The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

Advances in Virology
Andrey A AygininKamil Khafizov

Abstract

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment...Continue Reading

References

Jul 1, 1996·Journal of Clinical Microbiology·D R VanDevanterT M Rose
Jan 16, 1998·The American Journal of Tropical Medicine and Hygiene·M PfefferO R Kaaden
Oct 19, 2004·Critical Reviews in Clinical Laboratory Sciences·Stephan Günther, Oliver Lenz
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Oct 19, 2011·Nucleic Acids Research·Brett E PickettRichard H Scheuermann
Jan 21, 2012·Emerging Infectious Diseases·Sabrina WeissDetlev H Kruger
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Mar 16, 2013·Current Opinion in Virology·John S Mackenzie, Martyn Jeggo
May 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Bryony A JonesDirk Udo Pfeiffer
Aug 31, 2013·The Journal of Infectious Diseases·Chengmin WangHongxuan He
Sep 5, 2013·MBio·Simon J AnthonyW Ian Lipkin
Apr 9, 2015·Pharmaceutical Biology·V A ParvathyB Sasikumar
Mar 22, 2016·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·V G DedkovG A Shipulin
Jan 20, 2017·Nucleic Acids Research·Michael Y GalperinDaniel J Rigden
Feb 9, 2017·Archives of Pathology & Laboratory Medicine·Robert SchlabergUNKNOWN Microbiology Resource Committee of the College of American Pathologists

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Citations

Feb 23, 2020·Viruses·Daniel KiselevKamil Khafizov
Dec 4, 2021·Journal of Animal Science and Biotechnology·Christiana Eleojo AruwaSaheed Sabiu

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Methods Mentioned

BETA
PCR
PCRs
electrophoresis
Assay
amplicon sequencing
RNA-seq

Software Mentioned

BWA
PRINSEQ
HIT
CD
BLAST
lite
Primer3
ClustalW

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