Next-generation sequencing reveals endosymbiont variability in cassava whitefly,Bemisia tabaci, across the agro-ecological zones of Kerala, India

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 571-584 ◽  
Author(s):  
E.R. Harish ◽  
ManiChellappan ◽  
T. MakeshKumar ◽  
Deepu Mathew ◽  
M.T. Ranjith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bemisia Tabaci ◽  
Bacterial Communities ◽  
Insect Pests ◽  
Virus Transmission ◽  
Silverleaf Whitefly ◽  
Next Generation ◽  
Dominant Group ◽  
Bacterial Phyla ◽  
Generation Sequencing

Silverleaf whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), is one of the most notorious invasive insect pests, infesting more than 900 species of plants and spreading more than 200 viral diseases. This polyphagous agricultural pest harbours diverse bacterial communities in its gut, which perform multiple functions in whiteflies, including nutrient provisioning, amino acid biosynthesis, and virus transmission. The present exploratory study compares the bacterial communities associated with silverleaf whitefly infesting cassava, also known as cassava whitefly, collected from two different zones (zone P: plains; zone H: high ranges), from Kerala, India, using next-generation sequencing of 16S rDNA. The data sets for these two regions consisted of 1 321 906 and 690 661 high-quality paired-end sequences with mean length of 150 bp. Highly diverse bacterial communities were present in the sample, containing approximately 3513 operational taxonomic units (OTUs). Sequence analysis showed a marked difference in the relative abundance of bacteria in the populations. A total of 16 bacterial phyla, 27 classes, 56 orders, 91 families, 236 genera, and 409 species were identified from the P population, against 16, 31, 60, 88, 225, and 355, respectively, in the H population. Arsenophonus sp. (Enterobacteriaceae), which is important for virus transmission by whiteflies, was relatively abundant in the P population, whereas in the H population Bacillus sp. was the most dominant group. The association of whitefly biotypes and secondary symbionts suggests a possible contribution of these bacteria to host characteristics such as virus transmission, host range, insecticide resistance, and speciation.

scholarly journals Leafhopper Viral Pathogens: Ultrastructure of salivary gland infection of Taastrup-like virus inPsammotettix alienusDahlbom; and a novel Rhabdovirus inHomalodisca vitripennis(Germar) Hemiptera: Cicadellidae

2018 ◽  
Author(s):  
Thorben Lundsgaard ◽  
Wayne B. Hunter ◽  
Scott Adkins
Keyword(s):  
Next Generation Sequencing ◽  
Plant Pathogens ◽  
Insect Pests ◽  
Economic Losses ◽  
Type I ◽  
Next Generation ◽  
Viral Pathogen ◽  
Thin Sections ◽  
Wide Range ◽  
Generation Sequencing

AbstractViruses that are pathogenic to insect pests can be exploited as biological control agents. Viruses that are pathogenic to beneficial insects and other arthropods, as in honey bees, silk worms, and shrimp, cause millions of dollars of losses to those industries. Current advances in next generation sequencing technologies along with molecular and cellular biology have produced a wealth of information about insect viruses and their potential applications. Leafhoppers cause economic losses as vectors of plant pathogens which significantly reduce the worlds’ food crops. Each year more viruses are discovered primarily through the use of next generation sequencing of the leafhopper hosts. The diversity of viruses from leafhoppers demonstrates a wide range of taxonomic members that includes genomes of DNA or RNA from families like: Reoviridae, Iridoviridae, Dicistroviridae, Iflaviridae, and others yet to be classified. Discussed is a recent viral pathogen isolated from the leafhopperPsammotettix alienus, name Taastrup Virus. Taastrup virus (TV) is a novel virus with a RNA genome, a Filovirus-like morphology, being tentatively placed within theMononegavirales. AdultPsammotettix alienusinfected with TV, showed the highest concentration of virions in salivary glands, consisting of a principal gland (type I-VI-cells) and an accessory gland. Examination of thin sections revealed enveloped particles, about 1300 nm long and 62 nm in diameter, located singly or in paracrystalline arrays in canaliculi of type III- and IV-cells. In gland cells with TV particles in canaliculi, granular masses up to 15 μm in diameter were present in the cytoplasm. These masses are believed to be viroplasms, the sites for viral replication. TV particles were observed at the connection between a canaliculus and the salivary duct system. A TV-like virus with strongly similar morphology was discovered in the ornamental plant,Liriope, near Fort Pierce, Florida, USA. When the virus was inoculated to a leafhopper cell culture, HvWH, made from the glassy-winged sharpshooter,Homalodisca vitripennis(Germar), the cells rapidly degraded with 100% mortality in 48 hours. These two instances are the only reported cases of this newly discovered viral pathogen of leafhoppers.

scholarly journals Characterization of Leishmania Ulcers Microbiota Using Next Generation Sequencing: Leishmania Ulcers Microbiota

2021 ◽  
Vol 01 (1) ◽  
pp. 68-78
Author(s):  
Suheir Ereqat
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Pathogenic Bacteria ◽  
Healing Process ◽  
Leishmania Infection ◽  
Skin Microbiome ◽  
Next Generation ◽  
Subsequent Formation ◽  
Acinetobacter Species ◽  
Generation Sequencing

The human skin microbiome is a major source of bacteria in cutaneous leishmaniasis (CL) ulcers following the fall of the crust and the subsequent formation of a shallow depression in the epidermis and dermis of the skin. As a result, secondary bacterial infections are frequently observed which impair the healing process. Our study aimed at studying the bacterial communities in CL lesions using next-generation sequencing. A total of 298 patients (178 males and 120 females; median age of 17) presenting ulcerated skin lesions suspected with CL were included in this study. CL was confirmed in 153 (51%) cases by ITS1-PCR and/ or microscopy. Based on bacterial 16S rRNA-PCR, 92 samples were positive for the presence of bacteria, while 206 samples were negative and excluded from the microbiome study. A total of 925 Operational Taxonomic Units (OTUs) were identified and assigned to 215 genera. Despite insignificant difference in the microbiome composition between CL and non-CL lesions, the phylum level analysis revealed that Actinobacteria was significantly higher in CL ulcers while Protoeobacteria was significantly higher in non-CL ulcers (X2, P=0.039). The relative abundance of the most commonly encountered skin pathogens i. e E coli, Pseudomonas aeruginosa, Enterobacter, Enterococcus and Acinetobacter species were significantly higher in non-CL ulcers (X2, P<0.05) compared to Staphylococcus aureus and Proteus mirabilis which were higher in CL ulcers (P<0.05). Our data showed that bacterial communities did not cluster according to the Leishmania infection. Nonetheless, bacterial diversity was lower in CL compared to non-CL lesions. Presence of pathogenic bacteria in CL lesions such as S. aureus might exacerbate lesions, hinder diagnosis, and delay healing.

scholarly journals High throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.

2021 ◽  
Author(s):  
Nikhil Shri Sahajpal ◽  
Ashis K Mondal ◽  
Allan Njau ◽  
Zachary Petty ◽  
Jiani Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Performance Metrics ◽  
Limit Of Detection ◽  
Virus Transmission ◽  
Respiratory Viruses ◽  
Clinical Samples ◽  
Current Phase ◽  
Next Generation ◽  
Generation Sequencing

Background: In the current phase of the COVID-19 pandemic, we are facing two serious public health challenges that include deficits in SARS-CoV-2 variant monitoring and neglection of other co-circulation respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak are required to understand the transmission of the virus amongst seemingly unrelated cases and provide critical epidemiological information. To address these challenges, we evaluated a new high-throughput next-generation sequencing (NGS) panel that includes 40 viral pathogens to analyze viral subtypes, mutational variants of SARS-CoV-2, model to understand the spread of the virus in the state of Georgia, USA, and to assess other circulating viruses in the same population. Methods This study evaluated a total of 522 samples that included 483 patient samples and 42 synthetic positive control materials. The performance metrics were calculated for both clinical and reference control samples by comparing detection results with the RT-PCR assay. The limit of detection (LoD) studies were conducted as per the FDA guidelines. Inference and visualization of the phylogeny of the SARS-CoV-2 sequences were performed through the Nextstrain Command-Line Interface (CLI) tool, utilizing the associated augur and auspice toolkits. Result The performance metric was calculated using both the clinical samples and the reference control with a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The LoD was determined to be 10 copies/ml with all 25 replicates detected across two different runs. The clade for pangolin lineage B contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a and, S84L in ORF8 covarying with the D614G spike protein mutation were found to be prevalent in the early pandemic in Georgia, USA. Isolates from the same county formed paraphyletic groups in our analysis, which indicated virus transmission between counties. Conclusion The study demonstrates the clinical utility of the NGS panel to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats, models that provide insights into viral transmission patterns and predict transmission/ resurgence of regional outbreaks and provide critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.

scholarly journals High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2063
Author(s):  
Nikhil S. Sahajpal ◽  
Ashis K. Mondal ◽  
Allan Njau ◽  
Zachary Petty ◽  
Jiani Chen ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Performance Metrics ◽  
Virus Transmission ◽  
Health Utility ◽  
Respiratory Viruses ◽  
Next Generation ◽  
Public Health Challenges ◽  
Generation Sequencing

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.

scholarly journals Investigation of Biofilms Formed on Steelmaking Slags in Marine Environments for Water Depuration

2020 ◽  
Vol 21 (18) ◽  
pp. 6945
Author(s):  
Akiko Ogawa ◽  
Reiji Tanaka ◽  
Nobumitsu Hirai ◽  
Tatsuki Ochiai ◽  
Ruu Ohashi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Steelmaking Slag ◽  
Marine Environments ◽  
Next Generation ◽  
Ise Bay ◽  
Steelmaking Slags ◽  
Sequencing Technique ◽  
Sulfur Oxidizing ◽  
Generation Sequencing

Steelmaking slags are a promising resource as artificial seaweed beds for the reconstitution of marine environments. To grow seaweed well, the formation of biofilms is an essential process in biofouling. This study focused on the formation of initial biofilms on steelmaking slag samples and analyzed the resulting bacterial communities using the next-generation sequencing technique. Three types of steelmaking slag were submerged in an area of Ise Bay in Mie Prefecture, Japan, for 3 and 7 days in the summer and winter seasons to allow the formation of biofilms. The bacterial communities of these biofilms were richer in sulfur-oxidizing bacteria compared to the biofilms formed on polyurethane sponges. It was found that Helicobacteraceae dominantly grew on the biofilms formed on the slag samples. This shows that steelmaking slags have potential to be used as artificial seaweed beds and marine water purifiers.

scholarly journals Identification of Hepatitis C Virus Transmission Using a Next-Generation Sequencing Approach

2012 ◽  
Vol 50 (4) ◽  
pp. 1461-1463 ◽  
Author(s):  
A. Escobar-Gutierrez ◽  
M. Vazquez-Pichardo ◽  
M. Cruz-Rivera ◽  
P. Rivera-Osorio ◽  
J. C. Carpio-Pedroza ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Next Generation Sequencing ◽  
Virus Transmission ◽  
Next Generation ◽  
Generation Sequencing ◽  
Hepatitis C Virus Transmission
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