Njeru, Regina, Mugo, Robert, Ngama, Mwanajuma, Otieno, Grieven P., Nokes, D. James and Agoti, C.N. (2018) Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013. Wellcome Open Research, 3 . 150. doi:doi:10.12688/wellcomeopenres.14908.1

2017

(2017) Global respiratory syncytial virus-associated mortality in young children (RSV GOLD) : a retrospective case series. The Lancet Global Health, 5 (10). e984-e991. doi:10.1016/s2214-109x(17)30344-3

(2017) Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015 : a systematic review and modelling study. The Lancet, 390 (10098). pp. 946-958. doi:10.1016/S0140-6736(17)30938-8

Flasche, Stefan, Ojal, John, Le Polain de Waroux, Olivier, Otiende, Mark, O’Brien, Katherine L., Kiti, Moses, Nokes, D. James, Edmunds, W John and Scott, J. Anthony G. (2017) Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine : a modelling study based on data from PCV10 introduction in Kilifi, Kenya. BMC Medicine, 15 (1). 113. doi:10.1186/s12916-017-0882-9

Adetifa, Ifedayo M.O., Bwanaali, Tahreni, Wafula, Jackline, Mutuku, Alex, Karia, Boniface, Makumi, Anne, Mwatsuma, Pauline, Bauni, Evasius, Hammitt, Laura L., Nokes, D. James, Maree, Ephantus, Tabu, Collins, Kamau, Tatu, Mataza, Christine, Williams, Thomas N. and Scott, J. Anthony G. (2017) Cohort profile : the Kilifi vaccine monitoring study. International Journal of Epidemiology, 46 (3). 792-792h. doi:10.1093/ije/dyw202

Nyiro, Joyce U., Kombe, Ivy K., Sande, Charles J., Kipkoech, James, Kiyuka, Patience K., Onyango, Clayton O., Munywoki, Patrick K., Kinyanjui, Timothy M. and Nokes, D. James (2017) Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya. PLoS One, 12 (5). e0177803. doi:10.1371/journal.pone.0177803

Nokes, D. James and Otieno, James R. (2017) Data for Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya. [Dataset]

Nokes, D. James and Kamau, Evelyn (2017) Data for Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. [Dataset]

Nokes, D. James and Otieno, James R. (2017) Data for Spread and evolution of respiratory syncytial virus A genotype ON1, coastal Kenya, 2010–2015. [Dataset]

Ngari, Moses M., Fegan, Greg, Mwangome, Martha K., Ngama, Mwanajuma J., Mturi, Neema, Scott, John Anthony Gerard, Bauni, Evasius, Nokes, D. James and Berkley, James A. (2017) Mortality after inpatient treatment for severe pneumonia in children : a cohort study. Paediatric and Perinatal Epidemiology, 31 (3). pp. 233-242. doi:10.1111/ppe.12348

Atkins, Katie, Baguelin, Marc, Brand, Samuel, Jit, Mark, Keeling, Matthew James, Kibinge, Nelson, Kinyanjui, Timothy, Medley, Graham, Melegaro, Alessia, Munywoki, Patrick, Nokes, D. James, Panovska-Griffiths, Jasmina, Pan-Ngum, Wurichada , Pellis, Lorenzo and White, Lisa (2017) RSV modelling meeting. University of Warwick, Coventry: School of Life Science and Zeeman Institute SBIDER Centre, University of Warwick, UK and KEMRI-Wellcome Trust Research Programme , Kilifi, Kenya. (Unpublished)

Wathuo, Miriam, Medley, Graham, Nokes, D. James and Munywoki, Patrick K. (2017) Quantification and determinants of the amount of respiratory syncytial virus (RSV) shed using real time PCR data from a longitudinal household study. Wellcome Open Research, 1 . 27. doi:10.12688/wellcomeopenres.10284.2

Agoti, Charles N., Munywoki, Patrick K., Phan, My V. T., Otieno, James R., Kamau, Everlyn, Bett, Anne, Kombe, Ivy, Githinji, George, Medley, Graham, Cane, Patricia A., Kellam, Paul, Cotten, Matthew and Nokes, D. James (2017) Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. Virus Evolution, 3 (1). vex006. doi:10.1093/ve/vex006

Kamau, Everlyn, Agoti, Charles N., Lewa, Clement S., Oketch, John, Owor, Betty E., Otieno, Grieven P., Bett, Anne, Cane, Patricia A. and Nokes, D. James (2017) Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. Journal of clinical virology . doi:10.1016/j.jcv.2016.12.011

Otieno, James R., Kamau, Everlyn M., Agoti, Charles N., Lewa, Clement, Otieno, Grieven, Bett, Ann, Ngama, Mwanajuma, Cane, Patricia A. and Nokes, D. James (2017) Spread and evolution of respiratory syncytial virus A genotype ON1, coastal Kenya, 2010–2015. Emerging Infectious Diseases, 23 (2). pp. 264-271. doi:10.3201/eid2302.161149

Pan-Ngum, Wirichada, Kinyanjui, Timothy M., Kiti, Moses C., Taylor, Sylvia, Toussaint, Jean-François, Saralamba, Sompob, Van Effelterre, Thierry, Nokes, D. James and White, Lisa J. (2017) Predicting the relative impacts of maternal and neonatal respiratory syncytial virus (RSV) vaccine target product profiles : a consensus modelling approach. Vaccine, 35 (2). pp. 403-409. doi:10.1016/j.vaccine.2016.10.073

2016

Nyiro, Joyce Uchi, Sande, Charles Jumba, Mutunga, Martin, Kiyuka, Patience Kerubo, Munywoki, Patrick Kioo, Scott, John Anthony G. and Nokes, D. James (2016) Absence of association between cord specific antibody levels and severe respiratory syncytial virus (RSV) disease in early infants : a case control study from coastal Kenya. PLoS One, 11 (11). e0166706. doi:10.1371/journal.pone.0166706

Emukule, Gideon O. , Mott, Joshua A., Spreeuwenberg, Peter, Viboud, Cecile, Commanday, Alexander, Muthoka, Philip, Munywoki, Patrick K., Nokes, D. James, Velden, Koos van der and Paget, John W. (2016) Influenza activity in Kenya, 2007-2013 : timing, association with climatic factors, and implications for vaccination campaigns. Influenza and Other Respiratory Viruses, 10 (5). pp. 375-385. doi:10.1111/irv.12393

Agoti, Charles N., Kiyuka, Patience K., Kamau, Everlyn, Munywoki, Patrick K., Bett, Anne, van der Hoek, Lia, Kellam, Paul, Nokes, D. James and Cotten, Matthew (2016) Human Rhinovirus B and C genomes from rural coastal Kenya. Genome Announcements, 4 (4). pp. 1-2. e00751. doi:10.1128/genomeA.00751-16

Owor, Betty E., Masankwa, Geoffrey N., Mwango, Lilian C., Njeru, Regina W., Agoti, Charles N. and Nokes, D. James (2016) Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11. BMC Infectious Diseases, 16 (1). doi:10.1186/s12879-016-1605-0

Kiti, Moses C., Tizzoni, Michele, Kinyanjui, Timothy M., Koech, Dorothy C., Munywoki, Patrick K., Meriac, Milosch, Cappa, Luca, Panisson, André, Barrat, Alain, Cattuto, Ciro and Nokes, D. James (2016) Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors. EPJ Data Science, 5 (1). doi:10.1140/epjds/s13688-016-0084-2

Otieno, James R., Agoti, Charles N., Gitahi, Caroline W., Bett, Ann, Ngama, Mwanajuma, Medley, Graham F, Cane, Patricia A. and Nokes, D. James (2016) Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya. Journal of Virology, 90 (10). pp. 4990-5002. doi:10.1128/JVI.03105-15

WHO RSV Vaccine Consultation Expert Group (Including: Modjarrad, Kayvon, Giersing, Birgitte, Kaslow, David C., Smith, Peter G. and Moorthy, Vasee S.). (2016) WHO consultation on Respiratory Syncytial Virus Vaccine Development Report from a World Health Organization Meeting held on 23–24 March 2015. Vaccine, 34 (2). pp. 190-197. doi:10.1016/j.vaccine.2015.05.093

2015

Hollingsworth, T. Déirdre, Langley, Ivor, Nokes, D. James, Macpherson, Eleanor E., McGivern, Gerry, Adams, Emily R., Bockarie, Moses J., Mortimer, Kevin, Reimer, Lisa J, Squire, Bertie, Torr, Stephen J. and Medley, Graham (2015) Infectious disease and health systems modelling for local decision making to control neglected tropical diseases. BMC Proceedings, 9 (Suppl 10). S6. doi:10.1186/1753-6561-9-S10-S6

Munywoki, Patrick K., Koech, Dorothy C., Agoti, Charles N., Bett, Ann, Cane, Patricia A., Medley, Graham F. and Nokes, D. James (2015) Frequent asymptomatic respiratory syncytial virus infections during an epidemic in a rural Kenyan household cohort. Journal of Infectious Diseases, 212 (11). pp. 1711-1718. doi:10.1093/infdis/jiv263

Kinyanjui, Timothy M., House, Thomas A., Kiti, Moses C., Cane, Patricia, Nokes, D. James and Medley, Graham (2015) Vaccine induced herd immunity for control of respiratory syncytial virus disease in a low-income country setting. PLoS One, 10 (9). pp. 1-16. e0138018. doi:10.1371/journal.pone.0138018

Agoti, Charles N., Otieno, James R., Ngama, Mwanajuma, Mwihuri, Alexander G., Medley, Graham, Cane, Patricia A., Nokes, D. James and Kirkegaard, K. (2015) Successive respiratory syncytial virus epidemics in local populations arise from multiple variant introductions, providing insights into virus persistence. Journal of Virology, 89 (22). pp. 11630-11642. doi:10.1128/JVI.01972-15

Agoti, Charles N., Otieno, James R., Munywoki, Patrick K., Mwihuri, Alexander G., Cane, Patricia, Nokes, D. James, Kellam, Paul, Cotten, Matthew and Perlman, S. (2015) Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. Journal of Virology, Volume 89 (Number 7). pp. 3444-3454. doi:10.1128/JVI.03391-14

Nyiro, Joyce U., Sande, Charles, Mutunga, Martin, Kiyuka, Patience K., Munywoki, Patrick K., Scott, J. Anthony G. and Nokes, D. James (2015) Quantifying maternally derived respiratory syncytial virus specific neutralising antibodies in a birth cohort from coastal Kenya. Vaccine, 33 (15). pp. 1797-1801. doi:10.1016/j.vaccine.2015.02.039

Poletti, Piero, Merler, Stefano, Ajelli, Marco, Manfredi, Piero, Munywoki, Patrick K., Nokes, D. James and Melegaro, Alessia (2015) Evaluating vaccination strategies for reducing infant respiratory syncytial virus infection in low-income settings. BMC Medicine, Volume 13 (Number 1). pp. 1-11. Article number 49. doi:10.1186/s12916-015-0283-x

Munywoki, Patrick Kiio, Koech, Dorothy C., Agoti, Charles N., Kibirige, N., Kipkoech, J., Cane, Patricia, Medley, Graham and Nokes, D. James (2015) Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding. Epidemiology and Infection, 143 (4). pp. 804-812. doi:10.1017/S0950268814001393

2014

Sande, Charles J., Cane, Patricia and Nokes, D. James (2014) The association between age and the development of respiratory syncytial virus neutralising antibody responses following natural infection in infants. Vaccine, Volume 32 (Number 37). pp. 4726-4729. doi:10.1016/j.vaccine.2014.05.038

Kiti, Moses Chapa, Kinyanjui, Timothy, Koech, Dorothy Chelagat, Munywoki, Patrick Kiio, Medley, Graham and Nokes, D. James (2014) Quantifying age-related rates of social contact using diaries in a rural coastal population of Kenya. PLoS One, Volume 9 (Number 8). Article number e104786. doi:10.1371/journal.pone.0104786

Munywoki, Patrick Kiio, Koech, Dorothy C., Agoti, Charles N., Lewa, Clement, Cane, Patricia, Medley, Graham and Nokes, D. James (2014) The source of respiratory syncytial virus infection in infants : a household cohort study in rural Kenya. Journal of Infectious Diseases, Volume 209 (Number 11). pp. 1685-1692. doi:10.1093/infdis/jit828

Agoti, Charles N., Otieno, James R., Gitahi, Caroline W., Cane, Patricia and Nokes, D. James (2014) Rapid spread and diversification of respiratory syncytial virus genotype ON1, Kenya. Emerging Infectious Diseases , Volume 20 (Number 6). pp. 950-959. doi:10.3201/eid2006.131438

Agoti, Charles N., Mayieka, Lillian M., Otieno, James R., Ahmed, Jamal A., Fields, Barry S., Waiboci, Lilian W., Nyoka, Raymond, Eidex, Rachel B., Marano, Nina, Burton, Wagacha, Montgomery, Joel M., Breiman, Robert F. and Nokes, D. James (2014) Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya. BMC Infectious Diseases, Volume 14 (Number 1). Article number 178. doi:10.1186/1471-2334-14-178

2013

Agoti, Charles N., Gitahi, Caroline W., Medley, Graham, Cane, Patricia and Nokes, D. James (2013) Identification of group B respiratory syncytial viruses that lack the 60-nucleotide duplication after six consecutive epidemics of total BA dominance at coastal Kenya. Influenza and Other Respiratory Viruses, Volume 7 (Number 6). pp. 1008-1012. doi:10.1111/irv.12131

Sande, Charles J., Mutunga, M. N., Okiro, Emelda A., Medley, Graham, Cane, Patricia and Nokes, D. James (2013) Kinetics of the neutralizing antibody response to respiratory syncytial virus infections in a birth cohort. Journal of Medical Virology, Volume 85 (Number 11). pp. 2020-2025. doi:10.1002/jmv.23696

Sande, C. J., Mutunga, M. N., Medley, Graham, Cane, Patricia and Nokes, D. James (2013) Group- and genotype-specific neutralizing antibody responses against respiratory syncytial virus in infants and young children with severe pneumonia. Journal of Infectious Diseases, Volume 207 (Number 3). pp. 489-492. doi:10.1093/infdis/jis700

Fuller, James A., Summers, Aimee, Katz, Mark A., Lindblade, Kim A., Njuguna, Henry, Arvelo, Wences, Khagayi, Sammy, Emukule, Gideon, Linares-Perez, Nivaldo, McCracken, John, Nokes, D. James, Ngama, Mwanajuma, Kazungu, Sidi, Mott, Joshua A., Olsen, Sonja J., Widdowson, Marc-Alain and Feikin, Daniel R. (2013) Estimation of the national disease burden of influenza-associated severe acute respiratory illness in Kenya and Guatemala : a novel methodology. PLoS One, Volume 8 (Mumber 2). Article number e56882. doi:10.1371/journal.pone.0056882

Munywoki, Patrick Kiio, Ohuma, Eric O., Ngama, Mwanajuma, Bauni, Evasius, Scott, J. Anthony G. and Nokes, D. James (2013) Severe lower respiratory tract infection in early infancy and pneumonia hospitalizations among children, Kenya. Emerging Infectious Diseases , Volume 19 (Number 2). pp. 223-229. doi:10.3201/eid1902.120940

Anderson, L. J., Dormitzer, P. R., Nokes, D. James, Rappuoli, R., Roca, A. and Graham, B.S. (2013) Strategic priorities for respiratory syncytial virus (RSV) vaccine development. Vaccine, Volume 31 . B209-B215. doi:10.1016/j.vaccine.2012.11.106

2012

Okiro, Emelda A., Ngama, Mwanajuma, Bett, Ann and Nokes, D. James (2012) The incidence and clinical burden of respiratory syncytial virus disease identified through hospital outpatient presentations in Kenyan children. PLoS One, Vol.7 (No.12). e52520. doi:10.1371/journal.pone.0052520

Agoti, Charles N., Mwihuri, Alexander G., Sande, Charles J., Onyango, Clayton O., Medley, Graham, Cane, Patricia and Nokes, D. James (2012) Genetic relatedness of infecting and reinfecting respiratory syncytial virus strains identified in a birth cohort from rural Kenya. Journal of Infectious Diseases, Volume 206 (Number 10). pp. 1532-1541. doi:10.1093/infdis/jis570

van Hoek, Albert Jan, Ngama, Mwanajuma, Ismail, Amina, Chuma, Jane, Cheburet, Samuel, Mutonga, David, Kamau, Tatu and Nokes, D. James (2012) A cost effectiveness and capacity analysis for the introduction of universal rotavirus vaccination in Kenya : comparison between Rotarix and RotaTeq vaccines. PLoS One, Vol.7 (No.10). e47511. doi:10.1371/journal.pone.0047511

Webb, Clare, Ngama, Mwanajuma, Ngatia, Anthony, Shebbe, Mohammed, Morpeth, Susan, Mwarumba, Salim, Bett, Ann, Nokes, D. James, Seale, Anna C., Kazungu, Sidi, Munywoki, Patrick, Hammitt, Laura L., Scott, J Anthony G. and Berkley, James A. (2012) Treatment failure among Kenyan children with severe pneumonia--a cohort study. The Pediatric infectious disease journal, Volume 31 (Number 9). e152-e157. doi:10.1097/INF.0b013e3182638012

Gravel, Genevieve (2012) The use of a pediatric prophylactic vaccine for respiratory syncytial virus in Kenya. KEMRI-Wellcome Trust Research Programme.

Onyango, Clayton O., Welch, Stephen R., Munywoki, Patrick K., Agoti, Charles N., Bett, Ann, Ngama, Mwanajuma, Myers, Richard, Cane, Patricia and Nokes, D. James (2012) Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya. Journal of Medical Virology, Volume 84 (Number 5). pp. 823-831. doi:10.1002/jmv.23251

Hammitt, L. L., Kazungu, S., Morpeth, S. C., Gibson, D. G., Mvera, B., Brent, A. J., Mwarumba, S., Onyango, C. O., Bett, A., Akech, D. O., Murdoch, D. R., Nokes, D. James and Scott, J. A. G. (2012) A preliminary study of pneumonia etiology among hospitalized children in Kenya. Clinical Infectious Diseases, Vol.54 (Suppl.2). S190-S199. doi:10.1093/cid/cir1071

Onyango, Clayton O., Njeru, Regina, Kazungu, Sidi, Achilla, Rachel, Bulimo, Wallace, Welch, Stephen R., Cane, Patricia, Gunson, Rory N., Hammitt, Laura L., Scott, J. Anthony G., Berkley, James A. and Nokes, D. James (2012) Influenza surveillance among children with pneumonia admitted to a district hospital in coastal Kenya, 2007-2010. Journal of Infectious Diseases, Volume 206 (Supplement 1). S61-S67. doi:10.1093/infdis/jis536

Ohuma, E. O., Okiro, E. A., Ochola, R., Sande, C. J., Cane, Patricia, Medley, Graham, Bottomley, C. and Nokes, D. James (2012) The natural history of respiratory syncytial virus in a birth cohort : the influence of age and previous infection on reinfection and disease. American Journal of Epidemiology, Vol.176 (No.9). pp. 794-802. doi:10.1093/aje/kws257

2011

Munywoki, Patrick, Hamid, Fauzat, Mutunga, Martin, Welch, Steve, Cane, Patricia and Nokes, D. James (2011) Improved detection of respiratory viruses in pediatric outpatients with acute respiratory illness by real-time PCR using nasopharyngeal flocked swabs. Journal of Clinical Microbiology, Vol.49 (No.9). pp. 3365-3367. doi:10.1128/JCM.02231-10

Nyiro, Joyce U., Sanders, Eduard J., Ngetsa, Caroline, Wale, Steve, Awuondo, Ken, Bukusi, Elizabeth Anne, Price, Matthew A., Amornkul, Pauli N. and Nokes, D. James (2011) Seroprevalence, predictors and estimated incidence of maternal and neonatal Herpes Simplex Virus Type 2 infection in semi-urban women in Kilifi, Kenya. BMC Infectious Diseases, Vol.11 (No.155). doi:10.1186/1471-2334-11-155

Hammitt, L. L., Kazungu, S., Welch, S. (Steve), Bett, Anne, Onyango, Clayton O., Gunson, R. N., Scott, J. Anthony G. and Nokes, D. James (2011) Added value of an oropharyngeal swab in detection of viruses in children hospitalized with lower respiratory tract infection. Journal of Clinical Microbiology, Volume 49 (Number 6). pp. 2318-2320. doi:10.1128/JCM.02605-10

Moïsi, Jennifer, Gatakaa, Hellen, Berkley, James A., Maitland, Kathryn, Mturi, Neema, Newton, Charles, Njuguna, Patricia, Nokes, D. James, Ojal, John, Bauni, Evasius, Tsofa, Benjamin, Peshu, Norbert, Marsh, Kevin, Williams, Thomas and Scott, J. Anthony G. (2011) Excess child mortality after discharge from hospital in Kilifi, Kenya: a retrospective cohort analysis. Bulletin of the World Health Organization, Vol.89 (No.10). pp. 725-732. doi:10.2471/BLT.11.089235

Moïsi, Jennifer C, Nokes, D. James, Gatakaa, Hellen, Williams, Thomas N, Bauni, Evasius, Levine, Orin S and Scott, J Anthony G (2011) Sensitivity of hospital-based surveillance for severe disease: a geographic information system analysis of access to care in Kilifi district, Kenya. Bulletin of the World Health Organization, Vol.89 (No.2). pp. 102-111. doi:10.2471/BLT.10.080796

Mwambi, H., Ramroop, S., White, L., Okiro, E., Nokes, D. James, Shkedy, Z. and Molenberghs, G. (2011) A frequentist approach to estimating the force of infection for a respiratory disease using repeated measurement data from a birth cohort. Statistical Methods in Medical Research , Vol.20 (No.5). pp. 551-570. doi:10.1177/0962280210385749

2010

Agoti, Charles N., Mbisa, Jean L., Bett, Ann, Medley, Graham, Nokes, D. James and Cane, Patricia (2010) Intrapatient variation of the respiratory syncytial virus attachment protein gene. Journal of Virology, Vol.84 (No.19). pp. 10425-10428. doi:10.1128/JVI.01181-10

Nair, Harish, Gessner, Bradford D., Nokes, D. James, Theodoratou, Evropi, Rudan, Igor, Madhi, Shabir A., Simoes, Eric A. F. and Campbell, Harry (2010) Childhood mortality due to respiratory syncytial virus - authors' reply. Lancet, Vol.376 (No.9744). pp. 872-873. doi:10.1016/S0140-6736(10)61410-9

Nokes, D. James, Peenze, Ina, Netshifhefhe, Lufuno, Abwao, John, De Beer, Mariet C., Seheri, Mapaseka, Williams, Thomas N., Page, Nicola and Steele, Duncan (2010) Rotavirus genetic diversity, disease association, and temporal change in hospitalized rural Kenyan children. The Journal of Infectious Diseases, Vol.202 (Suppl.1). S180-S186. doi:10.1086/653566

Berkley, James A., Munywoki, Patrick, Ngama, Mwanajuma, Kazungu, Sidi, Abwao, John, Bett, Anne, Lassauniere, Ria, Kresfelder, Tina, Cane, Patricia, Venter, Marietjie, Scott, J. Anthony G. and Nokes, D. James (2010) Viral etiology of severe pneumonia among Kenyan infants and children. JAMA: The Journal of the American Medical Association, Vol.303 (No.20). pp. 2051-2057. doi:10.1001/jama.2010.675

(2010) Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. The Lancet, Vol.375 (No.9725). pp. 1545-1555. doi:10.1016/S0140-6736(10)60206-1

Okiro, E. A., White, L. J., Ngama, Mwanajuma, Cane, Patricia, Medley, Graham and Nokes, D. James (2010) Duration of shedding of respiratory syncytial virus in a community study of Kenyan children. BMC Infectious Diseases, Vol.10 (Article 15). doi:10.1186/1471-2334-10-15

2009

Ochola, Rachel, Sande, Charles, Fegan, Greg, Scott, P. D. (Paul D.), Medley, Graham, Cane, Patricia and Nokes, D. James (2009) The level and duration of RSV-specific maternal IgG in infants in Kilifi Kenya. PLoS One, Vol.4 (No.12). e8088. doi:10.1371/journal.pone.0008088

Nokes, D. James, Ngama, Mwanajuma, Bett, Anne, Abwao, John, Munywoki, Patrick, English, M. (Mike), Scott, J. Anthony G., Cane, Patricia and Medley, Graham (2009) Incidence and severity of respiratory syncytial virus pneumonia in rural Kenyan children identified through hospital surveillance. Clinical Infectious Diseases, Vol.49 (No.9). pp. 1341-1349. doi:10.1086/606055

Anderson, Roy M., Hollingsworth, T. Déirdre and Nokes, D. James (2009) Mathematical models of transmission and control. In: Detels, Roger and Beaglehole, Robert and Gulliford, Mary Ann and Lansang, Martin, (eds.) Oxford Textbook of Public Health. Oxford ; New York: Oxford University Press. ISBN 9780199218707

Medley, Graham and Nokes, D. James (2009) Does viral diversity matter? Science, Vol.325 (No.5938). pp. 274-275. doi:10.1126/science.1177475

Ohuma, E. O., Okiro, E. A., Bett, A., Abwao, John, Were, S., Samuel, Dhan, Vyse, A. J., Gay, N. J., Brown, D. W. G. and Nokes, D. James (2009) Evaluation of a measles vaccine campaign by oral-fluid surveys in a rural Kenyan district: interpretation of antibody prevalence data using mixture models. Epidemiology and Infection, Vol.13 (No.2). pp. 227-233. doi:10.1017/S0950268808000848

2008

White, Lisa J., Buttery, J., Cooper, Ben S., Nokes, D. James and Medley, Graham (2008) Rotavirus within day care centres in Oxfordshire, UK : characterization of partial immunity. Journal of The Royal Society Interface, Vol.5 (No.29). pp. 1481-1490. doi:10.1098/rsif.2008.0115

Nokes, D. James and Cane, Patricia (2008) New strategies for control of respiratory syncytial virus infection. Current Opinion in Infectious Diseases, Vol.21 (No.6). pp. 639-643. doi:10.1097/QCO.0b013e3283184245

Nigatu, Wondatir, Samuel, Dhan, Cohen, Bernard, Cumberland, Phillippa, Lemma, Eshetu, Brown, David W. G. and Nokes, D. James (2008) Evaluation of a measles vaccine campaign in Ethiopia using oral-fluid antibody surveys. Vaccine, Vol.26 (No.37). pp. 4769-4774. doi:10.1016/j.vaccine.2008.07.005

Nokes, D. James, Abwao, John, Pamba, Allan, Peenze, Ina, Dewar, John, Maghenda, J. Kamino, Gatakaa, Hellen, Bauni, Evasius, Scott, J. Anthony G., Maitland, Kathryn and Williams, Thomas N. (2008) Incidence and clinical characteristics of group A rotavirus infections among children admitted to hospital in Kilifi, Kenya. PL o S Medicine, Vol.5 (No.7). doi:10.1371/journal.pmed.0050153

Okiro, Emelda A., Ngama, Mwanajuma, Bett, Ann, Cane, Patricia, Medley, Graham and Nokes, D. James (2008) Factors associated with increased risk of progression to respiratory syncytial virus-associated pneumonia in young Kenyan children. Tropical Medicine & International Health, Volume 13 (Number 7). pp. 914-926. doi:10.1111/j.1365-3156.2008.02092.x

Okiro, Emelda A., Sande, Charles, Mutunga, Martin, Medley, Graham, Cane, Patricia and Nokes, D. James (2008) Identifying infections with respiratory syncytial virus by using specific immunoglobulin G (IgG) and IgA enzyme-linked immunosorbent assays with oral-fluid samples. Journal of Clinical Microbiology, Vol.46 (No.5). pp. 1659-1662. doi:10.1128/JCM.02190-07

Nokes, D. James, Okiro, Emelda A., Ngama, Mwanajuma, Ochola, Rachel, White, Lisa J., Scott, P. D. (Paul D.), English, M. (Mike), Cane, Patricia and Medley, Graham (2008) Respiratory syncytial virus infection and disease in infants and young children observed from birth in Kilifi district, Kenya. Clinical Infectious Diseases, Vol.46 (No.1). pp. 50-57. doi:10.1086/524019

2007

Scott, P. D. (Paul D.), Ochola, Rachel, Sande, Charles, Ngama, Mwanajuma, Okiro, Emelda A., Medley, Graham, Nokes, D. James and Cane, Patricia (2007) Comparison of strain-specific antibody responses during primary and secondary infections with respiratory syncytial virus. Journal of Medical Virology, Vol.79 (No.12). pp. 1943-1950. doi:10.1002/jmv.20999

White, L. J., Mandl, J. N., Gomes, M. G. M., Bodley-Tickell, A. T., Cane, Patricia, Perez-Brena, P., Aguilar, J. C., Siqueira, M. M., Portes, S. A., Straliotto, S. M., Waris, M., Nokes, D. James and Medley, Graham (2007) Understanding the transmission dynamics of respiratory syncytial virus using multiple time series and nested models. Mathematical Biosciences, Vol.209 (No.1). pp. 222-239. doi:10.1016/j.mbs.2006.08.018

Wilson, Jamie N., Nokes, D. James, Medley, Graham and Shouval, Daniel (2007) Mathematical model of the antibody response to hepatitis B vaccines: implications for reduced schedules. Vaccine, Vol.25 (No.18). pp. 3705-3712. doi:10.1016/j.vaccine.2007.01.012

2006

Nigatu, W., Nokes, D. James, Afework, A., Brown, D. W. G., Cutts, F. T. and Jin, L. (2006) Serological and molecular epidemiology of measles virus outbreaks reported in Ethiopia during 2000-2004. JOURNAL OF MEDICAL VIROLOGY, 78 (12). pp. 1648-1655. doi:10.1002/jmv.20750

2005

White, L. J., Waris, M., Cane, Patricia, Nokes, D. James and Medley, Graham (2005) The transmission dynamics of groups A and B human respiratory syncytial virus (hRSV) in England & Wales and Finland: seasonality and cross-protection. Epidemiology and Infection, Vol.13 (No.2). pp. 279-289. doi:10.1017/S0950268804003450

2003

Abebe, A., Nokes, D. James, Dejene, A., Enquselassie, F., Messele, T. and Cutts, Felicity (2003) Seroepidemiology of hepatitis B virus in Addis Ababa Ethiopia: transmission patterns and vaccine control. Epidemiology and Infection, Vol.13 (No.1). pp. 757-770. doi:10.1017/S0950268803008574

Enquselassie, F., Ayele, W., Dejene, A., Messele, T., Abebe, A., Cutts, Felicity and Nokes, D. James (2003) Seroepidemiology of measles in Addis Ababa Ethiopia: implications for control through vaccination. Epidemiology and Infection, Vol.13 (No.3). pp. 507-519. doi:10.1017/S0950268803008446

Gay, N. J., Vyse, A. J., Enquselassie, F., Nigatu, Wondatir and Nokes, D. James (2003) Improving sensitivity of oral fluid testing in IgG prevalence studies: application of mixture models to a rubella antibody survey. Epidemiology and Infection, Vol.13 (No.2). pp. 285-291. doi:10.1017/S0950268802008051

2000

Cutts, Felicity, Abebe, A., Messele, T., Dejene, A., Enquselassie, F., Nigatu, Wondatir and Nokes, D. James (2000) Sero-epidemiology of rubella in the urban population of Addis Ababa Ethiopia. Epidemiology and Infection, Vol.12 (No.3). pp. 467-479. doi:10.1017/S0950268899003532

Wilson, J. N., Nokes, D. James and Carman, W. (William) (2000) Predictions of the emergence of vaccine-resistant hepatitis B in The Gambia using a mathematical model. Epidemiology and Infection, Vol.124 (No.2). pp. 295-307. doi:10.1017/S0950268800003605

1998

Cox, M. J., Azevedo, R. S., Nokes, D. James, Beards, G. M., McCrae, Malcolm A., Massad, Eduardo and Medley, Graham (1998) Seroepidemiology of group A rotavirus in suburban São Paulo, Brazil. Epidemiology and Infection, Vol.120 . pp. 327-334. doi:10.1017/S0950268898008759

1996

Edmunds, W. John , Medley, Graham, Nokes, D. James, O'Callaghan, C. J., Whittle, H. C. and Hall, A. J. (Andrew James) (1996) Epidemiological patterns of hepatitis B virus (HBV) in highly endemic areas. Epidemiology and Infection, Vol.117 (No.2). pp. 313-325. doi:10.1017/S0950268800001497