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Munguía-Ramírez B, Giménez-Lirola L, Zimmerman J. Assessment of Strategies for Preserving Swine Viral RNA Targets in Diagnostic Specimens. Microorganisms 2024; 12:410. [PMID: 38399814 PMCID: PMC10892022 DOI: 10.3390/microorganisms12020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper sample handling at the time the sample is collected on the farm, during transport, and in the laboratory until RNA extraction is performed. Options for proper handling are limited to maintaining the cold chain or using commercial specimen storage matrices. Herein, we reviewed the refereed literature for evidence that commercial specimen storage matrices can play a role in preserving swine viral RNA in clinical specimens. Refereed publications were included if they compared RNA detection in matrix-treated vs. untreated samples. At present, the small number of refereed studies and the inconsistency in reported results preclude the routine use of commercial specimen storage matrices. For example, specimen storage matrices may be useful under specific circumstances, e.g., where it is mandatory to render the virus inactive. In a broader view, statistically sound side-by-side comparisons between specimens, viral RNA targets, and storage conditions are needed to establish if, when, and how commercial specimen storage matrices could be used in diagnostic medicine.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (L.G.-L.); (J.Z.)
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E-2 Glycoprotein Structural Variations Analysed within the CSFV 2.2. Genogroup in a “Closed Grid” Sampling Study from Meghalaya, India. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
CSF is enzootic in most of pig-producing states, particularly in the NorthEastern (NE) region of India. In this study, a total of 249 sera and 190 tissue samples were collected from different parts of Meghalaya. Samples were processed by ELISA and RT-PCR for serological and molecular diagnosis. Representative positive samples from the Khasi Hills region were selected for sequencing and “close grid” phylogenetic relationship using partial genomic regions of 5′UTR and E2. High seroprevalence (74.7%) of CSFV was recorded. Detection of the CSFV genome in serologically positive serum samples and tissue samples was 61.29% and 18.94%, respectively. BLAST and phylogenetic analyses indicate the clustering of all the field samples in subgroup 2.2, with high identity with EF014334 from China. Molecular structural modelling of the E2 partial sequence using representative sequences MG563797 from Meghalaya and EF014334 from China indicate potential changes in the protein motif and its conformation, which may explain the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in NorthEast India. The epidemiological information presented in this study may be helpful for determination of disease incidence in this region, whereas the virus profile may be useful for framing disease control programs.
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Lu X, Ward MP. Spatiotemporal analysis of reported classical swine fever outbreaks in China (2005-2018) and the influence of weather. Transbound Emerg Dis 2022; 69:e3183-e3195. [PMID: 35007396 PMCID: PMC9787383 DOI: 10.1111/tbed.14452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/30/2022]
Abstract
Classical swine fever (CSF) is a viral disease that causes enormous economic losses in the swine industry in endemic countries including China. The aims of the current study were to describe the spatial distribution of annual CSF reports in China from 2005 to 2018, identify spatiotemporal clusters of annual CSF reports during this time period and to investigate the correlations between climate factors (rainfall, wind speed, temperature, vapour pressure and relative humidity) and the occurrence of CSF outbreaks. The strongest (Moran's index > 0.19), significant (p < .05) spatial clustering of reported outbreaks was observed during the first 4 years of the study period. This clustering was apparent in the four southern provinces of Guizhou, Guangxi, Guangdong and Yunnan. Five of the six significant (p ≤ .0001) spatiotemporal clusters occurred during the period 2005-2012. These were widely dispersed, with four clusters persisting for only 1 or 2 years, whereas two clusters (Jiangxi and Yunnan) persisted for 8 and 7 years, respectively. As a result of implementation of a national animal disease control plan and increasing coverage of vaccination, CSF outbreaks in China have generally been controlled and reduced, becoming sporadic in most provinces by 2018. We also confirmed that low relative humidity and high wind speed were significant weather variables associated with the occurrence of CSF. Furthermore, our study has confirmed that CSF is still endemic in some Chinese provinces, and we recommend that the national CSF control protocol be updated and standardized.
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Affiliation(s)
- Xiao Lu
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | - Michael P. Ward
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
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Bai H, Zhao J, Ma C, Wei H, Li X, Fang Q, Yang P, Wang Q, Wang D, Xin L. Impact of RNA degradation on influenza diagnosis in the surveillance system. Diagn Microbiol Infect Dis 2021; 100:115388. [PMID: 34030102 DOI: 10.1016/j.diagmicrobio.2021.115388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/22/2021] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND The continuous evolution of influenza viruses is monitored by the World Health Organization Global Influenza Surveillance and Response System. Sample quality is essential for surveillance quality. METHODS To evaluate the RNA degradation of clinical samples, influenza-like illness samples were collected from four sentinel hospitals, and seasonal influenza was tested by real-time reverse transcription polymerase chain reaction and quantified by digital reverse transcription polymerase chain reaction at different time points. RESULTS RNA degradation was observed in the majority of samples eight days after sample collection. A significant and faster rate of RNA content reduction was observed in low viral load samples (<10 copies/µl) than in high viral load samples (>10 copies/μl), stored at 2 to 8°C for up to eight days. RNase P (RNP) RNA, which is a key indicator to evaluate sample collection quality, was detected. Sample collection quality was uneven in different hospitals. CONCLUSION Low viral load samples increase the risk of false negatives due to RNA degradation to undetectable levels.
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Affiliation(s)
- Hongyan Bai
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China
| | - Jiashen Zhao
- Beijing Center for Disease Prevention and Control, Beijing, People's Republic of China
| | - Chunyan Ma
- Beijing Center for Disease Prevention and Control, Beijing, People's Republic of China
| | - Hejiang Wei
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China
| | - Xiyan Li
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China
| | - Qiongqiong Fang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China
| | - Peng Yang
- Beijing Center for Disease Prevention and Control, Beijing, People's Republic of China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, People's Republic of China
| | - Dayan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China
| | - Li Xin
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing, People's Republic of China.
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Wille M, Yin H, Lundkvist Å, Xu J, Muradrasoli S, Järhult JD. RNAlater ® is a viable storage option for avian influenza sampling in logistically challenging conditions. J Virol Methods 2017; 252:32-36. [PMID: 29129490 DOI: 10.1016/j.jviromet.2017.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 11/28/2022]
Abstract
Surveillance of wild birds is critical in monitoring for highly pathogenic avian influenza A viruses (AIVs). However, a successful surveillance regime requires proper treatment of samples in the field - rapid placement of samples in -80°C and subsequent maintenance of cold-chain. Given the logistical difficulties of this, many avian taxa and/or geographic locations are not sampled, or, when sampled may result in false negatives due to poor sample treatment in the field. Here, we assessed the utility of RNAlater® as a stabilization agent for AIV sampling. We found no difference in real time PCR performance between virus transport media at optimal conditions and RNAlater® at -80°C, -20°C, 4°C or room temperature up to two weeks, at either low or high virus load. Not only was RNAlater® useful in comparison of spiked samples or those from duck experiments, it was employed successfully in a field study of backyard birds in China. We detected AIV in cloacal and oropharyngeal samples from chickens and a sample with a low Cq was successfully subtyped as H9, although sample storage conditions were suboptimal. Thus, despite limitations in downstream characterization such virus isolation and typing, RNAlater® is a viable option for AIV sampling under logistically challenging circumstances.
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Affiliation(s)
- Michelle Wille
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Hong Yin
- Department of Laboratory Medicine, Division of Clinical Microbiology, Dalarna County, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Juan Xu
- Xuanwu Hospital, Capital Medical University, China
| | - Shaman Muradrasoli
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Josef D Järhult
- Section for Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
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Shin HH, Hwang BH, Cha HJ. Multiplex 16S rRNA-derived geno-biochip for detection of 16 bacterial pathogens from contaminated foods. Biotechnol J 2016; 11:1405-1414. [PMID: 27492058 PMCID: PMC5132059 DOI: 10.1002/biot.201600043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/25/2016] [Accepted: 07/25/2016] [Indexed: 11/21/2022]
Abstract
Foodborne diseases caused by various pathogenic bacteria occur worldwide. To prevent foodborne diseases and minimize their impacts, it is important to inspect contaminated foods and specifically detect many types of pathogenic bacteria. Several DNA oligonucleotide biochips based on 16S rRNA have been investigated to detect bacteria; however, a mode of detection that can be used to detect diverse pathogenic strains and to examine the safety of food matrixes is still needed. In the present work, a 16S rRNA gene-derived geno-biochip detection system was developed after screening DNA oligonucleotide specific capture probes, and it was validated for multiple detection of 16 pathogenic strains that frequently occur with a signature pattern. rRNAs were also used as detection targets directly obtained from cell lysates without any purification and amplification steps in the bacterial cells separated from 8 food matrixes by simple pretreatments. Thus, the developed 16S rRNA-derived geno-biochip can be successfully used for the rapid and multiple detection of the 16 pathogenic bacteria frequently isolated from contaminated foods that are important for food safety.
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Affiliation(s)
- Hwa Hui Shin
- Department of Chemical EngineeringPohang University of Science and TechnologyPohangKorea
| | - Byeong Hee Hwang
- Department of Chemical EngineeringPohang University of Science and TechnologyPohangKorea
- Division of BioengineeringIncheon National UniversityIncheonKorea
| | - Hyung Joon Cha
- Department of Chemical EngineeringPohang University of Science and TechnologyPohangKorea
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Zhang XC, Liu S, Hou GY, Zhuang QY, Wang KC, Jiang WM, Wang SC, Li JP, Yu JM, Du X, Huang BX, Chen JM. Comparison of three media for transport and storage of the samples collected for detection of avian influenza virus. J Virol Methods 2015; 222:202-5. [PMID: 26159628 DOI: 10.1016/j.jviromet.2015.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/25/2015] [Accepted: 07/02/2015] [Indexed: 10/23/2022]
Abstract
Detection of avian influenza viruses (AIVs) is important for diagnosis, surveillance and control of avian influenza which is of great economic and public health significance. Proper transport and storage of samples is critical for the detection when the samples cannot be detected immediately. As recommended by some international or national authoritative entities and some publications, phosphate buffered saline (PBS), PBS-glycerol and brain heart infusion broth (BHIB) are frequently used for transport and storage of the samples collected for detection of AIVs worldwide. In this study, we compared these three media for transport and storage of simulated and authentic swab and feces samples collected for detection of AIVs using virus isolation and reverse transcription-PCR. The results suggest that PBS-glycerol is superior to PBS and BHIB as the sample transport and storage media. The results also suggest that the samples collected for detection of AIVs should be detected as soon as possible because the virus concentration of the samples may decline rapidly during storage within days at 4 or -20°C.
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Affiliation(s)
- Xiao-Chun Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Shuo Liu
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Guang-Yu Hou
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Qing-Ye Zhuang
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Kai-Cheng Wang
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Wen-Ming Jiang
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Su-Chun Wang
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Jin-Ping Li
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Jian-Min Yu
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Xiang Du
- China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Bao-Xu Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; China Animal Health & Epidemiology Center, Qingdao 266032, China
| | - Ji-Ming Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex. J Virol Methods 2014; 202:69-72. [PMID: 24657552 PMCID: PMC7113650 DOI: 10.1016/j.jviromet.2014.02.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 02/25/2014] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
Abstract
Sample quality is a critical consideration in nucleic acid-based diagnostic assay performance. Educational efforts are important to ensure that specimen collection occurs in the correct disease timeframe. FTA paper stabilizes nucleic acids for veterinary diagnostic testing.
In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI = 0.89–0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (−27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P ≥ 0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency.
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Reiser V, Smith RC, Xue J, Kurtz MM, Liu R, Legrand C, He X, Yu X, Wong P, Hinchcliffe JS, Tanen MR, Lazar G, Zieba R, Ichetovkin M, Chen Z, O'Neill EA, Tanaka WK, Marton MJ, Liao J, Morris M, Hailman E, Tokiwa GY, Plump AS. High-throughput simultaneous analysis of RNA, protein, and lipid biomarkers in heterogeneous tissue samples. Clin Chem 2011; 57:1545-55. [PMID: 21914789 DOI: 10.1373/clinchem.2010.157743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND With expanding biomarker discovery efforts and increasing costs of drug development, it is critical to maximize the value of mass-limited clinical samples. The main limitation of available methods is the inability to isolate and analyze, from a single sample, molecules requiring incompatible extraction methods. Thus, we developed a novel semiautomated method for tissue processing and tissue milling and division (TMAD). METHODS We used a SilverHawk atherectomy catheter to collect atherosclerotic plaques from patients requiring peripheral atherectomy. Tissue preservation by flash freezing was compared with immersion in RNAlater®, and tissue grinding by traditional mortar and pestle was compared with TMAD. Comparators were protein, RNA, and lipid yield and quality. Reproducibility of analyte yield from aliquots of the same tissue sample processed by TMAD was also measured. RESULTS The quantity and quality of biomarkers extracted from tissue prepared by TMAD was at least as good as that extracted from tissue stored and prepared by traditional means. TMAD enabled parallel analysis of gene expression (quantitative reverse-transcription PCR, microarray), protein composition (ELISA), and lipid content (biochemical assay) from as little as 20 mg of tissue. The mean correlation was r = 0.97 in molecular composition (RNA, protein, or lipid) between aliquots of individual samples generated by TMAD. We also demonstrated that it is feasible to use TMAD in a large-scale clinical study setting. CONCLUSIONS The TMAD methodology described here enables semiautomated, high-throughput sampling of small amounts of heterogeneous tissue specimens by multiple analytical techniques with generally improved quality of recovered biomolecules.
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Affiliation(s)
- Vladimír Reiser
- Merck Sharp & Dohme Corporation, Whitehouse Station, NJ, USA.
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Martin C, Letellier C, Caij B, Gauthier D, Jean N, Shaffii A, Saegerman C. Epidemiology of Pestivirus infection in wild ungulates of the French South Alps. Vet Microbiol 2011; 147:320-8. [DOI: 10.1016/j.vetmic.2010.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/05/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
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Weesendorp E, Willems EM, Loeffen WL. The effect of tissue degradation on detection of infectious virus and viral RNA to diagnose classical swine fever virus. Vet Microbiol 2010; 141:275-81. [DOI: 10.1016/j.vetmic.2009.09.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/04/2009] [Accepted: 09/22/2009] [Indexed: 11/27/2022]
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Development and evaluation of a rapid immunomagnetic bead assay for the detection of classical swine fever virus antigen. Trop Anim Health Prod 2008; 41:913-20. [DOI: 10.1007/s11250-008-9279-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 05/06/2007] [Indexed: 11/25/2022]
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13
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Rader JS, Malone JP, Gross J, Gilmore P, Brooks RA, Nguyen L, Crimmins DL, Feng S, Wright JD, Taylor N, Zighelboim I, Funk MC, Huettner PC, Ladenson JH, Gius D, Townsend RR. A unified sample preparation protocol for proteomic and genomic profiling of cervical swabs to identify biomarkers for cervical cancer screening. Proteomics Clin Appl 2008; 2:1658-69. [PMID: 21136816 DOI: 10.1002/prca.200780146] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Indexed: 01/04/2023]
Abstract
Cervical cancer screening is ideally suited for the development of biomarkers due to the ease of tissue acquisition and the well-established histological transitions. Furthermore, cell and biologic fluid obtained from cervix samples undergo specific molecular changes that can be profiled. However, the ideal manner and techniques for preparing cervical samples remains to be determined. To address this critical issue a patient screening protein and nucleic acid collection protocol was established. RNAlater was used to collect the samples followed by proteomic methods to identify proteins that were differentially expressed in normal cervical epithelial versus cervical cancer cells. Three hundred ninety spots were identified via 2-D DIGE that were expressed at either higher or lower levels (>three-fold) in cervical cancer samples. These proteomic results were compared to genes in a cDNA microarray analysis of microdissected neoplastic cervical specimens to identify overlapping patterns of expression. The most frequent pathways represented by the combined dataset were: cell cycle: G2/M DNA damage checkpoint regulation; aryl hydrocarbon receptor signaling; p53 signaling; cell cycle: G1/S checkpoint regulation; and the ER stress pathway. HNRPA2B1 was identified as a biomarker candidate with increased expression in cancer compared to normal cervix and validated by Western blot.
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Affiliation(s)
- Janet S Rader
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine and Alvin J. Siteman Cancer Center, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine and Alvin J. Siteman Cancer Center, St. Louis, MO, USA.
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14
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McClure C, Saksida S, Karreman G, Constantine J, Robinson J, Traxler G, Hammell L. Evaluation of a reverse transcriptase polymerase chain reaction test and virus isolation on field samples collected for the diagnosis of infectious hematopoietic necrosis virus in cultured Atlantic salmon in British Columbia. JOURNAL OF AQUATIC ANIMAL HEALTH 2008; 20:12-18. [PMID: 18536498 DOI: 10.1577/h06-045.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Infectious hematopoietic necrosis virus (IHNV) has been found to cause disease in cultured salmon of the Pacific Northwest region of North America. Diagnosis of IHNV by virus isolation (VI) can take over 2 weeks. Recently, a rapid reverse transcriptase (RT) polymerase chain reaction (PCR) test on fish tissues has been used for diagnosis. Test performances of the VI and RT PCR assays were compared using samples collected in the field. The effect of different storage conditions (tissue frozen with or without RNAlater [Ambion, Inc., Austin, Texas] versus fresh tissue) on the diagnostic tests was also evaluated. Based on the limited number of samples tested, the operating characteristics of RT PCR were very similar to those of VI; therefore, this method is likely suitable for testing field samples for IHNV. The ability of the tests to identify a positive fish ranged from 74% to 89%. Freezing samples at -80 degrees C before testing did not negatively affect the performance of RT PCR or VI. However, due to reduced test performance, RNAlater frozen storage is not recommended without further investigation.
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Affiliation(s)
- Carol McClure
- Centre for Aquatic Health Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island C1A 7J7, Canada.
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15
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The effect of sample type, temperature and RNAlater on the stability of avian influenza virus RNA. J Virol Methods 2008; 149:190-4. [PMID: 18294703 DOI: 10.1016/j.jviromet.2007.12.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 11/16/2007] [Accepted: 12/20/2007] [Indexed: 12/09/2022]
Abstract
As a result of continuing worldwide outbreaks of highly pathogenic avian influenza (HPAI) caused by the Asian lineage of H5N1, surveillance of targeted avian species in selected regions has been implemented. In these wild bird surveys, the use of real-time reverse transcription (rRT)-PCR has proved to be an invaluable tool as a frontline screening assay for the detection of avian influenza virus (AIV) RNA. However, verification of HPAI diagnosis, particularly in a primary outbreak situation, requires confirmation by a national, community or world reference laboratory. This may necessitate freezing and thawing of samples, sub-sampling and transportation to the reference laboratory. The deleterious effects of such handling on the infectivity of virus and the yield of viral RNA have been observed. The objective of this study was to investigate the effects of freezing and thawing, time, sample type and transportation on the yield of AIV RNA. Additionally, the effect of the RNA stabilisation agent, RNAlater was investigated. It was demonstrated that the quality of AIV RNA in faecal homogenate was markedly reduced by freezing and thawing, but that treatment with RNAlater protected the viral RNA from deterioration. When using RNAlater even low titre AIV samples were protected from the detrimental effects of time and transportation conditions.
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16
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Khounsy S, Gleeson LJ, Van Aken D, Westbury HA, Blacksell SD. Diagnosis of classical swine fever virus in a limited resource setting: the influence of pig breed on methodology and sample selection. Trop Anim Health Prod 2007; 39:21-5. [PMID: 17941484 DOI: 10.1007/s11250-006-4442-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S Khounsy
- Department of Livestock and Fisheries, Ministry of Agriculture and Forestry, Vientiane, Lao People's Democratic Republic
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17
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Kurth A. Possible biohazard risk from infectious tissue and culture cells preserved with RNAlater. Clin Chem 2007; 53:1389-90. [PMID: 17582155 DOI: 10.1373/clinchem.2007.085894] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Greiser-Wilke I, Blome S, Moennig V. Diagnostic methods for detection of Classical swine fever virus—Status quo and new developments. Vaccine 2007; 25:5524-30. [PMID: 17229496 DOI: 10.1016/j.vaccine.2006.11.043] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 10/25/2006] [Indexed: 11/27/2022]
Abstract
Classical swine fever (CSF) is a highly contagious disease causing major losses in pig populations almost worldwide. The disease occurs in many regions of Asia, Central and South America and parts of Europe and Africa. Some countries have eradicated the disease (Australia, USA, Canada, within the EU), yet it keeps recurring sporadically (South Africa, Germany, Netherlands, England). The causative virus is a member of the genus Pestivirus, family Flaviviridae. The first diagnosis of CSF is based on the recognition of clinical signs by the veterinarian in the field and by post mortem findings. Many signs are not exclusively associated with CSF and they may vary with the strain of virus, age and health status of the pigs. Since clinical signs may be confused with other pig diseases, laboratory diagnosis of CSF is indispensable. Both the Office International des Epizooties (OIE) and the European Union, have approved diagnostic manuals establishing sampling methods and diagnostic procedures for the confirmation of the disease. In this review, experiences with current tests will be analyzed and complemented with new developments, with emphasis on the polymerase chain reaction after reverse transcription of the RNA genome (RT-PCR).
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Affiliation(s)
- Irene Greiser-Wilke
- Institute of Virology, EU Reference Laboratory for Classical Swine Fever, Department of Infectious Diseases, University of Veterinary Medicine, Buenteweg 17, 30559 Hannover, Germany.
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Cha SH, Choi EJ, Park JH, Yoon SR, Kwon JH, Yoon KJ, Song JY. Phylogenetic characterization of classical swine fever viruses isolated in Korea between 1988 and 2003. Virus Res 2007; 126:256-61. [PMID: 17328983 DOI: 10.1016/j.virusres.2007.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 01/23/2007] [Accepted: 01/24/2007] [Indexed: 11/25/2022]
Abstract
Twenty-four isolates of classical swine fever (CSF) virus which were obtained from CSF outbreaks during 1988 and 2003 in the Republic of Korea were genetically characterized for partial E2 gene (190 nucleotides) and compared with CSF viruses reported by other countries. Phylogenetic analyses classified Korean field isolates between1988 and 1999 into subgroup 3.2, forming an independent clade distinct from CSF viruses identified in other countries. In contrast, the viruses isolated during 2002-2003 CSF epidemics were classified into a different subgroup (2.1). The 2.1 viruses showed a close genetic relationship (92.1-100% nucleotide similarity) with CSF viruses reported from China and Taiwan in 1998-2001. As no evidence of CSF virus infection was detected in the wild boar (Sus scrofa coreanus) population that inhabits Korea, the results of molecular characterization strongly suggest that CSF epidemic outbreaks in Korean swine populations during 2002-2003 were attributed to the introduction of a new strain or strains, likely from neighboring countries.
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Affiliation(s)
- Sang-Ho Cha
- Virology Division, National Veterinary Research and Quarantine Service, 480, Anyang 6-dong, Anyang, Gyeonggido, Republic of Korea
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Blacksell SD, Khounsy S, Boyle DB, Gleeson LJ, Westbury HA, Mackenzie JS. Genetic typing of classical swine fever viruses from Lao PDR by analysis of the 5' non-coding region. Virus Genes 2005; 31:349-55. [PMID: 16175340 DOI: 10.1007/s11262-005-3253-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 05/11/2005] [Indexed: 12/01/2022]
Abstract
The 5' non-coding region (5'-NCR) of 27 classical swine fever virus (CSFV) isolates from Lao People's Democratic Republic (Lao PDR) during 1997 and 1999 were amplified by RT-PCR. A 150-bp region of the 5'-NCR amplicons was analysed and compared with reference CSFV of European and Asian origin and a phylogenetic dendrogram constructed. Following analysis, all viruses were determined to belong to genogroup 2. Viruses from Lao PDR grouped on a geographical basis with the majority of northern/central isolates falling into subgroup 2.1 and southern/central isolates falling into subgroup 2.2. These results concur with previous studies of CSF viruses from Lao PDR, although this study recognized the first occurrence of subgroup 2.1 in southern Lao PDR.
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Affiliation(s)
- Stuart D Blacksell
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Private Bag 24, 3220, Geelong, Victoria, Australia.
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Flück M, Däpp C, Schmutz S, Wit E, Hoppeler H. Transcriptional profiling of tissue plasticity: role of shifts in gene expression and technical limitations. J Appl Physiol (1985) 2005; 99:397-413. [PMID: 16020435 DOI: 10.1152/japplphysiol.00050.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reprogramming of gene expression has been recognized as a main instructive modality for the adjustments of tissues to various kinds of stress. The recent application of gene expression profiling has provided a powerful tool to elucidate the molecular pathways underlying such tissue remodeling. However, the biological interpretations of expression profiling results critically depend on normalization of transcript signals to mRNA standards before statistical evaluation. A hypothesis is proposed whereby the “fluctuating nature” of gene expression represents an inherent limitation of the test system used to quantify RNA levels. Misinterpretation of gene expression data occurs when RNA quantities are normalized to a subset of mRNAs that are subject to strong regulation. The contention of contradictory biological outcomes using different RNA-normalization schemes is demonstrated in two models of skeletal muscle plasticity with data from custom-designed microarrays and biochemical and ultrastructural evidence for correspondingly altered RNA content and nucleolar activity. The prevalence of these biological constraints is underlined by a literature survey in different models of tissue plasticity with emphasis on the unique malleability of skeletal muscle. Finally, recommendations on the optimal experimental layout are given to control biological and technical variability in microarray and RT-PCR studies. It is proposed to approach normalization of transcript signals by measuring total RNA and DNA content per sample weight and by correcting for concurrently estimated endogenous standards such as major ribosomal RNAs and spiked RNA and DNA species. This allows for later conversion to diverse tissue-relevant references and should improve the physiological interpretations of phenotypic plasticity.
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Affiliation(s)
- Martin Flück
- Dept. of Anatomy, Baltzerstrasse 2, 3000 Bern 9, Switzerland.
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Rouquet P, Froment JM, Bermejo M, Kilbourn A, Karesh W, Reed P, Kumulungui B, Yaba P, Délicat A, Rollin PE, Leroy EM. Wild animal mortality monitoring and human Ebola outbreaks, Gabon and Republic of Congo, 2001-2003. Emerg Infect Dis 2005; 11:283-90. [PMID: 15752448 PMCID: PMC3320460 DOI: 10.3201/eid1102.040533] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
All human Ebola virus outbreaks during 2001-2003 in the forest zone between Gabon and Republic of Congo resulted from handling infected wild animal carcasses. After the first outbreak, we created an Animal Mortality Monitoring Network in collaboration with the Gabonese and Congolese Ministries of Forestry and Environment and wildlife organizations (Wildlife Conservation Society and Programme de Conservation et Utilisation Rationnelle des Ecosystemes Forestiers en Afrique Centrale) to predict and possibly prevent human Ebola outbreaks. Since August 2001, 98 wild animal carcasses have been recovered by the network, including 65 great apes. Analysis of 21 carcasses found that 10 gorillas, 3 chimpanzees, and 1 duiker tested positive for Ebola virus. Wild animal outbreaks began before each of the 5 human Ebola outbreaks. Twice we alerted the health authorities to an imminent risk for human outbreaks, weeks before they occurred.
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Affiliation(s)
- Pierre Rouquet
- Centre International de Recherches Médicales de Franceville, (CIRMF) BP 769, Franceville, Gabon.
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