scholarly journals Genetic diversity of begomoviruses infecting soybean, bean and associated weeds in Northwestern Argentina

2006 ◽  
Vol 31 (4) ◽  
pp. 342-348 ◽  
Author(s):  
Patricia E. Rodríguez-Pardina ◽  
F. Murilo Zerbini ◽  
Daniel A. Ducasse
Keyword(s):  
Genetic Diversity ◽  
Protein Gene ◽  
Weed Species ◽  
Capsid Protein Gene ◽  
High Sequence Identity ◽  
Northwestern Argentina ◽  
Sequence Identity ◽  
High Incidence ◽  
Northwestern Region ◽  
Prevalent Virus

The subtropical Northwestern region of Argentina (provinces of Tucumán, Salta, Jujuy, Santiago del Estero and Catamarca) suffers from a high incidence of the whitefly Bemisia tabaci, and the detection of begomoviruses is also common. The Northwest is the main bean-growing region of the country, and approximately 10% of Argentina's soybean crop is grown in this area. We have used a PCR-based assay to establish the identity and genetic diversity of begomoviruses associated with bean and soybean crops in Northwestern Argentina. Universal begomovirus primers were used to direct the amplification of a fragment encompassing the 5' portion of the capsid protein gene. Amplified fragments were cloned, sequenced and subjected to phylogenetic analysis to determine the sequence identity to known begomoviruses. The data indicated the presence of four distinct begomoviruses, all related to other New World begomoviruses. The prevalent virus, which was present in 94% of bean and soybean samples and also in two weed species, is closely related to Sida mottle virus (SiMoV). A virus with high sequence identity with Bean golden mosaic virus (BGMV) was found in beans. The two remaining viruses displayed less than 89% identity with other known begomoviruses, indicating that they may constitute novel species. One of these putative novel viruses was detected in bean, soybean and tomato samples.

In silico Prediction and Designing of Potential siRNAs to be Used as Antivirals Against SARS-CoV-2

2021 ◽  
Vol 27 ◽  
Author(s):  
Sayed Sartaj Sohrab ◽  
Sherif Aly El-Kafrawy ◽  
Aymn T. Abbas ◽  
Leena H. Bajrai ◽  
Esam Ibraheem Azhar
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
In Silico ◽  
Full Genome ◽  
In Silico Prediction ◽  
High Sequence Identity ◽  
Minor Parent ◽  
Sequence Identity ◽  
The City

Background:: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods:: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results:: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions:: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.

scholarly journals Genetic diversity of enteroviruses in patients with respiratory infection

2021 ◽  
Vol 66 (4) ◽  
pp. 444-452
Author(s):  
N. V. Paklonskaya ◽  
T. V. Amvrosieva ◽  
Yu. A. Shilova ◽  
E. P. Kishkurno
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Respiratory Infection ◽  
Protein Gene ◽  
Phylogenetic Reconstruction ◽  
Epidemiological Surveillance ◽  
Rt Pcr ◽  
Capsid Protein Gene ◽  
Coxsackievirus B4 ◽  
High Level

Enterovirus genetic variability underlies the variety of clinical forms of diseases they cause. The aim of the presented study was to establish the genetic diversity of enteroviruses (EVs) that caused acute respiratory infection (ARI) in 2016–2019. Biological samples were obtained from 203 patients with various forms of ARI, EV detection was carried out by RT-PCR, followed by sequencing of the main capsid protein gene and phylogenetic reconstruction. EV RNA was detected in 34.4 % of samples, most often in children aged 1–6 years (53.1–54.8 %). Coxsackieviruses B were found in patients with respiratory enterovirus infection (EVI) significantly more often than other EVs, the dominant serotypes were Coxsackievirus B4, B5. Despite the significant genetic diversity of EVs identified in patients with ARI (three genetic lines of Coxsackievirus B5, two genotypes of Coxsackievirus B2, one genotype of Coxsackievirus B3, three genovariant Coxsackievirus B4, one genovariant Coxsackievirus B1), there is no evidence of their connection with the formation of the respiratory form of EVI.The high level of genetic variability of EVs requires regular molecular-epidemiological surveillance for the identification of emerging genetic variants and assessment of their epidemic potential.

scholarly journals Genetic diversity of the attachment (H) protein gene of current field isolates of canine distemper virus.

1997 ◽  
Vol 78 (2) ◽  
pp. 367-372 ◽  
Author(s):  
G Bolt ◽  
P Arctander ◽  
T D Jensen ◽  
M J Appel ◽  
E Gottschalck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Canine Distemper Virus ◽  
Protein Gene ◽  
Canine Distemper ◽  
Current Field ◽  
Field Isolates ◽  
H Protein

scholarly journals Genetic diversity of cutaneous human papillomaviruses

2007 ◽  
Vol 88 (10) ◽  
pp. 2662-2669 ◽  
Author(s):  
Ola Forslund
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Human Skin ◽  
Human Papillomaviruses ◽  
Sequence Identity ◽  
Hpv Types

Human papillomaviruses (HPVs) of the genera Betapapillomavirus and Gammapapillomavirus are common on human skin. Sequencing of subgenomic amplicons of cutaneous HPVs has revealed a large number of novel putative HPV types within these genera. Phylogenetic analysis based on these amplicons revealed 133 putative HPV types with <90 % sequence identity to any known HPV type or to each other. As there are already 34 characterized HPV types described within the genera Betapapillomavirus and Gammapapillomavirus, they appear to be the most genetically diverse of the HPVs, apparently comprising at least 167 different HPV types.

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.

scholarly journals Onorchard habitats for Nysius huttoni an important kiwifruit passenger pest

2014 ◽  
Vol 67 ◽  
pp. 326-326
Author(s):  
C.A. Rowe ◽  
M.G. Hill ◽  
D.P. Logan
Keyword(s):  
Native Species ◽  
Host Plants ◽  
Ground Vegetation ◽  
Preliminary Survey ◽  
Weed Species ◽  
Quarantine Pest ◽  
Polygonum Aviculare ◽  
Brassica Crops ◽  
Wide Range ◽  
High Incidence

Nysius huttoni is a native species of wheat bug which is an occasional quarantine pest on export kiwifruit Wheat bug has a wide range of host plants including wheat and brassica crops as well as many weed species The kiwifruit harvest of 2013 had a high incidence of wheat bug finds on fruit in packhouses In response an orchard survey was undertaken to identify orchard habitats used by wheat bug Twentyfive orchards where wheat bug was found during packing in 2013 were surveyed from the Te Puke area from February to March At each orchard four habitats were searched (1) ground vegetation under the kiwifruit canopy (2) the loadout zone (3) edge of the loadout zone and (4) grassland surrounding the was found in and around the loadout zone associated with weed species notably Polygonum aviculare the dominant weed species in loadout zones No wheat bug was found under the kiwifruit canopy and the remaining 4 were found in grassland This preliminary survey suggests that the risk of wheat bug infestation can be reduced considerably by keeping loadout zones free of weeds during spring and summer

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