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Estimates of immunity and severity for the SARS-CoV-2 omicron subvariant BA.5 are important to assess the public health impact associated with its rapid global spread despite vaccination. We estimated natural and vaccine immunity and severity of BA.5 relative to BA.2 in Denmark, a country with high mRNA-vaccination coverage and free-of-charge RT-PCR testing.This nation-wide population-based study in Denmark included residents aged 18 years or older who had taken an RT-PCR test between 10 April and 30 June, 2022 (ie, the outcome period), and who the national COVID-19 surveillance system identified as having information since February 2020 on RT-PCR tests, whole-genome sequencing, vaccinations, and hospitalisation with a positive RT-PCR test and COVID-19 as the main diagnosis. First, we used a case-control design, in which cases were people infected with BA.5 or BA.2 during the outcome period and controls were people who tested negative for SARS-CoV-2 infection during the outcome period. We calculated the protection provided by a previous PCR-confirmed omicron infection against BA.5 and BA.2 infection and hospitalisation among triple-vaccinated individuals. Second, we compared vaccination status in people infected with BA.5 versus BA.2 and estimated relative vaccine protection against each subvariant. Third, we compared rates of hospitalisation for COVID-19 among people infected with BA.5 versus BA.2. We estimated effects using logistic regression with adjustment for sex, age, region, PCR-test date, comorbidity and, as appropriate, vaccination and previous infection status.A total of 210 (2·4%) of 8678 of BA.5 cases, 192 (0·7%) of 29 292 of BA.2 cases, and 33 972 (19·0%) of 178 669 PCR-negative controls previously had an omicron infection, which was estimated in the adjusted analyses to offer 92·7% (95% CI 91·6-93·7) protection against BA.5 infection and 97·1% (96·6-97·5) protection against BA.2 infection. We found similarly high amounts of protection against hospitalisation owing to infection with BA.5 (96·4% [95% CI 74·2-99·5]) and BA.2 (91·2% [76·3-96·7]). Vaccine coverage (three mRNA doses vs none) was 9307 (94·2%) of 9878 among BA.5 cases and 30 581 (94·8%) of 32 272 among BA.2 cases, although in the adjusted analysis, there was a trend towards slightly higher vaccination coverage among BA.5 cases than BA.2 cases (OR 1·18 [95% CI 0·99-1·42]; p=0·064), possibly suggesting marginally poorer vaccine protection against BA.5. The rate of hospitalisation due to COVID-19 was higher among the BA.5 cases (210 [1·9%] of 11 314) than among the BA.2 cases (514 [1·4%] of 36 805), with an OR of 1·34 (95% CI 1·14-1·57) and an adjusted OR of 1·69 (95% CI 1·22-2·33), despite low and stable COVID-19 hospitalisation numbers during the study period.The study provides evidence that a previous omicron infection in triple-vaccinated individuals provides high amounts of protection against BA.5 and BA.2 infections. However, protection estimates greater than 90% might be too high if individuals with a previous infection were more likely than those without one to come forward for a test for reasons other than suspicion of COVID-19. Our analysis also showed that vaccine protection against BA.5 infection was similar to, or slightly weaker than, protection against BA.2 infection. Finally, there was evidence that BA.5 infections were associated with an increased risk of hospitalisation compared with BA.2 infections.There was no funding source for this study.

Background: Estimates of the severity of the SARS-CoV-2 omicron variant (B.1.1.529) are crucial to assess the public health impact associated with its rapid global dissemination. We estimated the risk of SARS-CoV-2-related hospitalisations after infection with omicron compared with the delta variant (B.1.617.2) in Denmark, a country with high mRNA vaccination coverage and extensive free-of-charge PCR testing capacity. Methods: In this observational cohort study, we included all RT-PCR-confirmed cases of SARS-CoV-2 infection in Denmark, with samples taken between Nov 21 (date of first omicron-positive sample) and Dec 19, 2021. Individuals were identified in the national COVID-19 surveillance system database, which included results of a variant-specific RT-PCR that detected omicron cases, and data on SARS-CoV-2-related hospitalisations (primary outcome of the study). We calculated the risk ratio (RR) of hospitalisation after infection with omicron compared with delta, overall and stratified by vaccination status, in a Poisson regression model with robust SEs, adjusted a priori for reinfection status, sex, age, region, comorbidities, and time period. Findings: Between Nov 21 and Dec 19, 2021, among the 188 980 individuals with SARS-CoV-2 infection, 38 669 (20·5%) had the omicron variant. SARS-CoV-2-related hospitalisations and omicron cases increased during the study period. Overall, 124 313 (65·8%) of 188 980 individuals were vaccinated, and vaccination was associated with a lower risk of hospitalisation (adjusted RR 0·24, 95% CI 0·22–0·26) compared with cases with no doses or only one dose of vaccine. Compared with delta infection, omicron infection was associated with an adjusted RR of hospitalisation of 0·64 (95% CI 0·56–0·75; 222 [0·6%] of 38 669 omicron cases admitted to hospital vs 2213 [1·5%] of 150 311 delta cases). For a similar comparison by vaccination status, the RR of hospitalisation was 0·57 (0·44–0·75) among cases with no or only one dose of vaccine, 0·71 (0·60–0·86) among those who received two doses, and 0·50 (0·32–0·76) among those who received three doses. Interpretation: We found a significantly lower risk of hospitalisation with omicron infection compared with delta infection among both vaccinated and unvaccinated individuals, suggesting an inherent reduced severity of omicron. Our results could guide modelling of the effect of the ongoing global omicron wave and thus health-care system preparedness. Funding: None.

Early detection of pathogens at the point of care helps reduce the threats to human and animal health from emerging pathogens. Initially, the disease-causing agent will be unknown and needs to be identified; this often requires specific laboratory facilities. Here we describe the development of an unbiased detection assay for RNA and DNA viruses using metagenomic Nanopore sequencing and simple methods that can be transferred into a field setting. Human clinical samples containing the RNA virus SARS-CoV-2 or the DNA viruses human papillomavirus (HPV) and molluscum contagiosum virus (MCV) were used as a test of concept. Firstly, the virus detection potential was optimized by investigating different pretreatments for reducing non-viral nucleic acid components. DNase I pretreatment followed by filtration increased the proportion of SARS-CoV-2 sequenced reads > 500-fold compared with no pretreatments. This was sufficient to achieve virus detection with high confidence and allowed variant identification. Next, we tested individual SARS-CoV-2 samples with various viral loads (measured as CT-values determined by RT-qPCR). Lastly, we tested the assay on clinical samples containing the DNA virus HPV and co-infection with MCV to show the assay's detection potential for DNA viruses. This protocol is fast (same day results). We hope to apply this method in other settings for point of care detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.

Knowledge about agricultural crops and their mechanisms is crucial in a time focused on climate. Flavonoids are plant secondary metabolites present in many plant species, including narrow-leafed lupin (Lupinus angustifolius L.). To gain a better understanding of the biological effect of flavonoids in the soil, the link between roots and soil must be elucidated. Plants were grown in a long-term crop rotation field experiment, where roots and rhizosphere soil were sampled under L. angustifolius and reference spring barley (Hordeum vulgare L.). Three high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) methods were developed and validated for the identification and quantification of 27 flavonoids in roots and rhizosphere soil, with flavonoids present in the soil representing exudation. Soil extraction using acetonitrile (ACN) and methanol (MeOH) was compared to 70% MeOH. In addition, to elucidate the bioavailable flavonoids, water-based extractions were investigated. The optimal soil extraction method was using 70% MeOH, achieving acceptable recoveries for several compounds. L. angustifolius roots contained 14 of 27 flavonoids at concentrations of 0.05–736 μg/g DW; genistein, genistin, and luteone being the most abundant. Four flavonoids were detected in L. angustifolius soil, but not in H. vulgare soil. None of the water-based extractions resulted in flavonoid quantities similar to those obtained with 70% MeOH extraction. L. angustifolius roots contained larger quantities of flavonoids than H. vulgare roots. The presence of four flavonoids in L. angustifolius soil, and not in H. vulgare soil, suggests that the flavonoids were exuded from the L. angustifolius roots. Sonication using 70% MeOH was an efficient soil extraction method, and enabled quantification of the flavonoid pool present in soil at the sampling time point.

Background: The more infectious SARS-CoV-2 virus lineage B.1.1.7, rapidly spread in Europe after December 2020, and a concern of B.1.1.7 causing more severe disease has been raised. Denmark has one of Europe´s highest capacities per capita of SARS-CoV-2 reverse transcription polymerase chain reaction (RT PCR) test and whole genome sequencing (WGS). We used national health register-data to explore whether B.1.1.7 increases the risk of COVID-19 hospitalisation. Methods and Findings: In an observational cohort study we included all SARS-CoV-2 RT PCR test-positive individuals in Denmark sampled between the 1st January and until the 9th February, 2021, identified in the national COVID-19 surveillance system. The surveillance system includes national individual RT PCR test results and viral WGS analyses and data from national health registers including COVID-19 related hospital admissions defined as first admission within 14 days of the test-positive swab. The odds ratio (OR) of admission according to infection with B.1.1.7, vs other co-existing lineages, was calculated in a logistic regression model adjusted for sex, age, period, follow-up time less than 14 days, region, and comorbidities. A total of 35,887 test-positive individuals were identified, 23,057 (64%) had WGS performed, of whom 18,499 (80%) resulted in a viral genome and a total of 2,155 of these were lineage B.1.1.7. The proportion of individuals with B.1.1.7 increased from 4% in early January to 45% in early February. Among the individuals with viral genome data, B.1.1.7 was associated with a crude OR of admission of 0.87 (95%CI, 0.72-1.05) and an adjusted OR of 1.64 (95%CI, 1.32-2.04) based on 128 admissions after B.1.1.7 infection and 1,107 admissions after infection with other lineages. The adjusted OR was increased in all strata of age and calendar time - the two most important confounders of the crude OR. Conclusions: Infection with lineage B.1.1.7 was associated with an increased risk of hospitalisation compared with other lineages. This finding may have serious public health impact in countries with spread of B.1.1.7 and can support hospital preparedness and modelling of projected impact of the epidemic. Funding Statement: The authors received no specific funding for this work. Declaration of Interests: The authors declare that they have no competing interest. Ethics Approval Statement: This study was conducted on administrative register data. According to Danish law, ethics approval is not needed for such research.

Background: Influenza A virus in swine herds represents a major problem for the swine industry and poses a constant threat for the emergence of novel pandemic viruses and the development of more effective influenza vaccines for pigs is desired. By optimizing the vector backbone and using a needle-free delivery method, we have recently demonstrated a polyvalent influenza DNA vaccine that induces a broad immune response, including both humoral and cellular immunity. Objectives: To investigate the protection of our polyvalent influenza DNA vaccine approach in a pig challenge study. Methods: By intradermal needle-free delivery to the skin, we immunized pigs with two different doses (500 μg and 800 μg) of an influenza DNA vaccine based on six genes of pandemic origin, including internally expressed matrix and nucleoprotein and externally expressed hemagglutinin and neuraminidase as previously demonstrated. Two weeks following immunization, the pigs were challenged with the 2009 pandemic H1N1 virus. Results: When challenged with 2009 pandemic H1N1, 0/5 vaccinated pigs (800 μg DNA) became infected whereas 5/5 unvaccinated control pigs were infected. The pigs vaccinated with the low dose (500 μg DNA) were only partially protected. The DNA vaccine elicited binding-, hemagglutination inhibitory (HI) − as well as crossreactive neutralizing antibody activity and neuraminidase inhibiting antibodies in the immunized pigs, in a dosedependent manner. Conclusion: The present data, together with the previously demonstrated immunogenicity of our influenza DNA vaccine, indicate that naked DNA vaccine technology provides a strong approach for the development of improved pig vaccines, applying realistic low doses of DNA and a convenient delivery method for mass vaccination. info:eu-repo/semantics/publishedVersion

The presence of bioactive benzoxazinoids (BXs) in mature whole grain and experimental bread products was recently shown. The aim of this study was to reveal the level of BXs in a broad range of commercial cereal products and discuss these findings in relation to ingredients and preparation processes. The concentrations of 11 BX compounds were determined by liquid chromatography–triple quadrupole mass spectrometry (LC–MS/MS) in 25 supermarket-available cereal food products. The total BX content varied from below the limit of detection to >500 μg/g dry matter (DM) with some degree of variation among different lots. The products W (Rugsandwich), H (Gulerodsrugbrod), L (Morke Multikerneboller) and AA (Solsikkeklapper), which were all rich in rye-based ingredients, had a total BX concentration >300 μg/g DM. Double hexose derivatives of 2-hydroxy-1,4-benzoxazin-3-one (HBOA), 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2-β- d -glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one (DIBOA-glc) were the major BXs in most products. Further studies into the health effects of BXs should be conducted, and future exploitation of these compounds seems possible.

OBJECTIVES: Prostate cancer is a common cancer diagnosis among men, but the role of diet and food components remains controversial. Benzoxazinoids (BXs) is a potent group of bioactive compounds found in rye foods that seem to have the potential to inhibit prostate cancer growth in vitro but studies in humans are lacking. We therefore aimed to investigate the concentrations of different BXs and their metabolites after whole grain rye consumption in comparison to refined wheat and to correlate these compounds to PSA levels in men with indolent prostate cancer. METHODS: In a randomized controlled crossover study, men with prostate cancer (n = 24) consumed 485 gram of whole grain/bran rye and refined wheat foods for six weeks, with two weeks of washout in-between. The diets were isocaloric and contained the same amount of fiber by addition of cellulose in the refined wheat intervention. BXs in plasma samples were analyzed with HPLC- QTRAP/MS-ESI. RESULTS: Seventeen men finished the trial and were included in data analysis. For most BXs, the concentrations were significantly higher after the whole grain rye compared to the refined wheat intervention. The BXs or BXs metabolites HBOA-glc, HHPAA, HBOA-glcA, HPAA-glcA (∼19.4–0.4 nmol/L in plasma after interventions) were significantly inversely correlated to PSA level. CONCLUSIONS: In men with indolent prostate cancer, most BXs were significantly higher after an intervention with whole grain rye compared to refined wheat. The inverse correlation between four BXs or BXs metabolites and PSA may indicate on an inhibitory effect on prostate cancer cell growth. This could open for new preventive food-based strategies, but results would need to be replicated. FUNDING SOURCES: Independent Research Fund Denmark - Technology and Production Formas Swedish Research Council.

BACKGROUND: Pigs are natural hosts for influenza A viruses, and the infection is widely prevalent in swine herds throughout the world. Current commercial influenza vaccines for pigs induce a narrow immune response and are not very effective against antigenically diverse viruses. To control influenza in pigs, the development of more effective swine influenza vaccines inducing broader cross-protective immune responses is needed. Previously, we have shown that a polyvalent influenza DNA vaccine using vectors containing antibiotic resistance genes induced a broadly protective immune response in pigs and ferrets using intradermal injection followed by electroporation. However, this vaccination approach is not practical in large swine herds, and DNA vaccine vectors containing antibiotic resistance genes are undesirable.OBJECTIVES: To investigate the immunogenicity of an optimized version of our preceding polyvalent DNA vaccine, characterized by a next-generation expression vector without antibiotic resistance markers and delivered by a convenient needle-free intradermal application approach.METHODS: The humoral and cellular immune responses induced by three different doses of the optimized DNA vaccine were evaluated in groups of five to six pigs. The DNA vaccine consisted of six selected influenza genes of pandemic origin, including internally expressed matrix and nucleoprotein and externally expressed hemagglutinin and neuraminidase.RESULTS: Needle-free vaccination of growing pigs with the optimized DNA vaccine resulted in specific, dose-dependent immunity down to the lowest dose (200μg DNA/vaccination). Both the antibody-mediated and the recall lymphocyte immune responses demonstrated high reactivity against vaccine-specific strains and cross-reactivity to vaccine-heterologous strains.CONCLUSION: The results suggest that polyvalent DNA influenza vaccination may provide a strong tool for broad protection against swine influenza strains threatening animal as well as public health. In addition, the needle-free administration technique used for this DNA vaccine will provide an easy and practical approach for the large-scale vaccination of swine.

Fusarium head blight (FHB) is a devastating disease of wheat (Triticum aestivum L.) caused by a mycotoxigenic fungus Fusarium graminearum resulting in significantly decreased yields and accumulation of toxic trichothecenes in grains. We tested 7 major secondary metabolites from wheat for their effect on trichothecene production in liquid cultures of F. graminearum producing trichothecene 15-acetyldeoxynivalenol (15-ADON). 2,4-Dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) benzoxazinoid completely abolished toxin production without any apparent effect on fungal growth. DIMBOA strongly affected the expression of Tri6, encoding a major transcriptional regulator of several genes of the trichothecene biosynthesis pathway. DIMBOA also repressed expression of Tri5, encoding trichodiene synthase, the first enzyme in the trichothecene biosynthesis pathway. Thus, DIMBOA could play an important role against the accumulation of trichothecenes in wheat grain. Breeding or engineering of wheat with increased levels of benzoxazinoids could provide varieties with increased resistance against trichothecene contamination of grain and lower susceptibility to FHB.

Benzoxazinoids are important phytochemicals found in wheat and rye that are associated with plant resistance against pathogens, and recent studies have emphasized the potential health-promoting role of these compounds i.e. anti-cancer, anti-allergy and anti-inflammation. Accordingly, an understanding of their distribution in seeds and the effect of different processing techniques on their transformation will be helpful in identifying the mechanisms of their production and distribution and will support the on-going efforts to utilize these compounds in health-promoting food products.The analysis of seed fractions obtained from the milling of wheat and rye showed significantly higher concentrations of these bioactive compounds in the germ than in the other fractions, i.e. the bran and endosperm. Di-hexoses of 2,4-dihydroxy-1, 4-benzoxazin-3-one (DIBOA-glc-hexose) and 2-hydroxy-1, 4-benzoxazin-3-one (HBOA-glc-hexose) were the predominant compounds found in the different wheat and rye seed fractions followed by DIBOA-glc and DIBOA.The soaking and boiling of three rye-based breakfast cereals resulted in considerable changes in the benzoxazinoid contents. The soaking of pearled rye promoted the conversion of DIBOA-glc-hexose into DIBOA-glc. When these cereals were boiled, the increase in the DIBOA-glc content was much lower than that observed for soaking. For rye flakes, the pattern of these benzoxazinoids was different from that in pearled rye seeds. A considerable amount of the benzoxazinoids was also leached into the water during soaking or boiling. This study contributes to the understanding of the underlying processes involved in the biochemical changes of benzoxazinoids and will be the basis for future studies on other food-processing techniques.

In line of the development of a food composition database for Bangladesh, 10 minor indigenous fruits were analysed for their nutrient composition comprising ascorbic acid, carotenoids and mineral values. Nutrient data obtained have been compared with published data reported in different literatures, book and United States Department of Agriculture-National Nutrient Database for Standard Reference. Ascorbic acid was highest in Wood apple and lowest in Roselle. Monkey jack contained the highest amount of carotenoids, zinc and copper. Content of calcium, magnesium and phosphorous were found highest in Antidesma velutinum. Potassium was the highest in Wood apple followed by in Moneky jack. It was noted that most of the minor fruits have much higher amount of ascorbic acid than the national fruit – Jack fruit ripe, the king fruit – Mango ripe of Bangladesh and exotic fruits – Apple and Grapes. The nutrient values of these minor fruits would make awareness among the people for their mass consumption for healthy life and to grow more minor fruit trees from extinction in order to maintain biodiversity.