The Omicron SARS-CoV-2 variant of concern (VOC lineage B.1.1.529), which became dominant in many countries during early 2022, includes several subvariants with strikingly different genetic characteristics. Several countries, including Denmark, have observed the two Omicron subvariants: BA.1 and BA.2. In Denmark the latter has rapidly replaced the former as the dominant subvariant. Based on nationwide Danish data, we estimate the transmission dynamics of BA.1 and BA.2 following the spread of Omicron VOC within Danish households in late December 2021 and early January 2022. Among 8,541 primary household cases, of which 2,122 were BA.2, we identified a total of 5,702 secondary infections among 17,945 potential secondary cases during a 1-7 day follow-up period. The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. We found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19; 95%-CI 1.58-3.04), fully vaccinated individuals (OR 2.45; 95%-CI 1.77-3.40) and booster-vaccinated individuals (OR 2.99; 95%-CI 2.11-4.24), compared to BA.1. We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62 (95%-CI 1.96-3.52). The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1. We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

Background The Covid-19 pandemic is one of the most serious global public health threats in recent times. Understanding transmission of SARS-CoV-2 is of utmost importance to be able to respond to outbreaks and take action against spread of the disease. Transmission within the household is a concern, especially because infection control is difficult to apply within the household domain. Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission risk and attack rate. Results We studied the testing dynamics for COVID-19 and found that the day after receiving a positive test result within the household, 35% of potential secondary cases were tested and 13% of these were positive. After a primary case in 6,782 households, 82% of potential secondary cases were tested within 14 days, of which 17% tested positive as secondary cases, implying an attack rate of 17%. Among primary cases, those aged 0-24 were underrepresented when compared with the total population. We found an approximately linearly increasing relationship between attack rate and age. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults, while the risk seems to decrease with age for children. Conclusions Although there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household.

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We use laser light shaped by a digital micro-mirror device to realize arbitrary optical dipole potentials for one-dimensional (1D) degenerate Bose gases of 87 Rb trapped on an atom chip. Superposing optical and magnetic potentials combines the high flexibility of optical dipole traps with the advantages of magnetic trapping, such as effective evaporative cooling and the application of radio-frequency dressed state potentials. As applications, we present a 160 µm long box-like potential with a central tuneable barrier, a box-like potential with a sinusoidally modulated bottom and a linear confining potential. These potentials provide new tools to investigate the dynamics of 1D quantum systems and will allow us to address exciting questions in quantum thermodynamics and quantum simulations.

Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

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We present an open-source Matlab framework, titled iFluid, for simulating the dynamics of integrable models using the theory of generalized hydrodynamics (GHD). The framework provides an intuitive interface, enabling users to define and solve problems in a few lines of code. Moreover, iFluid can be extended to encompass any integrable model, and the algorithms for solving the GHD equations can be fully customized. We demonstrate how to use iFluid by solving the dynamics of three distinct systems: (i) The quantum Newton's cradle of the Lieb-Liniger model, (ii) a gradual field release in the XXZ-chain, and (iii) a partitioning protocol in the relativistic sinh-Gordon model. 8 4.2 Charges and currents of XXZ model 13 4.3 Partitioning protocol in relativistic sinh-Gordon 15 5 Conclusion 17 A Thermodynamic Bethe ansatz of implemented models 18 A.1 Lieb-Liniger model 18 A.2 XXZ spin chain model 19 A.3 Relativistic sinh-Gordon model 19 B Numerical implementation of GHD equations 20 1 arXiv:2001.02547v1 [cond-mat.stat-mech] 8 Jan 2020 SciPost Physics Submission B.1 Tensor representation and index conventions 20 B.2 Discretized GHD equations 21 References 22