Spatial scales of COVID-19 transmission in Mexico (preprint)

During outbreaks of emerging infectious diseases, internationally connected cities often experience large and early outbreaks, while rural regions follow after some delay. This hierarchical structure of disease spread is influenced primarily by the multiscale structure of human mobility. However, during the COVID-19 epidemic, public health responses typically did not take into consideration the explicit spatial structure of human mobility when designing non-pharmaceutical interventions (NPIs). NPIs were applied primarily at national or regional scales. Here we use weekly anonymized and aggregated human mobility data and spatially highly resolved data on COVID-19 cases, deaths and hospitalizations at the municipality level in Mexico to investigate how behavioural changes in response to the pandemic have altered the spatial scales of transmission and interventions during its first wave (March - June 2020). We find that the epidemic dynamics in Mexico were initially driven by SARS-CoV-2 exports from Mexico State and Mexico City, where early outbreaks occurred. The mobility network shifted after the implementation of interventions in late March 2020, and the mobility network communities became more disjointed while epidemics in these communities became increasingly synchronised. Our results provide actionable and dynamic insights into how to use network science and epidemiological modelling to inform the spatial scale at which interventions are most impactful in mitigating the spread of COVID-19 and infectious diseases in general.

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

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 the 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. The indicators defined here allow the quantification of behavior changes across the rural/urban divide and highlight the statistical association of mobility and proximity indicators with metrics characterizing the pandemic's social and public health impact such as unemployment and deaths. This study provides a framework to study massive social distancing phenomena with potential uses in analyzing and monitoring the effects of pandemic mitigation plans at the national and international level.

Forecasting hospital-level COVID-19 admissions using real-time mobility data (preprint)

For each of the COVID-19 pandemic waves, hospitals have had to plan for deploying surge capacity and resources to manage large but transient increases in COVID-19 admissions. While a lot of effort has gone into predicting regional trends in COVID-19 cases and hospitalizations, there are far fewer successful tools for creating accurate hospital-level forecasts. At the same time, anonymized phone-collected mobility data proved to correlate well with the number of cases for the first two waves of the pandemic (spring 2020, and fall-winter 2021). In this work, we show how mobility data could bolster hospital-specific COVID-19 admission forecasts for five hospitals in Massachusetts during the initial COVID-19 surge. The high predictive capability of the model was achieved by combining anonymized, aggregated mobile device data about users' contact patterns, commuting volume, and mobility range with COVID hospitalizations and test-positivity data. We conclude that mobility-informed forecasting models can increase the lead-time of accurate predictions for individual hospitals, giving managers valuable time to strategize how best to allocate resources to manage forthcoming surges.

The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system (preprint)

During the first year of the COVID-19 pandemic, the number of incarcerated people in the United States decreased by at least 16%---the largest, fastest reduction in prison population in American history. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from this decrease in the U.S. prison population, and the fraction of incarcerated Black and Latino people sharply increased. This pattern deviates from a decade-long trend before 2020 and the onset of COVID-19, during which the proportion of incarcerated Black people was declining. Using case studies of select states, we explore and quantify mechanisms that could explain these disparities: temporary court closures that led to fewer prison admissions, changes in the frequency of police interactions, and state-level prison release policies that sought to de-densify congregate settings. These findings illuminate how systemic racism pervades juridical and penal institutions and is the engine of mass incarceration in America.

Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy (preprint)

With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories---socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts---a rich data state in our dataset---which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.

The effect of eviction moratoriums on the transmission of SARS-CoV-2 (preprint)

Massive unemployment during the COVID-19 pandemic could result in an eviction crisis in US cities. Here we model the effect of evictions on SARS-CoV-2 epidemics, simulating viral transmission within and among households in a theoretical metropolitan area. We recreate a range of urban epidemic trajectories and project the course of the epidemic under two counterfactual scenarios, one in which a strict moratorium on evictions is in place and enforced, and another in which evictions are allowed to resume at baseline or increased rates. We find, across scenarios, that evictions lead to significant increase in infections. Applying our model to Philadelphia using locally-specific parameters shows that the increase is especially profound in models that consider realistically heterogenous cities in which both evictions and contacts occur more frequently in poorer neighborhoods. Our results provide a basis to assess municipal eviction moratoriums and show that policies to stem evictions are a warranted and important component of COVID-19 control.

Mask Wearing and Control of SARS-CoV-2 Transmission in the United States (preprint)

Introduction: Cloth face coverings and surgical masks have become commonplace across the United States in response to the SARS-CoV-2 epidemic. While evidence suggests masks help curb the spread of respiratory pathogens, research is limited. Face masks have quickly become a topic of public debate as government mandates have started requiring their use. Here we investigate the association between self-reported mask wearing, social distancing and community SARS-CoV-2 transmission in the United States, as well as the effect of statewide mandates on mask uptake. Methods: Serial cross-sectional surveys were administered June 3 through July 31, 2020 via web platform. Surveys queried individuals' likelihood to wear a face mask to the grocery store or with family and friends. Responses (N=378,207) were aggregated by week and state and combined with measures of the instantaneous reproductive number (Rt), social distancing proxies, respondent demographics and other potential sources of confounding. We fit multivariate logistic regression models to estimate the association between mask wearing and community transmission control (Rt <1) for each state and week. Multiple sensitivity analyses were considered to corroborate findings across mask wearing definitions, Rt estimators and data sources. Additionally, mask wearing in 12 states was evaluated two weeks before and after statewide mandates. Results: We find an upward trend in mask usage across the U.S., although uptake varies by geography and demographic groups. A multivariate logistic model controlling for social distancing and other variables found a 10% increase in mask wearing was associated with a 3.53 (95% CI: 2.03, 6.43) odds of transmission control (Rt <1). We also find that communities with high mask wearing and social distancing have the highest predicted probability of a controlled epidemic. These positive associations were maintained across sensitivity analyses. Segmented regression analysis of mask wearing found no statistical change following mandates, however the positive trend of increased mask wearing over time was preserved. Conclusion: Widespread utilization of face masks combined with social distancing increases the odds of SARS-CoV-2 transmission control. Mask wearing rose separately from government mask mandates, suggesting supplemental public health interventions are needed to maximize mask adoption and disrupt the spread of SARS-CoV-2, especially as social distancing measures are relaxed.

The unintended consequences of inconsistent pandemic control policies (preprint)

Controlling the spread of COVID-19 -- even after a licensed vaccine is available -- requires the effective use of non-pharmaceutical interventions, e.g., physical distancing, limits on group sizes, mask wearing, etc.. To date, such interventions have neither been uniformly nor systematically implemented in most countries. For example, even when under strict stay-at-home orders, numerous jurisdictions granted exceptions and/or were in close proximity to locations with entirely different regulations in place. Here, we investigate the impact of such geographic inconsistencies in epidemic control policies by coupling search and mobility data to a simple mathematical model of SARS-COV2 transmission. Our results show that while stay-at-home orders decrease contacts in most areas of the United States of America (US), some specific activities and venues often see an increase in attendance. Indeed, over the month of March 2020, between 10 and 30% of churches in the US saw increases in attendance; even as the total number of visits to churches declined nationally. This heterogeneity, where certain venues see substantial increases in attendance while others close, suggests that closure can cause individuals to find an open venue, even if that requires longer-distance travel. And, indeed, the average distance travelled to churches in the US rose by 13% over the same period. Strikingly, our mathematical model reveals that, across a broad range of model parameters, partial measures can often be worse than no measures at all. In the most severe cases, individuals not complying with policies by traveling to neighboring jurisdictions can create epidemics when the outbreak would otherwise have been controlled. Taken together, our data analysis and modelling results highlight the potential unintended consequences of inconsistent epidemic control policies and stress the importance of balancing the societal needs of a population with the risk of an outbreak growing into a large epidemic.

The unintended consequences of inconsistent pandemic control policies (preprint)

Controlling the spread of COVID-19 - even after a licensed vaccine is available - requires the effective use of non-pharmaceutical interventions: physical distancing, limits on group sizes, mask wearing, etc. To date, such interventions have neither been uniformly nor systematically implemented in most countries. For example, even when under strict stay-at-home orders, numerous jurisdictions granted exceptions and/or were in close proximity to locations with entirely different regulations in place. Here, we investigate the impact of such geographic inconsistencies in epidemic control policies by coupling search and mobility data to a simple mathematical model of SARS-COV2 transmission. Our results show that while stay-at-home orders decrease contacts in most areas of the US, some specific activities and venues often see an increase in attendance. Indeed, over the month of March 2020, between 10 and 30% of churches in the US saw increases in attendance; even as the total number of visits to churches declined nationally. This heterogeneity, where certain venues see substantial increases in attendance while others close, suggests that closure can cause individuals to find an open venue, even if that requires longer-distance travel. And, indeed, the average distance travelled to churches in the US rose by 13% over the same period. Strikingly, our model reveals that across a broad range of model parameters, partial measures can often be worse than none at all where individuals not complying with policies by traveling to neighboring areas can create epidemics when the outbreak would otherwise have been controlled. Taken together, our data analysis and modelling results highlight the potential unintended consequences of inconsistent epidemic control policies and stress the importance of balancing the societal needs of a population with the risk of an outbreak growing into a large epidemic.

Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 (preprint)

SARS-CoV-2 causing COVID-19 disease has moved rapidly around the globe, infecting millions and killing hundreds of thousands. The basic reproduction number, which has been widely used and misused to characterize the transmissibility of the virus, hides the fact that transmission is stochastic, is dominated by a small number of individuals, and is driven by super-spreading events (SSEs). The distinct transmission features, such as high stochasticity under low prevalence, and the central role played by SSEs on transmission dynamics, should not be overlooked. Many explosive SSEs have occurred in indoor settings stoking the pandemic and shaping its spread, such as long-term care facilities, prisons, meat-packing plants, fish factories, cruise ships, family gatherings, parties and night clubs. These SSEs demonstrate the urgent need to understand routes of transmission, while posing an opportunity that outbreak can be effectively contained with targeted interventions to eliminate SSEs. Here, we describe the potential types of SSEs, how they influence transmission, and give recommendations for control of SARS-CoV-2.

The role of directionality, heterogeneity and correlations in epidemic risk and spread (preprint)

Most models of epidemic spread, including many designed specifically for COVID-19, implicitly assume that social networks are undirected, i.e., that the infection is equally likely to spread in either direction whenever a contact occurs. In particular, this assumption implies that the individuals most likely to spread the disease are also the most likely to receive it from others. Here, we review results from the theory of random directed graphs which show that many important quantities, including the reproductive number and the epidemic size, depend sensitively on the joint distribution of in- and out-degrees ("risk" and "spread"), including their heterogeneity and the correlation between them. By considering joint distributions of various kinds we elucidate why some types of heterogeneity cause a deviation from the standard Kermack-McKendrick analysis of SIR models, i.e., so called mass-action models where contacts are homogeneous and random, and some do not. We also show that some structured SIR models informed by complex contact patterns among types of individuals (age or activity) are simply mixtures of Poisson processes and tend not to deviate significantly from the simplest mass-action model. Finally, we point out some possible policy implications of this directed structure, both for contact tracing strategy and for interventions designed to prevent superspreading events. In particular, directed networks have a forward and backward version of the classic "friendship paradox" -- forward links tend to lead to individuals with high risk, while backward links lead to individuals with high spread -- such that a combination of both forward and backward contact tracing is necessary to find superspreading events and prevent future cascades of infection.

The intensity of COVID-19 outbreaks is modulated by SARS-CoV-2 free-living survival and environmental transmission (preprint)

Variation in free-living, microparasite survival can have a meaningful impact on the ecological dynamics of established and emerging infectious diseases. Nevertheless, resolving the importance of environmental transmission in the ecology of epidemics remains a persistent challenge, requires accurate measuring the free-living survival of pathogens across reservoirs of various kinds, and quantifying the extent to which interaction between hosts and reservoirs generates new infections. These questions are especially salient for emerging pathogens, where sparse and noisy data can obfuscate the relative contribution of different infection routes. In this study, we develop a mechanistic, mathematical model that permits both direct (host-to-host) and indirect (environmental) transmission and then fit this model to empirical data from 17 countries affected by an emerging virus (SARS-CoV-2). From an ecological perspective, our model highlights the potential for environmental transmission to drive complex, non-linear dynamics during infectious disease outbreaks. Summarizing, we propose that fitting such models with environmental transmission to real outbreak data from SARS-CoV-2 transmission highlights that variation in environmental transmission is an underappreciated aspect of the ecology of infectious disease, and an incomplete understanding of its role has consequences for public health interventions.

Seeding COVID-19 across sub-Saharan Africa: an analysis of reported importation events across 40 countries (preprint)

BackgroundThe first case of COVID-19 in sub-Saharan Africa (SSA) was reported by Nigeria on February 27, 2020. While case counts in the entire region remain considerably less than those being reported by individual countries in Europe, Asia, and the Americas, SSA countries remain vulnerable to COVID morbidity and mortality due to systemic healthcare weaknesses, less financial resources and infrastructure to address the new crisis, and untreated comorbidities. Variation in preparedness and response capacity as well as in data availability has raised concerns about undetected transmission events. MethodsConfirmed cases reported by SSA countries were line-listed to capture epidemiological details related to early transmission events into and within countries. Data were retrieved from publicly available sources, including institutional websites, situation reports, press releases, and social media accounts, with supplementary details obtained from news articles. A data availability score was calculated for each imported case in terms of how many indicators (sex, age, travel history, date of arrival in country, reporting date of confirmation, and how detected) could be identified. We assessed the relationship between time to first importation and overall Global Health Security Index (GHSI) using Cox regression. K-means clustering grouped countries according to healthcare capacity and health and demographic risk factors. ResultsA total of 13,201 confirmed cases of COVID-19 were reported by 48 countries in SSA during the 54 days following the first known introduction to the region. Out of the 2516 cases for which travel history information was publicly available, 1129 (44.9%) were considered importation events. At the regional level, imported cases tended to be male (65.0%), were a median 41.0 years old (Range: 6 weeks - 88 years), and most frequently had recent travel history from Europe (53.1%). The median time to reporting an introduction was 19 days; a countrys time to report its first importation was not related to GHSI, after controlling for air traffic. Countries that had, on average, the highest case fatality rates, lowest healthcare capacity, and highest probability of premature death due to non-communicable diseases were among the last to report any cases. ConclusionsCountries with systemic, demographic, and pre-existing health vulnerabilities to severe COVID-related morbidity and mortality are less likely to report any cases or may be reporting with limited public availability of information. Reporting on COVID detection and response efforts, as well as on trends in non-COVID illness and care-seeking behavior, is critical to assessing direct and indirect consequences and capacity needs in resource-constrained settings. Such assessments aid in the ability to make data-driven decisions about interventions, country priorities, and risk assessment. Key MessagesO_LIWe line-listed epidemiological indicators for the initial cases reported by 48 countries in sub-Saharan Africa by reviewing and synthesizing information provided by official institutional outlets and news sources. C_LIO_LIOur findings suggest that countries with the largest proportions of untreated comorbidities, as measured by probability of premature death due to non-communicable diseases, and the fewest healthcare resources tended to not be reporting any cases at one-month post-introduction into the region. C_LIO_LIUsing data availability as a measure of gaps in detection and reporting and relating them to COVID-specific parameters for morbidity and mortality provides a measure of vulnerability. C_LIO_LIAccurate and available information on initial cases in seeding local outbreaks is key to projecting case counts and assessing the potential impact of intervention approaches, such that support for local data teams will be important as countries make decisions about control strategies. C_LI

Mobile phone data and COVID-19: Missing an opportunity? (preprint)

This paper describes how mobile phone data can guide government and public health authorities in determining the best course of action to control the COVID-19 pandemic and in assessing the effectiveness of control measures such as physical distancing. It identifies key gaps and reasons why this kind of data is only scarcely used, although their value in similar epidemics has proven in a number of use cases. It presents ways to overcome these gaps and key recommendations for urgent action, most notably the establishment of mixed expert groups on national and regional level, and the inclusion and support of governments and public authorities early on. It is authored by a group of experienced data scientists, epidemiologists, demographers and representatives of mobile network operators who jointly put their work at the service of the global effort to combat the COVID-19 pandemic.

The effect of human mobility and control measures on the COVID-19 epidemic in China (preprint)

The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19.

Beyond R0: the importance of contact tracing when predicting epidemics (preprint)

The basic reproductive number --- R0 --- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same R0. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average R0 and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory~\cite{Newman2001} that relies on contact tracing data to simultaneously determine the first moment (R0) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. %, in the case of COVID-19 from 10-70\% of susceptible individuals. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond R0 when predicting epidemic size.

Beyond $R_0$: Heterogeneity in secondary infections and probabilistic epidemic forecasting (preprint)

The basic reproductive number -- $R_0$ -- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same $R_0$. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average $R_0$ and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory that relies on contact tracing data to simultaneously determine the first moment ($R_0$) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond $R_0$ when predicting epidemic size.