Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for ...phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies.
The ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response. Mobile phone data have been proposed to monitor effectiveness ...of non-pharmaceutical interventions, to assess potential drivers of spatiotemporal spread, and to support contact tracing efforts. While these data may be an important part of COVID-19 response, their use must be considered alongside a careful understanding of the behaviors and populations they capture. Here, we review the different applications for mobile phone data in guiding and evaluating COVID-19 response, the relevance of these applications for infectious disease transmission and control, and potential sources and implications of selection bias in mobile phone data. We also discuss best practices and potential pitfalls for directly integrating the collection, analysis, and interpretation of these data into public health decision making.
This article investigates the impact of land tenure insecurity on the migration decisions of China's rural residents from 1995 to 2003. The article appeals to a simple model to frame the relationship ...between migration and the probability that a reallocation of land in the village will occur in the following year. Empirically, the article first demonstrates that a village leader's support for an administrative land reallocation carries with it the risk of losing a future election. Exploiting election timing and village heterogeneity in lineage group composition, the article identifies the effect of reallocation risk on migration decisions. In response to an expected land reallocation in the following year, the probability that a rural resident migrates out of the county declines by 2.4 percentage points, which accounts for 15% of the annual share of village residents, aged 16 to 50, who worked as migrants during the period. This finding underscores the potential importance of secure property rights for facilitating labor market integration and the movement of labor out of agriculture.
Understanding the level and characteristics of protection from past SARS-CoV-2 infection against subsequent re-infection, symptomatic COVID-19 disease, and severe disease is essential for predicting ...future potential disease burden, for designing policies that restrict travel or access to venues where there is a high risk of transmission, and for informing choices about when to receive vaccine doses. We aimed to systematically synthesise studies to estimate protection from past infection by variant, and where data allow, by time since infection.
In this systematic review and meta-analysis, we identified, reviewed, and extracted from the scientific literature retrospective and prospective cohort studies and test-negative case-control studies published from inception up to Sept 31, 2022, that estimated the reduction in risk of COVID-19 among individuals with a past SARS-CoV-2 infection in comparison to those without a previous infection. We meta-analysed the effectiveness of past infection by outcome (infection, symptomatic disease, and severe disease), variant, and time since infection. We ran a Bayesian meta-regression to estimate the pooled estimates of protection. Risk-of-bias assessment was evaluated using the National Institutes of Health quality-assessment tools. The systematic review was PRISMA compliant and was registered with PROSPERO (number CRD42022303850).
We identified a total of 65 studies from 19 different countries. Our meta-analyses showed that protection from past infection and any symptomatic disease was high for ancestral, alpha, beta, and delta variants, but was substantially lower for the omicron BA.1 variant. Pooled effectiveness against re-infection by the omicron BA.1 variant was 45·3% (95% uncertainty interval UI 17·3–76·1) and 44·0% (26·5–65·0) against omicron BA.1 symptomatic disease. Mean pooled effectiveness was greater than 78% against severe disease (hospitalisation and death) for all variants, including omicron BA.1. Protection from re-infection from ancestral, alpha, and delta variants declined over time but remained at 78·6% (49·8–93·6) at 40 weeks. Protection against re-infection by the omicron BA.1 variant declined more rapidly and was estimated at 36·1% (24·4–51·3) at 40 weeks. On the other hand, protection against severe disease remained high for all variants, with 90·2% (69·7–97·5) for ancestral, alpha, and delta variants, and 88·9% (84·7–90·9) for omicron BA.1 at 40 weeks.
Protection from past infection against re-infection from pre-omicron variants was very high and remained high even after 40 weeks. Protection was substantially lower for the omicron BA.1 variant and declined more rapidly over time than protection against previous variants. Protection from severe disease was high for all variants. The immunity conferred by past infection should be weighed alongside protection from vaccination when assessing future disease burden from COVID-19, providing guidance on when individuals should be vaccinated, and designing policies that mandate vaccination for workers or restrict access, on the basis of immune status, to settings where the risk of transmission is high, such as travel and high-occupancy indoor settings.
Bill & Melinda Gates Foundation, J Stanton, T Gillespie, and J and E Nordstrom.
This article presents empirical evidence from household and firm survey data collected during 2009−2010 on the implementation of the 2008 Labor Contract Law and effects on China’s workers. The ...Government and local labor bureaus have made substantial efforts to enforce the provisions of the new Law, which has likely contributed to reversing a trend toward increasing informalization of the urban labor market. Enforcement of the Law, however, varies substantially across cities. The article analyzes the determinants of worker satisfaction with the Law’s enforcement, workers’ propensity to have a labor contract, their awareness of the Law’s content and their likelihood of initiating disputes, and finds that all are highly correlated with education level, especially for migrants. Although higher labor costs may have had a negative impact on manufacturing employment growth, this has not led to an overall increase in aggregate unemployment or prevented the rapid growth of real wages. Less progress has been made in increasing social insurance coverage, although signing a labor contract is more likely to be associated with participation in social insurance programs than in the past, particularly for migrant workers.
During recent decades, pathogens that originated in bats have become an increasing public health concern. A major challenge is to identify how those pathogens spill over into human populations to ...generate a pandemic threat
. Many correlational studies associate spillover with changes in land use or other anthropogenic stressors
, although the mechanisms underlying the observed correlations have not been identified
. One limitation is the lack of spatially and temporally explicit data on multiple spillovers, and on the connections among spillovers, reservoir host ecology and behaviour and viral dynamics. We present 25 years of data on land-use change, bat behaviour and spillover of Hendra virus from Pteropodid bats to horses in subtropical Australia. These data show that bats are responding to environmental change by persistently adopting behaviours that were previously transient responses to nutritional stress. Interactions between land-use change and climate now lead to persistent bat residency in agricultural areas, where periodic food shortages drive clusters of spillovers. Pulses of winter flowering of trees in remnant forests appeared to prevent spillover. We developed integrative Bayesian network models based on these phenomena that accurately predicted the presence or absence of clusters of spillovers in each of the 25 years. Our long-term study identifies the mechanistic connections between habitat loss, climate and increased spillover risk. It provides a framework for examining causes of bat virus spillover and for developing ecological countermeasures to prevent pandemics.
Humans can impact the spatial transmission dynamics of infectious diseases by introducing pathogens into susceptible environments. The rate at which this occurs depends in part on human-mobility ...patterns. Increasingly, mobile-phone usage data are used to quantify human mobility and investigate the impact on disease dynamics. Although the number of trips between locations and the duration of those trips could both affect infectious-disease dynamics, there has been limited work to quantify and model the duration of travel in the context of disease transmission. Using mobility data inferred from mobile-phone calling records in Namibia, we calculated both the number of trips between districts and the duration of these trips from 2010 to 2014. We fit hierarchical Bayesian models to these data to describe both the mean trip number and duration. Results indicate that trip duration is positively related to trip distance, but negatively related to the destination population density. The highest volume of trips and shortest trip durations were among high-density districts, whereas trips among low-density districts had lower volume with longer duration. We also analyzed the impact of including trip duration in spatial-transmission models for a range of pathogens and introduction locations. We found that inclusion of trip duration generally delays the rate of introduction, regardless of pathogen, and that the variance and uncertainty around spatial spread increases proportionally with pathogen-generation time. These results enhance our understanding of disease-dispersal dynamics driven by human mobility, which has potential to elucidate optimal spatial and temporal scales for epidemic interventions.
This paper uses a unique panel of data from rural China to analyze the impact of expanding connections to off-farm labor markets on the income and consumption of farm households. With stronger ...village ties to both migrant and local off-farm labor markets, households in previously autarkic village communities experience reduced exposure to shocks affecting agricultural production. The analyses presented in this paper control for the persistent effect of past shocks influencing income and consumption, household attrition potentially correlated with shocks, and endogeneity of household demographic composition, land holdings and village network connections to migrant and local labor markets.
Recent research has shown that participation in migrant labor markets has led to substantial increases in incomeforfamilies in rural China. This article addresses the question of how participation is ...affected by elderly parent health. We find that younger adults are less likely to work as migrants when a parent is ill. Poor health of an elderly parent has less impact on the probability of employment as a migrant when an adult child has siblings who may be available to provide care. We also highlight the potential importance of including information on nonresident family members when studying how parent illness and elder care requirements influence the labor supply decisions of adult children.
Citrullination, the post-translational conversion of arginine to citrulline by the enzyme family of peptidylarginine deiminases (PADs), is associated with several diseases, and specific citrullinated ...proteins have been shown to alter function while others act as auto-antigens. In this study, we identified citrullinated proteins in human myocardial samples, from healthy and heart failure patients, and determined several potential functional consequences. Further we investigated PAD isoform cell-specific expression in the heart.
A citrullination-targeted proteomic strategy using data-independent (SWATH) acquisition method was used to identify the modified cardiac proteins. Citrullinated-induced sarcomeric proteins were validated using two-dimensional gel electrophoresis and investigated using biochemical and functional assays. Myocardial PAD isoforms were confirmed by RT-PCR with PAD2 being the major isoform in myocytes. In total, 304 citrullinated sites were identified that map to 145 proteins among the three study groups: normal, ischaemia, and dilated cardiomyopathy. Citrullination of myosin (using HMM fragment) decreased its intrinsic ATPase activity and inhibited the acto-HMM-ATPase activity. Citrullinated TM resulted in stronger F-actin binding and inhibited the acto-HMM-ATPase activity. Citrullinated TnI did not alter the binding to F-actin or acto-HMM-ATPase activity. Overall, citrullination of sarcomeric proteins caused a decrease in Ca(2+) sensitivity in skinned cardiomyocytes, with no change in maximal calcium-activated force or hill coefficient.
Citrullination unique to the cardiac proteome was identified. Our data indicate important structural and functional alterations to the cardiac sarcomere and the contribution of protein citrullination to this process.
PDF
