scholarly journals Identification, full-length genome sequencing, and field survey of citrus vein enation virus in Italy

2021 ◽  
Vol 60 (2) ◽  
pp. 293-301
Author(s):  
Maria MINUTOLO ◽  
Maria CINQUE ◽  
Giuseppe ALTAMURA ◽  
Francesco DI SERIO ◽  
Daniela ALIOTO ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Field Survey ◽  
Geographic Origin ◽  
Full Length ◽  
Full Genome Sequence ◽  
Post Inoculation ◽  
Campania Region ◽  
Italian Isolate ◽  
Full Length Genome ◽  
First Time

Citrus vein enation virus (CVEV) was described in Spain and then it has been reported in several citrus growing areas of Asia, America and Australia. Here, the occurrence of CVEV in Italy has been documented for the first time. The full genome sequence of a CVEV Italian isolate (14Q) was determined by high-throughput sequencing and the presence of the virus was confirmed by RT-PCR and graft-transmission to indicator plants, from which the virus was recovered six-months post-inoculation. Phylogenetic analysis based on the full-length genome of CVEV isolates from different countries showed that they are phylogenetically related to each other based on their geographic origin, rather than on their host and that the Italian isolate is more closely related to the Spanish isolate than to the other ones. A field survey revealed the presence of CVEV in some areas of Campania region (southern Italy), prevalently infecting lemon trees. In the frame of this survey, kumquat was identified for the first time as a host of CVEV. No symptoms were observed in the field so far. The infection of asymptomatic hosts and the transmission by aphid species present in Italy increase the risk that the virus could further spread.

scholarly journals Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs

2020 ◽  
Vol 11 ◽  
Author(s):  
Huimin Liu ◽  
Zhibin Shi ◽  
Chunguo Liu ◽  
Pengfei Wang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Pseudorabies Virus ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Full Genome Sequence ◽  
Genome Sequences ◽  
Protein Coding ◽  
One Step ◽  
Human Infections ◽  
Full Length Genome

Pseudorabies viruses (PRVs) pose a great threat to the pig industry of many countries around the world. Human infections with PRV have also been reported occasionally in China. Therefore, understanding the epidemiology and evolution of PRVs is of great importance for disease control in the pig populations and humans as well. In this study, we isolated a PRV designated HLJ-2013 from PRV-positive samples that had been collected in Heilongjiang, China, in 2013. The full genome sequence of the virus was determined to be ∼143 kbp in length using high-throughput sequencing. The genomic sequence identities between this isolate and 21 other previous PRV isolates ranged from 92.4% (with Bartha) to 97.3% (with SC). Phylogenetic analysis based on the full-length genome sequences revealed that PRV HLJ-2013 clustered together with all the Chinese strains in one group belonging to Genotype II, but this virus occurred phylogenetically earlier than all the other Chinese PRV strains. Phylogenetic trees based on both protein-coding genes and non-coding regions revealed that HLJ-2013 probably obtained its genome sequences from three origins: a yet unknown parent virus, the European viruses, and the same ancestor of all Chinese PRVs. Recombination analysis showed that HLJ-2013-like virus possibly donated the main framework of the genome of the Chinese PRVs. HLJ-2013 exhibited cytopathic and growth characteristics similar to that of the Chinese PRV strains SC and HeN1, but its pathogenicity in mice was higher than that of SC and lower than that of HeN1. The identification of HLJ-2013 takes us one step closer to understanding the origin of PRVs in China and provides new knowledge about the evolution of PRVs worldwide.

scholarly journals Characterization of full-length hepatitis C virus sequences for subtypes 1e, 1h and 1l, and a novel variant revealed Cameroon as an area in origin for genotype 1

2013 ◽  
Vol 94 (8) ◽  
pp. 1780-1790 ◽  
Author(s):  
Chunhua Li ◽  
Richard Njouom ◽  
Jacques Pépin ◽  
Tatsunori Nakano ◽  
Phil Bennett ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Genotype 1 ◽  
Novel Variant ◽  
Hcv Genotype 1 ◽  
Full Length Genome ◽  
First Time

In this study, we characterized the full-length genome sequences of seven hepatitis C virus (HCV) isolates belonging to genotype 1. These represent the first complete genomes for HCV subtypes 1e, 1h, 1l, plus one novel variant that qualifies for a new but unassigned subtype. The genomes were characterized using 19–22 overlapping fragments. Each was 9400–9439 nt long and contained a single ORF encoding 3019–3020 amino acids. All viruses were isolated in the sera of seven patients residing in, or originating from, Cameroon. Predicted amino acid sequences were inspected and unique patterns of variation were noted. Phylogenetic analysis using full-length sequences provided evidence for nine genotype 1 subtypes, four of which are described for the first time here. Subsequent phylogenetic analysis of 141 partial NS5B sequences further differentiated 13 subtypes (1a–1m) and six additional unclassified lineages within genotype 1. As a result of this study, there are now seven HCV genotype 1 subtypes (1a–1c, 1e, 1g, 1h, 1l) and two unclassified genotype 1 lineages with full-length genomes characterized. Further analysis of 228 genotype 1 sequences from the HCV database with known countries is consistent with an African origin for genotype 1, and with the hypothesis of subsequent dissemination of some subtypes to Asia, Europe and the Americas.

scholarly journals Catching SARS-CoV-2 by sequence hybridization: a comparative analysis

2021 ◽  
Author(s):  
Alexandra Rehn ◽  
Peter Braun ◽  
Mandy Knüpfer ◽  
Roman Wölfel ◽  
Markus H. Antwerpen ◽  
...  
Keyword(s):  
Sequence Data ◽  
Full Length ◽  
High Quality ◽  
Essential Information ◽  
Droplet Pcr ◽  
Next Generation Sequencing Ngs ◽  
Full Length Genome ◽  
First Time ◽  
Generation Sequencing ◽  
New Mutations

AbstractControlling and monitoring the still ongoing SARS-CoV-2 pandemic regarding geographical distributions, evolution and emergence of new mutations of the SARS-CoV-2 virus is only possible due to continuous next-generation sequencing (NGS) and worldwide sequence data sharing. Efficient sequencing strategies enabling the retrieval of the maximum number of high quality, full-length genomes are hence indispensable. Here, we describe for the first time a combined approach of digital droplet PCR (ddPCR) and NGS to evaluate five commercially available sequence capture panels targeting SARS-CoV-2. In doing so, we were not only able to determine the most sensitive and specific capture panel, but to discriminate their mode of action and number of read pairs needed to recover a high quality full length genome. Thereby, we are providing essential information for all sequencing laboratories worldwide striving for maximizing the sequencing output and simultaneously minimizing time, costs and sequencing resources.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Functional Genomic Identification of Cadmium Resistance Genes from a High GC Clone Library by Coupling the Sanger and PacBio Sequencing Strategies

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 7
Author(s):  
Jinghao Chen ◽  
Chao Xing ◽  
Xin Zheng ◽  
Xiaofang Li
Keyword(s):  
High Throughput ◽  
Resistance Genes ◽  
Sanger Sequencing ◽  
Genomic Library ◽  
Full Length ◽  
Host Cells ◽  
Full Genome Sequence ◽  
Functional Screening ◽  
Functional Genomic ◽  
Pacbio Sequencing

Functional (meta) genomics allows the high-throughput identification of functional genes in a premise-free way. However, it is still difficult to perform Sanger sequencing for high GC DNA templates, which hinders the functional genomic exploration of a high GC genomic library. Here, we developed a procedure to resolve this problem by coupling the Sanger and PacBio sequencing strategies. Identification of cadmium (Cd) resistance genes from a small-insert high GC genomic library was performed to test the procedure. The library was generated from a high GC (75.35%) bacterial genome. Nineteen clones that conferred Cd resistance to Escherichia coli subject to Sanger sequencing directly. The positive clones were in parallel subject to in vivo amplification in host cells, from which recombinant plasmids were extracted and linearized by selected restriction endonucleases. PacBio sequencing was performed to obtain the full-length sequences. As the identities, partial sequences from Sanger sequencing were aligned to the full-length sequences from PacBio sequencing, which led to the identification of seven unique full-length sequences. The unique sequences were further aligned to the full genome sequence of the source strain. Functional screening showed that the identified positive clones were all able to improve Cd resistance of the host cells. The functional genomic procedure developed here couples the Sanger and PacBio sequencing methods and overcomes the difficulties in PCR approaches for high GC DNA. The procedure can be a promising option for the high-throughput sequencing of functional genomic libraries, and realize a cost-effective and time-efficient identification of the positive clones, particularly for high GC genetic materials.

scholarly journals Resolved Stellar Populations of the interacting galaxies of the M81 group

2016 ◽  
Vol 11 (S321) ◽  
pp. 22-24
Author(s):  
Sakurako Okamoto ◽  
Nobuo Arimoto ◽  
Annette M.N. Ferguson ◽  
Edouard J. Bernard ◽  
Mike J. Irwin ◽  
...  
Keyword(s):  
Main Sequence ◽  
Field Survey ◽  
State Of The Art ◽  
Young Stars ◽  
Interacting Galaxies ◽  
Wide Field ◽  
Red Giant ◽  
Tidal Streams ◽  
Stellar Associations ◽  
First Time

AbstractWe present the results from the state-of-the-art wide-field survey of the M81 galaxy group that we are conducting with Hyper Suprime-Cam on Subaru Telescope. Our photometry reaches about 2 mag below the tip of the red giant branch (RGB) and reveals the spatial distribution of both old and young stars over an area of 5°2around the M81. The young main-sequence (MS) stars closely follow the HI distribution and can be found in a stellar stream between M81 and NGC 3077 and in numerous outlying stellar associations. Our survey also reveals for the first time the very extended (>2 × R25) halos of RGB stars around M81, M82, and NGC 3077, as well as faint tidal streams that link these systems. The gravitational interactions between M81, M82 and NGC 3077 galaxies induced star formation in tidally stripped gas, and also significantly perturbed the older stellar components leading to disturbed halo morphologies.

scholarly journals Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1556
Author(s):  
Monika J. Hjortaas ◽  
Elena Fringuelli ◽  
Adérito L. Monjane ◽  
Aase B. Mikalsen ◽  
Christine M. Jonassen ◽  
...  
Keyword(s):  
Full Length ◽  
Genomic Diversity ◽  
Last Common Ancestor ◽  
Source Of Infection ◽  
New Variant ◽  
Genotype 2 ◽  
Boat Traffic ◽  
Horizontal Spread ◽  
Full Length Genome

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

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