2017
DOI: 10.1128/jcm.02121-16
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High-Throughput Next-Generation Sequencing of Polioviruses

Abstract: The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found… Show more

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Cited by 63 publications
(68 citation statements)
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“…Viral RNA extraction was performed using a QIAmp Viral RNA minikit extraction kit (Qiagen) with nuclease and DNase treatment as described previously (68). After random PCR amplification, cDNA libraries were generated using an Illumina Nextera XT DNA Library Prep kit, and sequencing was performed on an Illumina MiSeq platform (69,70).…”
Section: Methodsmentioning
confidence: 99%
“…Viral RNA extraction was performed using a QIAmp Viral RNA minikit extraction kit (Qiagen) with nuclease and DNase treatment as described previously (68). After random PCR amplification, cDNA libraries were generated using an Illumina Nextera XT DNA Library Prep kit, and sequencing was performed on an Illumina MiSeq platform (69,70).…”
Section: Methodsmentioning
confidence: 99%
“…These works aimed to amplify viral RNA of arboviruses that can cause disease in humans, and also viruses capable of causing disease in fishes and plants (Hall-Mendelin et al, 2010;Price et al, 2014;Flies et al, 2015;Yang et al, 2015;Navaneeth Krishnan et al, 2016;Hall-Mendelin et al, 2017;Melanson et al, 2017;Chikh-Ali et al, 2016). Viral specimens were derived from cell culture or from a commercial inactivated vaccine in 10.6% of the reports (Muthukrishnan et al, 2008;Li et al, 2012;Bankamp et al, 2013;Sakai et al, 2015;Montmayeur et al, 2017). Finally, two reports isolated virus using human samples: stool and blood.…”
Section: Resultsmentioning
confidence: 99%
“…The punches were directly soaked in the lysis and extraction solutions of different commercial kits, TRIzol reagent® or Guanidinium thiocyanate-phenol-chloroform method ( Table 1). Most of the studies used methods for total RNA extraction and only one study used a commercial kit for viral RNA isolation (Montmayeur et al, 2017). In this particular case, the genome of polioviruses, (Enterovirus C, genus Enterovirus, family Picornaviridae), a virus with a (+) ssRNA non-segmented genome of 6.7-10.1 kb with a poly(A) tail, was isolated from FTA cards®.…”
Section: Resultsmentioning
confidence: 99%
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