Diversity of single-stranded DNA containing viruses in shrimp

Dhar, Arun K.; Cruz‐Flores, Roberto; Aranguren, Luis Fernando; Siewiora, Halina M.; Jory, D. E.

doi:10.1007/s13337-019-00528-3

Cited by 25 publications

(21 citation statements)

References 66 publications

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“…Considering a high rate of nucleotide substitution (1.39 × 10 -4 substitutions/site/year) 20 of IHNNV, it is possible that the strain that caused massive mortalities of blue shrimp (P. stylirostris) in the early 80's in Mexico and later in the rest of the Americas is different from the strains that have been characterized later. Another interesting fact that supports this hypothesis is that the current strains of IHNNV do not cause mortalities or major histological alterations in P. vannamei and P. stylirostris shrimp and no major epizootics have been attributed to IHHNV in recent years 20,21 . This could be due to accumulation of mutations in the IHHNV genome and/or development of host resistant/tolerance over time.…”

Section: Discussionmentioning

confidence: 63%

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: 63%

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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“…It is presumed that in subsequent year as the population of P. stylirostris developed resistance/tolerance against IHHNV, harvest from wild catch returned to the level prior to IHHNV outbreak. IHHNV is now endemic in this region and has been reported to be highly prevalent in wild population in the Gulf of California and Gulf of Mexico (Dhar et al., 2019; Robles‐Sikisaka et al., 2010). In our study, IHHNV prevalence was found to be very low in both species.…”

Section: Discussionmentioning

confidence: 99%

A cross‐sectional study of shrimp pathogens in wild shrimp,Penaeus vannameiandPenaeus stylirostrisin Tumbes, Peru

et al. 2020

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We report the results of a longitudinal, cross‐sectional study on the prevalence of some of the most important shrimp pathogens in wild shrimp located near Tumbes, the most productive shrimp farming area in Peru. Two enteric pathogens (Baculovirus penaei, BP and Hepatobacter penaei, NHP) and two systemic pathogens (infectious hypodermal and haematopoietic necrosis virus, IHHNV and white spot syndrome virus, WSSV) were detected in wild shrimp Penaeus vannamei and Penaeus stylirostris. Shrimp (n = 9,030) were collected from seven tidal channels of mangrove over 9 months (April through December) during 2012 through 2016. Screening for H. penaei, BP, IHHNV and WSSV were conducted by PCR or qPCR following the OIE‐recommended methods. The prevalence of these pathogens was below 3% during the study period, with the prevalence trend being BP > H. penaei > WSSV > IHHNV. The overall trend in IHHNV, H. penaei and WSSV prevalence was similar in both species, P. stylirostris and P. vannamei (p > .05). It was interesting to note that BP prevalence was significantly higher in P. stylirostris than P. vannamei (p < .001). The presence of the enteric and systemic pathogens in the wild shrimp population partially explains the presence of the diseases in the nearby shrimp farming areas, which confirms the risk of wild shrimp as a potential carrier for shrimp pathogens in Tumbes, Peru.

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“…Infectious hypodermal and hematopoietic necrosis virus (IHHNV; genus, Penstyldensovirus ; subfamily, Densovirinae ; family, Parvoviridae ) is one of the smallest penaeid shrimp viruses ( 3 ). This virus was first reported in the 1980s in Hawaii ( 4 , 5 ).…”

Section: Announcementmentioning

confidence: 99%

“…P enaeus vannamei is the shrimp with the highest commercial value, and therefore it is the most widely cultivated species around the world, including Peru (1,2). Infectious hypodermal and hematopoietic necrosis virus (IHHNV; genus, Penstyldensovirus; subfamily, Densovirinae; family, Parvoviridae) is one of the smallest penaeid shrimp viruses (3). This virus was first reported in the 1980s in Hawaii (4,5).…”

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confidence: 99%

Near-Complete Genome Sequences of 12 Peruvian Strains of Infectious Hypodermal and Hematopoietic Necrosis Virus Infecting the Shrimp Penaeus vannamei

Salcedo-Mejía

Durán-Ramirez

Velazco-Peña

et al. 2021

Microbiol Resour Announc

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Diversity of single-stranded DNA containing viruses in shrimp

Cited by 25 publications

References 66 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

A cross‐sectional study of shrimp pathogens in wild shrimp,Penaeus vannameiandPenaeus stylirostrisin Tumbes, Peru

Near-Complete Genome Sequences of 12 Peruvian Strains of Infectious Hypodermal and Hematopoietic Necrosis Virus Infecting the Shrimp Penaeus vannamei

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