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  1. Article: Effectiveness of Rotarix

    Murunga, Nickson / P Otieno, Grieven / Maia, Marta / N Agoti, Charles

    Wellcome open research

    2020  Volume 5, Page(s) 187

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2020-09-24
    Publishing country England
    Document type Systematic Review
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.16174.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Infection patterns of endemic human coronaviruses in rural households in coastal Kenya.

    Nyaguthii, Dickson Machira / Otieno, Grieven P / Kombe, Ivy K / Koech, Dorothy / Mutunga, Martin / Medley, Graham F / Nokes, D James / Munywoki, Patrick K

    Wellcome open research

    2021  Volume 6, Page(s) 27

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2021-02-09
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.16508.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Effectiveness of Rotarix® vaccine in Africa in the first decade of progressive introduction, 2009-2019

    Nickson Murunga / Grieven P. Otieno / Marta Maia / Charles N. Agoti

    Wellcome Open Research, Vol

    systematic review and meta-analysis [version 2; peer review: 2 approved]

    2020  Volume 5

    Abstract: Background: Randomized controlled trials of licensed oral rotavirus group A (RVA) vaccines, indicated lower efficacy in developing countries compared to developed countries. We investigated the pooled effectiveness of Rotarix® in Africa in 2019, a decade ...

    Abstract Background: Randomized controlled trials of licensed oral rotavirus group A (RVA) vaccines, indicated lower efficacy in developing countries compared to developed countries. We investigated the pooled effectiveness of Rotarix® in Africa in 2019, a decade since progressive introduction began in 2009. Methods: A systematic search was conducted in PubMed to identify studies that investigated the effectiveness of routine RVA vaccination in an African country between 2009 and 2019. A meta-analysis was undertaken to estimate pooled effectiveness of the full-dose versus partial-dose of Rotarix® (RV1) vaccine and in different age groups. Pooled odds ratios were estimated using random effects model and the risk of bias assessed using Newcastle-Ottawa scale. The quality of the evidence was assessed using GRADE. Results: By December 2019, 39 (72%) countries in Africa had introduced RVA vaccination, of which 34 were using RV1. Thirteen eligible studies from eight countries were included in meta-analysis for vaccine effectiveness (VE) of RVA by vaccine dosage (full or partial) and age categories. Pooled RV1 VE against RVA associated hospitalizations was 44% (95% confidence interval (CI) 28-57%) for partial dose versus 58% (95% CI 50-65%) for full dose. VE was 61% (95% CI 50-69%), 55% (95% CI 32-71%), 56% (95% CI 43-67%), and 61% (95% CI 42-73%) for children aged <12 months, 12-23 months, <24 months and 12-59 months, respectively. Conclusion: RV1 vaccine use has resulted in a significant reduction in severe diarrhoea in African children and its VE is close to the efficacy findings observed in clinical trials. RV1 VE point estimate was higher for children who received full dose than those who received partial dose, and its protection lasted beyond the first year of life.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article ; Online: Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.

    Phan, My V T / Agoti, Charles N / Munywoki, Patrick K / Otieno, Grieven P / Ngama, Mwanajuma / Kellam, Paul / Cotten, Matthew / Nokes, D James

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 202

    Abstract: Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in ... ...

    Abstract Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
    MeSH term(s) Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Kenya ; Metagenome ; Metagenomics ; Missed Diagnosis ; Phylogeny ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/virology ; Predictive Value of Tests ; Respiratory System/virology ; Viruses/genetics ; Viruses/isolation & purification
    Language English
    Publishing date 2022-01-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-03987-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya.

    Adema, Irene Wangwa / Kamau, Everlyn / Uchi Nyiro, Joyce / Otieno, Grieven P / Lewa, Clement / Munywoki, Patrick K / Nokes, D James

    Wellcome open research

    2020  Volume 5, Page(s) 63

    Abstract: Background: ...

    Abstract Background:
    Keywords covid19
    Language English
    Publishing date 2020-09-24
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.15703.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya.

    Otieno, Grieven P / Murunga, Nickson / Agoti, Charles N / Gallagher, Katherine E / Awori, Juliet O / Nokes, D James

    Wellcome open research

    2020  Volume 5, Page(s) 150

    Abstract: Introduction: ...

    Abstract Introduction:
    Keywords covid19
    Language English
    Publishing date 2020-09-22
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.16037.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

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  7. Article ; Online: Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

    My V. T. Phan / Charles N. Agoti / Patrick K. Munywoki / Grieven P. Otieno / Mwanajuma Ngama / Paul Kellam / Matthew Cotten / D. James Nokes

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 11

    Abstract: Abstract Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus ... ...

    Abstract Abstract Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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

    Owor, Betty E / Mwanga, Mike J / Njeru, Regina / Mugo, Robert / Ngama, Mwanajuma / Otieno, Grieven P / Nokes, D J / Agoti, C N

    Wellcome open research

    2019  Volume 3, Page(s) 150

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2019-05-15
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.14908.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya [version 2; peer review

    Grieven P. Otieno / Nickson Murunga / Charles N. Agoti / Katherine E. Gallagher / Juliet O. Awori / D. James Nokes

    Wellcome Open Research, Vol

    2 approved]

    2020  Volume 5

    Abstract: Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal ... ...

    Abstract Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  10. Article ; Online: Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016.

    Oketch, John W / Kamau, Everlyn / Otieno, Grieven P / Otieno, James R / Agoti, Charles N / Nokes, D James

    BMC infectious diseases

    2019  Volume 19, Issue 1, Page(s) 757

    Abstract: ... in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup (p = 0.264 ...

    Abstract Background: Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities in low resource settings is limited.
    Methods: We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV subgroup was assessed using Fisher's exact test.
    Results: Over 10 years, 274/6756 (4.1%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2 to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing clades A2b (41.0%) and A2c (10.7%), and subgroups B1 (23.4%) and B2 (24.9%). The dominance patterns were: clade A2b between 2007 and 11, subgroup B1 between 2012 and 14, and clade A2c in more recent epidemics. Subgroup B2 viruses were present in all the years. Temporal phylogenetic clustering within the subgroups for both local and global sequence data was seen. Subgroups occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup (p = 0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection.
    Conclusion: Subgroup patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.
    MeSH term(s) Age of Onset ; Child, Preschool ; Epidemics ; Female ; Genotype ; Hospitals, Pediatric/statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Kenya/epidemiology ; Male ; Metapneumovirus/classification ; Metapneumovirus/genetics ; Metapneumovirus/isolation & purification ; Paramyxoviridae Infections/epidemiology ; Paramyxoviridae Infections/virology ; Patient Admission/statistics & numerical data ; Phylogeny ; Pneumonia/epidemiology ; Pneumonia/virology ; Population Surveillance ; Prevalence ; Real-Time Polymerase Chain Reaction ; Seasons
    Language English
    Publishing date 2019-08-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-019-4381-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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