MOOD publications

@article{doi:10.1126/science.abj0113,

title = {Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence},

author = {MUG Kraemer and V Hill and C Ruis and S Dellicour and S Bajaj and JT McCrone and G Baele and KV Parag and AL Battle and B Gutierrez and B Jackson and R Colquhoun and A O'Toole and B Klein and A Vespignani and COVID-19 Genomics UK (COG-UK) Consortium and E Volz and NR Faria and DM Aanensen and NJ Loman NJ and L du Plessis and S Cauchemez and A Rambaut A and SV Scarpino SV and OG Pybus },

url = {https://www.science.org/doi/abs/10.1126/science.abj0113},

doi = {10.1126/science.abj0113},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Science},

volume = {373},

number = {6557},

pages = {889-895},

abstract = {The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al. explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. Disentangling the factors that contribute to the rapid spread of virus variants is essential for understanding their epidemiological consequences. Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.},

keywords = {big data, COVID-19, genome, mobility, phylogenetic, United Kingdom, variants},

pubstate = {published},

tppubtype = {article}

}

@article{lemey2021untangling,

title = {Untangling introductions and persistence in COVID-19 resurgence in Europe},

author = {Philippe Lemey and Nick Ruktanonchai and Samuel L Hong and Vittoria Colizza and Chiara Poletto and Frederik Van den Broeck and Mandev S Gill and Xiang Ji and Anthony Levasseur and Bas B Oude Munnink and others},

doi = {https://doi.org/10.1038/s41586-021-03754-2},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Nature},

volume = {595},

number = {7869},

pages = {713--717},

publisher = {Nature Publishing Group},

abstract = {After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.},

keywords = {big data, COVID-19, epidemiology, Europe, measures, mobility},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/aje/kwab252,

title = {The pressure on healthcare system and intensive care utilization during the COVID-19 outbreak in the Lombardy region: a retrospective observational study on 43,538 hospitalized patients},

author = {Filippo Trentini and Valentina Marziano and Giorgio Guzzetta and Marcello Tirani and Danilo Cereda and Piero Poletti and Raffaella Piccarreta and Antonio Barone and Giuseppe Preziosi and Fabio Arduini and Petra Giulia Della Valle and Alberto Zanella and Francesca Grosso and Gabriele Castillo and Ambra Castrofino and Giacomo Grasselli and Alessia Melegaro and Alessandra Piatti and Aida Andreassi and Maria Gramegna and Marco Ajelli and Stefano Merler},

url = {https://doi.org/10.1093/aje/kwab252},

doi = {10.1093/aje/kwab252},

issn = {0002-9262},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {American Journal of Epidemiology},

abstract = {During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-March 13), the period of highest pressure on healthcare (March 14-April 25, when COVID-19 patients exceeded the ICU pre-pandemic bed capacity), and the declining phase (April 26-July 12).Compared to the early phase, patients above 70 years of age were admitted less often to an ICU during highest pressure on healthcare (odds ratio OR 0.47, 95%CI: 0.41-0.54) with longer delays (incidence rate ratio IRR 1.82, 95%CI: 1.52-2.18), and lower chances of death in ICU (OR 0.47, 95%CI: 0.34-0.64). Patients under 56 years of age reported more limited changes in the probability (OR 0.65, 95%CI: 0.56-0.76) and delay to ICU admission (IRR 1.16, 95%CI: 0.95-1.42) and an increased mortality (OR 1.43, 95%CI: 1.00-2.07). In the declining phase, all quantities decreased for all age groups.These patterns may suggest that limited healthcare resources during the peak epidemic phase in Lombardy forced a shift in ICU admission criteria to prioritize patients with higher chances of survival.},

note = {kwab252},

keywords = {big data, COVID-19, epidemiology, ICU, Italy, Public Health},

pubstate = {published},

tppubtype = {article}

}

@article{pullano2020evaluating,

title = {Evaluating the effect of demographic factors, socioeconomic factors, and risk aversion on mobility during the COVID-19 epidemic in France under lockdown: a population-based study},

author = {Giulia Pullano and Eugenio Valdano and Nicola Scarpa and Stefania Rubrichi and Vittoria Colizza},

doi = {10.1016/S2589-7500(20)30243-0 },

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {The Lancet Digital Health},

volume = {2},

number = {12},

pages = {e638--e649},

publisher = {Elsevier},

abstract = {Background: On March 17, 2020, French authorities implemented a nationwide lockdown to respond to the COVID-19 epidemic and curb the surge of patients requiring critical care. Assessing the effect of lockdown on individual displacements is essential to quantify achievable mobility reductions and identify the factors driving the changes in social dynamics that affected viral diffusion. We aimed to use mobile phone data to study how mobility in France changed before and during the lockdown, breaking down our findings by trip distance, user age and residency, and time of day, and analysing regional data and spatial heterogeneities. For this population-based study, we used temporally resolved travel flows among 1436 administrative areas of mainland France reconstructed from mobile phone trajectories. Data were stratified by age class (younger than 18 years, 18-64 years, and 65 years or older). We distinguished between residents and non-residents and used population data and regional socio-economic indicators from the French National Statistical Institute. We measured mobility changes before and during lockdown at both local and country scales using a case-crossover framework. We analysed all trips combined and trips longer than 100 km (termed long trips), and separated trips by daytime or night-time, weekdays or weekends, and rush hours.



Findings: Lockdown caused a 65% reduction in the countrywide number of displacements (from about 57 million to about 20 million trips per day) and was particularly effective in reducing work-related short-range mobility, especially during rush hour, and long trips. Geographical heterogeneities showed anomalous increases in long-range movements even before lockdown announcement that were tightly localised in space. During lockdown, mobility drops were unevenly distributed across regions (eg, Île-de-France, the region of Paris, went from 585 000 to 117 000 outgoing trips per day). They were strongly associated with active populations, workers employed in sectors highly affected by lockdown, and number of hospitalisations per region, and moderately associated with the socioeconomic level of the regions. Major cities largely shrank their pattern of connectivity, reducing it mainly to short-range commuting (95% of traffic leaving Paris was contained in a 201 km radius before lockdown, which was reduced to 29 km during lockdown).},

keywords = {big data, contac tracing, COVID-19, epidemiology, France, measures, mobility, transmission},

pubstate = {published},

tppubtype = {article}

}

@article{candido2020evolution,

title = {Evolution and epidemic spread of SARS-CoV-2 in Brazil},

author = {Darlan S Candido and Ingra M Claro and Jaqueline G De Jesus and William M Souza and Filipe RR Moreira and Simon Dellicour and Thomas A Mellan and Louis Du Plessis and Rafael HM Pereira and Flavia CS Sales and others},

doi = {10.1126/science.abd2161},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Science},

volume = {369},

number = {6508},

pages = {1255--1260},

publisher = {American Association for the Advancement of Science},

abstract = {Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.},

keywords = {big data, Brazil, Contact tracing, COVID-19, epidemiology, measures, mobility, transmission},

pubstate = {published},

tppubtype = {article}

}