SIR model for assessing the impact of the advent of Omicron and mitigating measures on infection pressure and hospitalization needs

Background: On 26 November 2021, the world health organization (WHO) designated the coronavirus SARS-CoV-2 B.1.1.529 a variant of concern, named Omicron (WHO, 2021a). As of December 16, Omicron has been detected in 89 countries (WHO, 2021b). The thread posed by Omicron is highly uncertain. Methods and findings: For the analysis of the impact of Omicron on infection pressure and hospitalization needs we developed an open-source stochastic SIR (Susceptible-Infectious-Removed) fast-model for simulating the transmission in the transition stage from the prevailing variant (most often Delta) to Omicron. The model is capable to predict trajectories of infection pressure and hospitalization needs, considering (a) uncertainties for the (Omicron) parametrization, (b) pre-existing vaccination and/or partial immunity status of the population, and demographic specific aspects regarding reference hospitalization needs, (c) effects of mitigating measures including social distancing and accelerated vaccination (booster) campaigns. Conclusions: The SIR model approach yields results in fair agreement with Omicron transmission characteristics observed in South Africa and prognosis results in Europe. The equations underlying the SIR formulation allows to effectively explore the effect of Omicron parametrization on anticipated infection growth rates and hospitalization rates relative to the prevailing variant. The models are online available as open source on GitHub.

Genomic associations with poxvirus across divergent island populations in Berthelot's pipit

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot’s pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses provide evidence that pathogen-mediated selection has shaped genomic variation among relatively recently colonised island bird populations, and highlights the utility of genotype-environment associations for identifying candidate genes involved in adaption to local pathogen pressures.

Resistance of modern spring barley cultivars to harmful organisms

Background. Diseases and pests cause great damage to barley stands and harvests. Harvest losses from harmful organisms reach 25–30%.Materials and methods. During 2017–2020, 46 spring barley cultivars from the VIR collection, listed in the State Register for Selection Achievements, were studied for their resistance to fritfly, net and spot blotches, brown rust, and powdery mildew. The tests were carried out in the field with provocative colonization by fritfly and under natural infection pressure of leaf pathogens.Results and conclusions. In 2017, net blotch predominated over other diseases. In 2018, there was an epyphytotic outburst of spot blotch, and cultivars with weak development of this disease were identified. In 2019 and 2020, the incidence of brown rust and powdery mildew was significant, and the virulence of fritfly increased greatly in the same years. Field tests resulted in identification of 3 barley accessions resistant to fritfly: ‘Odon’ (k-31118, Buryatia), ‘Miar’ (k-31203, Orenburg Province), and ‘Omsky 99’ (k-31230, Omsk Province). Cv. ‘Posada’ (k-31245, Germany) was weakly affected by fritfly, brown rust and powdery mildew. Cultivars were selected for their low susceptibility to powdery mildew (up to 5%): ‘Chiraz’ (k-31131, Denmark), ‘Cheerio’ (k-31297, Denmark), and ‘Odyssey’ (k-31333, England), and brown rust: ‘Chiraz’ (k-31131, Denmark), ‘Eifel’ (k-31249, France), ‘Ursa’ (k-31339), and ‘Sunshine’ (k-31129, Germany). Such long-term assessment results can be used in breeding programs to develop cultivars with group or complex resistance to harmful organisms.

Mental Well-Being During Stages of COVID-19 Lockdown Among Pregnant Women And New Mothers

Background: Pregnancy and early motherhood are sensitive times where epidemic disease outbreaks can affect mental health negatively. Countries and health care systems handled the pandemic and lockdowns differently and knowledge about how the COVID-19 pandemic affected the mental well-being of pregnant women and new mothers is limited and points in different directions. Aim. to investigate symptoms of anxiety and depression in a population of pregnant women and new mothers in various stages of infection pressure and lock down during the first 15 months of the COVID-19 pandemic in Denmark. Methods: The study population was nested an inception cohort of women recruited in their first trimester of pregnancy. Data about mental health of the woman was obtained in relation to pregnancy and child development (first trimester, 8 weeks postpartum and 5 months postpartum), and data were analysed cross-sectionally according to calendar time (periods defined by infection rate and lock-down during the COVID-19 epidemic).Results: No differences in reported levels of depressive symptoms between the six examined time periods of the pandemic were observed. Specifically, symptoms remained unchanged after the first lock-down. No major changes in anxiety symptoms were observed in relation to increased infection pressure or lockdowns, but a small increase was observed during the second lockdown in women 8 weeks postpartum. Conclusion: No clear change in mood among pregnant women was seen between during the stages of Covid-19 pandemic in Denmark.

Grapevine Rpv3-, Rpv10- and Rpv12-mediated defense responses against Plasmopara viticola and the impact of their deployment on fungicide use in viticulture

Background The high susceptibility of European grapevine cultivars (Vitis vinifera) to downy mildew (Plasmopara viticola) leads to the intensive use of fungicides in viticulture. To reduce this input, breeding programs have introgressed resistance loci from wild Vitis species into V. vinifera, resulting in new fungus-resistant grapevine cultivars (FRC). However, little is known about how these different resistance loci confer resistance and what the potential reduction in fungicide applications are likely to be if these FRCs are deployed. To ensure a durable and sustainable resistance management and breeding, detailed knowledge about the different defense mechanisms mediated by the respective Rpv (Resistance to P. viticola) resistance loci is essential. Results A comparison of the resistance mechanisms mediated by the Rpv3–1, Rpv10 and/or Rpv12-loci revealed an early onset of programmed cell death (PCD) at 8 hours post infection (hpi) in Rpv12-cultivars and 12 hpi in Rpv10-cultivars, whereas cell death was delayed in Rpv3-cultivars and was not observed until 28 hpi. These temporal differences correlated with an increase in the trans-resveratrol level and the formation of hydrogen peroxide shortly before onset of PCD. The differences in timing of onset of Rpv-loci specific defense reactions following downy mildew infection could be responsible for the observed differences in hyphal growth, sporulation and cultivar-specific susceptibility to this pathogen in the vineyard. Hereby, Rpv3- and Rpv12/Rpv3-cultivars showed a potential for a significant reduction of fungicide applications, depending on the annual P. viticola infection pressure and the Rpv-loci. Furthermore, we report on the discovery of a new P. viticola isolate that is able to overcome both Rpv3- and Rpv12-mediated resistance. Conclusion This study reveals that differences in the timing of the defense reaction mediated by the Rpv3-, Rpv10- and Rpv12-loci, result in different degrees of natural resistance to downy mildew in field. Vineyard trials demonstrate that Rpv12/Rpv3- and Rpv3-cultivars are a powerful tool to reduce the dependence of grape production on fungicide applications. Furthermore, this study indicates the importance of sustainable breeding and plant protection strategies based on resistant grapevine cultivars to reduce the risk of new P. viticola isolates that are able to overcome the respective resistance mechanism.

Resistance of synthetic hexaploid wheat to the leaf rust pathogen

Background. One of the promising sources for enrichment of the common wheat (Triticum aestivum L.) gene pool with new alleles is synthetic hexaploid wheat (SHW), or allopolyploids from crossing tetraploid wheats (2n = 4x = 28, BBAA) with accessions of Aegilops tauschii Coss. (2n = 2x = 14, DD), and subsequent doubling of the chromosome number in the hybrids. Objectives of the study were to evaluate the SHW accessions from the VIR collection for resistance to Puccinia triticina Erikss. populations collected in Russia; genotype the accessions; and summarize information from the published sources concerning the resistance of the studied accessions to other harmful diseases and pests.Materials and methods. Resistance of 36 SHW accessions from the VIR collection to the populations of P. triticina was assessed in the laboratory and in the field, under artificial infection pressure, using the techniques developed by the Institute of Plant Protection. A phytopathological test and PCR markers were used to identify the Lr genes.Results and conclusion. The SHW accessions were characterized according to their resistance to the Russian populations of the wheat leaf rust pathogen. The sources of resistance in the phase of emergence and in adult plants were identified. The phytopathological test isolated three accessions with Lr23; the PCR marker of Lr21=Lr40 was found in 11 accessions, Lr39=Lr41 in 19, and Lr22a in 3. At the same time, k-65496, k-65515 and k-65517 had si multaneously Lr21=Lr40 and Lr39=Lr41, while k-65497, k-65503 and k-65508 had Lr22a and Lr39=Lr41. The analysis of published data showed that many of the studied SHW accessions were also resistant to other harmful diseases and insect pests, so they are of interest for further studying and possible use in domestic breeding.

Powdery mildew resistance of barley accessions from Dagestan

Powdery mildew caused by the parasitic fungus Blumeria graminis (DC.) Golovin ex Speer f. sp. hordei Marchal is one of the most common diseases of barley. Growing resistant varieties can significantly minimize harmful effects of the pathogen. The specificity in the interaction between the fungus and its host plant requires a continuous search for new donors of the resistance trait. The powdery mildew resistance of 264 barley accessions from Dagestan and genetic control of the trait in resistant forms were studied under field and laboratory conditions. Forty-seven barley lines carrying previously identified powdery mildew resistance genes were also examined. During three years, the experimental material was evaluated under severe infection pressure at the Dagestan Experiment Station of VIR (North Caucasus, Derbent). Juvenile resistance against the Northwest (St. Petersburg, Pushkin) pathogen population was evaluated in a climatic chamber. The genetic control of B. graminis resistance in the selected accessions was studied with the application of hybridological and molecular analyses. The level of genetic diversity of Dagestan barley for effective resistance to powdery mildew is very low. Only two accessions, VIR-23787 and VIR-28212, are resistant against B. graminis at both seedling and adult plant stages. The high-level resistance of breeding line VIR-28212 originating from barley landrace VIR-17554 (Ep-80 Abyssinien) from Ethiopia is controlled by the recessive gene mlo11. Accession VIR-17554 is heterogeneous for the studied trait, with the powdery mildew resistant genotypes belonging to two varieties, dupliatrum (an awnless phenotype) and nigrinudum (an awned phenotype). In accession VIR-23787, a recessive resistance gene distinct from the mlo11 allele was identified. This accession is supposed to be protected by a new, effective pathogen resistance gene.

Development of spring durum wheat cultivars resistant to stem rust in Western Siberia

Background. Stem rust of wheat, caused by the biotrophic fungus Puccinia graminis Pers. f. sp. tritici Eriks. et Henn., is a dangerous disease that afflicts serious economic damage to the cultivation of durum wheat.Materials and methods. Cultivars and promising materials developed at the Spring Durum Wheat Breeding Laboratory, Omsk Agrarian Scientific Center (OASC), lines obtained under the CIMMYT and KASIB programs, and accessions from the VIR collection were the objects of research. Field experiments, phenological observations, and assessment of stem rust resistance were carried out from 1990 through 2019 in the OASC experimental fields using conventional methods. Resistance to the Ug99 race was evaluated under natural infection pressure at the Kenya Agricultural and Livestock Research Organization (KALRO).Results. Promising source material was identified and included in the Laboratory’s breeding program. The ways were shown to develop stable cultivars of spring durum wheat for the environments of Western Siberia. A strategy was proposed for the selection of genotypes in hybrid combinations of spring durum wheat: it would include early selection (starting from F2 ) for disease resistance with simultaneous screening for quantitative traits and pasta-making qualities. The description and advantages of cv. ‘Omsky korall’, submitted to the State Variety Trials in 2018, are presented. This cultivar combines high yield, adaptability, resistance to the local population and the Ug99 race of the stem rust pathogen, and excellent pasta-making qualities.Conclusion. As a result of these studies under heavy stem rust pressure in Western Siberia, all breeding nurseries obtained source material resistant to the Omsk population of P. graminis. The released cultivars ‘Omskaya yantarnaya’ and ‘Omsky izumrud’ demonstrate resistance to the Omsk population of the stem rust causative agent.

Atlantic salmon farms are a likely source of Tenacibaculum maritimum infection in migratory Fraser River sockeye salmon

Infectious disease from domestic hosts, held for agriculture, can impact wild species that migrate in close proximity, potentially reversing selective advantages afforded by migration. For sockeye salmon in British Columbia, Canada, juveniles migrate past numerous Atlantic salmon farms from which they may acquire a number of infectious agents. We analyse patterns of molecular detection in juvenile sockeye salmon for one bacterial pathogen, Tenacibaculum maritimum, known to cause disease in fish species around the globe and to cause mouthrot disease in farmed Atlantic salmon in BC. Our data show a clear peak in T. maritimum detections in the Discovery Islands region of BC, where sockeye migrate close to salmon farms. Using well established differential-equation models to describe sockeye migration and T. maritimum infection spread, we fit models to our detection data to assess support for multiple hypotheses describing farm- and background-origin infection. Despite a data-constrained inability to resolve certain epidemiological features of the system, such as the relative roles of post-infection mortality and recovery, our models clearly support the role of Discovery-Islands salmon farms in producing the observed patterns. Our best models (with 99.8% empirical model support) describe relatively constant (background) infection pressure, except around Discovery-Islands salmon farms, where farm-origin infection pressure peaked at 12.7 (approximate 95% CI: 4.5 to 31) times background levels. Given the evidence for farm-origin transfer of T. maritimum to Fraser-River sockeye salmon, the severity of associated disease in related species, and the imperilled nature of Fraser River sockeye generally, our results suggest the need for a more precautionary approach to managing farm/wild interactions in sockeye salmon.