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Philos Trans R Soc Lond B Biol Sci ; 376(1829): 20200275, 2021 07 19.
Article in English | MEDLINE | ID: covidwho-1309693


This study demonstrates that an adoption of a segmenting and shielding strategy could increase the scope to partially exit COVID-19 lockdown while limiting the risk of an overwhelming second wave of infection. We illustrate this using a mathematical model that segments the vulnerable population and their closest contacts, the 'shielders'. Effects of extending the duration of lockdown and faster or slower transition to post-lockdown conditions and, most importantly, the trade-off between increased protection of the vulnerable segment and fewer restrictions on the general population are explored. Our study shows that the most important determinants of outcome are: (i) post-lockdown transmission rates within the general and between the general and vulnerable segments; (ii) fractions of the population in the vulnerable and shielder segments; (iii) adherence to protective measures; and (iv) build-up of population immunity. Additionally, we found that effective measures in the shielder segment, e.g. intensive routine screening, allow further relaxations in the general population. We find that the outcome of any future policy is strongly influenced by the contact matrix between segments and the relationships between physical distancing measures and transmission rates. This strategy has potential applications for any infectious disease for which there are defined proportions of the population who cannot be treated or who are at risk of severe outcomes. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

COVID-19/epidemiology , Pandemics , COVID-19/transmission , COVID-19/virology , Communicable Disease Control/trends , Humans , Models, Theoretical , SARS-CoV-2/pathogenicity , United Kingdom/epidemiology
Science ; 371(6530): 708-712, 2021 02 12.
Article in English | MEDLINE | ID: covidwho-1066806


The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

COVID-19/epidemiology , COVID-19/virology , Genome, Viral , SARS-CoV-2/genetics , COVID-19/prevention & control , COVID-19/transmission , Chain of Infection , Communicable Disease Control , Communicable Diseases, Imported/epidemiology , Communicable Diseases, Imported/virology , Epidemics , Humans , Phylogeny , Travel , United Kingdom/epidemiology
Science ; 369(6508): 1255-1260, 2020 09 04.
Article in English | MEDLINE | ID: covidwho-675945


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.

Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Basic Reproduction Number , Bayes Theorem , Betacoronavirus/classification , Brazil/epidemiology , COVID-19 , COVID-19 Testing , Cities/epidemiology , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Europe , Evolution, Molecular , Genome, Viral , Humans , Models, Genetic , Models, Statistical , Pandemics/prevention & control , Phylogeny , Phylogeography , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , SARS-CoV-2 , Spatio-Temporal Analysis , Travel , Urban Population