scholarly journals Genetic diversity of vector-borne pathogens in spotted and brown hyenas from Namibia and Tanzania relates to ecological conditions rather than host taxonomy

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jürgen Krücken ◽  
Gábor Á. Czirják ◽  
Sabrina Ramünke ◽  
Maria Serocki ◽  
Sonja K. Heinrich ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Sub Saharan Africa ◽  
Anthropogenic Factors ◽  
High Genetic Diversity ◽  
Acinonyx Jubatus ◽  
Ecological Conditions ◽  
Vector Borne ◽  
Babesia Lengau

Abstract Background Improved knowledge on vector-borne pathogens in wildlife will help determine their effect on host species at the population and individual level and whether these are affected by anthropogenic factors such as global climate change and landscape changes. Here, samples from brown hyenas (Parahyaena brunnea) from Namibia (BHNA) and spotted hyenas (Crocuta crocuta) from Namibia (SHNA) and Tanzania (SHTZ) were screened for vector-borne pathogens to assess the frequency and genetic diversity of pathogens and the effect of ecological conditions and host taxonomy on this diversity. Methods Tissue samples from BHNA (n = 17), SHNA (n = 19) and SHTZ (n = 25) were analysed by PCRs targeting Anaplasmataceae, Rickettsia spp., piroplasms, specifically Babesia lengau-like piroplasms, Hepatozoidae and filarioids. After sequencing, maximum-likelihood phylogenetic analyses were conducted. Results The relative frequency of Anaplasmataceae was significantly higher in BHNA (82.4%) and SHNA (100.0%) than in SHTZ (32.0%). Only Anaplasma phagocytophilum/platys-like and Anaplasma bovis-like sequences were detected. Rickettsia raoultii was found in one BHNA and three SHTZ. This is the first report of R. raoultii from sub-Saharan Africa. Babesia lengau-like piroplasms were found in 70.6% of BHNA, 88.9% of SHNA and 32.0% of SHTZ, showing higher sequence diversity than B. lengau from South African cheetahs (Acinonyx jubatus). In one SHTZ, a Babesia vogeli-like sequence was identified. Hepatozoon felis-like parasites were identified in 64.7% of BHNA, 36.8% of SHNA and 44.0% of SHTZ. Phylogenetic analysis placed the sequences outside the major H. felis cluster originating from wild and domestic felids. Filarioids were detected in 47.1% of BHNA, 47.4% of SHNA and 36.0% of SHTZ. Phylogenetic analysis revealed high genetic diversity and suggested the presence of several undescribed species. Co-infections were frequently detected in SHNA and BHNA (BHNA median 3 pathogens, range 1–4; SHNA median 3 pathogens, range 2–4) and significantly rarer in SHTZ (median 1, range 0–4, 9 individuals uninfected). Conclusions The frequencies of all pathogens groups were high, and except for Rickettsia, multiple species and genotypes were identified for each pathogen group. Ecological conditions explained pathogen identity and diversity better than host taxonomy. Graphic Abstract

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

scholarly journals Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

2021 ◽  
pp. 1-11
Author(s):  
Andrea Highfield ◽  
Angela Ward ◽  
Richard Pipe ◽  
Declan C. Schroeder
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Dunaliella Salina ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Hypersaline Environments ◽  
Rdna Its ◽  
Β Carotene ◽  
Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

scholarly journals Genetic diversity and phylogeographic analysis of human herpesvirus type 8 (HHV-8) in two distant regions of Argentina: association with the genetic ancestry of the population

2020 ◽  
Author(s):  
MARIA LAURA HULANIUK ◽  
LAURA MOJSIEJCZUK ◽  
FEDERICO JAUK ◽  
CARLOS REMONDEGUI ◽  
LILIA MAMMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Latin American ◽  
Phylogenetic Analyses ◽  
Human Herpesvirus ◽  
Kaposi Sarcoma ◽  
Genetic Ancestry ◽  
Sub Saharan Africa ◽  
Herpesvirus Type ◽  
Phylogeographic Analysis

Background: The genetic diversity of persistent infectious agents, such as HHV-8, correlates closely with the migration of modern humans out of East Africa which makes them useful to trace human migrations. However, there is scarce data about the evolutionary history of HHV-8 particularly in multiethnic Latin American populations. Objectives: The aim of this study was to characterize the genetic diversity and the phylogeography of HHV-8 in two distant geographic regions of Argentina and to establish potential associations with the genetic ancestry of the population. Study design: A total of 605 HIV-1 infected subjects, Kaposi Sarcoma (KS) patients and blood donors were recruited in the metropolitan (MET) and north-western regions of Argentina (NWA). After HHV-8 DNA detection, ORF-26 and ORF-K1 were analyzed for subtype assignment. Uniparental and biparental ancestry markers were evaluated in samples in which subtypes could be assigned. Phylogeographic analysis was performed in the ORF-K1 sequences from this study combined with 388 GenBank sequences. Results: HHV-8 was detected in 24.8% of samples. ORF-K1 phylogenetic analyses showed that subtypes A (A1-A5), B1, C (C1-C3) and F were present in 46.9%, 6.25%, 43.75% and 3.1% of cases, respectively. Analyses of ORF-26 fragment revealed that 81.95% of strains were subtypes A/C followed by J, B2, R, and K. Among KS patients, subtype A/C was more commonly detected in MET whereas subtype J was the most frequent in NWA. Subtypes A/C was significantly associated with Native American maternal haplogroups (p=0.004), whereas subtype J was related to non-Native American haplogroups (p<0.0001). Sub-Saharan Africa, Europe and Latin America were the most probable locations from where HHV-8 was introduced to Argentina. Conclusions: These results give evidence of the geographic circulation of HHV-8 in Argentina, provide new insights about its relationship with ancient and modern human migrations and identify the possible origins of this virus in Argentina.

scholarly journals Bluetongue in Europe – the risk of animal import from restricted zones

2019 ◽  
Vol 75 (05) ◽  
pp. 6254-2019
Author(s):  
ANNA ORŁOWSKA ◽  
MARCIN SMRECZAK ◽  
JERZY ROLA
Keyword(s):  
Genetic Diversity ◽  
20Th Century ◽  
Bluetongue Virus ◽  
Viral Disease ◽  
Economic Losses ◽  
High Genetic Diversity ◽  
Key Factor ◽  
Vector Borne ◽  
Sentinel Animals ◽  
Free Status

Bluetongue (BT) is a vector-borne viral disease effecting ruminants caused by bluetongue virus (BTV), transmitted mainly by bites from midges of the genus Culicoides. Since the end of 20th century, BTV is endemic in several European countries and the disease is caused mainly by BTV-8 and BTV-4 infections. Bluetongue virus is characterized by high genetic diversity. To date, over 29 BTV serotypes have been documented, including recently discovered atypical serotypes BTV (25–27). The disease has a high economic impact as it causes economic losses due to animal mortality, reduced productivity and restrictions on the movement of animals. Several reports and numerous observations indicate the contribution of animal movements to the spread of BTV infections. Thus, bluetongue surveillance that includes testing of sentinel animals as well as virological testing of animals susceptible to BTV infection imported from restricted zones due to the presence of BTV is a key factor in maintaining a BT-free status

scholarly journals Distribution and phylogenetic diversity of Anopheles species in malaria endemic areas of Honduras in an elimination setting

2020 ◽  
Author(s):  
Denis Escobar ◽  
Krisnaya Ascencio ◽  
Andrés Ortiz ◽  
Adalid Palma ◽  
Gustavo Fontecha
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Public Health Problem ◽  
Abundant Species ◽  
Malaria Vectors ◽  
Morphological Identification ◽  
High Genetic Diversity ◽  
Homogeneous Population ◽  
Molecular Approaches ◽  
Endemic Areas

Abstract Background: Anopheles mosquitoes are the vectors of malaria, one of the most important infectious diseases in the tropics. More than 500 Anopheles species have been described worldwide, and more than 30 are considered a public health problem. In Honduras, information on the distribution of Anopheles spp. and its genetic diversity is scarce. This study aimed to describe the distribution and genetic diversity of Anopheles mosquitoes in Honduras. Methods: Mosquitoes were captured in 8 locations in 5 malaria endemic departments during 2019. Two collection methods were used. Adult anophelines were captured outdoors using CDC light traps and by aspiration of mosquitoes at rest. The morphological identification was performed using taxonomic keys. Genetic analyses included the sequencing of a partial region of the cytochrome oxidase I gene (COI) and the ribosomal internal transcribed spacer 2 (ITS2). Results: A total of 1320 anophelines were collected and identified through morphological keys. Seven Anopheles species were identified. Anopheles albimanus was the most widespread and abundant species (74.02%). To confirm the morphological identification of the specimens, 175 and 122 sequences were obtained for COI and ITS2 respectively. Both markers confirmed the morphological identification. COI showed a greater nucleotide diversity than ITS2 in all species. High genetic diversity was observed within the populations of An. albimanus while An. darlingi proved to be a highly homogeneous population. Phylogenetic analyses revealed clustering patterns in An. darlingi and An. neivai in relation to specimens from South America. New sequences for An. crucians, An. vestitipennis, and An. neivai are reported in this study.Conclusions: Here we report the distribution and genetic diversity of Anopheles species in endemic areas of malaria transmission in Honduras. According to our results, both taxonomic and molecular approaches are useful tools in the identification of anopheline mosquitoes. However, both molecular markers differ in their ability to detect intraspecific genetic diversity. These results provide supporting data for a better understanding of the distribution of malaria vectors in Honduras.

Genetic diversity ofFrankiastrains in root nodules fromHippophae¨ rhamnoidesL.

Botany ◽  
2008 ◽  
Vol 86 (3) ◽  
pp. 240-247 ◽  
Author(s):  
Li-hong Chen ◽  
Jian Liu ◽  
Gui-min Yao ◽  
Wei Yan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Restriction Analysis ◽  
Root Nodules ◽  
Plant Cover ◽  
Practical Importance ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Northern China ◽  
High Genetic Diversity

The Hippophae¨ rhamnoides L. – Frankia symbiosis is of ecological and practical importance, but very little is known about H. rhamnoides-infective Frankia strains. To address this problem, we have used PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of nifD–nifK intergenic spacer (IGS) to estimate their genetic diversity at 19 sites in Northern China. Restriction analysis indicated that H. rhamnoides-infective Frankia had a high genetic diversity; the samples were divided into nine RFLP patterns (A–I). Elevation and precipitation likely affect the distribution of different Frankia patterns in root nodules. The patterns A and D were present in relatively large areas, which were located at various elevations; however, the distribution of patterns B, C, E, F, G, H, and I generally followed a geographic range. The richness of Frankia diversity was influenced by plant cover and geographic factors such as elevation and precipitation. H. rhamnoides cover had a higher diversity than that of natural vegetation cover. The center part of the geographical range, with intermediate elevation and precipitation, had a higher level of Frankia diversity than that of the west part and east part with high or low elevations and precipitations, respectively. The nifD–nifK IGS regions were sequenced from 28 nodule samples. Phylogenetic analysis showed that H. rhamnoides-infective Frankia strains were all clustered with the Elaeagnus group, and the diversity of this group was quite extensive. Phylogenetic relationships between Hippophae¨ and Elaeagnus-infective Frankia strains were relatively close to each other. Although not very close to either Hippophae¨- or Elaeagnus-infective Frankia strains, Shepherdia -infective strain SCN10a was closer to Hippophae¨-infective strains than to Elaeagnus- infective strains. This is the first detailed report on the genetic diversity and phylogenetic analysis of H. rhamnoides-infective Frankia.

scholarly journals High genetic diversity of hepatitis delta virus in eastern Turkey

2014 ◽  
Vol 8 (01) ◽  
pp. 074-078 ◽  
Author(s):  
Yasemin Bulut ◽  
Ibrahim Halil Bahcecioglu ◽  
Cem Aygun ◽  
Pinar Demirel Oner ◽  
Ibrahim Ozercan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Restriction Enzyme ◽  
Hepatitis Delta Virus ◽  
Rt Pcr ◽  
Genotype I ◽  
High Genetic Diversity ◽  
Hepatitis Delta ◽  
Hdv Genotype ◽  
Delta Virus

Introduction: Hepatitis delta virus (HDV) is a serious cause of liver-related mortality in patients infected with hepatitis B virus (HBV). Determination of genotypes of HDV and phylogenetic analysis are important for better understanding the pathogenesis of the liver diseases associated with HBV infection. The aim of this study was to determine the genotype or genotypes of HDV among chronically infected patients with HBV in eastern Turkey. Methodology: A group of 113 patients infected with HBV and HDV were included in this study. The samples taken from the patients were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction enzyme cleavage. Results: According to the results of the restriction enzyme analysis, all of the RT-PCR products were determined to be HDV genotype I. Furthermore, for phylogenetic analysis and genotyping, 40 of HDV RT-PCR positive products were sequenced. Phylogenetic analysis of the sequences showed that all of the samples were infected with HDV genotype I. In addition, the results of the alignment analysis showed that the sequences of clinical samples were 82%-95% similar. Conclusion: These results indicate that high genetic diversity of the virus is possible in endemic areas such as Turkey.

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

Microbiology ◽  
2000 ◽  
Vol 81 (1) ◽  
pp. 243-255 ◽  
Author(s):  
M. Bousalem ◽  
E. J. P. Douzery ◽  
D. Fargette
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
High Genetic Diversity ◽  
Single Clade ◽  
Cultivated Species ◽  
Selection Of

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis–Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3′-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis–D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

scholarly journals Genetic diversity and SNP’s from the chloroplast coding regions of virus-infected cassava

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8632
Author(s):  
Bruno Rossitto De Marchi ◽  
Tonny Kinene ◽  
Renate Krause-Sakate ◽  
Laura M. Boykin ◽  
Joseph Ndunguru ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
East Africa ◽  
Target Genes ◽  
Rna Extraction ◽  
Plant Viruses ◽  
Sub Saharan Africa ◽  
Cassava Mosaic Disease ◽  
Chloroplast Genomes ◽  
Cassava Varieties

Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.

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