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

Comparison of Near-infrared Spectroscopy with other options for total carotenoids content phenotyping in fresh cassava roots

This study compared the relationship of different phenotyping methods including iCheckTM CAROTENE (iCheck), Chromameter, colour chart and visible/near-infrared spectroscopy (Vis/NIRS) used in quantifying total carotenoids content (TCC) in fresh cassava roots. Using a total of 194 cassava clones harvested from the International Institute of Tropical Agriculture (IITA), Ibadan, we compared the repeatability precision, accuracy of measurement and correlations of these phenotyping methods. From the results, Vis/NIRS-analyzed TCC had high and positive correlations with Chromameter and Color chart (r = 0.91 and 0.71, respectively). On the other hand, the result revealed somewhat moderate correlation (r = 0.67) between Vis/NIRS and iCheck measurements. Vis/NIRS, iCheck and chromameter methods gave high and nearly equal heritability estimates (0.95, 0.98 and 0.98, respectively) illustrating high repeatability precision of these methods; an indication that they can be used for germplasm selection in the early stages of breeding. Conversely, with Bland-Altman plot at 95% confidence level, the accuracy of iCheck was not comparable with that of Vis/ NIRS. The information derived from this analysis directly contributes towards the genetic improvement of root quality traits in cassava and facilitates the sharing of data across cassava breeding consortium

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

Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR

Background Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. Objectives Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. Study design Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. Results N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. Conclusions An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy

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

A new African streak virus species from Nigeria

The African streak viruses (AfSVs) are a diverse group of mastrevirus species (family Geminiviridae) that infect a wide variety of annual and perennial grass species across the African continent and its nearby Indian Ocean islands. Six AfSV species (of which maize streak virus is the best known) have been described. Here we report the full genome sequences of eight isolates of a seventh AfSV species: Urochloa streak virus (USV), sampled from various locations in Nigeria. Despite there being good evidence of recombination in many other AfSV species, we found no convincing evidence that any of the USV sequences were either inter- or intra-species recombinants. The USV isolates, all of which appear to be variants of the same strain (their genome sequences are all more than 98% identical), share less than 69% nucleotide sequence identity with other currently described AfSV species

Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Background. Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur. Results. We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10 -4substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift. Conclusion. The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts. © 2009 Harkins et al; licensee BioMed Central Ltd

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.