scholarly journals Distribution and Genetic Diversity of Aedes aegypti Subspecies across the Sahelian Belt in Sudan

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 78
Author(s):  
Sara Abdelrahman Abuelmaali ◽  
Jamsari Amirul Firdaus Jamaluddin ◽  
Kheder Noaman ◽  
Mushal Allam ◽  
Hind Mohammad Abushama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aedes Aegypti ◽  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Haplotype Network ◽  
Mitochondrial Marker ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Disease Vector ◽  
Arboviral Disease

Aedes aegypti is the most important arboviral disease vector worldwide. In Africa, it exists as two morphologically distinct forms, often referred to as subspecies, Aaa and Aaf. There is a dearth of information on the distribution and genetic diversity of these two forms in Sudan and other African Sahelian region countries. This study aimed to explore the distribution and genetic diversity of Aedes aegypti subspecies using morphology and Cytochrome oxidase-1 mitochondrial marker in a large Sahelian zone in Sudan. An extensive cross-sectional survey of Aedes aegypti in Sudan was performed. Samples collected from eight locations were morphologically identified, subjected to DNA extraction, amplification, sequencing, and analyses. We classified four populations as Aaa and the other four as Aaf. Out of 140 sequence samples, forty-six distinct haplotypes were characterized. The haplotype and nucleotide diversity of the collected samples were 0.377–0.947 and 0.002–0.01, respectively. Isolation by distance was significantly evident (r = 0.586, p = 0.005). The SAMOVA test indicated that all Aaf populations are structured in one group, while the Aaa clustered into two groups. AMOVA showed 53.53% genetic differences within populations and 39.22% among groups. Phylogenetic relationships indicated two clusters in which the two subspecies were structured. Thus, the haplotype network consisted of three clusters.

scholarly journals Distribution and genetic diversity of Enterovirus G (EV-G) on pig farms in Thailand

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Taveesak Janetanakit ◽  
Supassama Chaiyawong ◽  
Kamonpan Charoenkul ◽  
Ratanaporn Tangwangvivat ◽  
Ekkapat Chamsai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Rt Pcr ◽  
Cross Sectional Survey ◽  
High Genetic Diversity ◽  
Cross Sectional ◽  
Predominant Genotype ◽  
Diarrhea Virus ◽  
Pig Farms

Abstract Background Enterovirus G (EV-G) causes subclinical infections and is occasionally associated with diarrhea in pigs. In this study, we conducted a cross-sectional survey of EV-G in pigs from 73 pig farms in 20 provinces of Thailand from December 2014 to January 2018. Results Our results showed a high occurrence of EV-Gs which 71.6 % of fecal and intestinal samples (556/777) and 71.2 % of pig farms (52/73) were positive for EV-G by RT-PCR specific to the 5’UTR. EV-Gs could be detected in all age pig groups, and the percentage positivity was highest in the fattening group (89.7 %), followed by the nursery group (89.4 %). To characterize the viruses, 34 EV-G representatives were characterized by VP1 gene sequencing. Pairwise sequence comparison and phylogenetic analysis showed that Thai-EV-Gs belonged to the EV-G1, EV-G3, EV-G4, EV-G8, EV-G9 and EV-G10 genotypes, among which the EV-G3 was the predominant genotype in Thailand. Co-infection with different EV-G genotypes or with EV-Gs and porcine epidemic diarrhea virus (PEDV) or porcine deltacoronavirus (PDCoV) on the same pig farms was observed. Conclusions Our results confirmed that EV-G infection is endemic in Thailand, with a high genetic diversity of different genotypes. This study constitutes the first report of the genetic characterization of EV-GS in pigs in Thailand.

scholarly journals Hubungan Tempat Perindukan dengan Kepadatan Larva Aedes aegypti sebagai Vektor Penyakit Demam Berdarah Dengue di Wilayah Kerja Puskesmas Kalumata Kota Ternate (Relationship of the Breeding Place with the Density of Aedes aegypti Larva as a Dengue Haemorhagic Fever Disease Vector in the Working Area of Kalumata Puskesmas Ternate City)

2019 ◽  
Vol 9 (2) ◽  
pp. 62
Author(s):  
Sitti Washliyah ◽  
Dantje Tarore ◽  
Christina Salaki
Keyword(s):  
Aedes Aegypti ◽  
Aedes Albopictus ◽  
Larval Density ◽  
Chi Square ◽  
Cross Sectional ◽  
Breeding Sites ◽  
Disease Vector ◽  
Relationship Of ◽  
Used Goods ◽  
Breeding Place

Hubungan Tempat Perindukan dengan Kepadatan Larva Aedes aegypti sebagai Vektor Penyakit Demam Berdarah Dengue di Wilayah Kerja Puskesmas Kalumata Kota Ternate (Relationship of the Breeding Place with the Density of Aedes aegypti Larva as a Dengue Haemorhagic Fever Disease Vector in the Working Area of Kalumata Puskesmas Ternate City) Sitti Washliyah¹*), Dantje Tarore1), Christina Salaki1**)¹)Program Studi Entomologi Pascasarjana Universitas Sam Ratulangi Manado, 95115*Email:[email protected]**Email korespondensi: [email protected] Diterima 2 Juli 2019, diterima untuk dipublikasi 5 Agustus 2019 Abstrak Demam berdarah dengue merupakan salah satu penyakit yang disebabkan oleh nyamuk Aedes aegypti dan Aedes albopictus sebagai vektor primer. Pengendalian tempat perindukan nyamuk Ae. aegypti lebih banyak dititikberatkan pada penutupan dan abatisasi bak mandi serta penguburan barang-barang bekas di sekitar rumah penduduk yang berpeluang sebagai penampung air hujan, sementara penampung air lainnya belum mendapat perhatian yang lebih memadai, padahal peluang untuk dijadikan sebagai habitat Ae. aegypti cukup besar. Tujuan penelitian ini yaitu untuk menganalisis hubungan tempat perindukan dengan kepadatan larva dan membandingkan kepadatan populasi larva pada setiap tempat perindukan nyamuk Ae. aegypti. Jenis penelitian kuantitatif dengan pendekatan cross sectional dan analisa uji chi square yang dilaksanakan di wilayah kerja Puskesmas Kalumata Kota Ternate. Hasil penelitian menunjukan bahwa ada hubungan antara tempat perindukan nyamuk dengan kepadatan larva berdasarkan karakteristik jenis, warna, bahan, letak dan kondisi. Kesimpulannya yaitu terdapat hubungan antara tempat perindukan dengan kepadatan larva Ae.aegypti sebagai vektor penyakit demam berdarah dengue.Kata kunci: Identifikasi, tempat penampungan air, survey jentik.  AbstractDengue hemorrhagic fever is a disease caused by mosquitoes species Aedes aegypti and Aedes albopictus as primary vectors. Control of breeding sites for Ae mosquitoes. aegypti is more focused on the closure and abatement of bathtubs and the burial of used goods around people's homes that have the opportunity to collect rainwater, while other water reservoirs have not received more adequate attention, even though the opportunity to be used as Ae habitat. aegypti is quite large. The purpose of this study was to determine the relationship between breeding sites with larval density and compare larval population densities at each breeding site of the Ae mosquito. aegypti. Type of quantitative research method with cross sectional approach and analysis of chi square test conducted in the working area of Kalumata Health Center, Ternate City. The results showed that there was a relationship between mosquito breeding sites and larval density based on the characteristics of the species, color, material, location and condition. The conclusion is that there is a relationship between breeding sites and the density of Ae.aegypti larvae as a vector of dengue hemorrhagic fever.Keywords: Identification, water reservoir, larva survey.

scholarly journals Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis A virus isolates from the West Bank, Palestine during the period between 2014 and 2016

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240339
Author(s):  
Kamal Dumaidi ◽  
Hayah Qaraqe ◽  
Amer Al-Jawabreh ◽  
Rasmi Abu-Helu ◽  
Fekri Samarah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Hepatitis A ◽  
Nucleotide Diversity ◽  
Hepatitis A Virus ◽  
West Bank ◽  
Haplotype Network ◽  
Hand Washing ◽  
The West

Background Hepatitis A virus (HAV) infection is one of the major causes of acute viral hepatitis. HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide. Aims The aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West Bank, Palestine. Study design A cohort of 161 clinically and laboratory-confirmed HAV (IgM-positive) cases and 170 apparently healthy controls from all the districts of the West Bank, Palestine during the period of 2014 to 2016 were tested for HAV infection using IgM antibodies, RT-PCR and sequence analysis of the VP3/VP1 junction region of the HAV genome. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences. Results All the 34 sequences of the HAV were found to be of HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%), but with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h = 8), but low haplotype (gene) diversity (Hd = 0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n = 10) and closer to others haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, infrequent hand washing before meals, and drinking of un-treated water were considered the major HAV risk factors in the present study. Conclusion Haplotype network analysis revealed haplotype variation among the HAV Palestinian sequences despite low genetic variation and nucleotide diversity. In addition, this study reconfirmed that age and parent’s level of education as HAV risk factors, while hand washing and treating drinking water as protective factors.

scholarly journals Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis a virus (HAV) isolates from the West Bank, Palestine during the period between 2014 and 2016

2020 ◽  
Author(s):  
Kamal Dumaidi ◽  
Hayah Qaraqe ◽  
Amer Al-Jawabreh ◽  
Rasmi Abu-Helu ◽  
Fekri Samarah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Network Analysis ◽  
Nucleotide Diversity ◽  
Hepatitis A Virus ◽  
West Bank ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
The West

AbstractBackgroundHAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.Aimsthe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West bank, Palestine.Study designa cohort of 161 clinically and laboratory confirmed HAV (IgM-positive) cases and 170 IgM negative individuals from all the districts of the West Bank, Palestine during the period of 2014-2016 were tested for VP3/VP1 junction of the HAV genome using RT-PCR and sequence analysis. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsOverall, all the 34 sequences of the HAV was found to be HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%) with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h=8), but low haplotype (gene) diversity (Hd=0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n=10) and closer to haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, poor hand washing and drinking of un-treated water was considered the major HAV risk factors in the present study.ConclusionHAV-IB subgentype is endemic in Palestine. HAV showed low genetic variation and nucleotide diversity. Furthermore, haplotype network analysis revealed haplotype variation among the Palestinian sequences.

scholarly journals Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct?

2021 ◽  
Vol 12 ◽  
Author(s):  
J. Brooks ◽  
N. P. Makunga ◽  
K. L. Hull ◽  
M. Brink-Hull ◽  
R. Malgas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Cape Floristic Region ◽  
Conservation Strategies ◽  
Clinal Variation ◽  
Survival Strategy ◽  
Western Cape ◽  
Northern Cape

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618–0.723; Ho: 0.528–0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286–0.900) and nucleotide diversity (π = 0.006–0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.

Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 845-864
Author(s):  
Raquel C. Buranelli ◽  
Fernando L. Mantelatto
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Dna Barcode ◽  
Population Expansion ◽  
Haplotype Network ◽  
Sudden Expansion ◽  
Restricted Gene Flow ◽  
Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

scholarly journals A cross-sectional survey of Aedes aegypti immature abundance in urban and rural household containers in central Colombia

2017 ◽  
Vol 10 (1) ◽  
Author(s):  
Hans J. Overgaard ◽  
Víctor Alberto Olano ◽  
Juan Felipe Jaramillo ◽  
María Inés Matiz ◽  
Diana Sarmiento ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Rural Household ◽  
Cross Sectional Survey ◽  
Cross Sectional

scholarly journals Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis a virus (HAV) isolates from the West Bank, Palestine during the period between 2014 and 2016

2020 ◽  
Author(s):  
Kamal Dumaidi ◽  
Hayah Qaraqe ◽  
Amer Al-Jawabreh ◽  
Rasmi Abu-Helu ◽  
Fekri Samarah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Network Analysis ◽  
Nucleotide Diversity ◽  
Hepatitis A Virus ◽  
West Bank ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
The West

AbstractBackgroundHAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.Aimsthe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West bank, Palestine.Study designa cohort of 161 clinically and laboratory confirmed HAV (IgM-positive) cases and 170 IgM negative individuals from all the districts of the West Bank, Palestine during the period of 2014-2016 were tested for VP3/VP1 junction of the HAV genome using RT-PCR and sequence analysis. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsOverall, all the 34 sequences of the HAV was found to be HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%) with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h=8), but low haplotype (gene) diversity (Hd=0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n=10) and closer to haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, poor hand washing and drinking of un-treated water was considered the major HAV risk factors in the present study.ConclusionHAV-IB subgentype is endemic in Palestine. HAV showed low genetic variation and nucleotide diversity. Furthermore, haplotype network analysis revealed haplotype variation among the Palestinian sequences.

Testing the Strain Theory of Suicide – The Moderating Role of Social Support

Crisis ◽  
2020 ◽  
Vol 41 (2) ◽  
pp. 82-88 ◽  
Author(s):  
Bob Lew ◽  
Ksenia Chistopolskaya ◽  
Yanzheng Liu ◽  
Mansor Abu Talib ◽  
Olga Mitina ◽  
...  
Keyword(s):  
Social Support ◽  
Suicidal Behavior ◽  
Online Survey ◽  
Perceived Social Support ◽  
Strain Theory ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Psychological Strains ◽  
Moderating Role

Abstract. Background: According to the strain theory of suicide, strains, resulting from conflicting and competing pressures in an individual's life, are hypothesized to precede suicide. But social support is an important factor that can mitigate strains and lessen their input in suicidal behavior. Aims: This study was designed to assess the moderating role of social support in the relation between strain and suicidality. Methods: A sample of 1,051 employees were recruited in Beijing, the capital of China, through an online survey. Moderation analysis was performed using SPSS PROCESS Macro. Social support was measured with the Multidimensional Scale of Perceived Social Support, and strains were assessed with the Psychological Strains Scale. Results: Psychological strains are a good predictor of suicidality, and social support, a basic need for each human being, moderates and decreases the effects of psychological strains on suicidality. Limitations: The cross-sectional survey limited the extent to which conclusions about causal relationships can be drawn. Furthermore, the results may not be generalized to the whole of China because of its diversity. Conclusion: Social support has a tendency to mitigate the effects of psychological strains on suicidality.

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