AutoVEM2: a flexible automated tool to analyze candidate key mutations and epidemic trends for virus

In our previous work, we developed an automated tool, AutoVEM, for real-time monitoring the candidate key mutations and epidemic trends of SARS-CoV-2. In this research, we further developed AutoVEM into AutoVEM2. AutoVEM2 is composed of three modules, including call module, analysis module, and plot module, which can be used modularly or as a whole for any virus, as long as the corresponding reference genome is provided. Therefore, it is much more flexible than AutoVEM. Here, we analyzed three existing viruses by AutoVEM2, including SARS-CoV-2, HBV and HPV-16, to show the functions, effectiveness and flexibility of AutoVEM2. We found that the N501Y locus was almost completely linked to the other 16 loci in SARS-CoV-2 genomes from the UK and Europe. Among the 17 loci, 5 loci were on the S protein and all of the five mutations cause amino acid changes, which may influence the epidemic traits of SARS-CoV-2. And some candidate key mutations of HBV and HPV-16, including T350G of HPV-16 and C659T of HBV, were detected. In brief, we developed a flexible automated tool to analyze candidate key mutations and epidemic trends for any virus, which would become a standard process for virus analysis based on genome sequences in the future.

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Unique and Universal Proteins in Human Genome

International Journal of Online and Biomedical Engineering (iJOE) ◽

10.3991/ijoe.v16i11.16059 ◽

2020 ◽

Vol 16 (11) ◽

pp. 45

Author(s):

Essam Al-Daoud ◽

Ghadeer Albesani

Keyword(s):

Comparative Analysis ◽

Amino Acid ◽

Human Genome ◽

Reference Genome ◽

Amino Acid Sequences ◽

The Other ◽

Entire Genome ◽

Whole Genomes ◽

The Common ◽

Similar Amino Acid

<span>One of the major troubles with a comparative analysis between human and other species is that only similar amino acid sequences are selected for analysis. To find the connection among the species and find out the unique, the common and the universal proteins, the entire genome of 40 species are compared with the human genome which is utilized as reference genome. More than 11 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 330 unique proteins in human genome and have insignificant hits in all tested genomes, the number of universal proteins in human genome and conserved in all tested species is 82, and there are 180 proteins common in vertebrates genomes, but have insignificant hits in the other tested species. In contrary to the previous studies which use selected set of the genes and do not consider the whole genomes, this study proves that the similarity between human and chimpanzee is only 94.8.</span>

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Papaya Ringspot Virus Isolates From Papaya in Bangladesh: Detection, Characterization, and Distribution

Plant Disease ◽

10.1094/pdis-12-18-2186-re ◽

2019 ◽

Vol 103 (11) ◽

pp. 2920-2924 ◽

Cited By ~ 2

Author(s):

Islam Hamim ◽

Maher Al Rwahnih ◽

Wayne B. Borth ◽

Jon Y. Suzuki ◽

Michael J. Melzer ◽

...

Keyword(s):

Amino Acid ◽

Full Length ◽

Ringspot Virus ◽

The Other ◽

Papaya Ringspot Virus ◽

Virus Infections ◽

Genome Sequences ◽

Sequence Comparisons ◽

Reverse Transcription Pcr ◽

Recombinant Event

Papaya ringspot virus (PRSV) is the major constraint to papaya (Carica papaya) production in Bangladesh. Disease symptoms occurred in 90 to 100% of the plants surveyed. Full-length genomes of PRSV strains from severely infected papaya plants were determined using the Illumina NextSeq 500 platform, followed by Sanger DNA sequencing of viral genomes obtained by reverse-transcription PCR(RT-PCR). The genome sequences of two distinct PRSV strains, PRSV BD-1 (10,300 bp) and PRSV BD-2 (10,325 bp) were 74 and 83% identical to each other, respectively, at the nucleotide and amino acid levels. PRSV BD-1 and PRSV BD-2 were 74 to 75% and 79 to 88% identical, respectively, to other full-length PRSV sequences at the nucleotide level. Based on phylogenetic analysis, PRSV BD-2 was most closely related to PRSV-Meghalaya (MF356497) from papaya in India. PRSV BD-1 formed a branch distinct from the other PRSV sequences based on nucleotide and amino acid sequence comparisons. Comparisons of the genome sequences of these two strains with other sequenced PRSV genomes indicated two putative recombination events in PRSV BD-2. One recombinant event contained a 2,766-nucleotide fragment highly identical to PRSV-Meghalaya (MF356497). The other recombinant event contained a 5,105-nucleotide fragment highly identical to PRSV-China (KY933061). The occurrence rates of PRSV BD-1 and PRSV BD-2 in the sampled areas of Bangladesh were approximately 19 and 69%, respectively. Plants infected with both strains (11%) exhibited more severe symptoms than plants infected with either strain alone. The full-length genome sequences of these new PRSV strains and their distribution provide important information regarding the dynamics of papaya ringspot virus infections in papaya in Bangladesh.

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Establishment of specifcations of the multiplex real-time PCR kit (NIHE-RealtimePCR hrHPV) for the detection of high-risk HPV genotypes

Tạp chí Y học Dự phòng ◽

10.51403/0868-2836/2021/333 ◽

2021 ◽

Vol 31 (4) ◽

pp. 28-36

Author(s):

Chu Thi Ngoc Mai ◽

Nguyen Van Chien ◽

Luu Thi Dung ◽

Tran Thi Nguyet Lan ◽

Le Thi Khanh Ly ◽

...

Keyword(s):

High Risk ◽

Real Time ◽

Real Time Pcr ◽

The Other ◽

World Health ◽

Real Time Systems ◽

Hpv 16 ◽

Hpv Genotypes ◽

Time Systems ◽

Hpv 18

High-risk human papillomavirus (HPV) genotypes are the leading causes of anogenital cancer, including cervical cancer. Screening these genotypes will potentially alleviate the disease burden that HPV causes. Therefore, NIHERealtime PCR hrHPV was developed based on the principle of multiplex real-time PCR. The objective of this study is to establish the specifcations of this assay in detecting and identifying 14 high-risk genotypes of HPV. The specifcations of this assay including cross-reactivity, sensitivity and specifcity, the limit of detection and stability, were evaluated with clinical samples, HPV positive control code 06/202 and 06/206 (National Institute for Biological Standards and Control) and in-house plasmids. Four different real-time systems and two commercial assays were applied for comparison. No cross detection of bacteria and viruses related to other genital-anal was observed. The sensitivity and the specifcity of this kit both reached 100% for HPV-18, 92.3% and 100% for HPV-16, and ranged from 90.0% - 100% for the other 12 high-risk genotypes (n = 92) with the detection limit of 5 copies/µl for HPV-16 and HPV-18, and 10 copies/µl for the other 12 high-risk genotypes HPV. This test was stable for up to 12 months under -20oC condition. Equivalent performance was demonstrated on all four real-time systems. Finally, the product was highly comparable with the Sacace kit, Italy (HPV Genotypes 14 Real-™ Quant, V67-100FRT), evaluated by the World Health Organization. The NIHE kit has the potential to be used in the early detection of HPV infection to improve control, prevention and treatment of HPV-related anogenital diseases.

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1618: Real-Time Monitoring of Nitric Oxide and Blood Flow During Ischemia-Reperfusion in the Rat Testis

The Journal of Urology ◽

10.1016/s0022-5347(18)33810-2 ◽

2006 ◽

Vol 175 (4S) ◽

pp. 521-521

Author(s):

Motoaki Saito ◽

Tomoharu Kono ◽

Yukako Kinoshita ◽

Itaru Satoh ◽

Keisuke Satoh

Keyword(s):

Nitric Oxide ◽

Blood Flow ◽

Real Time ◽

Ischemia Reperfusion ◽

Real Time Monitoring ◽

Rat Testis

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GaN heteroepitaxy by remote plasma MOCVD : Real time monitoring by laser reflectance interferometry

Journal de Physique IV (Proceedings) ◽

10.1051/jp4:20013148 ◽

2001 ◽

Vol 11 (PR3) ◽

pp. Pr3-1175-Pr3-1182 ◽

Cited By ~ 4

Author(s):

M. Losurdo ◽

A. Grimaldi ◽

M. Giangregorio ◽

P. Capezzuto ◽

G. Bruno

Keyword(s):

Real Time ◽

Real Time Monitoring ◽

Remote Plasma ◽

Laser Reflectance

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Non-invasive real-time monitoring of the Collateral Network oxygenation prior to, during and after open, endovascular and hybrid repair of descending and thoracoabdominal aortic aneurysms

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0031-1297712 ◽

2012 ◽

Vol 60 (S 01) ◽

Author(s):

CD Etz ◽

S Gudehus ◽

MA Borger ◽

J Ender ◽

M Luehr ◽

...

Keyword(s):

Real Time ◽

Aortic Aneurysms ◽

Real Time Monitoring ◽

Non Invasive ◽

Hybrid Repair ◽

Collateral Network

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From the “Judicialization of Politics” to the “Politicization of Justice” in the UK and Switzerland

BORDER CROSSING ◽

10.33182/bc.v6i2.487 ◽

2016 ◽

Vol 6 (2) ◽

pp. 118-135

Author(s):

Lucia Della Torre

Keyword(s):

General Rule ◽

The State ◽

The Other ◽

Specific Field ◽

Widespread Phenomenon ◽

Judicialization Of Politics ◽

The Uk ◽

Migration Law

Not very long ago, scholars saw it fit to name a new and quite widespread phenomenon they had observed developing over the years as the “judicialization” of politics, meaning by it the expanding control of the judiciary at the expenses of the other powers of the State. Things seem yet to have begun to change, especially in Migration Law. Generally quite a marginal branch of the State's corpus iuris, this latter has already lent itself to different forms of experimentations which then, spilling over into other legislative disciplines, end up by becoming the new general rule. The new interaction between the judiciary and the executive in this specific field as it is unfolding in such countries as the UK and Switzerland may prove to be yet another example of these dynamics.

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