Molecular Epidemiology of Human Metapneumovirus in Riyadh Province, Saudi Arabia

2016 ◽  
Vol 26 (6) ◽  
pp. 414-421 ◽  
Author(s):  
Haitham Mohamed Amer
Keyword(s):  
Genetic Diversity ◽  
Saudi Arabia ◽  
Purifying Selection ◽  
Variable Number ◽  
Human Metapneumovirus ◽  
F Gene ◽  
Circulation Patterns ◽  
Respiratory Tract Illness ◽  
High Degree ◽  
Current Report

Human metapneumovirus (HMPV) is an important cause of respiratory tract illness in children. Two HMPV subgroups, A and B, and four genotypes, A1, A2, B1 and B2, have been identified. Concurrent circulation of the different genotypes in yearly epidemics has been recorded globally, but not in Saudi Arabia. The current report was designed to study HMPV epidemiology in Saudi children and to analyze the genetic diversity and circulation patterns. Nasopharyngeal aspirates (n = 174) were collected from hospitalized children in Riyadh (2008-2009). The screening of samples using real-time RT-PCR identified 19 HMPV strains. The majority of the strains belonged to subgroup B, while all strains of subgroup A were members of genotype A2. In 2008, only subgroup B was recognized, whereas in 2009 both subgroups were identified to be cocirculating at similar rates. The full-length attachment (G) gene and a partial sequence of the fusion (F) gene of positive samples were sequenced. The G gene showed a high degree of genetic diversity and exhibited a variable number of positively selected sites in different lineages. In contrast, the F gene demonstrated an extensive genetic stability with a higher tendency toward purifying selection. This is the first report on HMPV genotype circulation in Saudi Arabia; however, the exact circulation kinetics requires further retrospective and prospective study.

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity.

Genetics ◽  
1988 ◽  
Vol 119 (4) ◽  
pp. 981-990
Author(s):  
S Jana ◽  
L N Pietrzak
Keyword(s):  
Genetic Diversity ◽  
Eastern Mediterranean ◽  
Hordeum Spontaneum ◽  
Hordeum Vulgare L ◽  
Closely Related Species ◽  
Mediterranean Countries ◽  
Isozyme Loci ◽  
Cultivated Barley ◽  
Multilocus Associations ◽  
High Degree

Abstract Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species.

scholarly journals Genetic Diversity and Potential Vectors and Reservoirs of Cucurbit aphid-borne yellows virus in Southeastern Spain

2013 ◽  
Vol 103 (11) ◽  
pp. 1188-1197 ◽  
Author(s):  
Mona A. Kassem ◽  
Miguel Juarez ◽  
Pedro Gómez ◽  
Carmen M. Mengual ◽  
Raquel N. Sempere ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aphis Gossypii ◽  
Purifying Selection ◽  
Aphid Species ◽  
Open Reading Frames ◽  
Weed Species ◽  
Nucleotide Substitutions ◽  
Multiple Introductions ◽  
Spatial And Temporal Scales ◽  
Southeastern Spain

The genetic variability of a Cucurbit aphid-borne yellows virus (CABYV) (genus Polerovirus, family Luteoviridae) population was evaluated by determining the nucleotide sequences of two genomic regions of CABYV isolates collected in open-field melon and squash crops during three consecutive years in Murcia (southeastern Spain). A phylogenetic analysis showed the existence of two major clades. The sequences did not cluster according to host, year, or locality of collection, and nucleotide similarities among isolates were 97 to 100 and 94 to 97% within and between clades, respectively. The ratio of nonsynonymous to synonymous nucleotide substitutions reflected that all open reading frames have been under purifying selection. Estimates of the population's genetic diversity were of the same magnitude as those previously reported for other plant virus populations sampled at larger spatial and temporal scales, suggesting either the presence of CABYV in the surveyed area long before it was first described, multiple introductions, or a particularly rapid diversification. We also determined the full-length sequences of three isolates, identifying the occurrence and location of recombination events along the CABYV genome. Furthermore, our field surveys indicated that Aphis gossypii was the major vector species of CABYV and the most abundant aphid species colonizing melon fields in the Murcia (Spain) region. Our surveys also suggested the importance of the weed species Ecballium elaterium as an alternative host and potential virus reservoir.

Isolation of Aeromonas hydrophila from Bottled Waters and Domestic Water Supplies in Saudi Arabia

1986 ◽  
Vol 49 (6) ◽  
pp. 471-476 ◽  
Author(s):  
PETER J. SLADE ◽  
MOHAMMED A. FALAH ◽  
AHMED M. R. AI-GHADY
Keyword(s):  
Saudi Arabia ◽  
Aeromonas Hydrophila ◽  
Mineral Water ◽  
False Negative ◽  
Domestic Water ◽  
Selective Method ◽  
Arginine Dihydrolase ◽  
Presumptive Identification ◽  
High Degree ◽  
Bottled Mineral Water

A total of 139 replicate samples of water were tested for Aeromonas hydrophila and coliforms. These consisted of 95 replicates from bottled mineral water, 13 replicates from flower petal infusions and 31 samples of domestic municipality supplies. Of these, 59 (43%) were positive for A. hydrophila, 15 (11%) were positive for coliforms and 11 (8%) positive for both A. hydrophila and coliforms. Most of the isolates of A. hydrophila came from various batches of one brand of bottled mineral water, none of which contained coliforms. The organism was isolated more frequently from newer samples, particularly those bottled for 59 d or less. Samples of treated water from one municipality were free from coliforms and A. hydrophila. Chlorinated water from another town was free from coliforms, but some samples contained A. hydrophila. In unchlorinated water from a third municipal source, there was a high degree of correlation between incidence of A. hydrophila and presence of coliforms. A selective method, using media without antibiotics, for isolation of A. hydrophila was used. A novel medium for the presumptive identification of A. hydrophila, gelatin arginine dihydrolase (GAD) medium, was assessed, with confirmation of suspected isolates using the API 20E system. Of 109 isolates from two selective agars identified with the organism on API strips, 18 (16.5%) were falsely gelatinase negative in GAD medium, of which 9 (8.3%) also gave false-negative arginine dihydrolase reactions. Of those presumptively identified as A. hydrophila in GAD, 4/95 isolates (4.2% false-positives) were not confirmed.

scholarly journals Human immunodeficiency virus 1. Predominance of a group-specific neutralizing epitope that persists despite genetic variation.

1989 ◽  
Vol 170 (5) ◽  
pp. 1681-1695 ◽  
Author(s):  
I Berkower ◽  
G E Smith ◽  
C Giri ◽  
D Murphy
Keyword(s):  
Genetic Diversity ◽  
Human Immunodeficiency Virus ◽  
Neutralizing Antibodies ◽  
Neutralizing Epitope ◽  
Vaccine Strategy ◽  
Disease Pathogenesis ◽  
Immunodeficiency Virus ◽  
High Degree ◽  
Hiv 1 ◽  
Human Immunodeficiency Virus 1

HIV-1 is known to show a high degree of genetic diversity, which may have major implications for disease pathogenesis and prevention. If every divergent isolate represented a distinct serotype, then effective vaccination might be impossible. However, using a sensitive new plaque-forming assay for HIV-1, we have found that most infected patients make neutralizing antibodies, predominantly to a group-specific epitope shared among three highly divergent isolates. This epitope persists among divergent isolates and rarely mutates, despite the rapid overall mutation rate of HIV-1, suggesting that it may participate in an essential viral function. These findings, plus the rarity of reinfections among these patients, suggest that HIV-1 may be more susceptible to a vaccine strategy based on a group-specific neutralizing epitope than was previously suspected.

scholarly journals Family’s Role in Achieving Language Affiliation among Children: A Comparative Study Applied to Some Families

2021 ◽  
Vol 12 (3) ◽  
pp. 111-128
Author(s):  
Aljohara Fahad Al Saud
Keyword(s):  
Social Media ◽  
Saudi Arabia ◽  
Comparative Study ◽  
Analytical Approach ◽  
Kingdom Of Saudi Arabia ◽  
Language Identity ◽  
Study Population ◽  
High Degree ◽  
Very High

Identifying language affiliation among children for family immigrants is crucial for one’s language identity. This study aimed to determine the role played by Arab families in the Kingdom of Saudi Arabia, Austria, and Britain to attain language affiliation among their children. It also aims to identify the challenges facing families living in these countries in achieving language affiliation among their children. The study population consisted of all the families that live in the Kingdom of Saudi Arabia, in addition to all the Arab families that live in Austria and Britain and the study sample included (120) parents. The researcher adopted the descriptive-analytical approach and used the questionnaire as the study tool. The study reached several results; first, the role played by families in the Kingdom of Saudi Arabia, Austria, and United Kingdom to attain language affiliation among their children got a high degree of response. Second, the challenges facing activating the family’s role in attaining language affiliation of their children in the Kingdom of Saudi Arabia and Austria have got a high degree of response, while in Britain, they obtained a very high degree of response. The study recommended involving all family members in accessing different and creative ways of practicing their native language and activating the role of social media in developing the language affiliation of children.

scholarly journals Difficulties of Teaching Based on Differentiated Instruction from the Viewpoint of Arabic Language Teachers in Qatif Governorate, Saudi Arabia: صعوبات التدريس المتمايز من وجهة نظر معلمي اللغة العربية بمحافظة القطيف بالمملكة العربية السعودية

2020 ◽  
Vol 4 (44) ◽  
Author(s):  
Mohammed Abdullah Alnasser
Keyword(s):  
Saudi Arabia ◽  
Differentiated Instruction ◽  
Arabic Language ◽  
Language Teachers ◽  
Study Phase ◽  
Impact Study ◽  
Kingdom Of Saudi Arabia ◽  
Level Of Significance ◽  
High Degree ◽  
The Impact

The present study aims to identify the Difficulties of Teaching Based On Differentiated Instruction Viewpoint Of Arabic Teachers In Qatif Governorate In the Kingdom of Saudi Arabia. In order to achieve these objectives, a questionnaire was designed, It consisted of (33) items distributed to five Domains. It was distributed to the study Sample wish was formed from (172) Arabic teachers chosen randomly from all study phases. The study found that the whole mean of Difficulties of Teaching Based On Differentiated Instruction Viewpoint Of Arabic Teachers In Qatif Governorate was (3.60). At the domains level: The difficulties of the environment of the school was the first with a mean (3.97), then the difficulties of a teacher with a mean (3.73).Booth with a high degree of difficulty. Difficulties of Curriculum was the third with a mean of (3.58), Then The difficulties of Administrative Regulation with a mean of (3.43), Finally The difficulties of Students with a mean of (3.28). All final three domains with a Medium degree of difficulty. The study also found that there were no significant differences between the average of these answers at the level of significance (α ≤ 0.05) due to the impact study phase. Based on these results The researcher recommended to train teachers and supply schools with suitable facilities and materials to teach the Arabic language based on Differentiated Instruction.

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