A comparative evaluation of the sensitivity of two automated and two manual nucleic acid extraction methods for the detection of norovirus by RT-PCR

Witlox, Kristie J.; Nguyen, Taylor; Bruggink, Leesa D.; Catton, Michael; Marshall, John A.

doi:10.1016/j.jviromet.2008.02.010

Cited by 31 publications

(19 citation statements)

References 3 publications

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“…Faecal specimens were prepared as a 20% (vol/vol) suspension in Hanks' complete balanced salt solution, and clarified by centrifugation [18]. RNA extraction was then carried out using the Corbett (now Qiagen GmbH, Hilden, Germany) automated nucleic acid extraction procedure [19]. …”

Section: Figmentioning

confidence: 99%

The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014

Bruggink

Moselen²,

Marshall³

2016

Intervirology

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The comparative molecular epidemiology of the related GII.P7_GII.6 and GII.P7_GII.7 noroviruses has not been examined in detail. ORF 1, ORF 2 and ORF 1/ORF 2 RT-PCR as well as sequencing and phylogeny analysis were carried out on faecal specimens from 873 gastroenteritis outbreaks in Victoria, Australia (2012-2014). There were 575 (66%) detected as positive for norovirus by means of ORF 1 RT-PCR and/or ORF 2 RT-PCR. Of these, 24 (4.2%) were GII.6 (ORF 2) outbreaks, 7 (1.2%) were GII.7 (ORF 2) outbreaks, and 1 outbreak (0.2%) involved both GII.6 (ORF 2) and GII.7 (ORF 2) noroviruses. The median age of patients identified with GII.6 (ORF 2) (84 years) was significantly different from that of patients identified with GII.7 (ORF 2) (39 years). ORF 2 GII.6 and ORF 2 GII.7 sequences were always associated with a GII.P7 ORF 1 sequence, and GII.P7 sequences fell into two clusters, with one corresponding to the GII.6 ORF 2 genotype and the other to the GII.7 ORF 2 genotype, thereby indicating that the ORF 1 has been evolving separately for the two viruses. Thus, two closely related noroviruses can have a markedly different incidence and epidemiology.

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Section: Figmentioning

confidence: 99%

The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014

Bruggink

Moselen²,

Marshall³

2016

Intervirology

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“…RNA extraction, prior to NoV ORF 1 reverse transcription-PCR (RT-PCR), was then carried out using either the manual QIAamp viral RNA kit (23,24) or the Corbett automated nucleic acid extraction procedure (23).…”

Section: Outbreakmentioning

confidence: 99%

Molecular Changes Associated with Altered Patterns of Norovirus Outbreak Epidemics in Victoria, Australia, in 2006 to 2007

Bruggink

Marshall

2010

J Clin Microbiol

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Noroviruses (NoVs) are now considered the most common cause of outbreaks of nonbacterial gastroenteritis, but the factors which control the incidence of NoVs are poorly understood. In 2006, the pattern of NoV outbreak epidemics in Victoria, Australia, changed compared to the pattern for 2002 to 2005 and 2007. This study examined molecular correlates of the changed NoV periodicity. For the period of 2002 to 2007, 8,507 fecal specimens from 1,495 gastroenteritis outbreaks were tested for NoV by reverse transcription-PCR, and 1,018 NoV outbreaks were identified. Nucleotide sequence analysis was used to define genotypes and GII.4 variants. For 2002 to 2007, GII.4 was the predominant genotype. For the period of 2002 to 2005 and 2007, a single NoV outbreak epidemic occurred in warmer months of each year, but in 2006 two epidemics occurred in 1 year, one in colder months and one in warmer months of the year. For 2002 to 2007, four major GII.4 variants, “2002 Oxford/Farmington Hills,” “2004 Hunter,” “2006a,” and “2006b,” were identified. Each NoV outbreak epidemic was linked principally to one of these four variants, and there was a time link, a delay of 2 to 6 months, between the first detection of a GII.4 variant and the first outbreak epidemic in which it was the principal variant. The unusual 2006 pattern of outbreak epidemics can then be correlated with the appearance of two GII.4 variants within a short space of time, resulting in two outbreak epidemics in a short space of time, i.e., in the 1 year. This study provides a potentially greater ability to predict the characteristics of NoV epidemics.

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“…In general, these investigations reveal a slight advantage for manually extracted DNA regarding technical issues such as yield and purity of DNA even when identical chemistries were used. 2,12,13 The results 11 ( Fig. 4) indicated that automated extraction method was comparable in sensitivity with the manual Chelex method.…”

Section: Dna Extraction and Purificationmentioning

confidence: 88%

Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples

Stangegaard

Frøslev

Frank-Hansen

et al. 2011

JALA: Journal of the Association for Laboratory Automation

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W e have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, M€ annedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpF[STR Identifiler, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, WI). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5 h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput. ( JALA 2011;16:134-40)

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A comparative evaluation of the sensitivity of two automated and two manual nucleic acid extraction methods for the detection of norovirus by RT-PCR

Cited by 31 publications

References 3 publications

The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014

The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014

Molecular Changes Associated with Altered Patterns of Norovirus Outbreak Epidemics in Victoria, Australia, in 2006 to 2007

Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples

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