SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers

Accurately estimating relative transmission rates of SARS-CoV-2 Variant of Concern and Variant of Interest viruses remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological behavior of SARS-CoV-2. Here, we extend methods for inferring the effective reproduction number of an epidemic using confirmed case data to jointly estimate variant-specific effective reproduction numbers and frequencies of co-circulating variants using case data and genetic sequences across states in the US from January to October 2021. Our method can be used to infer structured relationships between effective reproduction numbers across time series allowing us to estimate fixed variant-specific growth advantages. We use this model to estimate the effective reproduction number of SARS-CoV-2 Variants of Concern and Variants of Interest in the United States and estimate consistent growth advantages of particular variants across different locations.

Combining epidemiological and ecological methods to quantify social effects on Escherichia coli transmission

Enteric microparasites like Escherichia coli use multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships and direct physical contact between individuals is paramount for understanding how microparasites like E. coli spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal E. coli transmission experiments in two cattle ( Bos taurus ) herds, wherein all individuals were equipped with real-time location tracking devices. Following transmission experiments in this model system, we derived temporally dynamic social and contact networks from location data. Estimated social affiliations and dyadic contact frequencies during transmission experiments informed pairwise accelerated failure time models that we used to quantify effects of these sociobehavioural variables on weekly E. coli colonization risk in these populations. We found that sociobehavioural variables alone were ultimately poor predictors of E. coli colonization in feedlot cattle, but can have significant effects on colonization hazard rates ( p ≤ 0.05). We show, however, that observed effects were not consistent between similar populations. This work demonstrates that transmission experiments can be combined with real-time location data collection and processing procedures to create an effective framework for quantifying sociobehavioural effects on microparasite transmission.

Prevalence of Transmitted HIV-1 Drug Resistance Among Treatment-naive Individuals in China, 2000-2016

HIV with transmitted drug-resistance (TDR) limits the therapeutic options available for treatment-naive HIV patients. This study aimed to further our understanding of the prevalence and transmission characteristics of HIV with TDR for the application of first-line antiretroviral regimens. A total of 6578 HIV-1 protease/reverse-transcriptase sequences from treatment-naive individuals in China between 2000 and 2016, were obtained from the Los Alamos HIV Sequence Database and were analyzed for TDR. Transmission networks were constructed to determine genetic relationships. The spreading routes of large TDR clusters were identified using a Bayesian phylogeographic framework. TDR mutations were detected in 274 (4.51%) individuals, with 1.40% harboring TDR to nucleoside reverse transcriptase inhibitors, 1.52% to non-nucleoside reverse transcriptase inhibitors, and 1.87% to protease inhibitors. The most frequent mutation was M46L (58, 0.89%), followed by K103N (36, 0.55%), M46I (36, 0.55%), and M184V (26, 0.40%). The prevalence of total TDR initially decreased between 2000 and 2010 (OR = 0.83, 95% CI 0.73–0.95), and then increased thereafter (OR = 1.50, 95% CI 1.13–1.97). The proportion of sequences in a cluster (clustering rate) among HIV with TDR sequences was lower than that of sequences without TDR (40.5% vs. 48.8%, P = 0.023) and increased from 27.3% in 2005–2006 to 63.6% in 2015–2016 (P < 0.001). While most TDR mutations were associated with reduced relative transmission fitness, mutation M46I was associated with higher relative transmission fitness than the wild-type strain. This study identified a low-level prevalence of TDR HIV in China during the last two decades. However, the increasing TDR HIV rate sicn 2010, the persistent circulation of drug resistance mutations, and the expansion of self-sustaining drug resistance reservoirs may compromise the efficacy of antiretroviral therapy programs.

The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children

One of the significant unanswered questions about COVID-19 epidemiology relates to the role of children in transmission. This study uses data on infections within households in order to estimate the susceptibility and infectivity of children compared to those of adults. The data were collected from households in the city of Bnei Brak, Israel, in which all household members were tested for COVID-19 using PCR (637 households, average household size of 5.3). In addition, serological tests were performed on a subset of the individuals in the study. Inspection of the PCR data shows that children are less likely to be tested positive compared to adults (25% of children positive over all households, 44% of adults positive over all households, excluding index cases), and the chance of being positive increases with age. Analysis of joint PCR/serological data shows that there is under-detection of infections in the PCR testing, which is more substantial in children. However, the differences in detection rates are not sufficient to account for the differences in PCR positive rates in the two age groups. To estimate relative transmission parameters, we employ a discrete stochastic model of the spread of infection within a household, allowing for susceptibility and infectivity parameters to differ among children and adults. The model is fitted to the household data using a simulated maximum likelihood approach. To adjust parameter estimates for under-detection of infections in the PCR results, we employ a multiple imputation procedure using estimates of under-detection in children and adults, based on the available serological data. We estimate that the susceptibility of children (under 20 years old) is 43% (95% CI: [31%, 55%]) of the susceptibility of adults. The infectivity of children was estimated to be 63% (95% CI: [37%, 88%]) relative to that of adults.

Rectangular Glass Optical Fiber for Transmitting Sunlight in a Hybrid Concentrator Photovoltaic and Daylighting System

In this paper, we propose to use glass optical fibers with a rectangular cross-section for the application in a concentrator photovoltaic and daylighting system (CPVD) due to the unique characteristics of rectangular fibers with the capability to provide a uniform rectangular beam shape and a top-hat profile at the output. A mathematical model of rectangular optical fibers has been formulated in this study for different incident angles, and the results are compared with those of round optical fibers. Furthermore, the performance of the bundle of RGOFs is compared with that of the bundle of round optical fibers via simulation by using the ray-tracing method. The mathematical modelling and numerical simulation have demonstrated that the RGOF has advantages in terms of the improvement in relative transmission and reduction in energy leakage for the transmission through the optical fiber. The simulation result also shows that a higher flux of sunlight can be transmitted via the bundle of RGOFs as compared to the bundle of round optical fibers due to the higher coupling efficiency. The experiment results on the relative transmission in different incident angles for both round optical fibers and RGOFs have validated both the simulation and the mathematical modelling. The beam profile of our fabricated RGOF has also been measured via our laboratory facility. The flexibility test on the fabricated RGOF has been carried out to bend at a radius of 150 mm and twist at 90° at a fiber length of 2.2 m.

Rationing social contact during the COVID-19 pandemic: Transmission risk and social benefits of US locations

To prevent the spread of coronavirus disease 2019 (COVID-19), some types of public spaces have been shut down while others remain open. These decisions constitute a judgment about the relative danger and benefits of those locations. Using mobility data from a large sample of smartphones, nationally representative consumer preference surveys, and economic statistics, we measure the relative transmission reduction benefit and social cost of closing 26 categories of US locations. Our categories include types of shops, entertainments, and service providers. We rank categories by their trade-off of social benefits and transmission risk via dominance across 13 dimensions of risk and importance and through composite indexes. We find that, from February to March 2020, there were larger declines in visits to locations that our measures indicate should be closed first.

Rationing Social Contact During the COVID-19 Pandemic: Transmission Risk and Social Benefits of US Locations

To prevent the spread of COVID-19, some types of stores and gathering places have been shut down while others remain open. The decision to shut down one type of location and leave another open constitutes a judgement about the relative danger and benefits of those locations. Using location data from a large sample of smartphones, nationally representative consumer preference surveys, and government statistics, we measure the relative transmission risk benefit and social cost of closing about thirty different location categories in the US. Our categories include types of shops, entertainments, and public spaces. Our main analysis ranks twenty-six categories by those which should face stricter regulation via dominance across eight dimensions of risk and importance and through composite indexes. We find that from February to March, there were larger declines in visits to locations that our measures imply should be closed first. We hope this analysis will help policymakers decide how to reopen their economies.

CODE-BASED HYBRID CRYPTOSYSTEM: COMPARATIVE STUDIES AND ANALYSIS OF EFFICIENCY

In this paper the basic principles of construction and operation of McEliece and Niederreiter cryptosystems based on the use of error-correcting codes were considered. A new hybrid cryptosystem that combines the rules of encryption according to the above-mentioned schemes is proposed. Also, this paper presents the analysis and comparative studies from the standpoint of stability, the volume of public and private keys, length of ciphertext and relative speed of information transmission of the new proposed scheme and McEliece and Niederreiter cryptosystems. It is considered from an analytical point of view and with the help of graphic images. Comparative studies revealed that the hybrid cryptosystem retains the positive aspects of its predecessors, as well as allows us to increase the relative transmission rate with the preservation of the stability indicator to the classical and quantum cryptanalysis. One disadvantage is the increase in decoding time by adding information extracted as in Niederreiter scheme, but the increase in this indicator is not critical. Despite the demonstrated benefits, it remains open to all cryptosystems to reduce the amount of the used key data, which, in the case of quantum computers to maintain stability, still needs to be increased once.

Projecting the impact of variable MDR-TB transmission efficiency on long-term epidemic trends in South Africa and Vietnam

Whether multidrug-resistant tuberculosis (MDR-TB) is less transmissible than drug-susceptible (DS-)TB on a population level is uncertain. Even in the absence of a genetic fitness cost, the transmission potential of individuals with MDR-TB may vary by infectiousness, frequency of contact, or duration of disease. We used a compartmental model to project the progression of MDR-TB epidemics in South Africa and Vietnam under alternative assumptions about the relative transmission efficiency of MDR-TB. Specifically, we considered three scenarios: consistently lower transmission efficiency for MDR-TB than for DS-TB; equal transmission efficiency; and an initial deficit in the transmission efficiency of MDR-TB that closes over time. We calibrated these scenarios with data from drug resistance surveys and projected epidemic trends to 2040. The incidence of MDR-TB was projected to expand in most scenarios, but the degree of expansion depended greatly on the future transmission efficiency of MDR-TB. For example, by 2040, we projected absolute MDR-TB incidence to account for 5% (IQR: 4–9%) of incident TB in South Africa and 14% (IQR: 9–26%) in Vietnam assuming consistently lower MDR-TB transmission efficiency, versus 15% (IQR: 8–27%)and 41% (IQR: 23–62%), respectively, assuming shrinking transmission efficiency deficits. Given future uncertainty, specific responses to halt MDR-TB transmission should be prioritized.

Coupling Waveguide-Based Micro-Sensors and Spectral Multivariate Analysis to Improve Spray Deposit Characterization in Agriculture

The leaf coverage surface is a key measurement of the spraying process to maximize spray efficiency. To determine leaf coverage surface, the development of optical micro-sensors that, coupled with a multivariate spectral analysis, will be able to measure the volume of the droplets deposited on their surface is proposed. Rib optical waveguides based on Ge-Se-Te chalcogenide films were manufactured and their light transmission was studied as a response to the deposition of demineralized water droplets on their surface. The measurements were performed using a dedicated spectrophotometric bench to record the transmission spectra at the output of the waveguides, before (reference) and after drop deposition, in the wavelength range between 1200 and 2000 nm. The presence of a hollow at 1450 nm in the relative transmission spectra has been recorded. This corresponds to the first overtone of the O–H stretching vibration in water. This result tends to show that the optical intensity decrease observed after droplet deposition is partly due to absorption by water of the light energy carried by the guided mode evanescent field. The probe based on Ge-Se-Te rib optical waveguides is thus sensitive throughout the whole range of volumes studied, i.e., from 0.1 to 2.5 μL. Principal Component Analysis and Partial Least Square as multivariate techniques then allowed the analysis of the statistics of the measurements and the predictive character of the transmission spectra. It confirmed the sensitivity of the measurement system to the water absorption, and the predictive model allowed the prediction of droplet volumes on an independent set of measurements, with a correlation of 66.5% and a precision of 0.39 μL.