Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

Bodewes, Rogier; Run, Peter R. W. A. van; Schürch, Anita C.; Osterhaus, Albert D. M. E.; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L.

doi:10.1016/j.jviromet.2015.02.002

Cited by 24 publications

(24 citation statements)

References 35 publications

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Section: Discussionmentioning

confidence: 99%

“…Detection and characterization of novel viruses is frequently hampered by the lack of properly stored materials 5 . For the retrospective identification of viruses associated with disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available 5 . Retrieving genomic information from FFPE has always been a challenge but the availability of genome sequencing technologies such as NGS has now made it possible to reconstruct genetic information from archived samples.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, the availability of novel genome sequencing technologies have increased the chance and speed of detection of unknown viruses in samples collected from humans and animals. In particular NGS played an important role in the discovery and characterization of many novel viruses 5,[24][25][26] . Next generation sequencing using DNA isolated from FFPE tissue enabled pathogen detection, identification of endogenous viral elements, genome sequencing, exome and transcriptome sequencing in animals and humans [1][2][3][4][5]7,12,14,16,27,28 .…”

Section: Discussionmentioning

confidence: 99%

“…Although FFPE tissues have been used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is very limited. Recently, Bodewes et al 5 showed that sequence-independent amplification in combination with NGS can be used to detect sequences of known and unknown viruses in herring gull and ferrets, although with relatively low sensitivity. The findings of Bodewes et al 5 indicate that NGS from FFPE is a viable approach to detect known DNA (Adenovirus) and RNA (influenza A/H1N1) viruses, and unknown RNA viruses (novel herring gull rotavirus).…”

Section: Discussionmentioning

confidence: 99%

“…The virus species involved in 1918 pandemics showed large differences to the contemporary human influenza H1N1 strain 15 . Recently, FFPE tissue has been used for the detection and discovery of a novel rotavirus 5 . In another recently published retrospective study, FFPE tissue was used to sequence the RNA genome of ~ 15 kb length of the Newcastle disease virus (NDV) that naturally infects many avian species 16 .…”

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confidence: 99%

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Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson’s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue

Cruz‐Flores

Hùng

Kanrar

et al. 2020

Sci Rep

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Formalin-fixed paraffin-embedded (FFPE) tissues are a priceless resource for diagnostic laboratories worldwide. However, DNA extracted from these tissues is often not optimal for most downstream molecular analysis due to fragmentation and chemical modification. In this study, the complete genome of white spot syndrome virus (WSSV) was reconstructed from ~ 2-year-old archived Davidson's-fixed paraffin-embedded (DFPE) shrimp tissue using Next Generation Sequencing (NGS). A histological analysis was performed on archived DFPE shrimp tissue and a sample showing a high level of WSSV infection was selected for molecular analysis. The viral infection was further confirmed by molecular methods. DNA isolated from DFPE and fresh frozen (FF) tissues were sequenced by NGS. The complete genome reconstruction of WSSV (~ 305 kbp) was achieved from both DFPE and FF tissue. Single nucleotide polymorphisms, insertion and deletions were compared between the genomes. Thirty-eight mutations were identified in the WSSV genomes from the DFPE and FF that differed from the reference genome. This is the first study that has successfully sequenced the complete genome of a virus of over 300 kbp from archival DFPE tissue. These findings demonstrate that DFPE shrimp tissue represents an invaluable resource for prospective and retrospective studies, evolutionary studies and opens avenues for pathogen discovery. Formalin-fixed paraffin-embedded (FFPE) archived tissues in human and animal pathology laboratories are an invaluable resource for clinical research, genetic studies and pathogen discovery 1-3. In human cancer research, the utilization of preserved material from tissue banks has helped circumvent the need to rely upon frozen tissue and has enabled the reanalysis of samples from diverse clinical trials 1,2,4. The most common and suitable way to store tissues over prolonged periods of time is to fix them in formaldehyde and embed them in paraffin. However, the extraction of high quality nucleic acids from fixed tissues that is required for Next Generation Sequencing (NGS) has proven challenging. Formalin is the mostly widely used fixative that allows the preservation of tissues at room temperature and maintains the structure of cells and other components 5,6. However, formalin fixation presents one major drawback as it cross-links macromolecules, including DNA and RNA, which greatly complicates the extraction of intact DNA and RNA from FFPE tissues 5,6. Formalin fixation also causes hydrolysis of phosphodiester bonds, leading to varying degrees of DNA fragmentation 6,7. In addition, the degradation of nucleic acids increases during storage depending on the pH value of the fixative 8. Histopathological evaluation of shrimp tissues requires the fixation of tissue in Davidson´s fixative (alcohol, formalin and glacial acetic acid) 9. This type of fixation is fundamental in histopathology studies involving shrimp tissue since acetic acid enables the softening of the chitinous exoskeleton of shrimp. The major drawback of this fixative is its ac...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson’s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue

Cruz‐Flores

Hùng

Kanrar

et al. 2020

Sci Rep

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Quantification and persistence of COVID‐19 virus in recently deceased individuals before and after embalming

Gitto

Middleton

Reynolds

et al. 2023

Anatomical Sciences Ed

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The COVID‐19 pandemic severely affected the medical education worldwide. The infection risk for medical students and healthcare personnel who work with COVID‐19 positive cadavers or tissues remains unclear. Moreover, COVID‐19 positive cadavers have been rejected by medical schools, adversely impacting the continuum of medical education. Herein, the viral genome abundance in tissues from four COVID‐19 positive donors before and after embalming were compared. Tissue samples were collected from the lungs, liver, spleen, and brain both pre‐ and postembalming. The possible presence of infectious COVID‐19 was determined by inoculating human tissue homogenates onto a monolayer of human A549‐hACE2 cells and observing for cytopathic effects up to 72 h postinoculation. A real‐ time quantitative reverse transcription polymerase chain reaction was performed to quantify COVID‐19 present in culture supernatants. Fully intact viral genome sequence was possible to obtain in samples with higher levels of virus, even several days postmortem. The embalming procedure described above substantially reduces the abundance of viable COVID‐19 genomes in all tissues, sometimes even to undetectable levels. However, in some cases, COVID‐19 RNA can still be detected, and a cytopathic effect can be seen both pre‐ and postembalmed tissues. This study suggests that embalmed COVID‐19 positive cadavers might be used safely with appropriate precautions followed in gross anatomy laboratories and in clinical and scientific research. Deep lung tissue is the best specimen to test for the virus. If the tests on the lung tissues are negative, there is a very low likelihood that other tissues will show positive results.

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Rotavirus F and G circulating in chickens in Southeastern Brazil

Pinheiro

Dias

Cunha

et al. 2022

Trop Anim Health Prod

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Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

Cited by 24 publications

References 35 publications

Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson’s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue

Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson’s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue

Quantification and persistence of COVID‐19 virus in recently deceased individuals before and after embalming

Rotavirus F and G circulating in chickens in Southeastern Brazil

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