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The emerging N501Y mutation in severe acute respiratory syndrome coronavirus 2, which becomes prevalent in the UK rapidly, is one of the major challenges of COVID-19 control. To explore the transmission advantage, we estimate that the N501Y substitution increases the infectivity by 52% (95% confidence interval: 46, 58) in terms of the reproduction number.

Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.

Background The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. Characterizing the role of the mutation activities is of importance to understand how the evolution of pathogen shapes the epidemiological outcomes at population scale. Methods We developed a statistical framework to reconstruct variant-specific reproduction numbers and estimate transmission advantage associated with the mutation activities marked by single substitution empirically. Using likelihood-based approach, the model is exemplified with the COVID-19 surveillance data from January 1 to June 30, 2020 in California, USA. We explore the potential of this framework to generate early warning signals for detecting transmission advantage on a real-time basis. Results The modelling framework in this study links together the mutation activity at molecular scale and COVID-19 transmissibility at population scale. We find a significant transmission advantage of COVID-19 associated with the D614G substitution, which increases the infectivity by 54% (95%CI: 36, 72). For the early alarming potentials, the analytical framework is demonstrated to detect this transmission advantage, before the mutation reaches dominance, on a real-time basis. Conclusions We reported an evidence of transmission advantage associated with D614G substitution, and highlighted the real-time estimating potentials of modelling framework.

Abstract Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth–death skyline model (BDSKY), BDSKY$\\lambda $, which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we show that BDSKY$\\lambda $ robustly infers the relative transmission rates under different epidemic scenarios. Using publicly available genome data of SARS-CoV-2, we apply BDSKY$\\lambda $ to quantify the transmission advantage of the Omicron over the Delta variant in Berlin, Germany. We find the overall transmission rate of Omicron to be scaled by a factor of two with pronounced variation between the individual clusters of each variant. These results quantify the transmission advantage of Omicron over the previously circulating Delta variant, in a crucial period of pre-established non-pharmaceutical interventions. By inferring variant- as well as cluster-specific transmission rate scaling factors, we show the differences in transmission dynamics for each variant. This highlights the importance of incorporating lineage-specific transmission differences in phylodynamic inference.

We examine the role that parental engagement with child’s education plays in the lifecourse dynamics of locus of control (LOC), one of the most widely studied non-cognitive skills related to economic decision-making. We focus on parental engagement as previous studies have shown that it is malleable, easy to measure, and often available for fathers, whose inputs are notably understudied in the received literature. We estimate a standard skill production function using rich British cohort data. Parental engagement is measured with information provided at age 10 by the teacher on whether the father or the mother is very interested in the child’s education. We deal with the potential endogeneity in parental engagement by employing an added-value model, using lagged measures of LOC as a proxy for innate endowments and unmeasured inputs. We find that fathers’, but not mothers’, engagement leads to internality, a belief associated with positive lifetime outcomes, in both young adulthood and middle age for female and socioeconomically disadvantaged cohort members. Fathers’ engagement also increases the probability of lifelong internality and fully protects against lifelong externality. Our findings highlight that fathers play a pivotal role in the skill production process over the lifecourse.

In theory, people who own real estate should have advantage finding a partner in the marriage market. Empirical analyses along this line, however, face three issues. First, it is difficult to identify any causality for whether housing facilitates marriage or expected marriage facilitates a housing purchase. Second, survey samples usually do not cover very wealthy people, and so the observations are top coding in the wealth dimension. Third, getting married is a dynamic life cycle decision, and rich life-history data are rarely available. This paper uses registry data from Taiwan to estimate the impact of males’housing wealth on their first-marriage duration, taking into account all three issues mentioned above. We find that a 10% increase in real estate wealth increases probability of a man getting married in any particular year by 3.92%. Our finding suggests that housing or real estate is a status good in the marriage market.

Parental income and wealth contribute to children's success but are at least partly endogenous to parents' cognitive and noncognitive skills. We estimate the degree to which mothers' skills measured in early adulthood confound the relationship between their economic resources and their children's postsecondary education outcomes. Analyses of National Longitudinal Survey of Youth 1979 suggest that maternal cognitive and noncognitive skills attenuate half of parental income's association with child baccalaureate college attendance, a fifth of its association with elite college attendance, and a quarter of its association with bachelor's degree completion. Maternal skills likewise attenuate a third of parental wealth's association with children's baccalaureate college attendance, half of its association with elite college attendance, and a fifth of its association with bachelor's degree completion. Observational studies of the relationship between parents' economic resources and children's postsecondary attainments that fail to account for parental skills risk seriously overstating the benefits of parental income and wealth.

We study the acting mechanism of an early-life social safety net program and quantify its impact on child health outcomes at birth. We consider both the equity and efficiency implications of program impacts and provide a metric to compare such programs around the world. In particular, we estimate the impact of participation in Chile Crece Contigo (ChCC), Chile’s flagship early-life health and social welfare program, using a difference-in-differences style model based on variation in program intensity and administrative birth data matched to social benefits usage. We find that this targeted social program had significant effects on birth weight (approximately 10 grams) and other early-life human capital measures. These benefits are largest among the most socially vulnerable groups but shift outcomes toward the middle of the distribution of health at birth. We show that the program is efficient when compared to other successful neonatal health programs around the world and find some evidence to suggest that maternal nutrition components and increased links to the social safety net are important action mechanisms.

Estimates of economic persistence and mobility in the United States, as measured by the intergenerational elasticity (IGE), cover a very wide range. Nevertheless, careful analyses of the evidence suggested until recently that as much as half, and possibly more, of economic advantages are passed on from parents to children. This “dominant hypothesis” was seriously challenged by the first-ever study of family-income mobility based on tax data (Chetty et al. 2014), which provided estimates of family-income IGEs indicating that only one-third of economic advantages are transmitted across generations and claimed that previous highly influential IGE estimates were upward biased. Using a different tax-based data set, this article provides estimates of family-income IGEs that strongly support the dominant hypothesis. The article also carries out a one-to-one comparison between IGEs estimated with the two tax-based data sets and shows that Chetty et al.’s estimates were driven downward by a combination of attenuation, life-cycle, selection, and functional-form biases. Lastly, the article determines the exact relationship between parental income inequality, economic persistence, and inequality of opportunity for income. This leads to the conclusion that, in the United States, at least half of income inequality among parents is transformed into inequality of opportunity among their children.