Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing

<i>Propionibacterium acnes: </i>disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition

Cutavirus in cutaneous malignant melanoma

A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated

“The people who are out of ‘right’ English”: Japanese university students' social evaluations of English language diversity and the internationalisation of Japanese higher education

Previous research indicates that evaluations of speech forms reflect stereotypes of, and attitudes towards, the perceived group(s) of speakers of the language/variety under consideration. This study, employing both implicit and explicit attitude measures, investigates 158 Japanese university students' perceptions of forms of UK, US, Japanese, Chinese, Thai and Indian English speech. The results show a general convergence between students' explicit and implicit attitudes, for instance, regarding US and UK English as the most correct, and solidarity with Japanese speakers of English. The findings are discussed in relation to intergroup relations between the traditional Japanese cohort and specific groups of overseas students, particularly in light of recent internationalisation policies adopted by many Japanese universities, and the resultant increase in international students from South and East Asia

Identification of known and novel recurrent viral sequences in data from multiple patients and multiple cancers

Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified

Infectious Pancreatic NEcrosis Virus - Immunogenicity, Virion Integrity and Virus/Cell Interaction

Viruses are ubiquitous in all environments where life is present, also in aquatic environments. The fish-pathogenic virus, Infectious pancreatic necrosis virus (IPNV), has generally been studied because it causes high mortality amongst hatchery-reared salmonids in aqua culture facilities around the world. Today, no efficient vaccine is available to protect the fish from becoming infected. The virus is a double-stranded, unenveloped RNA virus. The icosahedral capsid is composed of multimeres of a single protein, VP2. Because of its external localization in the viral capsid, neutralizing antibodies target this protein. The position of VP2 makes it a good candidate in the research for a protective vaccine. We studied the properties of two sets of antibodies, obtained from rabbits immunized with either VP2 isolated from infectious virions, or recombinantly synthesized in Escherichia coli. Interestingly, despite that both sets of immunsera recognized and bound to VP2 with the same intensity and strength, only the sera obtained from rabbits immunized with authentic VP2 were able to neutralize the virus. We believe that the presence of O-linked sugar residues on the authentic VP2 is a part of the epitopes that are recognized by neutralizing antibodies. Neutralizing sera caused quantitative aggregation of virions. Immuno-goldlabelling studies in EM showed that a fraction of antibodies in this sera recognized the verticis of the virions. The lectin SBA also preferentially recognized this region. The virion stability might also depend on the low level of glycosylation. Virions treated with the oxidative reagent sodium periodate either lost their integrity and formed aggregates or displayed a reduction in specific infectivity as compared with control virus. The cellular receptor that IPNV utilizes for entry is not known. By using virus overlay protein binding assays (VOPBA) IPNV bound to three cellular components with a relative molecular weights of 210, 110 and 70 K

Rapid and reproducible infectivity end-point titration of virulent phage in a microplate system

The standard method for measuring the it umber of infectious phages in solution has traditionally been the plaque forming assay. An alternative method is described where the number of lytic, infectious phages is determined in an endpoint titration assay adapted for a microplate system. In this model system, susceptible Escherichia coli 136 at a density of 4 x 10(7) cells/ml, were mixed with an equal volume (100 mu l) of Phi X174 diluted serially in a microtest plate. After 3 h of incubation on a microplate shaker the endpoint was determined spectrophotornetrically and calculated according to the method of Reed and Muench. A well was considered positive for infection if the OD630-value was <= 10% compared to the OD630-value of the negative control Of uninfected cells. ID50-titers were 2.5 x higher than the PFU-titers (CV 15%) and the intra assay reproducibility revealed a CV of 9%. The method has several advantages as compared with the conventional PFU-titration. It is less time and material consuming with the possibility to assess several samples at the same time

Virion glycosylation governs integrity and infectivity of infectious pancreatic necrosis virus.

The possible importance of the O-linked glycosylation in virion stability and infectivity of infectious pancreatic necrosis virus (IPNV) was analysed. Enzymatic treatment with O-glycosidase of radiolabelled virions under different ionic conditions, to allow for possible alternative exposure of glycosidic enzyme cleavage sites, did not alter the specific infectivity of virions re-isolated after rate-zonal centrifugation in glycerol gradients. As an alternative method to assess the significance of carbohydrates in IPNV integrity, periodate oxidation in the presence of an aldehyde quencher was chosen. Following re-isolation of viruses, a 3-5 (10) log-unit reduction in specific infectivity was revealed and, at higher concentrations, a total disruption or virion aggregation was observed. The loss of infectivity of intact virions was not because of a lack of attachment to cells. Additionally, re-evaluation of reading values from UV-spectra of purified IPNV yielded a specific infectivity of 3 10(11) TCID(50) -units mg(-1) of protein and a ratio of 40 virions per TCID(50) -unit in the CHSE-214 cell system

Immunogenicity properties of authentic and heterologously synthesized structural protein VP2 of infectious pancreatic necrosis virus.

The sole coat protein VP2 of infectious pancreatic necrosis virus (IPNV) was isolated and purified from intact virions, propagated in CHSE-214 cells. Likewise was the full-length VP2 protein isolated and purified upon cloning and expression of the corresponding complete gene in E. coli. The two purified proteins of different synthetic origins carrying identical primary structures were utilized in an immunization program using a rabbit model. Sera obtained against both immunogens react equally well with authentic and recombinant VP2 in Western blots and ELISAs. Also, the total net binding forces as determined by avidity index (AI) calculations were high and of similar stature, exceeding 80. An IPNV infection of susceptible and permissive CHSE-214 cells could only be neutralized by IgG preparations obtained from rabbits immunized with authentic VP2. Only such antibodies were able to aggregate and sediment radiolabeled virions in glycerol gradients upon rate zonal centrifugations. The presence of sugar moieties on the authentic protein is suggested to be of pivotal importance in eliciting an immune response capable of preventing infection in cell cultures in vitro