scholarly journals Genetic Diversity and Zoonotic Potential of Blastocystis in Korean Water Deer, Hydropotes inermis argyropus

Pathogens ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 955
Author(s):  
Kyoo-Tae Kim ◽  
Gyeonguk Noh ◽  
Haeseung Lee ◽  
Seon-Hee Kim ◽  
Hyesung Jeong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Intestinal Tract ◽  
Protozoan Parasite ◽  
Domestic Animals ◽  
Nucleotide Sequencing ◽  
Zoonotic Potential ◽  
Infection Status ◽  
Korean Water Deer

Blastocystis is a protozoan parasite commonly detected in the intestinal tract of humans and animals. It has been actively studied worldwide; however, information on Blastocystis is limited in Korea. Because there is an increasing concern about the contact between wildlife and domestic animals or humans, we assessed the infection status and zoonotic potential of Blastocystis in Korean water deer (KWD, Hydropotes inermis argyropus) using genotyping and phylogenetic analysis. A total of 125 fresh fecal samples were collected from KWD which were killed by vehicles on highways or roadsides in this study. Among the 125 samples, 51 (40.8%) were PCR positive. We performed nucleotide sequencing and phylogenetic analysis of 26 of the 51 PCR-positive samples. By analyzing Blastocystis 18S rRNA, two subtypes (ST4 and ST14) were identified in this study. Of the 26 samples analyzed, 25 were identified as ST14 and one as ST4. Infection of ST14 in humans has not been reported. Although only one ST4 sample was detected in this study, ST4 has zoonotic potential without showing ruminant specificity. Thus, continuous attention should be provided to the potential of transmission between wildlife and domestic animals and humans.

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.

Genetic Diversity of Cryptosporidium Spp. in Njoro Sub County, Nakuru, Kenya

2021 ◽  
Author(s):  
Walter Miding'a Essendi ◽  
Charles Inyagwa Muleke ◽  
Miheso Manfred ◽  
Elick Onyango Otachi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Evolutionary Genetics ◽  
Domestic Animals ◽  
Local Alignment ◽  
Cryptosporidium Spp ◽  
Potential Source ◽  
Search Tool ◽  
Great Genetic Diversity

Abstract Cryptosporidium spp. cause Cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies have illustrated the significance of domestic animals as reservoirs of this parasite. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chicken, sheep and goats were assessed for presence of Cryptosporidium spp. Thirty-three positive samples were successfully sequenced. The sequences obtained were compared to Cryptosporidium sequences in the GenBank using NCBI’s (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The Cryptosporidium spp. present in the watershed showed great genetic diversity with nine (9) Cryptosporidium spp. namely: C. parvum, C. hominis, C. ubiquitum, C. meleagridis, C. andersoni, C. baileyi, C. muris, C. xiaoi and C. viatorum. Cattle were the biggest reservoirs of zoonotic Cryptosporidium spp. hence a potential source of zoonosis in humans while goats had the least species. This is the first study that reported presence of C. viatorum in Kenya.

scholarly journals Phylogenetic Analysis of the Hypervariable Region of the 18S rRNA Gene of Cryptosporidium Oocysts in Feces of Canada Geese (Branta canadensis): Evidence for Five Novel Genotypes

2004 ◽  
Vol 70 (1) ◽  
pp. 452-458 ◽  
Author(s):  
Kristen L. Jellison ◽  
Daniel L. Distel ◽  
Harold F. Hemond ◽  
David B. Schauer
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Hypervariable Region ◽  
Pcr Amplification ◽  
The United States ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Canada Geese ◽  
Pcr Products

ABSTRACT To assess genetic diversity in Cryptosporidium oocysts from Canada geese, 161 fecal samples from Canada geese in the United States were analyzed. Eleven (6.8%) were positive for Cryptosporidium spp. following nested PCR amplification of the hypervariable region of the 18S rRNA gene. Nine PCR products from geese were cloned and sequenced, and all nine diverged from previously reported Cryptosporidium 18S rRNA gene sequences. Five sequences were very similar or identical to each other but genetically distinct from that of Cryptosporidium baileyi; two were most closely related to, but genetically distinct from, the first five; and two were distinct from any other sequence analyzed. One additional sequence in the hypervariable region of the 18S rRNA gene isolated from a cormorant was identical to that of C. baileyi. Phylogenetic analysis provided evidence for new genotypes of Cryptosporidium species in Canada geese. Results of this study suggest that the taxonomy of Cryptosporidium species in geese is complex and that a more complete understanding of genetic diversity among these parasites will facilitate our understanding of oocyst sources and species in the environment.

scholarly journals Frequent Reassortments May Explain the Genetic Heterogeneity of Rotaviruses: Analysis of Finnish Rotavirus Strains

2002 ◽  
Vol 76 (23) ◽  
pp. 11793-11800 ◽  
Author(s):  
Leena Maunula ◽  
Carl-Henrik von Bonsdorff
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Heterogeneity ◽  
The Other ◽  
Nucleotide Sequencing ◽  
Genetic Reassortment ◽  
Genetic Clusters ◽  
Virus Isolates

ABSTRACT The predominant rotavirus electropherotypes (e-types) during 17 epidemic seasons (1980 through 1997) in Finland were established, and representative virus isolates were studied by nucleotide sequencing and phylogenetic analysis. The virus isolates were either P[8]G1 or P[8]G4 types. The G1 and G4 strains formed one G1 lineage (VP7-G1-1) and one G4 lineage, respectively. Otherwise, they belonged to two P[8] lineages (VP4-P[8]-1 and -2) unrelated to their G types. Phylogenetic analysis of partial sequences of all 11 RNA segments obtained from the strains also revealed genetic diversity among gene segments other than those defining P and G types. With the exception of segments 1, 3, and 10, the sequences of the other segments could be assigned to 2 to 4 different genetic clusters. The results of this study suggest that, in addition to the RNA segments encoding VP4 and VP7, the other RNA segments may segregate independently as well. In total, the 9 predominant e-types represented 7 different RNA segment combinations when the phylogenetic clusters of their 11 genes were determined. The extensive genetic diversity and number of e-types among rotaviruses are best explained by frequent genetic reassortment.

Molecular-Based Identification of Sarcocystis hominis in Belgian Minced Beef

2007 ◽  
Vol 70 (6) ◽  
pp. 1523-1526 ◽  
Author(s):  
L. VANGEEL ◽  
K. HOUF ◽  
K. CHIERS ◽  
J. VERCRUYSSE ◽  
K. D'HERDE ◽  
...  
Keyword(s):  
18S Rrna ◽  
Intestinal Tract ◽  
Protozoan Parasite ◽  
Sarcocystis Species ◽  
Rrna Sequence ◽  
Specific Sequence ◽  
Sarcocystis Spp ◽  
Minced Beef ◽  
Pcr Products ◽  
Human Intestinal Tract

Sarcocystis hominis, one of the three species of Sarcocystis that cause muscular cysts in cattle, is a protozoan parasite that can infect the human intestinal tract. The objective of the present study was to develop a new molecular identification method capable of discriminating among the bovine Sarcocystis species and to apply this tool in combination with stereo-microscopy to determine the presence of Sarcocystis spp. in minced beef in Belgium, with special attention to Sarcocystis hominis. A PCR technique based on the 18S rRNA sequence and by sequencing of the amplicon was highly specific. Sequence analysis of PCR products from thick-walled cysts collected from minced beef in Belgium revealed that S. hominis was present in 97.4% of the samples. Because the consumption of raw minced beef is common in Belgium and certain other European countries, these findings may point to an underestimated risk to public health.

scholarly journals Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

Insights into the genetic diversity and the phylogenetic analysis of Tunisian isolates of Tomato chlorosis virus

2014 ◽  
Vol 43 (1) ◽  
pp. 87-96 ◽  
Author(s):  
Charfeddine Gharsallah ◽  
Amina Ben Halima ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Tomato Chlorosis Virus

scholarly journals SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

2021 ◽  
Author(s):  
Juliana D Siqueira ◽  
Livia R Goes ◽  
Brunna M Alves ◽  
Pedro S de Carvalho ◽  
Claudia Cicala ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cancer Patients ◽  
Disease Severity ◽  
Healthcare Workers ◽  
Viral Population ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Consensus Sequences ◽  
Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

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