Crowding and the shape of COVID-19 epidemics

Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Canada: Longitudinal Trend Analysis

BACKGROUND

This study provides an update on the status of the COVID-19 pandemic in Canada, building upon our initial analysis conducted in 2020 by incorporating an additional 2 years of data.

OBJECTIVE

This study aims to (1) summarize the status of the pandemic in Canada when the World Health Organization (WHO) declared the end of the public health emergency for the COVID-19 pandemic on May 5, 2023; (2) use dynamic and genomic surveillance methods to describe the history of the pandemic in Canada and situate the window of the WHO declaration within the broader history; and (3) provide historical context for the course of the pandemic in Canada.

METHODS

This longitudinal study analyzed trends in traditional surveillance data and dynamic panel estimates for COVID-19 transmissions and deaths in Canada from June 2020 to May 2023. We also used sequenced SARS-CoV-2 variants from the Global Initiative on Sharing All Influenza Data (GISAID) to identify the appearance and duration of variants of concern. For these sequences, we used Nextclade nomenclature to collect clade designations and Pangolin nomenclature for lineage designations of SARS-CoV-2. We used 1-sided t tests of dynamic panel regression coefficients to measure the persistence of COVID-19 transmissions around the WHO declaration. Finally, we conducted a 1-sided t test for whether provincial and territorial weekly speed was greater than an outbreak threshold of 10. We ran the test iteratively with 6 months of data across the sample period.

RESULTS

Canada's speed remained below the outbreak threshold for 8 months by the time of the WHO declaration ending the COVID-19 emergency of international concern. Acceleration and jerk were also low and stable. While the 1-day persistence coefficient remained statistically significant and positive (1.074; P<.001), the 7-day coefficient was negative and small in magnitude (-0.080; P=.02). Furthermore, shift parameters for either of the 2 most recent weeks around May 5, 2023, were negligible (0.003 and 0.018, respectively, with P values of .75 and .31), meaning the clustering effect of new COVID-19 cases had remained stable in the 2 weeks around the WHO declaration. From December 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling 1-sided t test of speed equal to 10 became entirely insignificant from mid-October 2022 onward.

CONCLUSIONS

While COVID-19 continues to circulate in Canada, the rate of transmission remained well below the threshold of an outbreak for 8 months ahead of the WHO declaration. Both standard and enhanced surveillance metrics confirm that the pandemic had largely ended in Canada by the time of the WHO declaration. These results can inform future public health interventions and strategies in Canada, as well as contribute to the global understanding of the trajectory of the COVID-19 pandemic.

Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences

Pathogen genomics can provide insights into underlying infectious disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here, we leverage pairs of identical sequences to characterise fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that the location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this work improves our ability to leverage large pathogen genome datasets to understand the determinants of infectious disease spread.

Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile

Human mobility is strongly associated with the spread of SARS-CoV-2 via air travel on an international scale and with population mixing and the number of people moving between locations on a local scale. However, these conclusions are drawn mostly from observations in the context of the global north where international and domestic connectivity is heavily influenced by the air travel network; scenarios where land-based mobility can also dominate viral spread remain understudied. Furthermore, research on the effects of nonpharmaceutical interventions (NPIs) has mostly focused on national- or regional-scale implementations, leaving gaps in our understanding of the potential benefits of implementing NPIs at higher granularity. Here, we use Chile as a model to explore the role of human mobility on disease spread within the global south; the country implemented a systematic genomic surveillance program and NPIs at a very high spatial granularity. We combine viral genomic data, anonymized human mobility data from mobile phones and official records of international travelers entering the country to characterize the routes of importation of different variants, the relative contributions of airport and land border importations, and the real-time impact of the country's mobility network on the diffusion of SARS-CoV-2. The introduction of variants which are dominant in neighboring countries (and not detected through airport genomic surveillance) is predicted by land border crossings and not by air travelers, and the strength of connectivity between comunas (Chile's lowest administrative divisions) predicts the time of arrival of imported lineages to new locations. A higher stringency of local NPIs was also associated with fewer domestic viral importations. Our analysis sheds light on the drivers of emerging respiratory infectious disease spread outside of air travel and on the consequences of disrupting regular movement patterns at lower spatial scales.

A Coupled Spatial-Network Model: A Mathematical Framework for Applications in Epidemiology

There is extensive evidence that network structure (e.g., air transport, rivers, or roads) may significantly enhance the spread of epidemics into the surrounding geographical area. A new compartmental modeling framework is proposed which couples well-mixed (ODE in time) population centers at the vertices, 1D travel routes on the graph's edges, and a 2D continuum containing the rest of the population to simulate how an infection spreads through a population. The edge equations are coupled to the vertex ODEs through junction conditions, while the domain equations are coupled to the edges through boundary conditions. A numerical method based on spatial finite differences for the edges and finite elements in the 2D domain is described to approximate the model, and numerical verification of the method is provided. The model is illustrated on two simple and one complex example geometries, and a parameter study example is performed. The observed solutions exhibit exponential decay after a certain time has passed, and the cumulative infected population over the vertices, edges, and domain tends to a constant in time but varying in space, i.e., a steady state solution.

Non-suicidal self-injury in the COVID-19 pandemic: results from cross-sectional surveys among Brazilian adults from 2020 to 2023

The multilevel psychosocial stressors associated with COVID-19 pandemic set the stage to investigate risk factors and groups susceptible for non-suicidal self-injury (NSSI). A national sample of 9,929 Brazilian adults aged 36.1 years on average participated in the study. Cross-sectional data were collected in 2020, 2021, 2022, and 2023. NSSI levels were considered high in the total sample (13.2%) when compared to other studies in this context. The variables with the highest explanatory power in the regression models were age, anxiety, and depression. The main risk factors were being younger, living in the South or Southeast regions of Brazil, having lower educational attainment, and having higher rates of anxiety and depression. Respondents had the highest probability of NSSI in 2022. The sustained higher rates of NSSI in 2023 compared to the beginning of the pandemic underscores the need for continuous monitoring and the development of preventive actions for self-injurious behaviors.

Environmental and geographical factors influencing the spread of SARS-CoV-2 over 2 years: a fine-scale spatiotemporal analysis

Introduction

Since its emergence in late 2019, the SARS-CoV-2 virus has led to a global health crisis, affecting millions and reshaping societies and economies worldwide. Investigating the determinants of SARS-CoV-2 diffusion and their spatiotemporal dynamics at high spatial resolution is critical for public health and policymaking.

Methods

This study analyses 194,682 georeferenced SARS-CoV-2 RT-PCR tests from March 2020 and April 2022 in the canton of Vaud, Switzerland. We characterized five distinct pandemic periods using metrics of spatial and temporal clustering like inverse Shannon entropy, the Hoover index, Lloyd's index of mean crowding, and the modified space-time DBSCAN algorithm. We assessed the demographic, socioeconomic, and environmental factors contributing to cluster persistence during each period using eXtreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP), to consider non-linear and spatial effects.

Results

Our findings reveal important variations in the spatial and temporal clustering of cases. Notably, areas with flatter epidemics had higher total attack rate. Air pollution emerged as a factor showing a consistent positive association with higher cluster persistence, substantiated by both immission models and, to a lesser extent, tropospheric NO2 estimations. Factors including population density, testing rates, and geographical coordinates, also showed important positive associations with higher cluster persistence. The socioeconomic index showed no significant contribution to cluster persistence, suggesting its limited role in the observed dynamics, which warrants further research.

Discussion

Overall, the determinants of cluster persistence remained across the study periods. These findings highlight the need for effective air quality management strategies to mitigate air pollution's adverse impacts on public health, particularly in the context of respiratory viral diseases like COVID-19.

Evidence for Behavioral Autorepression in Covid-19 Epidemiological Dynamics

It has long been hypothesized that behavioral reactions to epidemic severity autoregulate infection dynamics, for example when susceptible individuals self-sequester based on perceived levels of circulating disease. However, evidence for such 'behavioral autorepression' has remained elusive, and its presence could significantly affect epidemic forecasting and interventions. Here, we analyzed early COVID-19 dynamics at 708 locations over three epidemiological scales (96 countries, 50 US states, and 562 US counties). Signatures of behavioral autorepression were identified through: (i) a counterintuitive mobility-death correlation, (ii) fluctuation-magnitude analysis, and (iii) dynamics of SARS-CoV-2 infection waves. These data enabled calculation of the average behavioral-autorepression strength (i.e., negative feedback 'gain') across different populations. Surprisingly, incorporating behavioral autorepression into conventional models was required to accurately forecast COVID-19 mortality. Models also predicted that the strength of behavioral autorepression has the potential to alter the efficacy of non-pharmaceutical interventions. Overall, these results provide evidence for the long-hypothesized existence of behavioral autorepression, which could improve epidemic forecasting and enable more effective application of non-pharmaceutical interventions during future epidemics.

Significance

Challenges with epidemiological forecasting during the COVID-19 pandemic suggested gaps in underlying model architecture. One long-held hypothesis, typically omitted from conventional models due to lack of empirical evidence, is that human behaviors lead to intrinsic negative autoregulation of epidemics (termed 'behavioral autorepression'). This omission substantially alters model forecasts. Here, we provide independent lines of evidence for behavioral autorepression during the COVID-19 pandemic, demonstrate that it is sufficient to explain counterintuitive data on 'shutdowns', and provides a mechanistic explanation of why early shutdowns were more effective than delayed, high-intensity shutdowns. We empirically measure autorepression strength, and show that incorporating autorepression dramatically improves epidemiological forecasting. The autorepression phenomenon suggests that tailoring interventions to specific populations may be warranted.

Utilizing disease transmission and response capacities to optimize covid-19 control in Malaysia

OBJECTIVES

Public Health Social Measures (PHSM) such as movement restriction movement needed to be adjusted accordingly during the COVID-19 pandemic to ensure low disease transmission alongside adequate health system capacities based on the COVID-19 situational matrix proposed by the World Health Organization (WHO). This paper aims to develop a mechanism to determine the COVID-19 situational matrix to adjust movement restriction intensity for the control of COVID-19 in Malaysia.

METHODS

Several epidemiological indicators were selected based on the WHO PHSM interim guidance report and validated individually and in several combinations to estimate the community transmission level (CT) and health system response capacity (RC) variables. Correlation analysis between CT and RC with COVID-19 cases was performed to determine the most appropriate CT and RC variables. Subsequently, the CT and RC variables were combined to form a composite COVID-19 situational matrix (SL). The SL matrix was validated using correlation analysis with COVID-19 case trends. Subsequently, an automated web-based system that generated daily CT, RC, and SL was developed.

RESULTS

CT and RC variables were estimated using case incidence and hospitalization rate; Hospital bed capacity and COVID-19 ICU occupancy respectively. The estimated CT and RC were strongly correlated [ρ = 0.806 (95% CI 0.752, 0.848); and ρ = 0.814 (95% CI 0.778, 0.839), p < 0.001] with the COVID-19 cases. The estimated SL was strongly correlated with COVID-19 cases (ρ = 0.845, p < 0.001) and responded well to the various COVID-19 case trends during the pandemic. SL changes occurred earlier during the increase of cases but slower during the decrease, indicating a conservative response. The automated web-based system developed produced daily real-time CT, RC, and SL for the COVID-19 pandemic.

CONCLUSIONS

The indicators selected and combinations formed were able to generate validated daily CT and RC levels for Malaysia. Subsequently, the CT and RC levels were able to provide accurate and sensitive information for the estimation of SL which provided valuable evidence on the progression of the pandemic and movement restriction adjustment for the control of Malaysia.

SARS-Cov-2 spike induces intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9

Background

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), as a typical tumor marker, has been found to exert immunomodulatory effects in many diseases. We previously reported the clinical and molecular evidences supporting that SARS-Cov-2 infected the gastrointestinal (GI) tract and found a reduction of CEACAM5 in COVID-19 patients' feces which associated with gut dysbiosis. Yet the role of CEACAM5 in GI infection is ill-defined.

Methods

Mice models were established through intraperitoneally injecting with recombinant viral spike-Fc to mimic the intestinal inflammation. We collected duodenum, jejunum, ileum and colon samples after 6h, 2 days, 4 days and 7 days of spike-Fc or control-Fc injection to perform proteomic analysis. Blood was collected from healthy donors and peripheral blood mononuclear cells (PBMC) were separated by density gradient centrifugation, then CD4+ T cells were isolated with magnetic beads and co-cultured with Caco-2 cells.

Results

In addition to intestinal CEACAM5, the expression of tight junction and the percent of CD4+ T lymphocytes were significantly decreased in spike-Fc group compared to control (p < 0.05), accompanied with increased level of inflammatory factors. The KEGG analysis revealed differentially expressed proteins were mainly enriched in the coronavirus disease (COVID-19), tight junction, focal adhesion, adherens junction and PI3K-Akt signaling pathway. Protein-protein interaction (PPI) network analysis identified the interaction between CEACAM5 and Galectin-9 that was also verified by molecular docking and co-IP assay. We further confirmed a reduction of CEACAM5 in SARS-CoV-2 spike stimulated enterocytes could promote the expression of Galectin-9 protein in CD4+T cells. Then it gave rise to the increasing release of inflammatory factors and increased apoptosis of CD4+T cells by inhibition of PI3K/AKT/mTOR pathway. Ultimately intestinal barrier dysfunction happened.

Conclusion

Our results indicated that CEACAM5 overexpression and Galectin-9 knockdown played a protective role in intestinal barrier injury upon spike-Fc stimulation. Collectively, our findings identified firstly that SARS-CoV-2 spike induced intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. The result provides potential therapeutic targets in intestinal barrier dysfunction for treating severe COVID patients.

Relative Role of Age Groups and Indoor Environments in Influenza Transmission Under Different Urbanization Rates in China

Exploring the relative role of different indoor environments in respiratory infections transmission remains unclear, which is crucial for developing targeted nonpharmaceutical interventions. In this study, a total of 2,583,441 influenza-like illness cases tested from 2010 to 2017 in China were identified. An agent-based model was built and calibrated with the surveillance data, to assess the roles of 3 age groups (children <19 years, younger adults 19-60 years, older adults >60 years) and 4 types of indoor environments (home, schools, workplaces, and community areas) in influenza transmission by province with varying urbanization rates. When the urbanization rates increased from 35% to 90%, the proportion of children aged <19 years among influenza cases decreased from 76% to 45%. Additionally, we estimated that infections originating from children decreased from 95.1% (95% confidence interval (CI): 92.7, 97.5) to 59.3% (95% CI: 49.8, 68.7). Influenza transmission in schools decreased from 80.4% (95% CI: 76.5, 84.3) to 36.6% (95% CI: 20.6, 52.5), while transmission in the community increased from 2.4% (95% CI: 1.9, 2.8) to 45.4% (95% CI: 35.9, 54.8). With increasing urbanization rates, community areas and younger adults contributed more to infection transmission. These findings could help the development of targeted public health policies. This article is part of a Special Collection on Environmental Epidemiology. This article is part of a Special Collection on Environmental Epidemiology.

A dynamic approach to support outbreak management using reinforcement learning and semi-connected SEIQR models

BACKGROUND

Containment measures slowed the spread of COVID-19 but led to a global economic crisis. We establish a reinforcement learning (RL) algorithm that balances disease control and economic activities.

METHODS

To train the RL agent, we design an RL environment with 4 semi-connected regions to represent the COVID-19 epidemic in Tokyo, Osaka, Okinawa, and Hokkaido, Japan. Every region is governed by a Susceptible-Exposed-Infected-Quarantined-Removed (SEIQR) model and has a transport hub to connect with other regions. The allocation of the synthetic population and inter-regional traveling is determined by population-weighted density. The agent learns the best policy from interacting with the RL environment, which involves obtaining daily observations, performing actions on individual movement and screening, and receiving feedback from the reward function. After training, we implement the agent into RL environments describing the actual epidemic waves of the four regions to observe the agent's performance.

RESULTS

For all epidemic waves covered by our study, the trained agent reduces the peak number of infectious cases and shortens the epidemics (from 165 to 35 cases and 148 to 131 days for the 5th wave). The agent is generally strict on screening but easy on movement, except for Okinawa, where the agent is easy on both actions. Action timing analyses indicate that restriction on movement is elevated when the number of exposed or infectious cases remains high or infectious cases increase rapidly, and stringency on screening is eased when the number of exposed or infectious cases drops quickly or to a regional low. For Okinawa, action on screening is tightened when the number of exposed or infectious cases increases rapidly.

CONCLUSIONS

Our experiments exhibit the potential of the RL in assisting policy-making and how the semi-connected SEIQR models establish an interactive environment for imitating cross-regional human flows.

Characterizing collective physical distancing in the U.S. during the first nine months of the COVID-19 pandemic

The COVID-19 pandemic offers an unprecedented natural experiment providing insights into the emergence of collective behavioral changes of both exogenous (government mandated) and endogenous (spontaneous reaction to infection risks) origin. Here, we characterize collective physical distancing-mobility reductions, minimization of contacts, shortening of contact duration-in response to the COVID-19 pandemic in the pre-vaccine era by analyzing de-identified, privacy-preserving location data for a panel of over 5.5 million anonymized, opted-in U.S. devices. We define five indicators of users' mobility and proximity to investigate how the emerging collective behavior deviates from typical pre-pandemic patterns during the first nine months of the COVID-19 pandemic. We analyze both the dramatic changes due to the government mandated mitigation policies and the more spontaneous societal adaptation into a new (physically distanced) normal in the fall 2020. Using the indicators here defined we show that: a) during the COVID-19 pandemic, collective physical distancing displayed different phases and was heterogeneous across geographies, b) metropolitan areas displayed stronger reductions in mobility and contacts than rural areas; c) stronger reductions in commuting patterns are observed in geographical areas with a higher share of teleworkable jobs; d) commuting volumes during and after the lockdown period negatively correlate with unemployment rates; and e) increases in contact indicators correlate with future values of new deaths at a lag consistent with epidemiological parameters and surveillance reporting delays. In conclusion, this study demonstrates that the framework and indicators here presented can be used to analyze large-scale social distancing phenomena, paving the way for their use in future pandemics to analyze and monitor the effects of pandemic mitigation plans at the national and international levels.

The Multi-temporal and Multi-dimensional Global Urban Centre Database to Delineate and Analyse World Cities

Monitoring sustainable urban development requires comparable geospatial information on cities across several thematic domains. Here we present the first global database combining such information with city extents. The Global Human Settlement Urban Centre Database (GHS-UCDB) is produced by geospatial data integration to characterise more than 10,000 urban centres worldwide. The database is multi-dimensional and multi-temporal, containing 28 variables across five domains and having multitemporal attributes for one or more epochs when the UC are delineated (1975-1990-2000-2015). Delineation of urban centres for the year 2015 is performed via a logic of grid cell population density, population size, and grid cell contiguity defined by the Degree of Urbanisation method. Each of the urban centres has 160 attributes, including a validation assessment. The novel aspects of this database concern the thematic richness and temporal depth of the variables (across geography, socio-economic, environmental, disaster risk reduction, and sustainable development domains) and the type of geo-information provided (location and extent), featuring an overall consistency that allows comparative analyses across locations and time.

People inflows as a pandemic trigger: Evidence from a quasi-experimental study

Although it has been established that population density can contribute to the outbreak of the COVID-19 virus, there is no evidence to suggest that economic activities, which imply a significant change in mobility, played a causal role in the unfolding of the pandemic. In this paper, we exploit the particular situation of Sardinia (Italy) in 2020 to examine how changes in mobility due to tourism inflows (a proxy of economic activities) influenced the development of the COVID-19 pandemic. Using a difference-in-differences approach, we identify a strong causal relationship between tourism flows and the emergence of COVID-19 cases in Sardinia. We estimate the elasticity of COVID-19 cases in relation to the share of tourists to be 4.1%, which increases to 5.1% when excluding local residents. Our analysis suggests that, in the absence of tools preventing the spread of infection, changes in population density due to economic activities trigger the pandemic spreading in previously unaffected locations. This work contributes to the debate on the complex relationship between COVID-19 and the characteristics of locations by providing helpful evidence for risk-prevention policies.

Where I am from matters: factors influencing behavioral and emotional changes in autistic individuals during COVID-19 in Latin America

Background

The COVID-19 pandemic brought an increased incidence of disease and mortality in the world at large, making it a particularly salient and stressful life event. For those individuals residing in Latin America, the pandemic was met with fragmented healthcare systems, economic downturn, and sociopolitical crisis which puts autistic individuals at risk for more detrimental outcomes. Behavioral and emotional challenges experienced by autistic individuals at the beginning of the pandemic could later develop into more severe symptomatology as the pandemic progresses. The present study aimed to explore changes in dysregulated (overt and internalizing) behaviors and preoccupation with getting sick during the COVID-19 pandemic among autistic children in 7 Latin American countries.

Method

Sample consisted of 1,743 caregivers, residing in: Argentina (n = 677, 38.8%) Brazil (n = 156, 9%), Chile (n = 251, 14.4%), Dominican Republic (n = 171, 9.8%), Mexico (n = 126, 7.2%), Uruguay (n = 259, 14.9%) and Venezuela (n = 103, 5.9%). The majority of caregivers who completed the questionnaire were mothers (85.1%), and most had a male autistic child (81.6%). A series of independent sample t-tests were conducted to assess country differences in dysregulated behaviors and preoccupation with getting sick. Linear regressions were conducted to identify which demographic characteristics and micro-level contextual factors predicted dysregulated overt behaviors and psychological changes.

Results

Contextual factors, such as country of residence, were related to preoccupation with getting sick and dysregulated behavior. Particularly, residing in Mexico and Brazil were related to changes in preoccupation with getting sick and mental health concerns. Coexistence predicted dysregulated internalizing behaviors, while being older significantly predicted preoccupation with getting sick. Increased screen time only predicted anxiety.

Conclusion

Our findings highlight differences and predictions of behavioral challenges and psychological changes based on certain contextual factors and individual characteristics while experiencing severe life stressors such as a worldwide pandemic. This knowledge could help inform policies and decrees aimed at protecting those most vulnerable due to their increased difficulty adapting to change.

Quantifying the benefits of healthy lifestyle behaviors and emotional expressivity in lowering the risk of COVID-19 infection: a national survey of Chinese population

BACKGROUND

COVID-19 is still prevalent in most countries around the world at the low level. Residents' lifestyle behaviors and emotions are critical to prevent COVID-19 and keep healthy, but there is lacking of confirmative evidence on how residents' lifestyle behaviors and emotional expressivity affected COVID-19 infection.

METHODS

Baseline study was conducted in August 2022 and follow-up study was conducted in February 2023. Baseline survey collected information on residents' basic information, as well as their lifestyle behaviors and emotions. Follow-up study was carried out to gather data on COVID-19 infection condition. Binary logistic regression was utilized to identify factors that may influence COVID-19 infection. Attributable risk (AR) was computed to determine the proportion of unhealthy lifestyle behaviors and emotional factors that could be attributed to COVID-19 infection. Sensitivity analysis was performed to test the robustness of the results.

RESULTS

A total of 5776 participants (46.57% males) were included in this study, yielding an overall COVID-19 infection rate of 54.8% (95%CI: 53.5 - 56.0%). The findings revealed that higher stress levels [aOR = 1.027 (95%CI; 1.005-1.050)] and lower frequency in wearing masks, washing hands, and keeping distance [aOR = 1.615 (95%CI; 1.087-2.401)], were positively associated with an increased likelihood of COVID-19 infection (all P < 0.05). If these associations were causal, 8.1% of COVID-19 infection would have been prevented if all participants had normal stress levels [Attributable Risk Percentage: 8.1% (95%CI: 5.9-10.3%)]. A significant interaction effect between stress and the frequency in wearing masks, washing hands, and keeping distance on COVID-19 infection was observed (β = 0.006, P < 0.001), which also was independent factor of COVID-19 infection.

CONCLUSIONS

The overall COVID-19 infection rate among residents is at a medium level. Residents' increasing stress and decreasing frequency in wearing masks and washing hands and keeping distance contribute to increasing risk of infection, residents should increase the frequency of mask-wearing, practice hand hygiene, keep safe distance from others, ensure stable emotional state, minimize psychological stress, providing evidence support for future responses to emerging infectious diseases.

COVID-19 in Baghdad, Iraq: adaptive and emotional findings in a household cluster survey

Purpose

The objective of this study was to assess the impact of COVID-19 infection on households in Baghdad, Iraq.

Methods

A cross-sectional household survey was conducted in early 2022; 41 clusters were selected proportional to population size from the districts of the Baghdad governorate. Households were randomly selected for inclusion. The head of household or senior female member present was interviewed to obtain a listing of COVID-19 infections, deaths, and vaccinations among members of the household and to understand if social and economic changes occurred during the pandemic. All analyses incorporated the complex survey design and sample weights for clustering.

Findings

The findings revealed that there were 1,464 cases of COVID-19 (37.1%) and 34 reported fatalities among the 927 households enrolled in this study. One or more COVID-19 immunizations were received by 50.9% of household members. Preventive measures against COVID-19 were widely reported to be being practiced but were not more commonly reported in households having reported a clinical case of infection. While some households where infections had occurred stated that their household expenses were increased, overall, infections were not associated with significantly increased household costs. In households where COVID-19 had occurred, senior members reported a substantial increase in emotional and psychological problems compared with uninfected households.

Implications

COVID-19 deaths were rare, though infections were common, suggesting an effect of vaccination and other efforts. The household economic implications were minimal in houses with and without COVID-19-infected members. COVID-19 had mental health consequences on affected and unaffected populations alike. It is conceivable that the fear and uncertainty generated by the pandemic had an effect on senior household members which was out of keeping with the other effects in the households sampled. This suggests that there may be a persisting need for mental health services for a protracted period to manage the consequences of mental health needs arising from the pandemic.

Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types

At-home rapid COVID-19 tests in the U.S. utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater transmission to contacts. We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity and/or non-nasal specimen types). In this observational cohort study, 370 individuals from 85 households with a recent COVID-19 case were screened at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). An aSAR of 53.6% (95% CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% 95% CI 19.5-35.0%, P = 0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95% CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may be less effective at limiting transmission to household contacts than other test types.

Metapopulation dynamics of SARS-CoV-2 transmission in a small-scale Amazonian society

The severity of infectious disease outbreaks is governed by patterns of human contact, which vary by geography, social organization, mobility, access to technology and healthcare, economic development, and culture. Whereas globalized societies and urban centers exhibit characteristics that can heighten vulnerability to pandemics, small-scale subsistence societies occupying remote, rural areas may be buffered. Accordingly, voluntary collective isolation has been proposed as one strategy to mitigate the impacts of COVID-19 and other pandemics on small-scale Indigenous populations with minimal access to healthcare infrastructure. To assess the vulnerability of such populations and the viability of interventions such as voluntary collective isolation, we simulate and analyze the dynamics of SARS-CoV-2 infection among Amazonian forager-horticulturalists in Bolivia using a stochastic network metapopulation model parameterized with high-resolution empirical data on population structure, mobility, and contact networks. Our model suggests that relative isolation offers little protection at the population level (expected approximately 80% cumulative incidence), and more remote communities are not conferred protection via greater distance from outside sources of infection, due to common features of small-scale societies that promote rapid disease transmission such as high rates of travel and dense social networks. Neighborhood density, central household location in villages, and household size greatly increase the individual risk of infection. Simulated interventions further demonstrate that without implausibly high levels of centralized control, collective isolation is unlikely to be effective, especially if it is difficult to restrict visitation between communities as well as travel to outside areas. Finally, comparison of model results to empirical COVID-19 outcomes measured via seroassay suggest that our theoretical model is successful at predicting outbreak severity at both the population and community levels. Taken together, these findings suggest that the social organization and relative isolation from urban centers of many rural Indigenous communities offer little protection from pandemics and that standard control measures, including vaccination, are required to counteract effects of tight-knit social structures characteristic of small-scale populations.

The unfinished agenda of communicable diseases among children and adolescents before the COVID-19 pandemic, 1990-2019: a systematic analysis of the Global Burden of Disease Study 2019

BACKGROUND

Communicable disease control has long been a focus of global health policy. There have been substantial reductions in the burden and mortality of communicable diseases among children younger than 5 years, but we know less about this burden in older children and adolescents, and it is unclear whether current programmes and policies remain aligned with targets for intervention. This knowledge is especially important for policy and programmes in the context of the COVID-19 pandemic. We aimed to use the Global Burden of Disease (GBD) Study 2019 to systematically characterise the burden of communicable diseases across childhood and adolescence.

METHODS

In this systematic analysis of the GBD study from 1990 to 2019, all communicable diseases and their manifestations as modelled within GBD 2019 were included, categorised as 16 subgroups of common diseases or presentations. Data were reported for absolute count, prevalence, and incidence across measures of cause-specific mortality (deaths and years of life lost), disability (years lived with disability [YLDs]), and disease burden (disability-adjusted life-years [DALYs]) for children and adolescents aged 0-24 years. Data were reported across the Socio-demographic Index (SDI) and across time (1990-2019), and for 204 countries and territories. For HIV, we reported the mortality-to-incidence ratio (MIR) as a measure of health system performance.

FINDINGS

In 2019, there were 3·0 million deaths and 30·0 million years of healthy life lost to disability (as measured by YLDs), corresponding to 288·4 million DALYs from communicable diseases among children and adolescents globally (57·3% of total communicable disease burden across all ages). Over time, there has been a shift in communicable disease burden from young children to older children and adolescents (largely driven by the considerable reductions in children younger than 5 years and slower progress elsewhere), although children younger than 5 years still accounted for most of the communicable disease burden in 2019. Disease burden and mortality were predominantly in low-SDI settings, with high and high-middle SDI settings also having an appreciable burden of communicable disease morbidity (4·0 million YLDs in 2019 alone). Three cause groups (enteric infections, lower-respiratory-tract infections, and malaria) accounted for 59·8% of the global communicable disease burden in children and adolescents, with tuberculosis and HIV both emerging as important causes during adolescence. HIV was the only cause for which disease burden increased over time, particularly in children and adolescents older than 5 years, and especially in females. Excess MIRs for HIV were observed for males aged 15-19 years in low-SDI settings.

INTERPRETATION

Our analysis supports continued policy focus on enteric infections and lower-respiratory-tract infections, with orientation to children younger than 5 years in settings of low socioeconomic development. However, efforts should also be targeted to other conditions, particularly HIV, given its increased burden in older children and adolescents. Older children and adolescents also experience a large burden of communicable disease, further highlighting the need for efforts to extend beyond the first 5 years of life. Our analysis also identified substantial morbidity caused by communicable diseases affecting child and adolescent health across the world.

FUNDING

The Australian National Health and Medical Research Council Centre for Research Excellence for Driving Investment in Global Adolescent Health and the Bill & Melinda Gates Foundation.

Vascular endothelial growth factor gene insertion/deletion polymorphism is associated with Vitamin D level in Turkish patients with coronavirus disease 2019

OBJECTIVE

Coronavirus disease 2019 emerges as a disease caused by severe acute respiratory syndrome coronavirus 2. It is a systemic disease associated with vascular inflammation and endothelial damage. In this study, we aimed to investigate whether vascular endothelial growth factor gene insertion/deletion polymorphism is associated with coronavirus disease 2019 in the Turkish population.

METHODS

The study included 179 participants (79 patients with coronavirus disease 2019 and 100 controls). DNA isolation was made from peripheral blood, and then the polymerase chain reaction analysis was performed.

RESULTS

When we analyze vascular endothelial growth factor gene insertion/deletion polymorphism in the study group, we found that the DD genotype and D allele were found to be statistically significantly different when compared to coronavirus disease 2019 patients with high vitamin D value (p=0.005 for DD genotype and p=0.006 for D allele) in the control group. In this high-level control group, when we analyze II+ID genotype versus DD, a statistically significant difference was also detected (p=0.007).

CONCLUSION

As a result of the study, we found that DD genotype and D allele were associated with vitamin D level in Turkish patients with coronavirus disease 2019.

Spatiotemporal Patterns of the Omicron Wave of COVID-19 in the United States

COVID-19 has undergone multiple mutations, with the Omicron variant proving to be highly contagious and rapidly spreading across many countries. The United States was severely hit by the Omicron variant. However, it was still unclear how Omicron transferred across the United States. Here, we collected daily COVID-19 cases and deaths in each county from 1 December 2021 to 28 February 2022 as the Omicron wave. We adopted space-time scan statistics, the Hoover index, and trajectories of the epicenter to quantify spatiotemporal patterns of the Omicron wave of COVID-19. The results showed that the highest and earliest cluster was located in the Northeast. The Hoover index for both cases and deaths exhibited phases of rapid decline, slow decline, and relative stability, indicating a rapid spread of the Omicron wave across the country. The Hoover index for deaths was consistently higher than that for cases. The epicenter of cases and deaths shifted from the west to the east, then southwest. Nevertheless, cases were more widespread than deaths, with a lag in mortality data. This study uncovers the spatiotemporal patterns of Omicron transmission in the United States, and its underlying mechanisms deserve further exploration.

Explaining the higher COVID-19 mortality rates among disproportionately Black counties: A decomposition analysis

Background

Why is COVID-19 mortality higher in counties with a disproportionately large (>13.4%) share of Black residents (hereafter "Black counties") relative to others ("non-Black counties")? Existing literature points to six categories of determinants: (1) social distancing, (2) COVID-19 testing, (3) socioeconomic characteristics, (4) environmental characteristics, (5) prevalence of (pre-existing) chronic health conditions, and (6) demographic characteristics. The relative importance of these determinants has not yet been thoroughly examined.

Methods

We built a dataset consisting of 21 sub-indicators across the six categories of determinants for 3108 US counties and their COVID-19 mortality over the period of January 22, 2020-December 31, 2020. Applying the Gelbach's decomposition, we quantified which determinants were most (or least) associated with the COVID-19 mortality disparity between Black and non-Black counties.

Results

We find that COVID-19 death rates were 26 percent higher in Black counties compared to non-Black counties. This disparity was almost completely explained by the six categories of determinants included in our model. Decomposition analyses indicate that county-level demographic and population health characteristics explained most of this disparity. Among all sub-indicators considered, the greater proportion of females and smaller proportion of rural residents in Black counties were the two largest contributors to the COVID-19 mortality gap between Black and non-Black counties. Proportions of diabetic residents, uninsured residents, and the degree of income inequality also significantly contributed to the gap in COVID-19 mortality.

Conclusion

The COVID-19 mortality gap between Black and non-Black counties was largely explained by pre-pandemic differences in demographic and population health characteristics. Policies aiming to reduce the prevalence of chronic conditions and uninsured residents in Black counties would have helped narrow the COVID-19 mortality gap between Black and non-Black counties in 2020.

Crime, inequality and public health: a survey of emerging trends in urban data science

Urban agglomerations are constantly and rapidly evolving ecosystems, with globalization and increasing urbanization posing new challenges in sustainable urban development well summarized in the United Nations' Sustainable Development Goals (SDGs). The advent of the digital age generated by modern alternative data sources provides new tools to tackle these challenges with spatio-temporal scales that were previously unavailable with census statistics. In this review, we present how new digital data sources are employed to provide data-driven insights to study and track (i) urban crime and public safety; (ii) socioeconomic inequalities and segregation; and (iii) public health, with a particular focus on the city scale.

Investigating the epidemiological and economic effects of a third-party certification policy for restaurants with COVID-19 prevention measures

This study investigates the effects of a third-party certification policy for restaurants (including bars) that comply with indoor infection-prevention measures on COVID-19 cases and economic activities. We focus on the case of Yamanashi Prefecture in Japan, which introduced a third-party certification policy that accredits facilities, predominantly restaurants, that comply with the designated guidelines. We employ a difference-in-differences design for each of our epidemiological and economic analyses. The estimation results show that, from July 2020 to April 2021, the certification policy reduced the total number of new infection cases by approximately 45.3% (848 cases), while increasing total sales and the number of customers per restaurant by approximately 12.8% (3.21 million Japanese yen or $30,000) and 30.3% (2909 customers), respectively, compared to the non-intervention scenarios. The results suggest that a third-party certification policy can be an effective policy to mitigate the trade-off between economic activities and infection prevention during a pandemic, especially when effective vaccines are not widely available.

The impact of COVID-19 on visitors' wayfinding within healthcare centers

The novel COVID-19 pandemic has caused substantial calamities in developing countries such as Iran, which initially suffered from inadequate infrastructure essential for the pandemic control. Due to the ongoing development of this malady, healthcare centers are recognized as one of the most significant hotspots within public settings so they are directly pertinent to the physical and mental health of visitors. The main objective for conducting the present study is to investigate the impact of the COVID-19 pandemic on the visitors' wayfinding procedure within Qa'em hospital, located in Rasht, northern Iran. The adopted methodology in the present study is based on a comparison between the collected data regarding the wayfinding behavior of visitors before and after the outbreak of the COVID-19 pandemic using mixed methods, namely Space Syntax, gate counting, people following, and semi-structured interviews. The obtained empirical results displayed that visitors were significantly confused and hesitant throughout their wayfinding process after the outbreak of the pandemic. Indeed, spatial accessibility and legibility were not found to be adequate for facilitating the wayfinding of the visitors. Moreover, the requirements for the reconfiguration of furniture layout in the waiting areas, according to the underlying notions of social distancing, became conspicuous as the pragmatic implications for the post-pandemic healthcare centers.

SARS-CoV-2 seroprevalence and living conditions in Bamako (Mali): a cross-sectional multistage household survey after the first epidemic wave, 2020

OBJECTIVES

In low-income settings with limited access to diagnosis, COVID-19 information is scarce. In September 2020, after the first COVID-19 wave, Mali reported 3086 confirmed cases and 130 deaths. Most reports originated from Bamako, with 1532 cases and 81 deaths (2.42 million inhabitants). This observed prevalence of 0.06% appeared very low. Our objective was to estimate SARS-CoV-2 infection among inhabitants of Bamako, after the first epidemic wave. We assessed demographic, social and living conditions, health behaviours and knowledges associated with SARS-CoV-2 seropositivity.

SETTINGS

We conducted a cross-sectional multistage household survey during September 2020, in three neighbourhoods of the commune VI (Bamako), where 30% of the cases were reported.

PARTICIPANTS

We recruited 1526 inhabitants in 3 areas, that is, 306 households, and 1327 serological results (≥1 years), 220 household questionnaires and collected answers for 962 participants (≥12 years).

PRIMARY AND SECONDARY OUTCOME MEASURES

We measured serological status, detecting SARS-CoV-2 spike protein antibodies in blood sampled. We documented housing conditions and individual health behaviours through questionnaires among participants. We estimated the number of SARS-CoV-2 infections and deaths in the population of Bamako using the age and sex distributions.

RESULTS

The prevalence of SARS-CoV-2 seropositivity was 16.4% (95% CI 15.1% to 19.1%) after adjusting on the population structure. This suggested that ~400 000 cases and ~2000 deaths could have occurred of which only 0.4% of cases and 5% of deaths were officially reported. Questionnaires analyses suggested strong agreement with washing hands but lower acceptability of movement restrictions (lockdown/curfew), and mask wearing.

CONCLUSIONS

The first wave of SARS-CoV-2 spread broadly in Bamako. Expected fatalities remained limited largely due to the population age structure and the low prevalence of comorbidities. Improving diagnostic capacities to encourage testing and preventive behaviours, and avoiding the spread of false information remain key pillars, regardless of the developed or developing setting.

ETHICS

This study was registered in the registry of the ethics committee of the Faculty of Medicine and Odonto-Stomatology and the Faculty of Pharmacy, Bamako, Mali, under the number: 2020/162/CA/FMOS/FAPH.

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

BACKGROUND

The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure.

RESULTS

Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323.

CONCLUSIONS

These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.

Computational decision-support tools for urban design to improve resilience against COVID-19 and other infectious diseases: A systematic review

The COVID-19 pandemic highlighted the need for decision-support tools to help cities become more resilient to infectious diseases. Through urban design and planning, non-pharmaceutical interventions can be enabled, impelling behaviour change and facilitating the construction of lower risk buildings and public spaces. Computational tools, including computer simulation, statistical models, and artificial intelligence, have been used to support responses to the current pandemic as well as to the spread of previous infectious diseases. Our multidisciplinary research group systematically reviewed state-of-the-art literature to propose a toolkit that employs computational modelling for various interventions and urban design processes. We selected 109 out of 8,737 studies retrieved from databases and analysed them based on the pathogen type, transmission mode and phase, design intervention and process, as well as modelling methodology (method, goal, motivation, focus, and indication to urban design). We also explored the relationship between infectious disease and urban design, as well as computational modelling support, including specific models and parameters. The proposed toolkit will help designers, planners, and computer modellers to select relevant approaches for evaluating design decisions depending on the target disease, geographic context, design stages, and spatial and temporal scales. The findings herein can be regarded as stand-alone tools, particularly for fighting against COVID-19, or be incorporated into broader frameworks to help cities become more resilient to future disasters.

A Spatiotemporal Solution to Control COVID-19 Transmission at the Community Scale for Returning to Normalcy: COVID-19 Symptom Onset Risk Spatiotemporal Analysis

BACKGROUND

Following the recent COVID-19 pandemic, returning to normalcy has become the primary goal of global cities. The key for returning to normalcy is to avoid affecting social and economic activities while supporting precise epidemic control. Estimation models for the spatiotemporal spread of the epidemic at the refined scale of cities that support precise epidemic control are limited. For most of 2021, Hong Kong has remained at the top of the "global normalcy index" because of its effective responses. The urban-community-scale spatiotemporal onset risk prediction model of COVID-19 symptom has been used to assist in the precise epidemic control of Hong Kong.

OBJECTIVE

Based on the spatiotemporal prediction models of COVID-19 symptom onset risk, the aim of this study was to develop a spatiotemporal solution to assist in precise prevention and control for returning to normalcy.

METHODS

Over the years 2020 and 2021, a spatiotemporal solution was proposed and applied to support the epidemic control in Hong Kong. An enhanced urban-community-scale geographic model was proposed to predict the risk of COVID-19 symptom onset by quantifying the impact of the transmission of SARS-CoV-2 variants, vaccination, and the imported case risk. The generated prediction results could be then applied to establish the onset risk predictions over the following days, the identification of high-onset-risk communities, the effectiveness analysis of response measures implemented, and the effectiveness simulation of upcoming response measures. The applications could be integrated into a web-based platform to assist the antiepidemic work.

RESULTS

Daily predicted onset risk in 291 tertiary planning units (TPUs) of Hong Kong from January 18, 2020, to April 22, 2021, was obtained from the enhanced prediction model. The prediction accuracy in the following 7 days was over 80%. The prediction results were used to effectively assist the epidemic control of Hong Kong in the following application examples: identified communities within high-onset-risk always only accounted for 2%-25% in multiple epidemiological scenarios; effective COVID-19 response measures, such as prohibiting public gatherings of more than 4 people were found to reduce the onset risk by 16%-46%; through the effect simulation of the new compulsory testing measure, the onset risk was found to be reduced by more than 80% in 42 (14.43%) TPUs and by more than 60% in 96 (32.99%) TPUs.

CONCLUSIONS

In summary, this solution can support sustainable and targeted pandemic responses for returning to normalcy. Faced with the situation that may coexist with SARS-CoV-2, this study can not only assist global cities in responding to the future epidemics effectively but also help to restore social and economic activities and people's normal lives.

Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations

Wastewater-based epidemiology (WBE), an emerging approach for community-wide COVID-19 surveillance, was primarily characterized at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be better implemented for a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population of 1471) from January to November 2021. Community testing data showed an average of 0.004 % incidence rate in these sewersheds (97 % of monitoring periods reported two or fewer daily infections). In 92 % of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. We statistically determined 10-2.6 as the threshold of the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (N/PMMOV) to alert high COVID-19 incidence rate in the studied sewershed. This threshold of N/PMMOV identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.2 %) with 82 % sensitivity and 51 % specificity. Importantly, neighborhood-scale WBE can discern local outbreaks that would not otherwise be identified by city-scale WBE. Our findings suggest that neighborhood-scale WBE is an effective community-wide disease surveillance tool when COVID-19 incidence is maintained at a low level.

The evolving roles of US political partisanship and social vulnerability in the COVID-19 pandemic from February 2020-February 2021

The COVID-19 pandemic has had intense, heterogeneous impacts on different communities and geographies in the United States. We explore county-level associations between COVID-19 attributed deaths and social, demographic, vulnerability, and political variables to develop a better understanding of the evolving roles these variables have played in relation to mortality. We focus on the role of political variables, as captured by support for either the Republican or Democratic presidential candidates in the 2020 elections and the stringency of state-wide governor mandates, during three non-overlapping time periods between February 2020 and February 2021. We find that during the first three months of the pandemic, Democratic-leaning and internationally-connected urban counties were affected. During subsequent months (between May and September 2020), Republican counties with high percentages of Hispanic and Black populations were most hardly hit. In the third time period -between October 2020 and February 2021- we find that Republican-leaning counties with loose mask mandates experienced up to 3 times higher death rates than Democratic-leaning counties, even after controlling for multiple social vulnerability factors. Some of these deaths could perhaps have been avoided given that the effectiveness of non-pharmaceutical interventions in preventing uncontrolled disease transmission, such as social distancing and wearing masks indoors, had been well-established at this point in time.

COVID-19 and the city: Did urbanized countries suffer more fatalities?

In this paper we derive a theoretical model of the spread of a viral infection which we use as basis for an estimation strategy to test four interrelated hypotheses on the relationship between country-level COVID-19 mortality rates and the extent of urban development. Using data covering 81 countries we find evidence that countries with a higher population density, a higher share of the urban population living in the largest city, and countries with a higher urbanization rate had on average the same or fewer COVID-19 fatalities compared to less urbanized countries in 2020. Even though COVID-19 spreads faster in cities, fatalities may be lower, conditional on economic development, trust in government, and a well-functioning health care system. Generally, urbanization and city development are associated with economic development: with the resources urbanized countries have, it is easier for them to manage and maintain stricter lockdowns, and to roll out effective pharmaceutical interventions.

An Overview of Anthropogenic Actions as Drivers for Emerging and Re-Emerging Zoonotic Diseases

Population growth and industrialization have led to a race for greater food and supply productivity. As a result, the occupation and population of forest areas, contact with wildlife and their respective parasites and vectors, the trafficking and consumption of wildlife, the pollution of water sources, and the accumulation of waste occur more frequently. Concurrently, the agricultural and livestock production for human consumption has accelerated, often in a disorderly way, leading to the deforestation of areas that are essential for the planet's climatic and ecological balance. The effects of human actions on other ecosystems such as the marine ecosystem cause equally serious damage, such as the pollution of this habitat, and the reduction of the supply of fish and other animals, causing the coastal population to move to the continent. The sum of these factors leads to an increase in the demands such as housing, basic sanitation, and medical assistance, making these populations underserved and vulnerable to the effects of global warming and to the emergence of emerging and re-emerging diseases. In this article, we discuss the anthropic actions such as climate changes, urbanization, deforestation, the trafficking and eating of wild animals, as well as unsustainable agricultural intensification which are drivers for emerging and re-emerging of zoonotic pathogens such as viral (Ebola virus, hantaviruses, Hendravirus, Nipah virus, rabies, and severe acute respiratory syndrome coronavirus disease-2), bacterial (leptospirosis, Lyme borreliosis, and tuberculosis), parasitic (leishmaniasis) and fungal pathogens, which pose a substantial threat to the global community. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to raise awareness and educate people about the science behind and the battle against zoonotic pathogens to mitigate the threat for both humans and animals.

COVID-19 outbreaks analysis in the Valencian Region of Spain in the prelude of the third wave

Introduction

The COVID-19 pandemic has led to unprecedented social and mobility restrictions on a global scale. Since its start in the spring of 2020, numerous scientific papers have been published on the characteristics of the virus, and the healthcare, economic and social consequences of the pandemic. However, in-depth analyses of the evolution of single coronavirus outbreaks have been rarely reported.

Methods

In this paper, we analyze the main properties of all the tracked COVID-19 outbreaks in the Valencian Region between September and December of 2020. Our analysis includes the evaluation of the origin, dynamic evolution, duration, and spatial distribution of the outbreaks.

Results

We find that the duration of the outbreaks follows a power-law distribution: most outbreaks are controlled within 2 weeks of their onset, and only a few last more than 2 months. We do not identify any significant differences in the outbreak properties with respect to the geographical location across the entire region. Finally, we also determine the cluster size distribution of each infection origin through a Bayesian statistical model.

Discussion

We hope that our work will assist in optimizing and planning the resource assignment for future pandemic tracking efforts.

Spatial modeling of vaccine deserts as barriers to controlling SARS-CoV-2

BACKGROUND

COVID-19 vaccine distribution is at risk of further propagating the inequities of COVID-19, which in the United States (US) has disproportionately impacted the elderly, people of color, and the medically vulnerable. We sought to measure if the disparities seen in the geographic distribution of other COVID-19 healthcare resources were also present during the initial rollout of the COVID-19 vaccine.

METHODS

Using a comprehensive COVID-19 vaccine database (VaccineFinder), we built an empirically parameterized spatial model of access to essential resources that incorporated vaccine supply, time-willing-to-travel for vaccination, and previous vaccination across the US. We then identified vaccine deserts-US Census tracts with localized, geographic barriers to vaccine-associated herd immunity. We link our model results with Census data and two high-resolution surveys to understand the distribution and determinates of spatially accessibility to the COVID-19 vaccine.

RESULTS

We find that in early 2021, vaccine deserts were home to over 30 million people, >10% of the US population. Vaccine deserts were concentrated in rural locations and communities with a higher percentage of medically vulnerable populations. We also find that in locations of similar urbanicity, early vaccination distribution disadvantaged neighborhoods with more people of color and older aged residents.

CONCLUSION

Given sufficient vaccine supply, data-driven vaccine distribution to vaccine deserts may improve immunization rates and help control COVID-19.

Actual conditions of person-to-object contact and a proposal for prevention measures during the COVID-19 pandemic

This study focused on human contact behavior with objects and discussed countermeasures during the COVID-19 pandemic across 15 location types. Reducing contact with objects and disinfecting items can be implemented at a relatively low cost. We created a protocol for organizing the objects, and 1260 subjects who went outside during a day between December 3-7, 2020 in Tokyo and Kanagawa, Japan were surveyed. The participants touched 7317 objects in total; the most common objects were doors, chairs, baskets, elevator equipment, and cash. One-way analysis of variance and Scheffé's multiple comparison test showed that supermarkets had the lowest mean and median values despite having the highest number of users, contact objects, and object types. Conversely, the values for hotels were the highest, significantly higher than that for other places, excluding amusement parks, workplaces, and schools and universities. Furthermore, the long-tailed frequency distribution of the number of objects suggests that the objects touched by many individuals are limited; thus, it is important to determine the objects to be prioritized for disinfection at each location. The data and protocol could inform infection countermeasures that properly address the contact realities as they pertain to people's behavior and objects.

Assessing the asymptomatic proportion of SARS-CoV-2 infection with age in China before mass vaccination

Some asymptomatic individuals carrying SARS-CoV-2 can transmit the virus and contribute to outbreaks of COVID-19. Here, we use detailed surveillance data gathered during COVID-19 resurgences in six cities of China at the beginning of 2021 to investigate the relationship between asymptomatic proportion and age. Epidemiological data obtained before mass vaccination provide valuable insights into the nature of pathogenicity of SARS-CoV-2. The data were collected by multiple rounds of city-wide PCR testing with contact tracing, where each patient was monitored for symptoms through the whole course of infection. The clinical endpoint (asymptomatic or symptomatic) for each patient was recorded (the pre-symptomatic patients were classified as symptomatic). We find that the proportion of infections that are asymptomatic declines with age (coefficient = −0.006, 95% CI: −0.008 to −0.003, p < 0.01), falling from 42% (95% CI: 6–78%) in age group 0–9 years to 11% (95% CI: 0–25%) in age group greater than 60 years. Using an age-stratified compartment model, we show that this age-dependent asymptomatic pattern, together with the distribution of cases by age, can explain most of the reported variation in asymptomatic proportions among cities. Our analysis suggests that SARS-CoV-2 surveillance strategies should take account of the variation in asymptomatic proportion with age.

Empiric recommendations for population disaggregation under different data scenarios

High-resolution population mapping is of high relevance for developing and implementing tailored actions in several fields: From decision making in crisis management to urban planning. Earth Observation has considerably contributed to the development of methods for disaggregating population figures with higher resolution data into fine-grained population maps. However, which method is most suitable on the basis of the available data, and how the spatial units and accuracy metrics affect the validation process is not fully known. We aim to provide recommendations to researches that attempt to produce high-resolution population maps using remote sensing and geospatial information in heterogeneous urban landscapes. For this purpose, we performed a comprehensive experimental research on population disaggregation methods with thirty-six different scenarios. We combined five different top-down methods (from basic to complex, i.e., binary and categorical dasymetric, statistical, and binary and categorical hybrid approaches) on different subsets of data with diverse resolutions and degrees of availability (poor, average and rich). Then, the resulting population maps were systematically validated with a two-fold approach using six accuracy metrics. We found that when only using remotely sensed data the combination of statistical and dasymetric methods provide better results, while highly-resolved data require simpler methods. Besides, the use of at least three relative accuracy metrics is highly encouraged since the validation depends on level and method. We also analysed the behaviour of relative errors and how they are affected by the heterogeneity of the urban landscape. We hope that our recommendations save additional efforts and time in future population mapping.

Vulnerable or resilient? The response of informal settlements to COVID-19: The case of urban village communities in Beijing

The COVID-19 pandemic has brought topics of the impact, response and adaptation of cities in emergencies to the forefront. When compared with formal settlements, the problems faced by informal settlements are more prominent. We propose the framework of an actor-network theory, substantiated by an empirical study of three typical informal settlements in Haidian District, Beijing, in which the process, characteristics and internal mechanism of the spatial reconstruction of the informal settlements in response to COVID-19 are closely scrutinised. Human actors such as local governments, community volunteers, landlords, tenants and non-human actors all participated in the response to COVID-19 according to their goal vision and political logic, with the local government as the core driving force, forming an integrated actor network. Rooted in the special locality of informal settlements, the actor network was both hierarchical and flexible, and its inherent dynamism has proven to be efficient during COVID-19, resulting in social adaptation and spatial reconstruction. This study contributes to the cautiously optimistic estimate of similar urban community resilience in terms of global epidemics and enriches the understanding of their interlacing dynamics from the perspective of spatial reconstruction.

Five common misconceptions regarding flattening-the-curve of COVID-19

In the fight against COVID-19 pandemic, the phrase "Flattening the curve" (FTC) has become a rallying cry, popularized by government leaders and journalist in the news and on the social media. FTC is a succinct way of communicating an important public health message that physical distancing, mask-wearing and other public health measures will decrease the peak number of cases and prevent the healthcare system from being overwhelmed. However, while the message of FTC is right in the sense that limiting transmission will reduce the peak number of cases, some visualizations used to illustrate its effect are incorrect from an infectious disease modelling point of view. The misconceptions are misinterpretations of flattened curves, the effect of FTC on the duration of the pandemic, the dynamics of the curve to be flattened, and the overestimation of the importance of FTC.

Data-driven contact network models of COVID-19 reveal trade-offs between costs and infections for optimal local containment policies

While several non-pharmacological measures have been implemented for a few months in an effort to slow the coronavirus disease (COVID-19) pandemic in the United States, the disease remains a danger in a number of counties as restrictions are lifted to revive the economy. Making a trade-off between economic recovery and infection control is a major challenge confronting many hard-hit counties. Understanding the transmission process and quantifying the costs of local policies are essential to the task of tackling this challenge. Here, we investigate the dynamic contact patterns of the populations from anonymized, geo-localized mobility data and census and demographic data to create data-driven, agent-based contact networks. We then simulate the epidemic spread with a time-varying contagion model in ten large metropolitan counties in the United States and evaluate a combination of mobility reduction, mask use, and reopening policies. We find that our model captures the spatial-temporal and heterogeneous case trajectory within various counties based on dynamic population behaviors. Our results show that a decision-making tool that considers both economic cost and infection outcomes of policies can be informative in making decisions of local containment strategies for optimal balancing of economic slowdown and virus spread.

COVID-19 in Latin America and the Caribbean: Two years of the pandemic

Worldwide, nations have struggled during the coronavirus disease 2019 (COVID-19) pandemic. However, Latin America and the Caribbean faced an unmatched catastrophic toll. As of March 2022, the region has reported approximately 15% of cases and 28% of deaths worldwide. Considering the relatively late arrival of SARS-CoV-2, several factors in the region were determinants of the humanitarian crisis that ensued. Pandemic unpreparedness, fragile healthcare systems, forthright inequalities, and poor governmental support facilitated the spread of the virus throughout the region. Moreover, reliance on repurposed and ineffective drugs such as hydroxychloroquine and ivermectin-to treat or prevent COVID-19-was publicised through misinformation and created a false sense of security and poor adherence to social distancing measures. While there were hopes that herd immunity could be achieved after the region's disastrous first peak, the emergence of the Gamma, Lambda, and Mu variants made this unattainable. This review explores how Latin America and the Caribbean fared during the first 2 years of the pandemic, and how, despite all the challenges, the region became a global leader in COVID-19 vaccination, with 63% of its population fully vaccinated.

Impact of pre-pandemic travel mobility patterns on the spatial diffusion of COVID-19 in South Korea

Introduction

Physical mobility is critical for the spread of infectious diseases in humans. However, few studies have conducted empirical investigations on the impact of pre-pandemic travel mobility patterns on the diffusion of coronavirus disease 2019 (COVID-19). Therefore, this study examines its impact at the city-county level on the diffusion by the wave period during the two-year pandemic in South Korea.

Methods

This study first employs factor analysis by using the travel origin-destination data by travel mode at the county level as of 2019 to derive pre-pandemic travel mobility patterns. Next, the study identifies how they had affected the diffusion of COVID-19 over time by employing the negative binomial regression models on confirmed COVID-19 cases for each wave, including the entire pandemic period.

Results

The study derived five pre-pandemic mobility patterns: 1) rail-oriented mobility, 2) intra-county bus-oriented mobility, 3) road-oriented mobility, 4) high-speed rail-oriented mobility, and 5) inter-county bus-oriented mobility. Among them, the biggest risk to the diffusion of COVID-19 was the rail-oriented mobility before the pandemic if controlling such measures as accessibility, physical environment, and demographic and socioeconomic indicators. In addition, the order of the magnitudes for the impact of pre-pandemic travel mobility factors on its spatial diffusion had not changed during experiencing the three different wave periods during the two-year pandemic in South Korea.

Conclusions

The study concludes that the rail-oriented travel mobility pattern before the pandemic could pose the greatest threat factor to the spatial spread of COVID-19 at any scale and time. Policymakers should develop strategies to prevent the spatial spread of COVID-19 by reducing human mobility for daily living in areas with strong rail mobility patterns formed before the pandemic.

Evaluating effectiveness of public health intervention strategies for mitigating COVID-19 pandemic

Coronavirus disease 2019 (COVID-19) pandemic is an unprecedented global public health challenge. In the United States (US), state governments have implemented various non-pharmaceutical interventions (NPIs), such as physical distance closure (lockdown), stay-at-home order, mandatory facial mask in public in response to the rapid spread of COVID-19. To evaluate the effectiveness of these NPIs, we propose a nested case-control design with propensity score weighting under the quasi-experiment framework to estimate the average intervention effect on disease transmission across states. We further develop a method to test for factors that moderate intervention effect to assist precision public health intervention. Our method takes account of the underlying dynamics of disease transmission and balance state-level pre-intervention characteristics. We prove that our estimator provides causal intervention effect under assumptions. We apply this method to analyze US COVID-19 incidence cases to estimate the effects of six interventions. We show that lockdown has the largest effect on reducing transmission and reopening bars significantly increase transmission. States with a higher percentage of non-White population are at greater risk of increasedR t $$ {R}_t $$ associated with reopening bars.

Mapping local variation in household overcrowding across Africa from 2000 to 2018: a modelling study

BACKGROUND

Household overcrowding is a serious public health threat associated with high morbidity and mortality. Rapid population growth and urbanisation contribute to overcrowding and poor sanitation in low-income and middle- income countries, and are risk factors for the spread of infectious diseases, including COVID-19, and antimicrobial resistance. Many countries do not have adequate surveillance capacity to monitor household overcrowding. Geostatistical models are therefore useful tools for estimating household overcrowding. In this study, we aimed to estimate household overcrowding in Africa between 2000 and 2018 by combining available household survey data, population censuses, and other country-specific household surveys within a geostatistical framework.

METHODS

We used data from household surveys and population censuses to generate a Bayesian geostatistical model of household overcrowding in Africa for the 19-year period between 2000 and 2018. Additional sociodemographic and health-related covariates informed the model, which covered 54 African countries.

FINDINGS

We analysed 287 surveys and population censuses, covering 78 695 991 households. Spatial and temporal variability arose in household overcrowding estimates over time. In 2018, the highest overcrowding estimates were observed in the Horn of Africa region (median proportion 62% [IQR 57-63]); the lowest regional median proportion was estimated for the north of Africa region (16% [14-19]). Overall, 474·4 million (95% uncertainty interval [UI] 250·1 million-740·7 million) people were estimated to be living in overcrowded conditions in Africa in 2018, a 62·7% increase from the estimated 291·5 million (180·8 million-417·3 million) people who lived in overcrowded conditions in the year 2000. 48·5% (229·9 million) of people living in overcrowded conditions came from six African countries (Nigeria, Ethiopia, Democratic Republic of the Congo, Sudan, Uganda, and Kenya), with a combined population of 538·3 million people.

INTERPRETATION

This study incorporated survey and population censuses data and used geostatistical modelling to estimate continent-wide overcrowding over a 19-year period. Our analysis identified countries and areas with high numbers of people living in overcrowded conditions, thereby providing a benchmark for policy planning and the implementation of interventions such as in infectious disease control.

FUNDING

UK Department of Health and Social Care, Wellcome Trust, Bill & Melinda Gates Foundation.

County-Level Social Vulnerability is Associated With In-Hospital Death and Major Adverse Cardiovascular Events in Patients Hospitalized With COVID-19: An Analysis of the American Heart Association COVID-19 Cardiovascular Disease Registry

BACKGROUND

The COVID-19 pandemic has disproportionately affected low-income and racial/ethnic minority populations in the United States. However, it is unknown whether hospitalized patients with COVID-19 from socially vulnerable communities experience higher rates of death and/or major adverse cardiovascular events (MACEs). Thus, we evaluated the association between county-level social vulnerability and in-hospital mortality and MACE in a national cohort of hospitalized COVID-19 patients.

METHODS

Our study population included patients with COVID-19 in the American Heart Association COVID-19 Cardiovascular Disease Registry across 107 US hospitals between January 14, 2020 to November 30, 2020. The Social Vulnerability Index (SVI), a composite measure of community vulnerability developed by Centers for Disease Control and Prevention, was used to classify the county-level social vulnerability of patients' place of residence. We fit a hierarchical logistic regression model with hospital-level random intercepts to evaluate the association of SVI with in-hospital mortality and MACE.

RESULTS

Among 16 939 hospitalized COVID-19 patients in the registry, 5065 (29.9%) resided in the most vulnerable communities (highest national quartile of SVI). Compared with those in the lowest quartile of SVI, patients in the highest quartile were younger (age 60.2 versus 62.3 years) and more likely to be Black adults (36.7% versus 12.2%) and Medicaid-insured (31.1% versus 23.0%). After adjustment for demographics (age, sex, race/ethnicity) and insurance status, the highest quartile of SVI (compared with the lowest) was associated with higher likelihood of in-hospital mortality (OR, 1.25 [1.03-1.53]; P=0.03) and MACE (OR, 1.26 [95% CI, 1.05-1.50]; P=0.01). These findings were not attenuated after accounting for clinical comorbidities and acuity of illness on admission.

CONCLUSIONS

Patients hospitalized with COVID-19 residing in more socially vulnerable communities experienced higher rates of in-hospital mortality and MACE, independent of race, ethnicity, and several clinical factors. Clinical and health system strategies are needed to improve health outcomes for socially vulnerable patients.

Disease-economy trade-offs under alternative epidemic control strategies

Public policy and academic debates regarding pandemic control strategies note disease-economy trade-offs, often prioritizing one outcome over the other. Using a calibrated, coupled epi-economic model of individual behavior embedded within the broader economy during a novel epidemic, we show that targeted isolation strategies can avert up to 91% of economic losses relative to voluntary isolation strategies. Unlike widely-used blanket lockdowns, economic savings of targeted isolation do not impose additional disease burdens, avoiding disease-economy trade-offs. Targeted isolation achieves this by addressing the fundamental coordination failure between infectious and susceptible individuals that drives the recession. Importantly, we show testing and compliance frictions can erode some of the gains from targeted isolation, but improving test quality unlocks the majority of the benefits of targeted isolation.

Evaluating the policy of closing bars and restaurants in Cataluña and its effects on mobility and COVID19 incidence

The world has gone through unprecedented changes since the global pandemic hit. During the early phase of the pandemic, the absence of known drugs or pharmaceutical treatments forced governments to introduce different policies in order to help reduce contagion rates and manage the economic consequences of the pandemic. This paper analyses the causal impact on mobility and COVID19 incidence from policy makers in Cataluña, Spain. We use anonymized phone-based mobility data together with reported incidence and apply a series of causal impact models frequently used in econometrics and policy evaluation in order to measure the policies impact. We analyse the case of Cataluña and the public policy decision of closing all bars and restaurants down for a 5 week period between 2020-16-10 and 2020-23-11. We find that this decision led to a significant reduction in mobility. It not only led to reductions in mobility but from a behavioural economics standpoint, we highlight how people responded to the policy decision. Moreover, the policy of closing bars and restaurants slowed the incidence rate of COVID19 after a time lag has been taken into account. These findings are significant since governments worldwide want to restrict movements of people in order to slow down COVID19 incidence without infringing on their rights directly.