Stability of hepatitis C virus RNA during specimen handling and storage prior to NASBA amplification

Damen, Marjolein; Sillekens, Peter; Sjerps, M; Melsert, Roel; Frantzen, Inge; Reesink, H. W.; Lelie, P. N.; Cuypers, H. T. M.

doi:10.1016/s0166-0934(98)00024-x

Cited by 37 publications

(29 citation statements)

References 26 publications

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“…Thus, the frequency of vRNA detection in the feces of SIVcpz-infected wild chimpanzees appears to be similar to that of captive SIVcpz-infected chimpanzees as well as SIVsminfected sooty mangabeys (30). Given the importance of fecal samples as a source of viral sequences, we tested different methods of fecal preservation previously reported to permit host genetic analyses (12,15,56). These studies showed that fecal treatment with 70% ethanol, guanidine thiocyanate, or silica did not preserve SIVcpz sequences (not shown); however, resuspension in RNAlater (Ambion), maintained viral as well as cellular nucleic acids, even in the absence of refrigeration.…”

Section: Discussionmentioning

confidence: 97%

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Santiago

Lukasik

Kamenya

et al. 2003

J Virol

114

116

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Simian immunodeficiency virus of chimpanzees (SIVcpz) is the immediate precursor to human immunodeficiency virus type 1 (HIV-1), yet remarkably, the distribution and prevalence of SIVcpz in wild ape populations are unknown. Studies of SIVcpz infection rates in wild chimpanzees are complicated by the species' endangered status and by its geographic location in remote areas of sub-Saharan Africa. We have developed sensitive and specific urine and fecal tests for SIVcpz antibody and virion RNA (vRNA) detection and describe herein the first comprehensive prevalence study of SIVcpz infection in five wild Pan troglodytes schweinfurthii communities in east Africa. In Kibale National Park in Uganda, 31 (of 52) members of the Kanyawara community and 39 (of ϳ145) members of the Ngogo community were studied; none were found to be positive for SIVcpz infection. In Gombe National Park in Tanzania, 15 (of 20) members of the Mitumba community, 51 (of 55) members of the Kasekela community, and at least 10 (of ϳ20) members of the Kalande community were studied. Seven individuals were SIVcpz antibody and/or vRNA positive, and two others had indeterminate antibody results. Based on assay sensitivities and the numbers and types of specimens analyzed, we estimated the prevalence of SIVcpz infection to be 17% in Mitumba (95% confidence interval, 10 to 40%), 5% in Kasekela (95% confidence interval, 4 to 7%), and 30% in Kalande (95% confidence interval, 15 to 60%). For Gombe as a whole, the SIVcpz prevalence was estimated to be 13% (95% confidence interval, 7 to 25%). SIVcpz infection was confirmed in five chimpanzees by PCR amplification of partial pol and gp41/nef sequences which revealed a diverse group of viruses that formed a monophyletic lineage within the SIVcpzPts radiation. Although none of the 70 Kibale chimpanzees tested SIVcpz positive, we estimated the likelihood that a 10% or higher prevalence existed but went undetected because of sampling and assay limitations; this possibility was ruled out with 95% certainty. These results indicate that SIVcpz is unevenly distributed among P. t. schweinfurthii in east Africa, with foci or "hot spots" of SIVcpz endemicity in some communities and rare or absent infection in others. This situation contrasts with that for smaller monkey species, in which infection rates by related SIVs are generally much higher and more uniform among different groups and populations. The basis for the wide variability in SIVcpz infection rates in east African apes and the important question of SIVcpz prevalence in west central African chimpanzees (Pan troglodytes troglodytes) remain to be elucidated.The origin and evolutionary history of human immunodeficiency virus type 1 (HIV-1) and the circumstances leading to the AIDS pandemic remain important questions for our understanding of emerging infectious diseases. Chimpanzees (Pan troglodytes) are widely regarded as a natural host for simian immunodeficiency virus SIVcpz and as the simian source of HIV-1, but the prevalence of SIVcpz in wild chimpanzee popul...

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Section: Discussionmentioning

confidence: 97%

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Santiago

Lukasik

Kamenya

et al. 2003

J Virol

114

116

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“…Most studies demonstrate no substantial loss of HIV-1 or HCV viral titer during storage over many years, although some studies show reductions with time (6,13,15,19). Ginocchio et al found significant decreases in the mean plasma HIV-1 load when the plasma was stored for over 6 months at Ϫ70°C, although these investigations used a lower acceptability range (0.3 log versus the 0.5 log used in this study) (10).…”

Section: Discussionmentioning

confidence: 99%

Stability of Hepatitis C Virus, HIV, and Hepatitis B Virus Nucleic Acids in Plasma Samples after Long-Term Storage at −20 ^o C and −70 ^o C

et al. 2011

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The storage of biological samples may affect detection of viral nucleic acid, yet the stability of viral nucleic acid at standard laboratory storage temperatures (؊70°C and ؊20°C) has not been comprehensively assessed. Deterioration of viral RNA and DNA during storage may affect the detection of viruses, thus leading to an increased likelihood of false-negative results on diagnostic testing. The viral loads of 99 hepatitis C virus (HCV), 41 HIV, and 101 hepatitis B virus (HBV) patient samples were measured before and after storage at ؊20°C and ؊70°C for up to 9.1 years using Versant branched DNA assays, Cobas Monitor assays, and/or AmpliPrep/AmpliScreen assays. Clinical samples stored at ؊20°C for up to 1.2 years and at ؊70°C for up to 9 years showed a statistically significant difference from baseline with respect to HCV RNA titer, although this difference was not greater than 0.5 log 10 unit. The concentration of HIV RNA in clinical samples stored at ؊20°C for 2.3 years and at ؊70°C for up to 9.1 years did not differ significantly from the baseline viral load. HBV DNA-positive clinical samples stored at ؊20°C for up to 5 years and at ؊70°C for up to 4 years differed significantly in viral load. In all studies, however, the loss of viral load of HCV, HIV, or HBV in clinical samples tested after storage at ؊20°C and ؊70°C for up to 9 years ranged from 0.01 to 0.35 log 10 IU/ml and did not exceed 0.5 log 10 , which is the estimated intra-assay variation for molecular tests. Hence, the loss was considered of minimal clinical impact and adequate for the detection of HCV, HIV-1, and HBV nucleic acids using nucleic acid assays for the assessment of the infectious risk of cell, blood, and tissue donors.

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“…This buffer instantly stabilizes DNA and RNA, permitting short-term transport and storage at ambient temperatures and enabling long-term preservation at 280°C. 33,34 EBV parameters in the brushing specimens were retrospectively analysed batch wise and in a blinded fashion at the department of Pathology, VU Medical Centre, Amsterdam, The Netherlands, uninformed about the NPC status of the patients. For this purpose NP brushing samples collected in Indonesia and stored in lysis buffer within 2 hr after collection were sent on dry ice to Amsterdam in 2 batches.…”

Section: Nasopharyngeal Brushing Samplesmentioning

confidence: 99%

“…It can assist in clinical patient management and it can be repeated more easily and frequently than the biopsy. NP brushing with direct storage of samples in the described DNA and RNA-stabilizing buffer 33,34 is a relatively cheap method that, combined with a portable nasendoscope, may be used ''in the field'' in regions with high NPC incidence, e.g., in developing countries such as Indonesia, where medical facilities are poor. Nasendoscopy may even not be required for experienced examiners.…”

Section: Np Brushings Of Npc Patients Contain Extremely High Ebv Dna mentioning

confidence: 99%

Noninvasive diagnosis of nasopharyngeal carcinoma: Nasopharyngeal brushings reveal high Epstein‐Barr virus DNA load and carcinoma‐specific viral BARF1 mRNA

Stevens

Verkuijlen

Hariwiyanto

et al. 2006

Intl Journal of Cancer

103

130

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Nasopharyngeal carcinoma (NPC) is the most prevalent ENTtumour in Indonesia. We investigated the primary diagnostic value of Epstein-Barr virus (EBV) DNA load and mRNA detection in noninvasive nasopharyngeal (NP) brushings, obtained prospectively from consecutive Indonesian ENT-patients with suspected NPC (N 5 106) and controls. A subsequent routine NP biopsy was taken for pathological examination and EBER-RISH, yielding 85 confirmed NPC and 21 non-NPC tumour patients. EBV DNA and human DNA load were quantified by real-time PCR. NP brushings from NPC patients contained extremely high EBV DNA loads compared to the 88 non-NPC controls (p < 0.0001). Using mean EBV DNA load in controls plus 3 SD as cut-off value, specificity, sensitivity, positive and negative predictive values were 98, 90, 97 and 91%, respectively. Epstein-Barr nuclear antigen 1 (EBNA1) and the carcinoma-specific BARF1 mRNA were detected by nucleic acid sequence based amplification and found in 86 and 74% of NP brushings, confirming NPC tumour cell presence. EBV RNA positivity was even higher in fresh samples stored at 280°C until RNA expression analyses (88% for both EBNA1 and BARF1). EBV RNA-negative NP brushings from proven NPC cases had the lowest EBV DNA loads, indicating erroneous sampling. No EBV mRNA was detected in NP brushings from healthy donors and non-NPC patients. In conclusion, EBV DNA load measurement combined with detection of BARF1 mRNA in simple NP brushings allows noninvasive NPC diagnosis. It reflects carcinoma-specific EBV involvement at the anatomical site of tumour development and reduces the need for invasive biopsies. This procedure may be useful for confirmatory diagnosis in large serological NPC screening programs and has potential as prognostic tool. ' 2006 Wiley-Liss, Inc.Key words: EBV; NPC; diagnosis; viral load; oncogene; carcinoma Undifferentiated nasopharyngeal carcinoma (NPC WHO type III) is virtually 100% associated with Epstein-Barr virus (EBV) and has a reported high incidence in most of South-East Asia and intermediate incidence in North-African populations and in Inuit. [1][2][3] In Indonesia, with an ethnically diverse population of 225 million people, NPC is the most common ENT tumour with high prevalence among native populations and a yearly overall incidence estimated at 6.2/100,000. 4 Extremely high incidence was recently documented in native populations living on the island of Sulawesi. 5 In Yogyakarta, Central Java, NPC is the most prevalent tumour among man and 4th most prevalent among females, with a male/female ratio of 2.4, constituting respectively 22 and 8% of all diagnosed malignancies. 4 The strong etiological link between EBV and NPC has been known for over 3 decades [1][2][3]6 and is reflected by abnormal anti-EBV antibody profiles, increased circulating EBV DNA levels and by distinct EBV gene expression in the tumour cells. 7-11 Classically, NPC is considered to have a latency type 2 EBV transcription, with expression of EBV-encoded small RNAs 1 and 2 (EBER1/2), BamHI A rightward transcript...

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Stability of hepatitis C virus RNA during specimen handling and storage prior to NASBA amplification

Cited by 37 publications

References 26 publications

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Stability of Hepatitis C Virus, HIV, and Hepatitis B Virus Nucleic Acids in Plasma Samples after Long-Term Storage at −20 ^o C and −70 ^o C

Noninvasive diagnosis of nasopharyngeal carcinoma: Nasopharyngeal brushings reveal high Epstein‐Barr virus DNA load and carcinoma‐specific viral BARF1 mRNA

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Stability of hepatitis C virus RNA during specimen handling and storage prior to NASBA amplification

Cited by 37 publications

References 26 publications

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

Stability of Hepatitis C Virus, HIV, and Hepatitis B Virus Nucleic Acids in Plasma Samples after Long-Term Storage at −20 o C and −70 o C

Noninvasive diagnosis of nasopharyngeal carcinoma: Nasopharyngeal brushings reveal high Epstein‐Barr virus DNA load and carcinoma‐specific viral BARF1 mRNA

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Product

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Stability of Hepatitis C Virus, HIV, and Hepatitis B Virus Nucleic Acids in Plasma Samples after Long-Term Storage at −20 ^o C and −70 ^o C