Modeling geographic vaccination strategies for COVID-19 in Norway.

Vaccination was a key intervention in controlling the COVID-19 pandemic globally. In early 2021, Norway faced significant regional variations in COVID-19 incidence and prevalence, with large differences in population density, necessitating efficient vaccine allocation to reduce infections and severe outcomes. This study explored alternative vaccination strategies to minimize health outcomes (infections, hospitalizations, ICU admissions, deaths) by varying regions prioritized, extra doses prioritized, and implementation start time. Using two models (individual-based and meta-population), we simulated COVID-19 transmission during the primary vaccination period in Norway, covering the first 7 months of 2021. We investigated alternative strategies to allocate more vaccine doses to regions with a higher force of infection. We also examined the robustness of our results and highlighted potential structural differences between the two models. Our findings suggest that early vaccine prioritization could reduce COVID-19 related health outcomes by 8% to 20% compared to a baseline strategy without geographic prioritization. For minimizing infections, hospitalizations, or ICU admissions, the best strategy was to initially allocate all available vaccine doses to fewer high-risk municipalities, comprising approximately one-fourth of the population. For minimizing deaths, a moderate level of geographic prioritization, with approximately one-third of the population receiving doubled doses, gave the best outcomes by balancing the trade-off between vaccinating younger people in high-risk areas and older people in low-risk areas. The actual strategy implemented in Norway was a two-step moderate level aimed at maintaining the balance and ensuring ethical considerations and public trust. However, it did not offer significant advantages over the baseline strategy without geographic prioritization. Earlier implementation of geographic prioritization could have more effectively addressed the main wave of infections, substantially reducing the national burden of the pandemic.

A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting.

The COVID-19 pandemic is challenging nations with devastating health and economic consequences. The spread of the disease has revealed major geographical heterogeneity because of regionally varying individual behaviour and mobility patterns, unequal meteorological conditions, diverse viral variants, and locally implemented non-pharmaceutical interventions and vaccination roll-out. To support national and regional authorities in surveilling and controlling the pandemic in real-time as it unfolds, we here develop a new regional mathematical and statistical model. The model, which has been in use in Norway during the first two years of the pandemic, is informed by real-time mobility estimates from mobile phone data and laboratory-confirmed case and hospitalisation incidence. To estimate regional and time-varying transmissibility, case detection probabilities, and missed imported cases, we developed a novel sequential Approximate Bayesian Computation method allowing inference in useful time, despite the high parametric dimension. We test our approach on Norway and find that three-week-ahead predictions are precise and well-calibrated, enabling policy-relevant situational awareness at a local scale. By comparing the reproduction numbers before and after lockdowns, we identify spatially heterogeneous patterns in their effect on the transmissibility, with a stronger effect in the most populated regions compared to the national reduction estimated to be 85% (95% CI 78%-89%). Our approach is the first regional changepoint stochastic metapopulation model capable of real time spatially refined surveillance and forecasting during emergencies.

Immune cell profiles associated with human exposure to perfluorinated compounds (PFAS) suggest changes in natural killer, T helper, and T cytotoxic cell subpopulations.

Per- and polyfluoroalkyl substances (PFAS) constitutes a group of highly persistent man-made substances. Recent evidence indicates that PFAS negatively impact the immune system. However, it remains unclear how different PFAS are associated with alterations in circulating leukocyte subpopulations. More detailed knowledge of such potential associations can provide better understanding into mechanisms of PFAS immunotoxicity in humans. In this exploratory study, associations of serum levels of common PFAS (perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), perfluorononanoic acid (PFNA), and perfluorohexane sulfonic acid (PFHxS)) and immune cell profiles of peripheral blood mononuclear cells, both with and without immunostimulation, were investigated. High-dimensional single cell analysis by mass cytometry was done on blood leukocytes from fifty participants in the Norwegian human biomonitoring EuroMix study. Different PFAS were associated with changes in various subpopulations of natural killer (NK), T helper (Th), and cytotoxic T (Tc) cells. Broadly, PFAS concentrations were related to increased frequencies of NK cells and activated subpopulations of NK cells. Additionally, increased levels of activated T helper memory cell subpopulations point to Th2/Th17 and Treg-like skewed profiles. Finally, PFAS concentrations were associated with decreased frequencies of T cytotoxic cell subpopulations with CXCR3+ effector memory (EM) phenotypes. Several of these observations point to biologically plausible mechanisms that may contribute to explaining the epidemiological reports of immunosuppression by PFAS. Our results suggest that PFAS exposures even at relatively low levels are associated with changes in immune cell subpopulations, a finding which should be explored more thoroughly in a larger cohort. Additionally, causal relationships should be confirmed in experimental studies. Overall, this study demonstrates the strength of profiling by mass cytometry in revealing detailed changes in immune cells at a single cell level.

Estimating vaccine effectiveness against COVID-19 using cause-specific sick leave as an indicator: a nationwide population-based cohort study, Norway, July 2021 - December 2022.

BACKGROUND: Due to changes in testing policy and increased use of rapid tests, other indicators for SARS-CoV-2 infections are needed to monitor vaccine effectiveness (VE). We aimed to estimate VE against COVID-19 sick leave (> 3 days, certified by a medical professional) among employed individuals (25-64-years-old) in Norway. METHODS: We performed a nationwide cohort study by collating data from the Emergency preparedness register for COVID-19. We used adjusted Cox proportional hazard models with vaccine status as a time-varying covariate and presented results as adjusted hazard ratios (aHRs) with corresponding 95% confidence intervals. Separate models were run against sick leave and against SARS-CoV-2 infections during the Delta period (June-December 2021), and against sick leave during the Omicron period (January-December 2022) when SARS-CoV-2 PCR-testing was replaced by rapid self-tests and infections were underreported. RESULTS: We included 2,236,419 individuals during the Delta period, of whom 73,776 (3.3%) had a reported infection and 54,334 (2.4%) were registered with sick leave. Of the 2,206,952 included individuals in the Omicron period, 300,140 (13.6%) were registered with sick leave. During the Delta period, 55% (26,611) of individuals who had registered sick leave also had a positive test, compared to 32% (96,445) during the Omicron period. The VE against sick leave during the Delta period followed a similar waning pattern to that against SARS-CoV-2 infections. After the second and third dose, the lowest aHRs were estimated for 2-7 days after vaccination for both sick leave (0.25; 95%CI 0.24-0.26 and 0.26; 95% CI 0.24-0.29) and infection ( 0.16; 95% CI 0.15-0.17 and 0.18; 95% CI 0.16-0.19) respectively. During the Omicron period, aHRs for sick leave were higher than during the Delta period, but the lowest aHRs were still found in 2-7 weeks after receiving the second (0.61; 95% CI 0.59-0.64) or third dose (0.63; 95% CI 0.62-0.64). CONCLUSION: Our results showed that sick leave could be a relevant indicator for VE in the surveillance of COVID-19 and a finding that may be important in the surveillance of other respiratory infection.

Frequency and risk of SARS-CoV-2 reinfections in Norway: a nation-wide study, February 2020 to January 2022.

BACKGROUND: SARS-CoV-2 reinfection rates have been shown to vary depending on the circulating variant, vaccination status and background immunity, as well as the time interval used to identify reinfections. This study describes the frequency of SARS-CoV-2 reinfections in Norway using different time intervals and assesses potential factors that could impact the risk of reinfections during the different variant waves. METHODS: We used linked individual-level data from national registries to conduct a retrospective cohort study including all cases with a positive test for SARS-CoV-2 from February 2020 to January 2022. Time intervals of 30, 60, 90 or 180 days between positive tests were used to define potential reinfections. A multivariable Cox regression model was used to assess the risk of reinfection in terms of variants adjusting for vaccination status, demographic factors, and underlying comorbidities. RESULTS: The reinfection rate varied between 0.2%, 0.6% and 5.9% during the Alpha, Delta and early Omicron waves, respectively. In the multivariable model, younger age groups were associated with a higher risk of reinfection compared to older age groups, whereas vaccination was associated with protection against reinfection. Moreover, the risk of reinfection followed a pattern similar to risk of first infection. Individuals infected early in the pandemic had higher risk of reinfection than individuals infected in more recent waves. CONCLUSIONS: Reinfections increased markedly during the Omicron wave. Younger individuals, and primary infections during earlier waves were associated with an increased reinfection risk compared to primary infections during more recent waves, whereas vaccination was a protective factor. Our results highlight the importance of age and post infection waning immunity and are relevant when evaluating vaccination polices.

Milder disease trajectory among COVID-19 patients hospitalised with the SARS-CoV-2 Omicron variant compared with the Delta variant in Norway.

Using individual-level national registry data, we conducted a cohort study to estimate differences in the length of hospital stay, and risk of admission to an intensive care unit and in-hospital death among patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, compared with patients infected with Delta variant in Norway. We included 409 (38%) patients infected with Omicron and 666 (62%) infected with Delta who were hospitalised with coronavirus disease 2019 (COVID-19) as the main cause of hospitalisation between 6 December 2021 and 6 February 2022. Omicron patients had a 48% lower risk of intensive care admission (adjusted hazard ratios (aHR): 0.52, 95% confidence interval (CI): 0.34-0.80) and a 56% lower risk of in-hospital death (aHR: 0.44, 95%CI: 0.24-0.79) compared with Delta patients. Omicron patients had a shorter length of stay (with or without ICU stay) compared with Delta patients in the age groups from 18 to 79 years and those who had at least completed their primary vaccination. This supports growing evidence of reduced disease severity among hospitalised Omicron patients compared with Delta patients.

eHealth: Disease activity measures are related to the faecal gut microbiota in adult patients with ulcerative colitis.

BACKGROUND/AIM: Microbial dysbiosis in inflammatory bowel disease (IBD) is poorly understood. Faecal samples collected for the purposes of microbiota analysis are not yet a part of everyday clinical practice. To explore associations between faecal microbiota and disease activity measures in adult IBD patients, for the purpose of possibly integrating microbiota measures in an existing IBD eHealth application for disease-monitoring. METHODS: We collected faecal samples from adult IBD patients for one year while they were home-monitoring for disease activity, using faecal calprotectin (FC) and the Simple Clinical Colitis Activity Index (SCCAI). Faecal samples were analysed in two different ways: commercially available test consisting of 54 pre-determined bacterial markers (DNA test) and 16S rRNA gene sequencing (16S-seq). Univariable linear mixed effect models were fitted to predict disease scores using normalised relative abundances as fixed effects. RESULTS: Seventy-eight IBD patients provided a total of 288 faecal samples for microbiota analysis. Two hundred and thirty-four of the samples were from patients with ulcerative colitis (UC). Peptostreptococcus anaerobius was found to correlate significantly with increasing FC, while an additional 24 genera were found to be associated with FC and/or SCCAI (16S-seq). Bacterial markers (DNA test) for Proteobacteria, Shigella spp. and Escherichia spp., were significantly correlated with increasing FC measures, while another 14 markers were found to be associated with FC and/or SCCAI. CONCLUSIONS: In patients with UC, results of both methods are associated with disease activity, correlating significantly with Peptostretococcus anaerobius (16S-seq) and with Proteobacteria, Shigella spp. and Escherichia spp. (DNA test).

The potential spread of severe footrot in Norway if no elimination programme had been initiated: a simulation model.

When severe footrot was detected in Norway in 2008, a surveillance programme was initiated and followed by an elimination programme. By 2013 the disease had spread to two of 19 counties and a total of 119 (1%) sheep flocks had been diagnosed with severe footrot. A simulation model was developed to estimate the potential spread of severe footrot in Norway and to estimate the relative importance of the different spreading routes. The model parameters were based on the rate of spread of the first 38 diagnosed cases and the management and climatic factors particular for Norway. The model showed that by 2013, severe footrot would have spread to six counties and infected 16% of the sheep flocks if no elimination programme had been initiated. If this is compared with the 1% of flocks that were diagnosed in Norway by 2013, there seems to be a large effect of the implemented footrot elimination programme. By 2035, it was estimated that severe footrot would have spread to 16 counties and 64% of the sheep flocks. Such an extensive spread would probably impose a large negative impact on the sheep industry and welfare of the sheep. The most effective way to curb the spread of severe footrot was by decreasing the within county infection rate. This could be achieved by decreasing the contact between flocks or by decreasing the environmental load of D. nodosus, for example by footbathing sheep, culling diseased sheep or eliminating severe footrot in the flock.

COVID-19 Vaccine Effectiveness Among Adolescents.

BACKGROUND: For adolescents, data on the long-term effectiveness of the BNT162b2 and mRNA-1273 vaccines against severe COVID-19 outcomes are scarce. Additionally, only a few studies have evaluated vaccine effectiveness (VE) for mRNA-1273 or heterologous mRNA vaccine schedules (ie, mixing BNT162b2 and mRNA-1273). METHODS: Nationwide register-based 1-to-1 matched cohort analyses were conducted in Denmark, Finland, Norway, and Sweden between May 28, 2021, and April 30, 2023, to estimate VE for primary COVID-19 vaccine (2-dose) schedules among adolescents aged 12 to 17 years. Cumulative incidences of COVID-19-related hospitalization (primary outcome) and laboratory-confirmed SARS-CoV-2 infection (secondary outcome) were compared for vaccinated and unvaccinated at 6 months of follow-up using the Kaplan-Meier estimator. Country-specific VE (1-risk ratio) and risk differences (RD) were combined by random-effects meta-analyses. RESULTS: The study included 526 966 primary schedule vaccinated adolescents. VE against COVID-19-related hospitalization was 72.6% (95% confidence interval [CI], 62.5-82.7) and RD was -2.8 (95% CI, -4.5 to -1.0) per 10 000 vaccinated for BNT162b2 at 6 months of follow-up compared with unvaccinated. The corresponding VE and RD were 86.0% (95% CI, 56.8-100.0) and -2.1 (95% CI, -4.0 to -0.2) per 10 000 vaccinated for mRNA-1273 and 80.7% (95% CI, 58.0-100.0) and -5.5 (95% CI, -15.5 to 4.6) per 10 000 vaccinated for heterologous mRNA vaccine schedules. Estimates were comparable when restricting to a period of omicron predominance and extending follow-up to 12 months. CONCLUSIONS: Across 4 Nordic countries, severe COVID-19 in adolescents was a rare event. Compared with unvaccinated, BNT162b2, mRNA-1273, and heterologous mRNA vaccination schedules provided high protection against COVID-19-related hospitalization, including hospitalizations during the omicron period.

Effectiveness of XBB.1.5 Monovalent COVID-19 Vaccines During a Period of XBB.1.5 Dominance in EU/EEA Countries, October to November 2023: A VEBIS-EHR Network Study.

Using a common protocol across seven countries in the European Union/European Economic Area, we estimated XBB.1.5 monovalent vaccine effectiveness (VE) against COVID-19 hospitalisation and death in booster-eligible ≥ 65-year-olds, during October-November 2023. We linked electronic records to construct retrospective cohorts and used Cox models to estimate adjusted hazard ratios and derive VE. VE for COVID-19 hospitalisation and death was, respectively, 67% (95%CI: 58-74) and 67% (95%CI: 42-81) in 65- to 79-year-olds and 66% (95%CI: 57-73) and 72% (95%CI: 51-85) in ≥ 80-year-olds. Results indicate that periodic vaccination of individuals ≥ 65 years has an ongoing benefit and support current vaccination strategies in the EU/EEA.

A mobile genetic element with unknown function found in distantly related viruses.

BACKGROUND: The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups. METHODS: We have searched GenBank in order to identify all viral accessions that have s2m(-like) sequence motifs. Rigorous phylogenetic analyses and constrained tree topology testing were also performed in order to investigate the apparently mobile nature of s2m. RESULTS: The stem-loop s2m structure can be found in four families of + ssRNA viruses; Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae. In all of these virus families, with the possible exception of Caliciviridae, multiple gains and/or losses of s2m would have to be postulated in order to explain the distribution of this character. CONCLUSIONS: s2m appears to be a mobile genetic element with a unique evolutionary history in all of the four virus families where it can be found. Based on our findings and a review of the current literature on s2m, a hypothesis implying an RNAi-like function for the s2m element is also outlined.

Effectiveness and durability of a second COVID-19 booster against severe outcomes among older people in Norway: a population-based cohort study comparing mono- and bivalent booster doses.

BACKGROUND: Evidence on the durability of the protection of a fourth dose of a monovalent or bivalent messenger ribonucleic acid (mRNA) vaccine against coronavirus disease 2019 (COVID-19) among older people during the predominant Omicron period is needed. METHODS: We performed a population-based cohort study in Norway covering the time from 1 July 2022 to 15 January 2023, including individuals ≥75 years of age who had received at least a third dose. Using Cox proportional hazard models on severe COVID-19-associated outcome measures and all-cause mortality, we estimated the vaccine effectiveness of mono- and bivalent vaccines, comparing fourth- to third-dose recipients (>24 weeks ago). Vaccine status was included as a time-varying covariate and models were adjusted for potential confounders. RESULTS: We included 408 073 individuals. A fourth dose with either monovalent or bivalent mRNA vaccine showed increased protection against COVID-19-associated mortality relative to a third dose in individuals ≥75 years of age. We estimated a protective effect for the bivalent BA.1 vaccine [adjusted hazard ratio (aHR) 0.08, 95% CI 0.02-0.32] relative to the bivalent BA.4-5 (aHR 0.27, 95% CI 0.14-0.56) and a monovalent dose (aHR 0.34, 95% CI 0.26-0.45) 2-9 weeks after vaccination compared with recipients with a third dose >24 weeks ago. The increased protective effect waned with no added protection for the monovalent vaccine after 33 weeks compared with a third dose. CONCLUSIONS: Our results indicate an increased protective effect of a fourth dose against severe outcomes compared with a third dose, with decreasing effect with time since the last dose.

Exploration of multivariate analysis in microbial coding sequence modeling.

BACKGROUND: Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focus on coding sequence modeling algorithms; that is, algorithms for identification and prediction of the actual coding sequences from genomic DNA. In this respect, we promote a novel multivariate method known as Canonical Powered Partial Least Squares (CPPLS) as an alternative to the commonly used Interpolated Markov model (IMM). Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties. RESULTS: The multivariate CPPLS approach classified coding sequence substantially better than the commonly used IMM on the same set of sequences. We also found that the use of CPPLS with codon representation gave significantly better classification results than both IMM with protein (p < 0.001) and with DNA (p < 0.001). Further, although the mean performance was similar, the variation of CPPLS performance on codon representation was significantly smaller than for IMM (p < 0.001). CONCLUSIONS: The performance of coding sequence modeling can be substantially improved by using an algorithm based on the multivariate CPPLS method applied to codon or DNA frequencies.

No evidence for added value of introducing mandatory COVID-19 testing for international travellers entering Norway with a valid EU digital COVID certificate.

BACKGROUND: As a response to the emergence of the new Omicron SARS-CoV-2 variant, on December 3, 2021, mandatory testing after entry to Norway was extended to include international travellers with a valid COVID-19 certificate. We aim to validate if mandatory testing upon arrival increased the proportion of travellers confirmed with a positive COVID-19 test after entry. METHODS: We used individual level data on registered travellers linked with data on COVID-19 testing and confirmed COVID-19 cases. The proportions of confirmed cases among international travellers before and after the requirement were introduced was analysed with an interrupted times series design. RESULTS: The proportion of travellers with an EU COVID-19 certificate tested at an official test station increased from 3% to 43% after mandatory testing was introduced. However, the proportion of all travellers confirmed with COVID-19 rose only marginally with 0.14 percentage point directly after the intervention (p-value .06). The results are limited by the absence of data on antigen tests taken by the traveller at home and missing data from travellers without a valid Norwegian ID. CONCLUSIONS: Our findings suggest that the benefit of mandatory testing of all international travellers to Norway was marginal in the period directly after the emergence of the omicron variant. This result must be understood in the context of free of charge testing at official test centres, a government recommendation on a low threshold to test when experiencing symptoms in addition to limited surveillance of the compliance of the test after arrival requirement.

Long-term effects of fecal microbiota transplantation (FMT) in patients with irritable bowel syndrome.

BACKGROUND: We recently found fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) patients to be an effective and safe treatment after 3 months. The present follow-up study investigated the efficacy and safety of FMT at 1 year after treatment. METHODS: This study included 77 of the 91 IBS patients who had responded to FMT in our previous study. Patients provided a fecal sample and completed five questionnaires to assess their symptoms and quality of life at 1 year after FMT. The dysbiosis index (DI) and fecal bacterial profile were analyzed using a 16S rRNA gene-based DNA probe hybridization. The levels of fecal short-chain fatty acids (SCFAs) were determined by gas chromatography. RESULTS: There was a persistent response to FMT at 1 year after treatment in 32 (86.5%) and 35 (87.5%) patients who received 30-g and 60-g FMT, respectively. In the 30-g FMT group, 12 (32.4%) and 8 (21.6%) patients showed complete remission at 1 year and 3 months, respectively; the corresponding numbers in the 60-g FMT group were 18 (45%) and 11 (27.5%), respectively. Abdominal symptoms and the quality of life were improved at 1 year compared with after 3 months. These findings were accompanied by comprehensive changes in the fecal bacterial profile and SCFAs. CONCLUSIONS: Most of the IBS patients maintained a response at 1 year after FMT. Moreover, the improvements in symptoms and quality of life increased over time. Changes in DI, fecal bacterial profile and SCFAs were more comprehensive at 1 year than after 3 months. www.clinicaltrials.gov (NCT03822299).

Increased transmissibility of the alpha SARS-CoV-2 variant: evidence from contact tracing data in Oslo, January to February 2021.

BACKGROUND: Information about the contagiousness of new SARS-CoV-2 variants, including the alpha lineage, and how they spread in various locations is essential. Country-specific estimates are needed because local interventions influence transmissibility. METHODS: We analysed contact tracing data from Oslo municipality, reported from January through February 2021, when the alpha lineage became predominant in Norway and estimated the relative transmissibility of the alpha lineage with the use of Poisson regression. RESULTS: Within households, we found an increase in the secondary attack rate by 60% (95% CI 20-114%) among cases infected with the alpha lineage compared to other variants; including all close contacts, the relative increase in the secondary attack rate was 24% (95% CI -6%-43%). There was a significantly higher risk of infecting household members in index cases aged 40-59 years who were infected with the alpha lineage; we found no association between transmission and household size. Overall, including all close contacts, we found that the reproduction number among cases with the alpha lineage was increased by 24% (95% CI 0%-52%), corresponding to an absolute increase of 0.19, compared to the group of index cases infected with other variants. CONCLUSION: Our study suggests that households are the primary locations for rapid transmission of the new lineage alpha.

No Evidence of the Vertical Transmission of Non-Virulent Infectious Salmon Anaemia Virus (ISAV-HPR0) in Farmed Atlantic Salmon.

The nonvirulent infectious salmon anaemia virus (ISAV-HPR0) is the putative progenitor for virulent-ISAV, and a potential risk factor for the development of infectious salmon anaemia (ISA). Understanding the transmission dynamics of ISAV-HPR0 is fundamental to proper management and mitigation strategies. Here, we demonstrate that ISAV-HPR0 causes prevalent and transient infections in all three production stages of Atlantic salmon in the Faroe Islands. Phylogenetic analysis of the haemagglutinin-esterase gene from 247 salmon showed a clear geographical structuring into two significantly distinct HPR0-subgroups, which were designated G2 and G4. Whereas G2 and G4 co-circulated in marine farms, Faroese broodfish were predominantly infected by G2, and smolt were predominantly infected by G4. This infection pattern was confirmed by our G2- and G4-specific RT-qPCR assays. Moreover, the HPR0 variants detected in Icelandic and Norwegian broodfish were never detected in the Faroe Islands, despite the extensive import of ova from both countries. Accordingly, the vertical transmission of HPR0 from broodfish to progeny is uncommon. Phylogenetic and statistical analysis suggest that HPR0 persists in the smolt farms as "house-strains", and that new HPR0 variants are occasionally introduced from the marine environment, probably by HPR0-contaminated sea-spray. Thus, high biosecurity-including water and air intake-is required to avoid the introduction of pathogens to the smolt farms.

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction.

BACKGROUND: When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. RESULTS: We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya). CONCLUSION: We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

Prescription of antimicrobial drugs in Norwegian aquaculture with an emphasis on "new" fish species.

The usage of antimicrobial (AM) drugs in farmed fish in Norwegian aquaculture for the period 2000-2005 was investigated by using prescription data. These data were validated against national sales data of AM drugs sold for use in farmed fish and were found to be highly valid. The defined course dose (DCD) was applied as the unit of measurement to correct for the variations in the dosages between different AM drugs. The DCD(kg) was the amount of an AM drug recommended for the treatment of a 1-kg fish. The calculated number of prescribed DCD(kg)s is an estimate of the biomass of farmed fish that can be treated with a certain amount AM drug. In the present study, the number of prescriptions issued (i.e., numbers of initiated treatments), weight of active substance prescribed and biomass treated were applied to describe the usage. An increase, although modest, in the AM drug usage in Norwegian aquaculture was observed from 2002 to 2005. This increase was accounted for by new-farmed fish species (other than Atlantic salmon and rainbow trout), especially Atlantic cod. The increased usage of AM drugs in cod in the study period was significantly positively correlated to the biomass produced; even so from 2001 to 2005 the number of prescriptions for cod relative to the produced biomass declined. The AM drug usage in Atlantic halibut as well as the production varied during the study period. For other species such as turbot, coalfish and wolffish the usage of AM drugs was found to be negligible. "Mono-therapy" with quinolones may present a selective pressure in regard to development of quinolone resistance.