scholarly journals Survey and Genetic Diversity of Grapevine Leafroll Associated Virus 2 in Algeria

2015 ◽  
Vol 4 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Arezki Lehad ◽  
Ilhem Selmi ◽  
Meriem Louanchi ◽  
Mouni Aitouada ◽  
Naima Mahfoudhi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Synonymous Site ◽  
Rt Pcr ◽  
Synonymous Substitutions ◽  
Representative Sequence ◽  
Polymerase Chain ◽  
Das Elisa ◽  
Similarity Plot

Vineyards in western and center regions of Algeria were surveyed for the Grapevine leafroll-associated virus 2 (GLRaV-2). Analyses by DAS-ELISA and Reverse Transcription Polymerase Chain Reaction (RT-PCR) reveal 15, 8% prevalence. The genetic diversity of the GLRaV-2 population was studied by phylogenetic analyses of the HSP70h gene region of seven samples sequenced in this study and other sequences downloaded from GenBank. Results reveal segregation of the GLRav-2 population into six distinct groups. An estimation of the ratio of non-synonymous substitutions per non-synonymous site to synonymous substitutions per synonymous site indicated that HSP70h gene evolve under positive selection. Similarity plot constructed with representative sequence from each group confirmed previous results.  All Algerian isolates belong to group PN. As far as we know, this is the first characterization of GLRaV-2 isolates from Algeria.

scholarly journals Detection and Characterization of Porcine Sapelovirus in Italian Pig Farms

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 966
Author(s):  
Eleonora Chelli ◽  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Fabio Ostanello ◽  
Ilaria Di Bartolo
Keyword(s):  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Genetic Characteristics ◽  
The Family ◽  
Polymerase Chain ◽  
Porcine Sapelovirus

Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6–7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.

scholarly journals Occurrence and molecular characterization of alfalfa mosaic virus in eggplant in Serbia

2021 ◽  
Vol 26 (51) ◽  
pp. 33-39
Author(s):  
Dragana Milošević ◽  
Maja Ignjatov ◽  
Zorica Nikolić ◽  
Gordana Tamindžić ◽  
Gordana Petrović ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Potato Virus Y ◽  
Chenopodium Quinoa ◽  
Alfalfa Mosaic Virus ◽  
Rt Pcr ◽  
Bright Yellow ◽  
Polymerase Chain ◽  
Test Plants ◽  
Das Elisa

In the 2018-19 growing season, a total of 51 leaves of eggplant plants grown under field conditions were collected randomly from nine private gardens at four different localities in the Province of Vojvodina. Eggplants with nearly 40% of plants showing bright yellow to white mosaic or mottling of leaves were found throughout the inspected fields (gardens). The collected samples were analyzed for the presence of alfalfa mosaic virus (AMV), cucumber mosaic virus (CMV) and potato virus Y (PVY) using commercial double-antibody sandwich (DAS)-ELISA kits. Serological analysis of eggplant samples revealed the presence of AMV in 80.39% collected samples. None of the analyzed samples was positive for CMV and PVY. The virus was successfully mechanically transmitted to test plants including Nicotiana benthamiana, Chenopodium quinoa, C. amaranticolor, as well as eggplant seedlings, confirming the infectious nature of the disease. The presence of AMV in eggplants was further verified by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing, using the primers CP AMV1 and CP AMV2 that amplify part of the coat protein (CP) gene. The phylogenetic analysis showed that Serbian AMV isolates grouped into a separate well-supported group together with AMV isolates from Italy, Croatia and previously characterized isolates from Serbia. To our knowledge, this is the first report of AMV infection of eggplant in Serbia.

scholarly journals Limited Genetic Variability Among American Isolates of Grapevine virus E from Vitis spp.

Plant Disease ◽  
2016 ◽  
Vol 100 (1) ◽  
pp. 159-163 ◽  
Author(s):  
J. Vargas-Asencio ◽  
M. Al Rwahnih ◽  
A. Rowhani ◽  
F. Celebi-Toprak ◽  
J. R. Thompson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Protein Gene ◽  
The United States ◽  
Nucleic Acid Binding ◽  
Grapevine Virus ◽  
Rt Pcr ◽  
Viral Cdna ◽  
Polymerase Chain ◽  
Binding Protein Gene

A survey for the presence of Grapevine virus E (GVE, genus Vitivirus, family Betaflexiviridae) in vineyards in New York and California was conducted using macroarray hybridization or reverse-transcription polymerase chain reaction (RT-PCR) assays. In New York, GVE was detected in 10 of 46 vines of Vitis labrusca, one V. riparia, and one Vitis hybrid. All GVE-infected New York vines were coinfected with Grapevine leafroll-associated virus-3. In California, GVE was detected in 8 of 417 vines of V. vinifera. All GVE-infected California vines were also coinfected by one of the leafroll-associated viruses and other vitiviruses. In order to assess the genetic diversity among GVE isolates, a viral cDNA was amplified by RT-PCR, and a 675-nucleotide region that included the 3′ terminus of the coat protein gene, a short intergenic region, and the 5′ terminus of the putative nucleic acid binding protein gene was sequenced. All 20 GVE isolates sequenced in this study were very closely related, with >98% nucleotide identity to the SA94 isolate from South Africa. These findings confirm the presence of GVE in major grape-growing regions of the United States and indicate a very low level of genetic diversity.

scholarly journals Analysis of Genetic Diversity of Fusarium tupiense, the Main Causal Agent of Mango Malformation Disease in Southern Spain

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 276-286 ◽  
Author(s):  
M. Crespo ◽  
F. M. Cazorla ◽  
A. de Vicente ◽  
E. Arrebola ◽  
J. A. Torés ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Southern Spain ◽  
Fusarium Fujikuroi ◽  
Dna Sequence Data ◽  
Fusarium Fujikuroi Species Complex ◽  
Polymerase Chain ◽  
Mango Malformation

Mango malformation disease (MMD) has become an important global disease affecting this crop. The aim of this study was to identify the main causal agents of MMD in the Axarquía region of southern Spain and determine their genetic diversity. Fusarium mangiferae was previously described in the Axarquía region but it represented only one-third of the fusaria recovered from malformed trees. In the present work, fusaria associated with MMD were analyzed by arbitrary primed polymerase chain reaction (ap-PCR), random amplified polymorphic DNA (RAPD), vegetative compatibility grouping (VCG), a PCR screen for mating type idiomorph, and phylogenetic analyses of multilocus DNA sequence data to identify and characterize the genetic diversity of the MMD pathogens. These analyses confirmed that 92 of the isolates were F. tupiense, which was previously only known from Brazil and Senegal. In addition, two isolates of a putatively novel MMD pathogen were discovered, nested within the African clade of the Fusarium fujikuroi species complex. The F. tupiense isolates all belonged to VCG I, which was first described in Brazil, and the 11 isolates tested showed pathogenicity on mango seedlings. Including the prior discovery of F. mangiferae, three exotic MMD pathogenic species have been found in southern Spain, which suggests multiple independent introductions of MMD pathogens in the Axarquía region.

scholarly journals Genetic Diversity and Aggressiveness of Ralstonia solanacearum Strains Causing Bacterial Wilt of Potato in Uruguay

Plant Disease ◽  
2011 ◽  
Vol 95 (10) ◽  
pp. 1292-1301 ◽  
Author(s):  
M. I. Siri ◽  
A. Sanabria ◽  
M. J. Pianzzola
Keyword(s):  
Genetic Diversity ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Potato Tubers ◽  
Bacterial Strains ◽  
Potato Plants ◽  
Polymerase Chain ◽  
First Time ◽  
Different Levels

Bacterial wilt, caused by Ralstonia solanacearum, is a major disease affecting potato (Solanum tuberosum) production worldwide. Although local reports suggest that the disease is widespread in Uruguay, characterization of prevalent R. solanacearum strains in that country has not been done. In all, 28 strains of R. solanacearum isolated from major potato-growing areas in Uruguay were evaluated, including 26 strains isolated from potato tubers and 2 from soil samples. All strains belonged to phylotype IIB, sequevar 1 (race 3, biovar 2). Genetic diversity of strains was assessed by repetitive-sequence polymerase chain reaction, which showed that the Uruguayan strains constituted a homogeneous group. In contrast, inoculation of the strains on tomato and potato plants showed, for the first time, different levels of aggressiveness among R. solanacearum strains belonging to phylotype IIB, sequevar 1. Aggressiveness assays were also performed on accessions of S. commersonii, a wild species native to Uruguay that is a source of resistance for potato breeding. No significant interactions were found between bacterial strains and potato and S. commersonii genotypes, and differences in aggressiveness among R. solanacearum strains were consistent with previously identified groups based on tomato and potato inoculations. Moreover, variation in responses to R. solanacearum was observed among the S. commersonii accessions tested.

Isolation and Characterization of Mesenchymal Stem Cells from Chicken Liver

2020 ◽  
Vol 10 (1) ◽  
pp. 8-16
Author(s):  
Xibin Liu ◽  
Shuang Zhang ◽  
Weijun Guan ◽  
Dong Zheng
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Protein Markers ◽  
Multilineage Differentiation ◽  
Rt Pcr ◽  
Multipotent Stem Cells ◽  
Isolation And Characterization ◽  
Potential Applications ◽  
Polymerase Chain

Hepatic mesenchymal stem cells (HMSCs) are multipotent stem cells that is a vital part of the regeneration of hepatocytes after injury. In this study, HMSCs were isolated in embryonic livers from of 12-day-old chick embryo using collagenase, and the primary HMSCs were sub-cultured to passage. The protein markers of HMSCs, namely CD71, CD29 and CD44, were tested with immunofluorescence and Reverse Transcription-Polymerase Chain Reaction (RT-PCR). The proliferation of HMSCs in different passages was detected using growth curve, which shown a typically sigmoidal. And then, the pluripotent of HMSCs was analyzed, the results showed that HMSCs could directly induce to differentiate into neural-like cells, adipocytes, and osteoblasts. Our data illustrated that the chick HMSCs have same characteristics to those obtained from other species. The capacity of these cells for multilineage differentiation shows promise for many potential applications.

scholarly journals Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study

2017 ◽  
Vol 146 (1) ◽  
pp. 11-18 ◽  
Author(s):  
P. R. PATIL ◽  
N. N. GANORKAR ◽  
V. GOPALKRISHNA
Keyword(s):  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Clinical Manifestations ◽  
Western India ◽  
Vp1 Gene ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Predominant Genotype ◽  
Stool Specimens ◽  
Polymerase Chain

SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

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 Genetic Diversity of Babesia bovis MSA-1, MSA-2b and MSA-2c in China

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 473
Author(s):  
Jinming Wang ◽  
Jifei Yang ◽  
Shandian Gao ◽  
Xiaoxing Wang ◽  
Hao Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Immune Responses ◽  
Nested Pcr ◽  
Phylogenetic Analyses ◽  
Apicomplexan Parasite ◽  
Amino Acid Sequences ◽  
Babesia Bovis ◽  
Chain Reaction ◽  
Merozoite Surface Antigen ◽  
Polymerase Chain

The apicomplexan parasite Babesia bovis is a tick-borne intracellular hemoprotozoan parasite that is widespread across China. Genetic diversity is an important strategy used by parasites to escape the immune responses of their hosts. In our present study, 575 blood samples, collected from cattle in 10 provinces, were initially screened using a nested PCR (polymerase chain reaction) for detection of B. bovis infection. To perform genetic diversity analyses, positive samples were further amplified to obtain sequences of three B. bovis merozoite surface antigen genes (MSA-1, MSA-2b, MSA-2c). The results of the nested PCR approach showed that an average of 8.9% (51/575) of cattle were positive for B. bovis infection. Phylogenetic analyses of the predicted amino acid sequences revealed that unique antigen variants were formed only by Chinese isolates. Our findings provide vital information for understanding the genetic diversity of B. bovis in China.

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