| 1. |
- Allander, Tobias
(författare)
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Hepatitis C virus infection : molecular analysis of transmission and immunity
- 1997
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Hepatitis C virus (HCV) is an important cause for chronic liver disease worldwide. Infection by HCV may resolve spontaneously, but in the majority of cases a chronic infection is established, that may result in liver cirrhosis and hepatocellular cancer. HCV is parenterally transmitted, but up to 50% of patients lack a history of known parenteral exposure. The present study is focused on two aspects of HCV infection: Detection of inapparent transmission of HCV in hospitals, and investigation of the role of the antibody response for control and resolution of the HCV infection. The prevalence and incidence of HCV infection were studied in 236 haemodialysis patients, and time of seroconversion to HCV was determined by retrospective analysis of stored serum samples. 36 patients (15%) were anti-HCV positive. Seroconversion was usually temporally associated to blood transfusions, but seroconversion more than 6 months after transfusion and lack of transfusion in some cases suggested additional routes of transmission. Subsequently, the HCV strains were investigated by sequencing of the hypervariable region (HVR1) of the E2 gene in 14 patients in one of the dialysis units. Five patients shared a common viral strain, and two patients were sharing a second strain. Blood donors could be ruled out as the source of infection. The patients had not shared dialysis machines, but were treated on the same shift. The same approach was utilised for analysing a high incidence of HCV infections in a haematology ward. The HCV strain was analysed in 37 patients. Five clusters of highly related viruses were found, involving 30 of the patients. Blood products could again be ruled out as the common source of infection. The pattern of new mutations in the virus suggested spread from patient to patient. All patients in each cluster had been treated in the ward during overlapping time periods. Thus, in the two investigated hospital settings, transmission between patients seemed to occur frequently, and was a major cause for infection also in multi-transfused patients. The antibody response to the HVRI during acute infection was analysed in five dialysis patients infected by the same viral strain. A new assay for HVRI antibody detection based on recombinant bacteriophage was developed for this purpose. Results indicated that early appearance of anti-HVRI antibodies - but not anti-HCV antibodies in general - may predict clearance of the infection. To further analyse the nature of protective antibodies to HCV, human monoclonal antibodies to the HCV envelope protein E2 were isolated from a combinatorial antibody library displayed on bacteriophage. The antibody library was derived from a chronically HCV infected individual. Seven distinct antibody clones directed to E2 were characterised. All bind a conformation dependent epitope that seems conserved between different isolates, and all clones inhibit the binding of recombinant E2 protein to target cells, indicating a potential neutralising activity. This suggests the existence of a conserved neutralising epitope in the HCV envelope. The cloned human antibodies directed to it may prove useful for immunotherapy or prophylaxis.
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| 2. |
- Barrientos-Somarribas, Mauricio, et al.
(författare)
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Discovering viral genomes in human metagenomic data by predicting unknown protein families
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.
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| 3. |
- Gustafsson, Britt, et al.
(författare)
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KI, WU, and Merkel Cell Polyomavirus DNA was not Detected in Guthrie Cards of Children who Later Developed Acute Lymphoblastic Leukemia
- 2012
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Ingår i: Journal of pediatric hematology/oncology (Print). - 1077-4114 .- 1536-3678. ; 34:5, s. 364-367
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Tidskriftsartikel (refereegranskat)abstract
- Background: Neonatal dried blood spots (Guthrie cards) have been used to demonstrate a prenatal origin of clonal leukemia-specific genetic aberrations in several subgroups of childhood acute lymphoblastic leukemia (ALL). One hypothesis suggests that an infectious agent could initiate genetic transformation already in utero. In search for a possible viral agent, Guthrie cards were analyzed for the presence of 3 newly discovered polyomavirus Karolinska Institutet polymavirus (KIPyV), Washington University polyomavirus (WUPyV), and Merkel cell polyomavirus (MCPyV). Methods: Guthrie cards from 50 children who later developed ALL and 100 matched controls were collected and analyzed by standard or real-time polymerase chain reaction for the presence of the VP1 region of KIPyV, WUPyV, and MCPyV, and the LT region for MCPyV. Results and Conclusions: DNA from KIPyV, WUPyV, and MCPyV was not detected in neonatal blood samples from children with ALL or controls. Prenatal infections with these viruses are not likely to be etiological drivers for childhood leukemogenesis.
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| 4. |
- Leijonhufvud, Gustaf, et al.
(författare)
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Better detection of Torque teno virus in children with leukemia by metagenomic sequencing than by quantitative PCR
- 2022
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Ingår i: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 94:2, s. 634-641
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Tidskriftsartikel (refereegranskat)abstract
- Torque teno virus (TTV) is a group of chronically persisting viruses with a short circular DNA genome. TTV demonstrates a wide sequence diversity and a large majority of humans are chronically infected by one or more types of TTV. As TTV is ubiquitous, and viral replication correlates with immune status, TTV has been studied as a marker to assess global functional immune competence in transplant recipients. Most studies of the prevalence, amounts, and variation in TTV have been performed using PCR assays. We here present a comparison of the most frequently used quantitative PCR (qPCR) assay for TTV with shotgun metagenomic sequencing for detection and characterization of TTV in a cohort of pediatric cancer patients. The results show that TTV is more common than the qPCR assays indicate, and analysis of the TTV genome sequences indicate that a qPCR with primers and probe designed on a conserved region of the TTV genome may fail to detect some of the TTV strains found in this study.
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| 5. |
- Lysholm, Fredrik, et al.
(författare)
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Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:2
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Tidskriftsartikel (refereegranskat)abstract
- The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
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| 6. |
- Messina, David, 1974-, et al.
(författare)
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Discovery of novel protein families in metagenomic samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Despite the steady rise in gene sequence information, there is a persistent, significant fraction of genes which do not match any previously known sequence. These genes are called ORFans, and metagenomic samples, where DNA is extracted from a mixed population of unknown and often uncultivable species, are a rich source of ORFans. Viral infections cause significant morbidity and mortality, and identifying ORFan viral gene families from human metagenomic samples represents a route to understanding molecular processes that affect human health. Few methods exist for metagenomic gene-finding, and most of them rely on sequence similarity, which cannot be used to detect ORFans. Furthermore, nonsimilarity-based methods are hard to apply to the complex mixture of short, higherror-rate sequence fragments which are typical of metagenomic projects. Here we present an approach to detect ORFan protein families in short-read data, and apply it to 937 Mbp (megabase pairs) of sequence from 17 virus-enriched libraries made from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. After isolating approximately 450 putative ORFan families from clusters of sequence contigs, we applied RNAcode, a gene finder developed for use on high-quality genome sequences, and calibrated it for errorprone short sequence reads. Additional predictive measures such as sequence complexity and length were then used to rank and filter candidates into a high-quality set of 32 putative novel gene families, only two of which show significant similarity to known genes.
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| 7. |
- Stranneheim, Henrik, et al.
(författare)
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Classification of DNA sequences using Bloom filters
- 2010
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 26:13, s. 1595-1600
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed. Results: A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.
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| 8. |
- Sullivan, Patrick F, et al.
(författare)
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An unbiased metagenomic search for infectious agents using monozygotic twins discordantfor chronic fatigue
- 2011
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Ingår i: BMC Microbiology. - : BMC. - 1471-2180. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chronic fatigue syndrome is an idiopathic syndrome widely suspected of having an infectious orimmune etiology. We applied an unbiased metagenomic approach to try to identify known or novel infectiousagents in the serum of 45 cases with chronic fatigue syndrome or idiopathic chronic fatigue. Controls were theunaffected monozygotic co-twins of cases, and serum samples were obtained at the same place and time.Results: No novel DNA or RNA viral signatures were confidently identified. Four affected twins and no unaffectedtwins evidenced viremia with GB virus C (8.9% vs. 0%, p = 0.019), and one affected twin had previously undetectedhepatitis C viremia. An excess of GB virus C viremia in cases with chronic fatigue requires confirmation.Conclusions: Current, impairing chronic fatigue was not robustly associated with viremia detectable in serum.
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| 9. |
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