25 results on '"Erima B"'
Search Results
2. Influenza and influenza like illness in human populations in Uganda
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Mworozi, E., primary, Byarugaba, D., additional, Erima, B., additional, Bwogi, J., additional, Luswa, L., additional, Mimbe, D., additional, Milland, M., additional, Kibuuka, H., additional, and Mangeni, W., additional
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- 2012
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3. H1N1 Pandemic: From imported cases in July 2009 to sustained transmission in school clusters in September, Uganda, 2009
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Lukwago, L., primary, Wamala, J., additional, Erima, B., additional, Okot, C., additional, Bakamutumaho, B., additional, Nabukenya, I., additional, and Lutwama, J.J., additional
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- 2010
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4. Predictors for Risk Factors for Spread of Avian Influenza Viruses by Poultry Handlers in Live bird markets in Uganda.
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Kirunda, H., Mugimba, K. K., Erima, B., Mimbe, D., Byarugaba, D. K., and Wabwire ‐ Mangen, F.
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AVIAN influenza ,RESPIRATORY infections ,PUBLIC health ,HEALTH education ,HEALTH literacy ,PREVENTIVE medicine ,PUBLIC health research - Abstract
Live bird markets (LBMs) are essential for marketing poultry, but have been linked to many outbreaks of avian influenza (AI) and its spread. In Uganda, it has been observed that demographic characteristics of poultry traders/handlers influence activities and decision-making in LBMs. The study investigated the influence of socio-demographic characteristics of poultry handlers: age, sex, religion, educational background, level of income, location of residence and region of operation on 20 potential risk factors for introduction and spread of AI in LBMs. Study sites included 39 LBMs in the four regions of Uganda. Data was collected using a semi-structured questionnaire administered to 424 poultry handlers. We observed that background of education was a predictor for slaughter and processing of poultry in open sites. Location of residence was associated with slaughter of poultry from open sites and selling of other livestock species. Region influenced stacking of cages, inadequate cleaning of cages, feeders and drinkers, and provision of dirty feed and water. Specifically, bird handlers with secondary level of education (OR = 12.9, 95% CI: 2.88-57.4, P < 0.01) were more likely to be involved in open site slaughter of poultry than their counterparts without formal education. Comparatively, urbanite bird handlers were less likely to share poultry equipment (OR = 0.4, 95% CI: 0.22-0.63, P < 0.01) than rural resident handlers. Poultry handlers in Northern were 3.5 times more likely to practise insufficient cleaning of cages (OR = 3.5, 95% CI: 1.52-8.09) compared to those in Central region. We demonstrated that some socio-demographic characteristics of poultry handlers were predictors to risky practices for introduction and spread of AI viruses in LBMs in Uganda. [ABSTRACT FROM AUTHOR]
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- 2015
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5. Genetic analysis of influenza B viruses isolated in Uganda during the 2009–2010 seasons
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Byarugaba Denis K, Erima Bernard, Millard Monica, Kibuuka Hannah, L Lukwago, Bwogi Josephine, Mimbe Derrick, Mworozi Edison A, Sharp Bridget, Krauss Scott, Webby Richard J, Webster Robert G, Martin Samuel K, Wabwire-Mangen Fred, and Ducatez Mariette F
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Influenza B ,Genetic analysis ,Uganda ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Influenza B viruses can cause morbidity and mortality in humans but due to the lack of an animal reservoir are not associated with pandemics. Because of this, there is relatively limited genetic sequences available for influenza B viruses, especially from developing countries. Complete genome analysis of one influenza B virus and several gene segments of other influenza B viruses isolated from Uganda from May 2009 through December 2010 was therefore undertaken in this study. Methods Samples were collected from patients showing influenza like illness and screened for influenza A and B by PCR. Influenza B viruses were isolated on Madin-Darby Canine Kidney cells and selected isolates were subsequently sequenced and analyzed phylogenetically. Findings Of the 2,089 samples collected during the period, 292 were positive by PCR for influenza A or B; 12.3% of the PCR positives were influenza B. Thirty influenza B viruses were recovered and of these 25 that grew well consistently on subculture were subjected to further analysis. All the isolates belonged to the B/Victoria-lineage as identified by hemagglutination inhibition assay and genetic analysis except one isolate that grouped with the B-Yamagata-lineage. The Ugandan B/Victoria-lineage isolates grouped in clade 1 which was defined by the N75K, N165K and S172P substitutions in hemagglutinin (HA) protein clustered together with the B/Brisbane/60/2008 vaccine strain. The Yamagata-like Ugandan strain, B/Uganda/MUWRP-053/2009, clustered with clade 3 Yamagata viruses such as B/Bangladesh/3333/2007 which is characterized by S150I and N166Y substitutions in HA. Conclusion In general there was limited variation among the Ugandan isolates but they were interestingly closer to viruses from West and North Africa than from neighboring Kenya. Our isolates closely matched the World Health Organization recommended vaccines for the seasons.
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- 2013
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6. Draft genome sequence of Acinetobacter haemolyticus strain MUWRP1017 isolated from the pus of a female inpatient at Bwera General Hospital in Uganda.
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Wokorach G, Erima B, Alafi S, Kabatesi HO, Muhindo JT, Najjuka F, Kiyengo J, Kibuuka H, Musinguzi AK, Wabwire-Mangen F, and Byarugaba DK
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The bacterium Acinetobacter haemolyticus , with a genome size of 3.4 Mb, was isolated from a pus swab of a wound on the left lower limb above the ankle joint of a female patient. This strain carries the antimicrobial resistance genes cephalosporinase blaADC-25 , oxallinase blaOXA-264 , floR , and sul2 and other resistance and virulence genes., Competing Interests: The authors declare no conflict of interest.
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- 2024
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7. Molecular detection of Coxiella burnetii in ticks collected from animals and the environment in Uganda.
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Eneku W, Erima B, Byaruhanga AM, Cleary N, Atim G, Tugume T, Ukuli QA, Kibuuka H, Mworozi E, Tweyongyere R, Douglas CE, Koehler JW, von Fricken ME, Wabwire-Mangen F, and Byarugaba DK
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Aims: Coxiella burnetii is a highly infectious organism that is easily spread through aerosols causing Q fever in humans. Ticks can harbour and transmit C. burnetii to animals, contributing to disease maintenance. Our aim was to examine the presence of C. burnetii in ticks in Uganda., Methods and Results: In this study, ticks were collected from five Ugandan districts and tested by real-time PCR for C. burnetii (Coxiella outer membrane protein 1 gene). A total of 859 tick pools (9602 individual ticks) were tested, and pool positivity for C. burnetii was 5.5% (n = 47). Pooled prevalence differed by district; the highest was Luwero (7.3%), then Gulu (6.6%), and Kasese had the lowest (1.3%). However, district variation was not statistically significant (Fisher's exact = 0.07). Ticks collected from dogs and cats had the highest positivity rates [23/47, (48.9%)] followed by livestock (cattle, goats, sheep, and pigs) [18/47, (38.3%)] and vegetation [6/47, (12.8%)]. Haemaphysalis elliptica had the highest infection rates, followed by Rhipicephalus appendiculatus, Amblyomma variegatum and Rhipicephalus decoloratus had similar prevalence., Conclusions: Although ticks are not the primary transmitters of C. burnetii to humans, pathogen detection in ticks can be an indirect indicator of risk among animal hosts. Vulnerable populations, including occupations with close animal contact such as farming, butchery, and veterinary practice, have an increased risk of C. burnetii exposure. Veterinarians and clinicians should be aware that C. burnetii may cause human and animal illness in these regions., (© 2024 The Author(s). Zoonoses and Public Health published by Wiley‐VCH GmbH.)
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- 2024
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8. Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan.
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Wokorach G, Erima B, Najjuka F, Kiyengo J, Kibuuka H, Musinguzi AK, Wabwire-Mangen F, and Byarugaba DK
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Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides ( erm(C ) and mph(C' )), aminoglycosides ( aac(6")-aph(2" )), tetracyclines ( tet(K )), and trimethoprim ( dfrG )., Competing Interests: The authors declare no conflict of interest.
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- 2024
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9. Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda.
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Musinguzi AK, Kiyengo J, Najjuka F, and Wabwire-Mangen F
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- Humans, Escherichia coli, Tertiary Healthcare, Uganda, Pandemics, Genotype, Anti-Bacterial Agents pharmacology, Virulence Factors genetics, beta-Lactamases genetics, Membrane Transport Proteins genetics, Extraintestinal Pathogenic Escherichia coli, Escherichia coli Infections drug therapy, Escherichia coli Infections epidemiology, Escherichia coli Infections microbiology, Escherichia coli Proteins genetics
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Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum β-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Byarugaba et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2023
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10. Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Najjuka F, Kiyengo J, Musinguzi AK, and Wabwire-Mangen F
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Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase ( bla
CTX-M-15 ) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae , low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.- Published
- 2023
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11. Wide distribution of Mediterranean and African spotted fever agents and the first identification of Israeli spotted fever agent in ticks in Uganda.
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Eneku W, Erima B, Byaruhanga AM, Atim G, Tugume T, Ukuli QA, Kibuuka H, Mworozi E, Douglas C, Koehler JW, Cleary NG, von Fricken ME, Tweyongyere R, Wabwire-Mangen F, and Byarugaba DK
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- Animals, Cattle, Humans, Dogs, Sheep, Cats, Swine, Uganda epidemiology, Israel, Real-Time Polymerase Chain Reaction veterinary, Goats, Cat Diseases, Dog Diseases, Rickettsia genetics, Ixodidae microbiology, Spotted Fever Group Rickettsiosis epidemiology, Rhipicephalus genetics
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Rickettsia microorganisms are causative agents of several neglected emerging infectious diseases in humans transmitted by arthropods including ticks. In this study, ticks were collected from four geographical regions of Uganda and pooled in sizes of 1-179 ticks based on location, tick species, life stage, host, and time of collection. Then, they were tested by real-time PCR for Rickettsia species with primers targeting gltA, 17kDa and ompA genes, followed by Sanger sequencing of the 17kDa and ompA genes. Of the 471 tick pools tested, 116 (24.6%) were positive for Rickettsia spp. by the gltA primers. The prevalence of Rickettsia varied by district with Gulu recording the highest (30.1%) followed by Luwero (28.1%) and Kasese had the lowest (14%). Tick pools from livestock (cattle, goats, sheep, and pigs) had the highest positivity rate, 26.9%, followed by vegetation, 23.1%, and pets (dogs and cats), 19.7%. Of 116 gltA-positive tick pools, 86 pools were positive using 17kDa primers of which 48 purified PCR products were successfully sequenced. The predominant Rickettsia spp. identified was R. africae (n = 15) in four tick species, followed by R. conorii (n = 5) in three tick species (Haemaphysalis elliptica, Rhipicephalus appendiculatus, and Rh. decoloratus). Rickettsia conorii subsp. israelensis was detected in one tick pool. These findings indicate that multiple Rickettsia spp. capable of causing human illness are circulating in the four diverse geographical regions of Uganda including new strains previously known to occur in the Mediterranean region. Physicians should be informed about Rickettsia spp. as potential causes of acute febrile illnesses in these regions. Continued and expanded surveillance is essential to further identify and locate potential hotspots with Rickettsia spp. of concern., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
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- 2023
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12. Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda.
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Byarugaba DK, Wokorach G, Alafi S, Erima B, Najjuka F, Mworozi EA, Kibuuka H, and Wabwire-Mangen F
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Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by bla
EC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.- Published
- 2023
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13. Molecular characterisation of human adenoviruses associated with respiratory infections in Uganda.
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Ukuli QA, Erima B, Mubiru A, Atim G, Tugume T, Kibuuka H, Mworozi E, Ducatez MF, Wabwire-Mangen F, and Byarugaba DK
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- Child, Adult, Humans, Infant, Uganda epidemiology, Sequence Analysis, DNA, Genotype, Phylogeny, Adenoviruses, Human, Adenovirus Infections, Human epidemiology, Respiratory Tract Infections epidemiology
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Human adenoviruses (HAdV) are a diverse group of viruses causing a broad range of infections of the respiratory, urogenital and gastrointestinal tracts and keratoconjunctivitis. There are seven species of human adenoviruses with 113 genotypes which may contain multiple genetic variants. This study characterised respiratory human adenoviruses and associated factors in samples collected from selected hospitals in Uganda. A total of 2,298 nasopharyngeal samples were collected between the period of 2008 to 2016 from patients seeking health care at tertiary hospitals for influenza-like illness. They were screened by polymerase chain reaction (PCR) to determine the prevalence of HAdV. HAdV was cultured in A549 cell lines and the hexon gene was sequenced for genotyping. Of the 2,298 samples tested, 225 (9.8%) were adenovirus-positive by PCR. Age was found to be significantly associated with HAdV infections (p = 0.028) with 98% (220/225) of the positives in children aged 5 years and below and none in adults above 25 years of age. The sequenced isolates belonged to species HAdV-B and HAdV-C with most isolates identified as genotype B3. The results showed a high prevalence and genetic diversity in respiratory HAdV circulating in Ugandan population. Deeper genomic characterization based on whole genome sequencing may be necessary to further elucidate possible transmission and impact of current adenovirus-vectored vaccines in Africa., (© 2023. The Author(s).)
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- 2023
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14. Genome Sequence Analysis of a Wohlfahrtiimonas chitiniclastica Strain Isolated from a Septic Wound of a Hospitalized Patient in Uganda.
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Byarugaba DK, Erima B, Wokorach G, Najjuka F, Kiyengo J, Kwak YI, Ong A, Maybank R, Preston L, Mills E, McGann P, Kibuuka H, Musinguzi AK, and Wabwire-Mangen F
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We report a genome sequence of Wohlfahrtiimonas chitiniclastica strain MUWRP0946, isolated from a hospitalized patient in Uganda. The genome size was 2.08 million bases, and the genome completeness was 94.22%. The strain carries tetracycline, folate pathway antagonist, β-lactam, and aminoglycoside antibiotic resistance genes.
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- 2023
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15. Genetic Evolution of Avian Influenza A (H9N2) Viruses Isolated from Domestic Poultry in Uganda Reveals Evidence of Mammalian Host Adaptation, Increased Virulence and Reduced Sensitivity to Baloxavir.
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Atim G, Tugume T, Ukuli QA, Erima B, Mubiru A, Kibuuka H, Mworozi E, McKenzie P, Turner JCM, Walker D, Jeevan T, Webster RG, Jones J, Webby RJ, Ducatez MF, Wabwire-Mangen F, and Byarugaba DK
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- Animals, Dibenzothiepins, Endonucleases genetics, Evolution, Molecular, Host Adaptation, Humans, Mammals, Morpholines, Nucleotides, Phylogeny, Poultry, Pyridones, Triazines, Uganda epidemiology, Virulence genetics, Influenza A Virus, H9N2 Subtype, Influenza in Birds epidemiology, Influenza, Human
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A (H9N2) avian influenza A viruses were first detected in Uganda in 2017 and have since established themselves in live bird markets. The aim of this study was to establish the subsequent genetic evolution of H9N2 viruses in Uganda. Cloacal samples collected from live bird market stalls in Kampala from 2017 to 2019 were screened by RT-PCR for influenza A virus and H9N2 viruses were isolated in embryonated eggs. One hundred and fifty H9N2 isolates were subjected to whole genome sequencing on the Illumina MiSeq platform. The sequence data analysis and comparison with contemporary isolates revealed that the virus was first introduced into Uganda in 2014 from ancestors in the Middle East. There has since been an increase in nucleotide substitutions and reassortments among the viruses within and between live bird markets, leading to variations in phylogeny of the different segments, although overall diversity remained low. The isolates had several mutations such as HA-Q226L and NS-I106M that enable mammalian host adaptation, NP-M105V, PB1-D3V, and M1-T215A known for increased virulence/pathogenicity and replication, and PA-E199D, NS-P42S, and M2-S31N that promote drug resistance. The PA-E199D substitution in particular confers resistance to the endonuclease inhibitor Baloxavir acid, which is one of the new anti-influenza drugs. Higher EC50 was observed in isolates with a double F105L+E199D substitution that may suggest a possible synergistic effect. These H9N2 viruses have established an endemic situation in live bird markets in Uganda because of poor biosecurity practices and therefore pose a zoonotic threat. Regular surveillance is necessary to further generate the needed evidence for effective control strategies and to minimize the threats.
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- 2022
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16. Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019.
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Fusade-Boyer M, Djegui F, Batawui K, Byuragaba DK, Jones JC, Wabwire-Mangeni F, Erima B, Atim G, Ukuli QA, Tugume T, Dogno K, Adjabli K, Nzuzi M, Adjin R, Jeevan T, Rubrum A, Go-Maro W, Kayali G, McKenzie P, Webby RJ, and Ducatez MF
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- Africa South of the Sahara, Animals, Antibodies, Viral immunology, Antigenic Variation, Chickens virology, Cross Reactions, Evolution, Molecular, Humans, Influenza A Virus, H9N2 Subtype pathogenicity, Influenza A Virus, H9N2 Subtype physiology, Influenza, Human virology, Phylogeny, Virulence, Virus Replication, Influenza A Virus, H9N2 Subtype genetics, Influenza A Virus, H9N2 Subtype immunology, Influenza in Birds virology, Poultry Diseases virology
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Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.
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- 2021
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17. Serological Surveillance of Influenza D Virus in Ruminants and Swine in West and East Africa, 2017-2020.
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Sanogo IN, Kouakou C, Batawui K, Djegui F, Byarugaba DK, Adjin R, Adjabli K, Wabwire-Mangen F, Erima B, Atim G, Ukuli QA, Tugume T, Dogno K, Go-Maro W, Couacy-Hymann E, Kayali G, McKenzie P, Webby RJ, and Ducatez MF
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- Africa, Eastern epidemiology, Africa, Western epidemiology, Animals, Cattle, Cattle Diseases epidemiology, Cattle Diseases immunology, Cattle Diseases virology, Female, Male, Seroepidemiologic Studies, Swine, Swine Diseases epidemiology, Swine Diseases immunology, Swine Diseases virology, Orthomyxoviridae Infections epidemiology, Orthomyxoviridae Infections immunology, Ruminants immunology, Ruminants virology, Thogotovirus immunology, Thogotovirus pathogenicity
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Influenza D virus (IDV) was first isolated in 2011 in Oklahoma, USA from pigs presenting with influenza-like symptoms. IDV is known to mainly circulate in ruminants, especially cattle. In Africa, there is limited information on the epidemiology of IDV, although the virus has likely circulated in the region since 2012. In the present study, we investigated the seropositivity of IDV among domestic ruminants and swine in West and East Africa from 2017 to 2020. Serum samples were analyzed using the hemagglutination inhibition (HI) assay. Our study demonstrated that IDV is still circulating in Africa, with variations in seropositivity among countries and species. The highest seropositivity was detected in cattle (3.9 to 20.9%). Our data highlights a need for extensive surveillance of IDV in Africa in order to better understand the epidemiology of the virus in the region.
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- 2021
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18. Seroprevalence of human coronaviruses among patients visiting hospital-based sentinel sites in Uganda.
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Mulabbi EN, Tweyongyere R, Wabwire-Mangen F, Mworozi E, Koehlerb J, Kibuuka H, Millard M, Erima B, Tugume T, Aquino UQ, and Byarugaba DK
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- Adolescent, Adult, Child, Child, Preschool, Cross Reactions, Enzyme-Linked Immunosorbent Assay, Female, Hospitals, Humans, Infant, Male, Sentinel Surveillance, Seroepidemiologic Studies, Uganda epidemiology, Young Adult, Antibodies, Viral blood, Coronavirus, Coronavirus Infections epidemiology, Immunoglobulin G blood
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Background: Human coronaviruses are causative agents of respiratory infections with several subtypes being prevalent worldwide. They cause respiratory illnesses of varying severity and have been described to be continuously emerging but their prevalence is not well documented in Uganda. This study assessed the seroprevalence of antibodies against the previously known human coronaviruses prior 2019 in Uganda., Methods: A total 377 serum samples collected from volunteers that showed influenza like illness in five hospital-based sentinel sites and archived were analyzed using a commercial Qualitative Human Coronavirus Antibody IgG ELISA kit. Although there is no single kit available that can detect the presence of all the circulating coronaviruses, this kit uses a nucleoprotein, aa 340-390 to coat the wells and since there is significant homology among the various human coronavirus strains with regards to the coded for proteins, there is significant cross reactivity beyond HCoV HKU-39849 2003. This gives the kit a qualitative ability to detect the presence of human coronavirus antibodies in a sample., Results: The overall seroprevalence for all the sites was 87.53% with no significant difference in the seroprevalence between the Hospital based sentinel sites (p = 0.8). Of the seropositive, the age group 1-5 years had the highest percentage (46.97), followed by 6-10 years (16.67) and then above 20 (16.36). An odds ratio of 1.6 (CI 0.863-2.97, p = 0.136) showed that those volunteers below 5 years of age were more likely to be seropositive compared to those above 5 years. The seropositivity was generally high throughout the year with highest being recorded in March and the lowest in February and December., Conclusions: The seroprevalence of Human coronaviruses is alarmingly high which calls for need to identify and characterize the circulating coronavirus strains so as to guide policy on the control strategies.
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- 2021
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19. Molecular Characterization of Closely Related H6N2 Avian Influenza Viruses Isolated from Turkey, Egypt, and Uganda.
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Mercan Y, Atim G, Kayed AE, Azbazdar ME, Kandeil A, Ali MA, Rubrum A, McKenzie P, Webby RJ, Erima B, Wabwire-Mangen F, Ukuli QA, Tugume T, Byarugaba DK, Kayali G, Ducatez MF, and Koçer ZA
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- Animal Migration, Animals, Animals, Wild virology, Chickens virology, Egypt, Genome, Viral, Humans, Influenza A virus isolation & purification, Influenza in Birds transmission, Poultry virology, Turkey, Uganda, Influenza A virus classification, Influenza A virus genetics, Influenza in Birds virology, Phylogeny, Reassortant Viruses genetics
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Genetic analysis of circulating avian influenza viruses (AIVs) in wild birds at different geographical regions during the same period could improve our knowledge about virus transmission dynamics in natural hosts, virus evolution as well as zoonotic potential. Here, we report the genetic and molecular characterization of H6N2 influenza viruses isolated from migratory birds in Turkey, Egypt, and Uganda during 2017-2018. The Egyptian and Turkish isolates were genetically closer to each other than they were to the virus isolated from Uganda. Our results also suggest that multiple reassortment events were involved in the genesis of the isolated viruses. All viruses contained molecular markers previously associated with increased replication and/or pathogenicity in mammals. The results of this study indicate that H6N2 viruses carried by migratory birds on the West Asian/East African and Mediterranean/Black Sea flyways have the potential to transmit to mammals including humans. Additionally, adaptation markers in these viruses indicate the potential risk for poultry, which also increases the possibility of human exposure to these viruses.
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- 2021
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20. Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears.
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Rowneki M, Aronson N, Du P, Sachs P, Blakemore R, Chakravorty S, Levy S, Jones AL, Trivedi G, Chebore S, Addo D, Byarugaba DK, Njobvu PD, Wabwire-Mangen F, Erima B, Ramos ES, Evans CA, Hale B, Mancuso JD, and Alland D
- Subjects
- Humans, DNA, Bacterial genetics, DNA, Bacterial isolation & purification, High-Throughput Nucleotide Sequencing, Mycobacterium tuberculosis genetics, Mycobacterium tuberculosis isolation & purification, Tuberculosis, Multidrug-Resistant microbiology
- Abstract
Background: Drug susceptibility testing for Mycobacterium tuberculosis (MTB) is difficult to perform in resource-limited settings where Acid Fast Bacilli (AFB) smears are commonly used for disease diagnosis and monitoring. We developed a simple method for extraction of MTB DNA from AFB smears for sequencing-based detection of mutations associated with resistance to all first and several second-line anti-tuberculosis drugs., Methods: We isolated MTB DNA by boiling smear content in a Chelex solution, followed by column purification. We sequenced PCR-amplified segments of the rpoB, katG, embB, gyrA, gyrB, rpsL, and rrs genes, the inhA, eis, and pncA promoters and the entire pncA gene., Results: We tested our assay on 1,208 clinically obtained AFB smears from Ghana (n = 379), Kenya (n = 517), Uganda (n = 262), and Zambia (n = 50). Coverage depth varied by target and slide smear grade, ranging from 300X to 12000X on average. Coverage of ≥20X was obtained for all targets in 870 (72%) slides overall. Mono-resistance (5.9%), multi-drug resistance (1.8%), and poly-resistance (2.4%) mutation profiles were detected in 10% of slides overall, and in over 32% of retreatment and follow-up cases., Conclusion: This rapid AFB smear DNA-based method for determining drug resistance may be useful for the diagnosis and surveillance of drug-resistant tuberculosis., Competing Interests: M.R. owns shares of Illumina, Inc.; D.A. and his laboratory receive licensing fees for use of primers and probes in molecular diagnostic assays from Cepheid Inc. Cepheid also provides research support in the form of grants, equipment, and consumables to D.A.’s laboratory. D.A. is listed as an inventor for US patent applications PCT/US18/48611 Therapeutic Indazoles and PCT/US18/48607 Therapeutic Indoles for treating tuberculosis; S.C. is employed by Cepheid, which makes diagnostic tests for identifying drug resistant Mycobacterium tuberculosis; N.A. is a member of the Advisory Committee for the Elimination of Tuberculosis (ACET) for the Centers for Disease Control and Prevention (CDC); all other authors report no competing interests. These affiliations do not alter our adherence toPLOS ONE policies on sharing data and materials.
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- 2020
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21. Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011.
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Byarugaba DK, Erima B, Millard M, Kibuuka H, Lkwago L, Bwogi J, Mimbe D, Kiconco JB, Tugume T, Mworozi EA, Turner J, Mckenzie PP, Webby RR, Webster RG, Foret C, Ducatez MF, Coldren R, Wabwire-Mangen F, and Krauss S
- Subjects
- Amino Acid Substitution, Antigens, Viral, Evolution, Molecular, Hemagglutinin Glycoproteins, Influenza Virus chemistry, Hemagglutinin Glycoproteins, Influenza Virus genetics, Humans, Influenza A Virus, H1N1 Subtype isolation & purification, Influenza, Human epidemiology, Neuraminidase chemistry, Neuraminidase genetics, Phylogeny, RNA, Viral genetics, Seasons, Sequence Analysis, RNA, Uganda epidemiology, Genome, Viral, Influenza A Virus, H1N1 Subtype genetics, Influenza, Human virology
- Abstract
We report a whole-genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248D in the neuraminidase proteins with consistent mutations in all gene segments distinguishing isolates from the 2009/2010 to 2010/2011 seasons. Phylogenetic analysis showed low genetic evolution, with genetic distances of 0%-1.3% and 0.1%-1.6% for HA and NA genes, respectively. The amino acid substitutions did not lead to antigenic differences from the reference strains., (© 2016 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)
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- 2016
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22. Epidemiology and Surveillance of Influenza Viruses in Uganda between 2008 and 2014.
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Wabwire-Mangen F, Mimbe DE, Erima B, Mworozi EA, Millard M, Kibuuka H, Lukwago L, Bwogi J, Kiconco J, Tugume T, Mulei S, Ikomera C, Tsui S, Malinzi S, Kasasa S, Coldren R, and Byarugaba DK
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- Child, Child, Preschool, Female, Humans, Humidity, Infant, Influenza A Virus, H1N1 Subtype genetics, Influenza A Virus, H1N1 Subtype isolation & purification, Influenza B virus genetics, Influenza B virus isolation & purification, Influenza, Human virology, Male, Nasopharynx virology, Oropharynx virology, Prevalence, RNA, Viral metabolism, Rain, Real-Time Polymerase Chain Reaction, Seasons, Temperature, Uganda epidemiology, Influenza, Human epidemiology
- Abstract
Introduction: Influenza surveillance was conducted in Uganda from October 2008 to December 2014 to identify and understand the epidemiology of circulating influenza strains in out-patient clinic attendees with influenza-like illness and inform control strategies., Methodology: Surveillance was conducted at five hospital-based sentinel sites. Nasopharyngeal and/or oropharyngeal samples, epidemiological and clinical data were collected from enrolled patients. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to identify and subtype influenza strains. Data were double-entered into an Epi Info 3.5.3 database and exported to STATA 13.0 software for analysis., Results: Of the 6,628 patient samples tested, influenza virus infection was detected in 10.4% (n = 687/6,628) of the specimens. Several trends were observed: influenza circulates throughout the year with two peaks; the major one from September to November and a minor one from March to June. The predominant strains of influenza varied over the years: Seasonal Influenza A(H3) virus was predominant from 2008 to 2009 and from 2012 to 2014; Influenza A(H1N1)pdm01 was dominant in 2010; and Influenza B virus was dominant in 2011. The peaks generally coincided with times of higher humidity, lower temperature, and higher rainfall., Conclusion: Influenza circulated throughout the year in Uganda with two major peaks of outbreaks with similar strains circulating elsewhere in the region. Data on the circulating strains of influenza and its patterns of occurrence provided critical insights to informing the design and timing of influenza vaccines for influenza prevention in tropical regions of sub-Saharan Africa., Competing Interests: The authors have declared that no competing interests exist.
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- 2016
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23. Prevalence of influenza A viruses in livestock and free-living waterfowl in Uganda.
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Kirunda H, Erima B, Tumushabe A, Kiconco J, Tugume T, Mulei S, Mimbe D, Mworozi E, Bwogi J, Luswa L, Kibuuka H, Millard M, Byaruhanga A, Ducatez MF, Krauss S, Webby RJ, Webster RG, Wurapa K, Byarugaba DK, and Wabwire-Mangen F
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- Animals, Female, Logistic Models, Male, Odds Ratio, Orthomyxoviridae Infections epidemiology, Orthomyxoviridae Infections veterinary, Orthomyxoviridae Infections virology, Risk Factors, Seroepidemiologic Studies, Uganda epidemiology, Animals, Wild, Anseriformes, Influenza A virus isolation & purification, Livestock
- Abstract
Background: Avian influenza viruses may cause severe disease in a variety of domestic animal species worldwide, with high mortality in chickens and turkeys. To reduce the information gap about prevalence of these viruses in animals in Uganda, this study was undertaken., Results: Influenza A virus prevalence by RT-PCR was 1.1% (45/4,052) while seroprevalence by ELISA was 0.8% (24/2,970). Virus prevalence was highest in domestic ducks (2.7%, 17/629) and turkeys (2.6%, 2/76), followed by free-living waterfowl (1.3%, 12/929) and swine (1.4%, 7/511). A lower proportion of chicken samples (0.4%, 7/1,865) tested positive. No influenza A virus was isolated. A seasonal prevalence of these viruses in waterfowl was 0.7% (4/561) for the dry and 2.2% (8/368) for the wet season. In poultry, prevalence was 0.2% (2/863) for the dry and 1.4% (24/1,713) for the wet season, while that of swine was 0.0% (0/159) and 2.0% (7/352) in the two seasons, respectively. Of the 45 RT-PCR positive samples, 13 (28.9%) of them were H5 but none was H7. The 19 swine sera positive for influenza antibodies by ELISA were positive for H1 antibodies by HAI assay, but the subtype(s) of ELISA positive poultry sera could not be determined. Antibodies in the poultry sera could have been those against subtypes not included in the HAI test panel., Conclusions: The study has demonstrated occurrence of influenza A viruses in animals in Uganda. The results suggest that increase in volumes of migratory waterfowl in the country could be associated with increased prevalence of these viruses in free-living waterfowl and poultry.
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- 2014
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24. Capacity-building efforts by the AFHSC-GEIS program.
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Sanchez JL, Johns MC, Burke RL, Vest KG, Fukuda MM, Yoon IK, Lon C, Quintana M, Schnabel DC, Pimentel G, Mansour M, Tobias S, Montgomery JM, Gray GC, Saylors K, Ndip LM, Lewis S, Blair PJ, Sjoberg PA, Kuschner RA, Russell KL, Blazes DL, Witt CJ, Money NN, Gaydos JC, Pavlin JA, Gibbons RV, Jarman RG, Stoner M, Shrestha SK, Owens AB, Iioshi N, Osuna MA, Martin SK, Gordon SW, Bulimo WD, Waitumbi DJ, Assefa B, Tjaden JA, Earhart KC, Kasper MR, Brice GT, Rogers WO, Kochel T, Laguna-Torres VA, Garcia J, Baker W, Wolfe N, Tamoufe U, Djoko CF, Fair JN, Akoachere JF, Feighner B, Hawksworth A, Myers CA, Courtney WG, Macintosh VA, Gibbons T, Macias EA, Grogl M, O'Neil MT, Lyons AG, Houng HS, Rueda L, Mattero A, Sekonde E, Sang R, Sang W, Palys TJ, Jerke KH, Millard M, Erima B, Mimbe D, Byarugaba D, Wabwire-Mangen F, Shiau D, Wells N, Bacon D, Misinzo G, Kulanga C, Haverkamp G, Kohi YM, Brown ML, Klein TA, Meyers M, Schoepp RJ, Norwood DA, Cooper MJ, Maza JP, Reeves WE, and Guan J
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- Global Health, Government Agencies, Humans, International Cooperation, Laboratories, United States, Influenza, Human epidemiology, Military Personnel, Public Health, Respiratory Tract Infections epidemiology, Sentinel Surveillance
- Abstract
Capacity-building initiatives related to public health are defined as developing laboratory infrastructure, strengthening host-country disease surveillance initiatives, transferring technical expertise and training personnel. These initiatives represented a major piece of the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) contributions to worldwide emerging infectious disease (EID) surveillance and response. Capacity-building initiatives were undertaken with over 80 local and regional Ministries of Health, Agriculture and Defense, as well as other government entities and institutions worldwide. The efforts supported at least 52 national influenza centers and other country-specific influenza, regional and U.S.-based EID reference laboratories (44 civilian, eight military) in 46 countries worldwide. Equally important, reference testing, laboratory infrastructure and equipment support was provided to over 500 field sites in 74 countries worldwide from October 2008 to September 2009. These activities allowed countries to better meet the milestones of implementation of the 2005 International Health Regulations and complemented many initiatives undertaken by other U.S. government agencies, such as the U.S. Department of Health and Human Services, the U.S. Agency for International Development and the U.S. Department of State.
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- 2011
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25. Molecular epidemiology of influenza A/H3N2 viruses circulating in Uganda.
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Byarugaba DK, Ducatez MF, Erima B, Mworozi EA, Millard M, Kibuuka H, Lukwago L, Bwogi J, Kaira BB, Mimbe D, Schnabel DC, Krauss S, Darnell D, Webby RJ, Webster RG, and Wabwire-Mangen F
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- Adolescent, Adult, Child, Child, Preschool, Genes, Viral genetics, Hemagglutinin Glycoproteins, Influenza Virus genetics, Humans, Infant, Infant, Newborn, Influenza A Virus, H3N2 Subtype isolation & purification, Molecular Epidemiology, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Uganda epidemiology, Young Adult, Influenza A Virus, H3N2 Subtype genetics, Influenza, Human epidemiology, Influenza, Human virology
- Abstract
The increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/Brisbane/10/07), instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09) in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.
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- 2011
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