Showing papers by "D. James Nokes published in 2016"

Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors

Abstract: Close proximity interactions between individuals influence how infections spread. Quantifying close contacts in developing world settings, where such data is sparse yet disease burden is high, can provide insights into the design of intervention strategies such as vaccination. Recent technological advances have enabled collection of time-resolved face-to-face human contact data using radio frequency proximity sensors. The acceptability and practicalities of using proximity devices within the developing country setting have not been investigated. We present and analyse data arising from a prospective study of 5 households in rural Kenya, followed through 3 consecutive days. Pre-study focus group discussions with key community groups were held. All residents of selected households carried wearable proximity sensors to collect data on their close (<1.5 metres) interactions. Data collection for residents of three of the 5 households was contemporaneous. Contact matrices and temporal networks for 75 individuals are defined and mixing patterns by age and time of day in household contacts determined. Our study demonstrates the stability of numbers and durations of contacts across days. The contact durations followed a broad distribution consistent with data from other settings. Contacts within households occur mainly among children and between children and adults, and are characterised by daily regular peaks in the morning, midday and evening. Inter-household contacts are between adults and more sporadic when measured over several days. Community feedback indicated privacy as a major concern especially regarding perceptions of non-participants, and that community acceptability required thorough explanation of study tools and procedures. Our results show for a low resource setting how wearable proximity sensors can be used to objectively collect high-resolution temporal data without direct supervision. The methodology appears acceptable in this population following adequate community engagement on study procedures. A target for future investigation is to determine the difference in contact networks within versus between households. We suggest that the results from this study may be used in the design of future studies using similar electronic devices targeting communities, including households and schools, in the developing world context.

Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya

Abstract: The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing efficiency of pre-existing immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 – 2012) in Kilifi (n=649), Kenya, and contemporaneous sequences (n=1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%) and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2, then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3.58 x 10-3 [95% HPD: 3.04 – 4.16] nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.

Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11

Abstract: Human metapneumovirus (HMPV) is an important global cause of severe acute respiratory infections in young children and the elderly. The epidemiology of HMPV in sub-Saharan Africa is poorly described and factors that allow its recurrent epidemics in communities not understood. We undertook paediatric inpatient surveillance for HMPV in Kilifi County Hospital (KCH) of Coastal Kenya between 2007 and 2011. Nasopharyngeal samples collected from children aged 1 day–59 months admitted with severe or very severe pneumonia, were tested for HMPV using real-time polymerase chain reaction (RT-PCR). Partial nucleotide sequences of the attachment (G) and fusion (F) surface proteins of positive samples were determined and phylogenetically analyzed. HMPV was detected in 4.8 % (160/3320) of children [73.8 % (118/160) of these less than one year of age], ranging between 2.9 and 8.8 % each year over the 5 years of study. HMPV infections were seasonal in occurrence, with cases predominant in the months of November through April. These months frequently coincided with low rainfall, high temperature and low relative humidity in the location. Phylogenetic analysis of partial F and G sequences revealed three subgroups of HMPV, A2 (74 %, 91/123), B1 (3.2 %, 4/123) and B2 (22.8 %, 28/123) in circulation, with subgroup A2 predominant in majority of the epidemic seasons. Comparison of G sequences (local and global) provided a greater phylogenetic resolution over comparison of F sequences and indicated presence of probable multiple G antigenic variants within the subgroups due to differences in amino acid sequence, encoded protein length and glycosylation patterns. The present study reveals HMPV is an important seasonal contributor to respiratory disease hospitalization in coastal Kenya, with an evolutionary pattern closely relating to that of respiratory syncytial virus.

Cohort Profile: The Kilifi Vaccine Monitoring Study

Abstract: Cohort Profile: The Kilifi Vaccine Monitoring Study Ifedayo M.O. Adetifa,* Tahreni Bwanaali, Jackline Wafula, Alex Mutuku, Boniface Karia, Anne Makumi, Pauline Mwatsuma, Evasius Bauni, Laura L. Hammitt, D. James Nokes, Ephantus Maree, Collins Tabu, Tatu Kamau, Christine Mataza, Thomas N. Williams J. Anthony G. Scott Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya, Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA, School of Life Sciences and WIDER, University of Warwick, Coventry, UK, Unit of Vaccines and Immunisation Services, Vector Borne Diseases Control Unit, Ministry of Health, Nairobi, Kenya, County Department of Health, Kilifi, Kenya, Department of Medicine, Imperial College, St Mary’s Hospital, London, UK, INDEPTH Network, Accra, Ghana

Human Rhinovirus B and C Genomes from Rural Coastal Kenya

Abstract: Primer-independent agnostic deep sequencing was used to generate three human rhinovirus (HRV) B genomes and one HRV C genome from samples collected in a household respiratory survey in rural coastal Kenya. The study provides the first rhinovirus genomes from Kenya and will help improve the sensitivity of local molecular diagnostics.