Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Kiselev, Daniel; Matsvay, Alina D.; Абрамов, И. С.; Dedkov, Vladimir G.; Шипулин, Г А; Khafizov, K.

doi:10.3390/v12020211

Cited by 50 publications

(36 citation statements)

References 219 publications

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“…Despite the deluge of viral genomes in the public databases, the SSR incidences/abundances and their relevance in viral genomes have been given a little attention including coronaviruses in particular. Elucidating the SSR landscape in viral members of Coronaviridae and their prospect relevance in evolution and pathogenesis, therefore, became crucial in the current scenario of the COVID-19 outbreak [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Deciphering the SSR incidences across viral members of Coronaviridae family

Satyam¹,

Jha

Kar

et al. 2020

Chemico-Biological Interactions

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Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae members. We successfully identified 919 SSRs with length≥12 bp across 55 reference genomes majority of which (838 S SRs) were found abundant in genic regions. The in-silico analysis further identified the preferential abundance of hexameric SSRs than any other size-based motif class. Our analysis shows that the genome size and GC content of the genome had a weak influence on SSR frequency and density. However, we find a positive correlation of SSRs GC content with genomic GC content. We also report relatively low abundances of all theoretically possible 501 repeat motif classes in all the genomes of Coronaviridae . The majority of SSRs were AT-rich. Overall, we see an underrepresentation of SSRs across the genomes of Coronaviridae . Besides, our integrative study highlights the presence of SSRs in ORF1ab (nsp3, nsp4, nsp5A_3CLpro and nsp5B_3CLpro, nsp6, nsp10, nsp12, nsp13, & nsp15 domains), S, ORF3a, ORF7a, N & 3′ UTR regions of SARS-CoV-2 and harbours multiple mutations (3′UTR and ORF1ab SSRs serving as major mutational hotspots). This indicates the genic SSRs are under selection pressure against mutations that might alter the reading frame and at the same time responsible for rapid protein evolution. Our preliminary results indicate the significance of the limited repertoire of SSRs in the genomes of Coronaviridae.

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Section: Introductionmentioning

confidence: 99%

Deciphering the SSR incidences across viral members of Coronaviridae family

Satyam¹,

Jha

Kar

et al. 2020

Chemico-Biological Interactions

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“…The DNA passing through the nanopore changes the current depending on the shape, size and length of the DNA sequence. Nanopore sequencing has several advantages such as the relatively low cost compared to other HTS technologies, high mobility due to the sequencer small size and rapid sample processing, without the need for reverse transcription for RNA viruses (Kiselev et al, 2020). This technology has been recently used to detect some plant viruses, such as plum pox virus (PPV) and tomato yellow leaf curl virus (TYLCV), and discover new plant viruses (Bronzato Badial et al, 2018;Chalupowicz et al, 2019;Naito et al, 2019).…”

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confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

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Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.

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“…These countries are usually well-represented in the field of patent filing due to their advanced technological and scientific sectors and, in this area, their strong records of innovation in the production of disease diagnosis methods. Moreover, a large number of healthcare and biotechnology companies (including startups) are based in these countries which are world leaders in the sector of diagnostics and molecular biology (17,18).…”

Section: Patent Search and Screeningmentioning

confidence: 99%

Trends in MERS-CoV, SARS-CoV, and SARS-CoV-2 (COVID-19) Diagnosis Strategies: A Patent Review

Nascimento

Santos

Oliveira

et al. 2020

Front. Public Health

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The emergence of a new coronavirus (SARS-CoV-2) outbreak represents a challenge for the diagnostic laboratories responsible for developing test kits to identify those infected with SARS-CoV-2. Methods with rapid and accurate detection are essential to control the sources of infection, to prevent the spread of the disease and to assist decision-making by public health managers. Currently, there is a wide variety of tests available with different detection methodologies, levels of specificity and sensitivity, detection time, and with an extensive range of prices. This review therefore aimed to conduct a patent search in relation to tests for the detection of SARS-CoV, MERS-CoV, and SARS-CoV-2. The greatest number of patents identified in the search were registered between 2003 and 2011, being mainly deposited by China, the Republic of Korea, and the United States. Most of the patents used the existing RT-PCR, ELISA, and isothermal amplification methods to develop simple, sensitive, precise, easy to use, low-cost tests that reduced false-negative or false-positive results. The findings of this patent search show that an increasing number of materials and diagnostic tests for the coronavirus are being produced to identify infected individuals and combat the growth of the current pandemic; however, there is still a question in relation to the reliability of the results of these tests.

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Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Cited by 50 publications

References 219 publications

Deciphering the SSR incidences across viral members of Coronaviridae family

Deciphering the SSR incidences across viral members of Coronaviridae family

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

Trends in MERS-CoV, SARS-CoV, and SARS-CoV-2 (COVID-19) Diagnosis Strategies: A Patent Review

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