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Agaoglu NB, Yildiz J, Akgun Dogan O, Kose B, Alkurt G, Kendir Demirkol Y, Irvem A, Doganay L, Dinler Doganay G. COVID-19 PCR test performance on samples stored at ambient temperature. J Virol Methods 2021; 301:114404. [PMID: 34921841 PMCID: PMC8673954 DOI: 10.1016/j.jviromet.2021.114404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 11/20/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022]
Abstract
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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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Medical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Pediatric Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Betsi Kose
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Alkurt
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Yasemin Kendir Demirkol
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Medical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Arzu Irvem
- Department of Microbiology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Gastroenterology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.
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Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma. PLoS Pathog 2021; 17:e1008594. [PMID: 33465147 PMCID: PMC7845968 DOI: 10.1371/journal.ppat.1008594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/29/2021] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
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. Kaposi sarcoma (KS) is a leading cancer in sub-Saharan Africa and in persons with HIV co-infection. Kaposi sarcoma-associated herpesvirus (KSHV, also referred to as human herpesvirus-8, or HHV-8) is the etiologic agent of KS, but the factors that contribute to the development of KS, which occurs in only a small subset of infected individuals, remain largely unknown. While strain differences or mutations in other tumor viruses are known to affect the risk and progression of their associated cancers, whether genetic variation in KSHV is important to the natural history of KS is unclear. Most studies of KSHV diversity have only characterized ~4% of its 165-kb genome, and the observed variation in some studies is likely to have been impacted by PCR or cloning artifacts. To precisely define genomic diversity of KSHV in vivo, we evaluated full-length viral genomes (except the internal repeat regions) using a technique that greatly lowers sequencing error rates and thus measures genomic diversity much more accurately than previous studies. In addition, we extended our analyses to look for potential tumor-specific changes in the KSHV genomes by examining viruses in both tumor and non-tumor tissues. To these ends, we performed highly sensitive, single-molecule sequencing of whole KSHV genomes in paired KS tumors and oral swabs from 9 individuals with KS. We found that KSHV genomes were virtually identical within the 9 individuals, with no evidence of quasispecies formation or multi-strain infection. However, KSHV genome aberrations and gene-inactivating mutations were found to be common in KS tumors, often impacting the same genes and genomic regions across individuals. Whether theses mutations influence KS tumorigenesis or result from genomic instability commonly found in tumors warrants further study. Lastly, aberrant KSHV genomes were found to be shared by distinct tumors within individuals, suggesting the capacity of KS tumor cells to metastasize and seed new lesions.
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Johnston C, Magaret A, Roychoudhury P, Greninger AL, Cheng A, Diem K, Fitzgibbon MP, Huang ML, Selke S, Lingappa JR, Celum C, Jerome KR, Wald A, Koelle DM. Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U L and U S regions from genital swabs collected from 3 continents. Virology 2017; 510:90-98. [PMID: 28711653 PMCID: PMC5565707 DOI: 10.1016/j.virol.2017.06.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS Genital lesion swabs containing ≥ 107log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction. RESULTS Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated UL_US segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids. CONCLUSIONS Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.
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Affiliation(s)
- Christine Johnston
- Department of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
| | - Amalia Magaret
- Department of Laboratory Medicine, University of Washington, USA; Department of Biostatistics, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | | | | | - Anqi Cheng
- Department of Biostatistics, University of Washington, USA
| | - Kurt Diem
- Department of Laboratory Medicine, University of Washington, USA
| | - Matthew P Fitzgibbon
- Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, USA
| | - Stacy Selke
- Department of Laboratory Medicine, University of Washington, USA
| | - Jairam R Lingappa
- Department of Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Department of Pediatrics, University of Washington, USA
| | - Connie Celum
- Department of Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Department of Global Health, University of Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | - Anna Wald
- Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | - David M Koelle
- Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA; Benaroya Research Institute, Seattle, WA, USA
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Yu R, Dan Y, Xiang X, Zhou Y, Kuang X, Yang G, Tang Y, Liu M, Kong W, Tan W, Deng G. Stability of Chronic Hepatitis-Related Parameters in Serum Samples After Long-Term Storage. Biopreserv Biobank 2016; 15:211-219. [PMID: 27960069 DOI: 10.1089/bio.2016.0043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Serum samples are widely used in clinical research, but a comprehensive research of the stability of parameters relevant to chronic hepatitis and the effect of a relatively long-term (up to 10 years) storage on the stability have rarely been studied. AIMS To investigate the stability of chronic hepatitis-related parameters in serum samples after long-term storage. MATERIALS AND METHODS The storage stability of common clinical parameters such as total bile acid (TBA), total bilirubin (TBIL), potassium, cholesterol, and protein parameters such as alanine aminotransferase (ALT), creatine kinase (CK), γ-glutamyltransferase (GGT), albumin, high-density lipoprotein (HDL) and also hepatitis B virus (HBV) DNA, hepatitis C virus (HCV) RNA, hepatitis B surface antigen (HBsAg), and chemokine (C-X-C motif) ligand 10 (CXCL10) were tested in serum samples after storing at -20°C or -70°C for 1, 2, 3, 7, 8, and 10 years. RESULTS Levels of TBA, TBIL, and protein parameters such as ALT, CK, GGT, HDL, and HBsAg decreased significantly, but levels of potassium and cholesterol increased significantly after long-term storage, whereas blood glucose and triglycerides were stable during storage. HBV DNA remained stable at -70°C but changed at -20°C, whereas HCV RNA was stable after 1-, 2-, and 3-year storage. CXCL10 was still detectable after 8-year storage. CONCLUSIONS Low temperatures (-70°C/80°C) are necessary for storage of serum samples in chronic hepatitis B research after long-term storage.
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Affiliation(s)
- Rentao Yu
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Yunjie Dan
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Xiaomei Xiang
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Yi Zhou
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Xuemei Kuang
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Ge Yang
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Yulan Tang
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Mingdong Liu
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Weilong Kong
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Wenting Tan
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China
| | - Guohong Deng
- 1 Department of Infectious Diseases, Southwest Hospital, The Third Military Medical University , Chongqing, China .,2 Chongqing Key Laboratory of Infectious Diseases, Southwest Hospital, Third Military Medical University , Chongqing, China .,3 Institute of Immunology, Third Military Medical University , Chongqing, China
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Bender Ignacio RA, Goldman JD, Magaret AS, Selke S, Huang ML, Gantt S, Johnston C, Phipps WT, Schiffer JT, Zuckerman RA, McClelland RS, Celum C, Corey L, Wald A, Casper C. Patterns of human herpesvirus-8 oral shedding among diverse cohorts of human herpesvirus-8 seropositive persons. Infect Agent Cancer 2016; 11:7. [PMID: 26865856 PMCID: PMC4748452 DOI: 10.1186/s13027-016-0052-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/28/2015] [Indexed: 12/28/2022] Open
Abstract
Background Human 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. Methods We 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. Results 248 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. Conclusions In 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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Affiliation(s)
- Rachel A Bender Ignacio
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Epidemiology, School of Public Health, Seattle, WA USA
| | - Jason D Goldman
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Epidemiology, School of Public Health, Seattle, WA USA
| | - Amalia S Magaret
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Department of Biostatistics, School of Public Health, Seattle, WA USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA USA
| | - Stacy Selke
- Department of Laboratory Medicine, University of Washington, Seattle, WA USA
| | - Meei-Li Huang
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA USA
| | - Soren Gantt
- Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC Canada
| | - Christine Johnston
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA
| | - Warren T Phipps
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA
| | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA
| | - Richard A Zuckerman
- Section of Infectious Disease and International Health, Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH USA
| | - R Scott McClelland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Epidemiology, School of Public Health, Seattle, WA USA.,Department of Global Health, University of Washington, Seattle, WA USA
| | - Connie Celum
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Global Health, University of Washington, Seattle, WA USA
| | - Larry Corey
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA USA
| | - Anna Wald
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Epidemiology, School of Public Health, Seattle, WA USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA USA
| | - Corey Casper
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA USA.,Department of Epidemiology, School of Public Health, Seattle, WA USA.,Department of Global Health, University of Washington, Seattle, WA USA
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