The origin and early spread of SARS-CoV-2 in Europe
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TLDR
A view on the early state of the epidemic in Europe and on migration patterns of the virus before border closures is offered, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions.Abstract:
The investigation of migratory patterns of the SARS-CoV-2 pandemic before border closures in Europe is a crucial first step towards an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions. We find that the predominant lineage spreading in Europe has a most recent common ancestor in Italy and was probably seeded by a transmission event in either Hubei or Germany. We do not find evidence for preferential migration paths from Hubei into different European regions or from each European region to the others. Sustained local transmission is first evident in Italy and then shortly thereafter in the other European regions considered. Before the first border closures in Europe, we estimate that the rate of occurrence of new cases from within-country transmission was within the bounds of the estimated rate of new cases from migration. In summary, our analysis offers a view on the early state of the epidemic in Europe and on migration patterns of the virus before border closures. This information will enable further study of the necessity and timeliness of border closures. Significance Statement We estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures based on viral genome sequences using a phylodynamic model with geographic structure. We confirm that the predominant European outbreak most likely started in Italy and spread from there. This outbreak was probably seeded by a transmission event in either Hubei or Germany. In particular, we find that before the first border closures in Europe, the rate of new cases occurring from within-country transmission was within the estimated bounds on the rate of new migration cases.read more
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Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions
Shannan N Rich,Veronica Richards,Carla Mavian,Brittany Rife Magalis,Nathan D. Grubaugh,Sonja Rasmussen,Simon Dellicour,Bram Vrancken,Christine V.F. Carrington,Rebecca Fisk-Hoffman,Demi Danso-Odei,Daniel Chacreton,Jerne Shapiro,Marie Nancy Séraphin,Crystal M. Hepp,Allison Black,Ann M Dennis,Nídia S. Trovão,Anne-Mieke Vandamme,Angela Rasmussen,Michael Lauzardo,Natalie E. Dean,Marco Salemi,Mattia Prosperi +23 more
TL;DR: In this paper , a focus group was organized to discuss the application of phylodynamic tools to inform public health responses to the COVID-19 pandemic in real-time data.
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References
More filters
Journal ArticleDOI
A new coronavirus associated with human respiratory disease in China.
Fan Wu,Su Zhao,Bin Yu,Yan-Mei Chen,Wen Wang,Zhi gang Song,Yi Hu,Zhao Wu Tao,Jun Hua Tian,Yuan Yuan Pei,Ming Li Yuan,Yu Ling Zhang,Fa Hui Dai,Yi Liu,Qi Min Wang,Jiao Jiao Zheng,Lin Xu,Edward C. Holmes,Edward C. Holmes,Yong-Zhen Zhang,Yong-Zhen Zhang +20 more
TL;DR: Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
Journal ArticleDOI
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
TL;DR: The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more.
Journal ArticleDOI
The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak.
Matteo Chinazzi,Jessica T. Davis,Marco Ajelli,Corrado Gioannini,Maria Litvinova,Stefano Merler,Ana Pastore y Piontti,Kunpeng Mu,Luca Rossi,Kaiyuan Sun,Cécile Viboud,Xinyue Xiong,Hongjie Yu,M. Elizabeth Halloran,M. Elizabeth Halloran,Ira M. Longini,Alessandro Vespignani,Alessandro Vespignani +17 more
TL;DR: The results suggest that early detection, hand washing, self-isolation, and household quarantine will likely be more effective than travel restrictions at mitigating this pandemic, and sustained 90% travel restrictions to and from mainland China only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community.
Journal ArticleDOI
The reproductive number of COVID-19 is higher compared to SARS coronavirus.
TL;DR: The authors' review found the average R0 for 2019-nCoV to be 3.28, which exceeds WHO estimates of 1.4 to 2.5, and is higher than expected.
Journal ArticleDOI
Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020.
Kenji Mizumoto,Kenji Mizumoto,Katsushi Kagaya,Katsushi Kagaya,Alexander E. Zarebski,Gerardo Chowell +5 more
TL;DR: On 5 February 2020, in Yokohama, Japan, a cruise ship hosting 3,711 people underwent a 2-week quarantine after a former passenger was found with COVID-19 post-disembarking, and the delay-adjusted asymptomatic proportion of infections, along with the infections’ timeline were derived.
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