Consistent viral DNA quantification after prolonged storage at ambient temperature

Zaniello, Benjamin; Huang, Meei Li; Cheng, Anqi; Selke, Stacy; Wald, Anna; Jerome, Keith R.; Magaret, Amalia

doi:10.1016/j.jviromet.2015.11.010

Cited by 7 publications

(5 citation statements)

References 16 publications

(15 reference statements)

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“…Recently many studies have investigated the effects of various factors on virus survival but, less is known on the impact of temperature on SARS-CoV-2 RNA detection by RT- PCR ( Eslami and Jalili, 2020 ; Kim et al, 2021 ; Li et al, 2020 ; Xie and Zhu, 2020 ; Xu et al, 2020 ). In a limited number of studies related to other viruses (enterovirus, HSV-2, HHV-8, adenovirus, influenza), it has been reported that the storage of the samples at ambient temperature did not affect the test results ( Druce et al, 2012 ; Zaniello et al, 2016 ). Our results showed that oropharyngeal/nasopharyngeal samples kept at room temperature remain positive in SARS-CoV-2 real-time PCR studies for at least six days.…”

Section: Discussionmentioning

confidence: 99%

COVID-19 PCR test performance on samples stored at ambient temperature

Ağaoğlu

Yildiz

Doğan

et al. 2022

Journal of Virological Methods

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The WHO-named Coronavirus Disease 2019 (COVID-19) infection had become a pandemic within a short time period since it was detected in Wuhan. The outbreak required the screening of millions of samples daily and overwhelmed diagnostic laboratories worldwide. During this pandemic, the handling of patient specimens according to the universal guidelines was extremely difficult as the WHO, CDC and ECDC required cold chain compliance during transport and storage of the swab samples. The aim of this study was to compare the effects of two different storage conditions on the COVID-19 real-time PCR assay on 30 positive nasopharyngeal and/or oropharyngeal samples stored at both ambient temperature (22 ± 2 °C) and +4 °C. The results revealed that all the samples stored at ambient temperature remain PCR positive for at least six days without any false-negative result. In conclusion, transporting and storing these types of swab samples at ambient temperature for six days under resource-limited conditions during the COVID-19 pandemics are acceptable.

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Section: Discussionmentioning

confidence: 99%

COVID-19 PCR test performance on samples stored at ambient temperature

Ağaoğlu

Yildiz

Doğan

et al. 2022

Journal of Virological Methods

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“…Briefly, a Dacron swab is inserted into the mouth and vigorously rubbed along the buccal mucosa, gums, and hard palate. The swab is then placed in 1 mL of filter-sterilized digestion buffer [ 59 ] and stored at ambient temperature [ 60 ] before being placed at -20°C for storage.…”

Section: Methodsmentioning

confidence: 99%

Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma

et al. 2021

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Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than that which occurs in the viral population, and these studies have only studied variable regions. Here, full-length KSHV genomes in tumors and/or oral swabs from 9 Ugandan adults with HIV-associated KS were characterized. Furthermore, we used deep, short-read sequencing using duplex unique molecular identifiers (dUMI)–random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors to ~10−9/base as well as afforded accurate determination of KSHV genome numbers sequenced in each sample. KSHV genomes were assembled de novo, and rearrangements observed were confirmed by PCR and Sanger sequencing. 131-kb KSHV genome sequences, excluding major repeat regions, were successfully obtained from 23 clinical specimens, averaging 2.3x104 reads/base. Strikingly, KSHV genomes were virtually identical within individuals at the point mutational level. The intra-host heterogeneity that was observed was confined to tumor-associated KSHV mutations and genome rearrangements, all impacting protein-coding sequences. Although it is unclear whether these changes were important to tumorigenesis or occurred as a result of genomic instability in tumors, similar changes were observed across individuals. These included inactivation of the K8.1 gene in tumors of 3 individuals and retention of a region around the first major internal repeat (IR1) in all instances of genomic deletions and rearrangements. Notably, the same breakpoint junctions were found in distinct tumors within single individuals, suggesting metastatic spread of rearranged KSHV genomes. These findings define KSHV intra-host heterogeneity in vivo with greater precision than has been possible in the past and suggest the possibility that aberrant KSHV genomes may contribute to aspects of KS tumorigenesis. Furthermore, study of KSHV with use of dUMI provides a proof of concept for utilizing this technique for detailed study of other virus populations in vivo.

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“…HHV-8 seropositivity was determined by positive test result on either immunofluorescence assay (IFA) against latent or lytic antibodies [ 39 ] or whole-virus enzyme immunoassay (EIA) [ 27 ]. Swabs were collected into lysis buffer containing 100 mM KCl (or NaCl), 25 mM EDTA (pH 8.0), 10 mM Tris (pH 8.0), and 1 % Igepal CA-630 and stored at −20 °C until testing, a process validated to be stable for extended storage [ 40 , 41 ]. Quantitative polymerase chain reaction (qPCR) was performed to quantitate HHV-8 DNA using previously described and validated methods [ 1 , 16 , 38 , 42 ].…”

Section: Methodsmentioning

confidence: 99%

Patterns of human herpesvirus-8 oral shedding among diverse cohorts of human herpesvirus-8 seropositive persons

Ignacio

Goldman

Magaret

et al. 2016

Infect Agents Cancer

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BackgroundHuman herpesvirus-8 (HHV-8), the etiologic agent of Kaposi sarcoma (KS), establishes lifelong latent infection with periodic lytic replication (“shedding”) at mucosal sites, especially the oropharynx. Patterns of HHV-8 shedding are not well understood, and require elucidation to better predict risk of HHV-8 related malignancies in those infected. We sought to characterize patterns of HHV-8 oropharyngeal shedding among diverse cohorts that enrolled HHV-8 seropositive persons.MethodsWe quantified HHV-8 oral shedding using PCR among HHV-8 seropositive persons who collected at least 14 days of oral swabs in 22 studies on 3 continents. We excluded persons taking antivirals during sampling or any prior use of antiretrovirals in those who were HIV-infected.Results248 participants were enrolled from the US, Peru, Cameroon, Uganda, and Kenya; 61 % were men, 58 % were HIV seropositive, and 16 % had KS. Overall, 3,123 of 10,557 samples (29.6 %) had HHV-8 detected. Quantity of virus shed was highly correlated with shedding rate, (ρ = 0.72, p < 0.0001). HHV-8 was detected in ≥1 sample in 55 % of participants with a median of 7 % of days in the US and Kenya, 0 % in Uganda and Peru, and 18 % in Cameroon. Median episode duration was three days, and episodes with high median quantity lasted longer (42 vs 3 days, p < 0.0001). In persons with multiple observations over time, 66 % of shedding rate variance was attributable to differences between individuals.ConclusionsIn HHV-8 infected individuals from diverse settings, oral mucosal shedding rate, quantity, and duration were correlated; individual shedding was highly variable. Studies are needed to determine factors accounting for between-person variation and the relationship of HHV-8 shedding to development of associated diseases.

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Consistent viral DNA quantification after prolonged storage at ambient temperature

Cited by 7 publications

References 16 publications

COVID-19 PCR test performance on samples stored at ambient temperature

COVID-19 PCR test performance on samples stored at ambient temperature

Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma

Patterns of human herpesvirus-8 oral shedding among diverse cohorts of human herpesvirus-8 seropositive persons

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