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Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic.

ABSTRACT: During the COVID-19 pandemic, governments faced difficulties in implementing mobility restriction measures, as no clear quantitative relationship between human mobility and infection spread in large cities is known. We developed a model that enables quantitative estimations of the infection risk for individual places and activities by using smartphone GPS data for the Tokyo metropolitan area. The effective reproduction number is directly calculated from the number of infectious social contacts defined by the square of the population density at each location. The difference in the infection rate of daily activities is considered, where the 'stay-out' activity, staying at someplace neither home nor workplace, is more than 28 times larger than other activities. Also, the contribution to the infection strongly depends on location. We imply that the effective reproduction number is sufficiently suppressed if the highest-risk locations or activities are restricted. We also discuss the effects of the Delta variant and vaccination.

SUBMITTER: Ozaki J

PROVIDER: S-EPMC9595098 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic.

Ozaki Jun'ichi J Shida Yohei Y Takayasu Hideki H Takayasu Misako M

Scientific reports 20221025 1

During the COVID-19 pandemic, governments faced difficulties in implementing mobility restriction measures, as no clear quantitative relationship between human mobility and infection spread in large cities is known. We developed a model that enables quantitative estimations of the infection risk for individual places and activities by using smartphone GPS data for the Tokyo metropolitan area. The effective reproduction number is directly calculated from the number of infectious social contacts d ...[more]

PMID: 36284166

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Project description:The reproduction number, R, defined as the average number of secondary cases generated by a primary case, is a crucial quantity for identifying the intensity of interventions required to control an epidemic. Current estimates of the reproduction number for seasonal influenza show wide variation and, in particular, uncertainty bounds for R for the pandemic strain from 1918 to 1919 have been obtained only in a few recent studies and are yet to be fully clarified. Here, we estimate R using daily case notifications during the autumn wave of the influenza pandemic (Spanish flu) in the city of San Francisco, California, from 1918 to 1919. In order to elucidate the effects from adopting different estimation approaches, four different methods are used: estimation of R using the early exponential-growth rate (Method 1), a simple susceptible-exposed-infectious-recovered (SEIR) model (Method 2), a more complex SEIR-type model that accounts for asymptomatic and hospitalized cases (Method 3), and a stochastic susceptible-infectious-removed (SIR) with Bayesian estimation (Method 4) that determines the effective reproduction number Rt at a given time t. The first three methods fit the initial exponential-growth phase of the epidemic, which was explicitly determined by the goodness-of-fit test. Moreover, Method 3 was also fitted to the whole epidemic curve. Whereas the values of R obtained using the first three methods based on the initial growth phase were estimated to be 2.98 (95% confidence interval (CI): 2.73, 3.25), 2.38 (2.16, 2.60) and 2.20 (1.55, 2.84), the third method with the entire epidemic curve yielded a value of 3.53 (3.45, 3.62). This larger value could be an overestimate since the goodness-of-fit to the initial exponential phase worsened when we fitted the model to the entire epidemic curve, and because the model is established as an autonomous system without time-varying assumptions. These estimates were shown to be robust to parameter uncertainties, but the theoretical exponential-growth approximation (Method 1) shows wide uncertainty. Method 4 provided a maximum-likelihood effective reproduction number 2.10 (1.21, 2.95) using the first 17 epidemic days, which is consistent with estimates obtained from the other methods and an estimate of 2.36 (2.07, 2.65) for the entire autumn wave. We conclude that the reproduction number for pandemic influenza (Spanish flu) at the city level can be robustly assessed to lie in the range of 2.0-3.0, in broad agreement with previous estimates using distinct data.

Project description:BackgroundTo suppress the COVID-19 outbreak, the Norwegian government closed all schools on March 13, 2020. The kindergartens reopened on April 20, and the schools on April 27 and May 11 of 2020. The effect of these measures is largely unknown since the role of children in the spread of the SARS-CoV-2 virus is still unclear. There are only a few studies of school closures as a separate intervention to other social distancing measures, and little research exists on the effect of school opening during a pandemic.ObjectiveThis study aimed to model the effect of opening kindergartens and the schools in Norway in terms of a change in the reproduction number (R). A secondary objective was to assess if we can use the estimated R after school openings to infer the rates of transmission between children in schools.MethodsWe used an individual-based model (IBM) to assess the reopening of kindergartens and schools in two Norwegian cities, Oslo, the Norwegian capital, with a population of approximately 680 000, and Tromsø, which is the largest city in Northern Norway, with a population of approximately 75 000. The model uses demographic information and detailed data about the schools in both cities. We carried out an ensemble study to obtain robust results in spite of the considerable uncertainty that remains about the transmission of SARS-CoV-2.ResultsWe found that reopening of Norwegian kindergartens and schools are associated with a change in R of 0.10 (95%CI 0.04-0.16) and 0.14 (95%CI 0.01-0.25) in the two cities under investigation if the in-school transmission rates for the SARS-CoV-2 virus are equal to what has previously been estimated for influenza pandemics.ConclusionWe found only a limited effect of reopening schools on the reproduction number, and we expect the same to hold true in other countries where nonpharmaceutical interventions have suppressed the pandemic. Consequently, current R-estimates are insufficiently accurate for determining the transmission rates in schools. For countries that have closed schools, planned interventions, such as the opening of selected schools, can be useful to infer general knowledge about children-to-children transmission of SARS-CoV-2.

Project description:BackgroundSpatio-temporal patterns of movement can characterize relationships between organisms and their surroundings, and address gaps in our understanding of species ecology, activity budgets, bioenergetics, and habitat resource management. Highly mobile waterfowl, which can exploit resources over large spatial extents, are excellent models to understand relationships between movements and resource usage, landscape interactions and specific habitat needs.MethodsWe tracked 3 species of dabbling ducks with GPS-GSM transmitters in 2015-17 to examine fine-scale movement patterns over 24 h periods (30 min interval), dividing movement pathways into temporally continuous segments and spatially contiguous patches. We quantified distances moved, area used and time allocated across the day, using linear and generalized linear mixed models. We investigated behavior through relationships between these variables.ResultsMovements and space-use were small, and varied by species, sex and season. Gadwall (Mareca strepera) generally moved least (FFDs: 0.5-0.7 km), but their larger foraging patches resulted from longer within-area movements. Pintails (Anas acuta) moved most, were more likely to conduct flights > 300 m, had FFDs of 0.8-1.1 km, used more segments and patches per day that they revisited more frequently, resulting in the longest daily total movements. Females and males differed only during the post-hunt season when females moved more. 23.6% of track segments were short duration (1-2 locations), approximately 1/3 more than would be expected if they occurred randomly, and were more dispersed in the landscape than longer segments. Distance moved in 30 min shortened as segment duration increased, likely reflecting phases of non-movement captured within segments.ConclusionsPacific Flyway ducks spend the majority of time using smaller foraging and resting areas than expected or previously reported, implying that foraging areas may be highly localized, and nutrients obtainable from smaller areas. Additionally, movement reductions over time demonstrates behavioral adjustments that represent divergent energetic demands, the detection of which is a key advantage of higher frequency data. Ducks likely use less energy for movement than currently predicted and management, including distribution and configuration of essential habitat, may require reconsideration. Our study illustrates how fine-scale movement data from tracking help understand and inform various other fields of research.

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Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic.

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Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic.

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