Prevalence of Group a Rotavirus before and after Vaccine Introduction in Mukuru Informal Settlement in Kenya

Background: Rotavirus vaccines have been shown to be a lifesaving and cost-effective public health intervention in Africa and have resulted in reduced rotavirus mortality. In Kenya, rotavirus diarrhea causes 19% of hospitalizations and 16% of clinic visits among children <5 years of age and causes 4471 deaths and 8,781 hospitalizations per year. Nationally, rotavirus disease costs the health care system $10.8 million annually. It is estimated that routine vaccination with a 2-dose rotavirus vaccination series would avert approximately 2,467 deaths (55%), 5,724 hospitalizations (65%), 852, 589 clinic visits (59%) and would save 58 disability-adjusted life-years (DALYs) per 1000 children annually. In July 2014, Kenya introduced rotavirus vaccine into its routine expanded programme  immunisation, with two doses given at 6 and 10ths week of age.WHO recommend having  surveillance studies before and after vaccine as baseline data and monitoring the possible effect after vaccine introductions. The aim of this study was to determine the prevalence of rotavirus in pre- and post-vaccine stool samples collected from children under five years, attending two selected clinics in Mukuru informal settlement in Nairobi, Kenya. Methods: Archived samples collected during a Salmonella surveillance study (SSC No. 2074) conducted between July 2013 and July 2015 were used for this study. A total of 270 samples (150 pre-vaccine and 120 post-vaccine) were tested for rotavirus using ELISA Prospect kit (Oxoid Ltd UK) and data analyzed using SPSS version 20. Results: Rotavirus prevalence was 10% (15/150) and 5% (6/120) in pre-vaccine and post-vaccine samples respectively. There was significant difference in prevalence pre and post vaccine samples for children less than 12 months (P=0.014), 13-24 months (P=0.002) and over 49 months (P=0.01). However, there was no difference in prevalence for age categories 25-36 and 37- 48 months. Conclusion: This study showed a reduction in prevalence of Group A rotavirus in Mukuru selected clinics one year after vaccine introduction into National immunization program in Kenya. Rotavirus prevalence differed significantly for cases less than 12 months, 13-24 months and over 49 months pre and post vaccine introduction. However, there was no difference in prevalence for age category 25-36 and 37- 48 months thus the vaccine proved to have a significant protection in the most vulnerable group of children. Keywords: Rotavirus, Kenya, vaccine, pre-vaccine, post-vaccine, prevalence, Kenya

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

Background: 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. Methods: 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. Results: 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. Conclusion: 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

4.胃平滑筋肉腫の1例(第526回千葉医学会例会・第9回佐藤外科例会)

A. Temporal distribution of HMPV subgroups by month isolated from Kilifi County Hospital in the 5 years of the study (2007-11). Numbers at the bottom indicate number of genotypes each year determined by a combined F and G gene sequencing (total of 123 out of the 160 positives) in Kilifi, Kenya in the period 2007–2011. (PPTX 86 kb

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

Background Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%). Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period. Conclusions The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks. These data will be useful in interpreting genotype patterns observed in the region during the vaccine er

Influenza surveillance among children with pneumonia admitted to a district hospital in coastal Kenya, 2007-2010

Background: Influenza data gaps in sub-Saharan Africa include incidence, case fatality, seasonal patterns, and associations with prevalent disorders. Methods: Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. Outpatient children provided comparative data. Results: Of 2002 admissions, influenza A virus infection was diagnosed in 3.5% (71), influenza B virus infection, in 0.9% (19); and influenza C virus infection, in 0.8% (11 of 1404 tested). Four patients with influenza died. Among outpatients, 13 of 331 (3.9%) with acute respiratory infection and 1 of 196 without acute respiratory infection were influenza positive. The annual incidence of severe or very severe pneumonia, of influenza (any type), and of influenza A, was 1321, 60, and 43 cases per 100 000 <5 years of age, respectively. Peak occurrence was in quarters 3–4 each year, and approximately 50% of cases involved infants: temporal association with bacteremia was absent. Hypoxia was more frequent among pneumonia cases involving influenza (odds ratio, 1.78; 95% confidence interval, 1.04–1.96). Influenza A virus subtypes were seasonal H3N2 (57%), seasonal H1N1 (12%), and 2009 pandemic H1N1 (7%). Conclusions: The burden of influenza was small during 2007–2010 in this pediatric hospital in Kenya. Influenza A virus subtype H3N2 predominated, and 2009 pandemic influenza A virus subtype H1N1 had little impact

ILRI In-House reconstituted SARS-CoV-2 RT-qPCR testing kit as an alternative to the commercial kits

Due to worldwide shortage and the increasing cost of COVID-19 testing kits, International Livestock Research Institute (ILRI) scientists have developed in-house reconstituted testing reagents based on the known primer sequences and their targets on the SARS-COV-2 genome. The ILRI In-House reconstituted kit reduces the cost of COVID-19 RT-qPCR testing by at least 50% compared to the cheapest commercial kits available. Our ILRI In-House reconstituted kit is a three-target multiplex formation consisting of IDT synthesized primer and probes targeting two SARS-COV-2 genes (ORF1ab and N) and an internal control targeting the human RNAse P gene. The reconstituted kit uses an RT-qPCR Mastermix with low Rox for RT-PCR amplification. We have thoroughly conducted validation tests on the ILRI In-House reconstituted kit by comparing results of the same/matching samples generated by approved commercial kits for SARS-COV-2 testing. The commercial kits used for validation experiments include DA0990-Detection Kit (Da An Gene) and TaqPath™ COVID-19 CE-IVD RT-PCR Kit (Applied Biosystems) to which we have obtained 98.96% concordance. Detailed documentation of our validation results is available

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations]

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.   Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era

Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores

Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy’s zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy’s zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation

Effectiveness of monovalent rotavirus vaccine against hospitalization with acute rotavirus gastroenteritis in Kenyan children

Rotavirus remains a leading cause of diarrheal illness and death among children worldwide. Data on rotavirus vaccine effectiveness in sub-Saharan Africa are limited. Kenya introduced monovalent rotavirus vaccine (RV1) in July 2014. We assessed RV1 effectiveness against rotavirus-associated hospitalization in Kenyan children. Between July-2014 and December-2017, we conducted surveillance for acute gastroenteritis (AGE) in three hospitals across Kenya. We analysed data from children age-eligible for ≥1 RV1 dose, with stool tested for rotavirus and confirmed vaccination history. We compared RV1 coverage among those who tested rotavirus-positive (cases) versus rotavirus-negative (controls) using multivariable logistic regression; effectiveness was 1-adjusted odds ratio for vaccination x100%. Among 677 eligible children, 110 (16%) were rotavirus-positive. Vaccination data were available for 91 (83%) cases; 51 (56%) had received 2 RV1 doses and 33 (36%) 0 doses. Among 567 controls, 418 (74%) had vaccination data; 308 (74%) had 2 doses and 69 (16%) 0 doses. Overall 2-dose effectiveness was 64% (95% confidence interval [CI]: 35-80%); for children aged <12 months 67% (95%CI: 30-84%) and children aged ≥12 months 72% (95%CI: 10-91%). Significant effectiveness was seen in children with normal weight-for-age (84% [95%CI: 62-93%]), length/height-for-age (75% [95%CI: 48-88%]) and weight-for-length/height (84% [95%CI: 64-93%]); however, no protection was found among underweight, stunted nor wasted children. RV1 in the routine Kenyan immunization program provides significant protection against rotavirus AGE hospitalization. Protection was sustained beyond infancy. Malnutrition appears to diminish vaccine effectiveness. Efforts to improve rotavirus vaccine uptake and nutritional status are important to maximize vaccine benefit. [Abstract copyright: © The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.