VirusDIP: Virus Data Integration Platform

Wang, Lina; Chen, Fengzhen; Guo, Xueqin; You, Lijin; Yang, Xiaoxia; Yang, Fan; Yang, Tao; Gao, Fei; Hua, Cong; Ding, Yuantong; Cai, Jia; Huang, Wei E.; Xu, Zhicheng; Wan, Bo; Tong, Jiawei; Peng, Chunhua; Yang, Yawen; Zhang, Lei; Liu, Ke; Zhou, Feiyu; Zhang, Minwen; Tan, Cong; Zeng, Wenjun; Wang, Bo; Wei, Xiaofeng

doi:10.1101/2020.06.08.139451

Cited by 7 publications

(4 citation statements)

References 18 publications

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“…The Virus Data Integration Platform (VirusDIP [ 50 ], https://db.cngb.org/virus/ncov ) is a system developed at CNGBdb to help researchers find, retrieve and analyze viruses quickly. It declares itself as a general resource for all kinds of viruses; however, to date includes only coronaviruses sequences.…”

Section: Sars-cov2 Search Systemsmentioning

confidence: 99%

A review on viral data sources and search systems for perspective mitigation of COVID-19

Bernasconi

Canakoglu

Masseroli

et al. 2020

Briefings in Bioinformatics

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With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the effects of the pandemic. In this context, we review the data integration efforts required for accessing and searching genome sequences and metadata of SARS-CoV2, the virus responsible for the COVID-19 disease, which have been deposited into the most important repositories of viral sequences. Organizations that were already present in the virus domain are now dedicating special interest to the emergence of COVID-19 pandemics, by emphasizing specific SARS-CoV2 data and services. At the same time, novel organizations and resources were born in this critical period to serve specifically the purposes of COVID-19 mitigation while setting the research ground for contrasting possible future pandemics. Accessibility and integration of viral sequence data, possibly in conjunction with the human host genotype and clinical data, are paramount to better understand the COVID-19 disease and mitigate its effects. Few examples of host-pathogen integrated datasets exist so far, but we expect them to grow together with the knowledge of COVID-19 disease; once such datasets will be available, useful integrative surveillance mechanisms can be put in place by observing how common variants distribute in time and space, relating them to the phenotypic impact evidenced in the literature.

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Section: Sars-cov2 Search Systemsmentioning

confidence: 99%

A review on viral data sources and search systems for perspective mitigation of COVID-19

Bernasconi

Canakoglu

Masseroli

et al. 2020

Briefings in Bioinformatics

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“…Although the origin sources provide well-organized data portals (NCBI Virus ( 10 ), the COVID-19 Data Portal https://www.covid19dataportal.org/ and GISAID EpiCoV TM data browser), these do not allow for an integrated search over multiple sources, nor they provide fast selection using sequence variants. A number of other integrated interfaces are being developed in alternative research contexts: UCSC SARS-CoV-2 Genome Browser ( 11 ); 2019nCoVR ( 12 ) at the Chinese National Genomics Data Center; VirusDIP ( 13 ) at the China National GeneBank; CovSeq ( 14 ); and CARD ( 15 ). Compared to other resources, ViruSurf has much stronger query and search capabilities; we use the power of conceptual modeling to structure metadata and to organize data integration and curation; we support search queries allowing to combine filters on metadata, nucleotide and amino acid mutations in an effective and scalable way, treating all of them as first-class citizens.…”

Section: Introductionmentioning

confidence: 99%

ViruSurf: an integrated database to investigate viral sequences

Canakoglu

Pinoli

Bernasconi

et al. 2020

Nucleic Acids Research

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ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

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“…Traditionally, the predominant approach to combat C. pomonella has been through the use of conventional insecticides (Hu et al, 2020). However, the efficacy of chemical insecticides in controlling this pest is limited due to factors like overlapping generations and the larvae's habit of tunneling into fruit (Huang et al, 2024;Ju et al, 2021). Furthermore, the widespread application of insecticides has led to the development of resistance in C. pomonella (Ju et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Previous research has indicated that male pupae irradiated with X-rays at a dose of 366 Gy resulted in complete sterility in C. pomonella, albeit with a low mating competitiveness index of 0.01 . The observed side effects of X-ray irradiation, such as reduced mating competitiveness, are likely attributed to its negative impact on flight ability (Huang et al, 2024).…”

Section: Introductionmentioning

confidence: 99%

Linalool fumigation improves mating competitiveness of males for population suppression of the global fruit pestCydia pomonella

Huang,

Wang,

Wang

et al. 2024

Preprint

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The implementation of sterile insect technique (SIT) has proven effective in the area-wide suppression of several significant agricultural and sanitary pests by employing traditional cobalt-60 (60Co-γ) as a radiation source. Recently, X-ray has been validated as a feasible alternative to60Co-γ radiation sources. Nonetheless, higher doses of X-ray irradiation lead to insect sterility but diminish mating competitiveness, thereby impacting the effectiveness of SIT applications. Thus, it is crucial to ascertain the optimal irradiation dose and develop strategies to enhance the mating competitiveness of sterile insects to enhance SIT efficacy. In this study, we determined the effect of various X-ray irradiation doses (ranging from 0 to 366 Gy) on the fecundity, fertility, and mating competitiveness ofCydia pomonella, a globally invasive fruit pest. Results demonstrated that the sterility rate of sterile males increased proportionally with irradiation dose up to 200 Gy, beyond which it plateaued. Notably, exposure to 200 Gy of irradiation notably decreased the mating competitiveness of male, as evidenced by a mating competitiveness index of 0.17 in laboratory and 0.096 in the orchard. This decline in mating competitiveness is likely linked to the down-regulation of genes associated with the recognition of sex pheromones, specificallyCpomOR3a,CpomOR3b, andCpomOR5, following X-ray irradiation. Fumigation of the plant volatile, linalool at varying concentrations (70, 83, and 96 μL/m ³) resulted in differential enhancements in male mating competitiveness, with the moderate concentration significantly improving the competitiveness of sterilized males, possibly by restoring their ability to recognize sex pheromones. Implementation of repeated releases of sterilized males on a pilot scale led to a notable reduction in the population ofC. pomonellain the field. These findings indicate that fumigation with plant volatiles has the potential to mitigate male sterility induced by X-ray irradiation, offering a promising approach to enhance the efficacy of SIT applications for the control ofC. pomonella.

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VirusDIP: Virus Data Integration Platform

Cited by 7 publications

References 18 publications

A review on viral data sources and search systems for perspective mitigation of COVID-19

A review on viral data sources and search systems for perspective mitigation of COVID-19

ViruSurf: an integrated database to investigate viral sequences

Linalool fumigation improves mating competitiveness of males for population suppression of the global fruit pestCydia pomonella

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