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1.
Data Science and Management ; 2022.
Article in English | ScienceDirect | ID: covidwho-2004024

ABSTRACT

A novel coronavirus emerged in Wuhan in late 2019 and has caused the COVID-19 pandemic announced by the World Health Organization on March 12, 2020. This study was originally conducted in January 2020 to estimate the potential risk and geographic range of COVID-19 spread within and beyond China at the early stage of the pandemic. A series of connectivity and risk analyses based on domestic and international travel networks were conducted using historical aggregated mobile phone data and air passenger itinerary data. We found that the cordon sanitaire of Wuhan was likely to have occurred during the latter stages of peak population numbers leaving the city, with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% uncertainty interval: 478–1349) had COVID-19 infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to the city’s lockdown. Most of these destinations were located in Asia, but major hubs in Europe, the US and Australia were also prominent, with a strong correlation seen between the predicted risks of importation and the number of imported cases found. Given the limited understanding of emerging infectious diseases in the very early stages of outbreaks, our approaches and findings in assessing travel patterns and risk of transmission can help guide public health preparedness and intervention design for new COVID-19 waves caused by variants of concern and future pandemics to effectively limit transmission beyond its initial extent.

2.
Nat Commun ; 13(1): 4784, 2022 08 15.
Article in English | MEDLINE | ID: covidwho-1991598

ABSTRACT

Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Middle East/epidemiology , Pandemics/prevention & control , Travel
3.
Nat Commun ; 12(1): 5769, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1447305

ABSTRACT

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.


Subject(s)
COVID-19/transmission , COVID-19/virology , SARS-CoV-2/genetics , Africa, Central/epidemiology , Antibodies, Neutralizing/immunology , COVID-19/epidemiology , Europe/epidemiology , Humans , Immune Evasion/genetics , Mutation , Phylogeny , Phylogeography , SARS-CoV-2/classification , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/genetics , Travel/statistics & numerical data
4.
J Travel Med ; 27(2)2020 03 13.
Article in English | MEDLINE | ID: covidwho-1335914

ABSTRACT

There is currently an outbreak of pneumonia of unknown aetiology in Wuhan, China. Although there are still several unanswered questions about this infection, we evaluate the potential for international dissemination of this disease via commercial air travel should the outbreak continue.


Subject(s)
Air Travel , Betacoronavirus/isolation & purification , Coronavirus Infections/transmission , Pneumonia, Viral/transmission , Animals , Betacoronavirus/genetics , COVID-19 , China/epidemiology , Contact Tracing , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Humans , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Public Health , SARS-CoV-2 , Zoonoses
5.
Cell ; 184(19): 4939-4952.e15, 2021 09 16.
Article in English | MEDLINE | ID: covidwho-1330684

ABSTRACT

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.


Subject(s)
COVID-19/epidemiology , Epidemics , SARS-CoV-2/physiology , COVID-19/transmission , Databases as Topic , Disease Outbreaks , Humans , Louisiana/epidemiology , Phylogeny , Risk Factors , SARS-CoV-2/classification , Texas , Travel , United States/epidemiology
6.
Wellcome Open Res ; 6: 121, 2021.
Article in English | MEDLINE | ID: covidwho-1259748

ABSTRACT

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

7.
Science ; 371(6530): 708-712, 2021 02 12.
Article in English | MEDLINE | ID: covidwho-1066806

ABSTRACT

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.


Subject(s)
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
8.
J Am Med Dir Assoc ; 22(3): 494-497, 2021 03.
Article in English | MEDLINE | ID: covidwho-1065277

ABSTRACT

OBJECTIVES: To assess changes in the mobility of staff between nursing homes in Ontario, Canada, before and after enactment of public policy restricting staff from working at multiple homes. DESIGN: Pre-post observational study. SETTING AND PARTICIPANTS: 623 nursing homes in Ontario, Canada, between March 2020 and June 2020. METHODS: We used GPS location data from mobile devices to approximate connectivity between all 623 nursing homes in Ontario during the 7 weeks before (March 1-April 21) and after (April 22-June 13) the policy restricting staff movement was implemented. We constructed a network diagram visualizing connectivity between nursing homes in Ontario and calculated the number of homes that had a connection with another nursing home and the average number of connections per home in each period. We calculated the relative difference in these mobility metrics between the 2 time periods and compared within-home changes using McNemar test and the Wilcoxon rank-sum test. RESULTS: In the period preceding restrictions, 266 (42.7%) nursing homes had a connection with at least 1 other home, compared with 79 (12.7%) homes during the period after restrictions, a drop of 70.3% (P < .001). Including all homes, the average number of connections in the before period was 3.90 compared to 0.77 in the after period, a drop of 80.3% (P < .001). In both periods, mobility between nursing homes was higher in homes located in larger communities, those with higher bed counts, and those part of a large chain. CONCLUSIONS AND IMPLICATIONS: Mobility between nursing homes in Ontario fell sharply after an emergency order by the Ontario government limiting long-term care staff to a single home, though some mobility persisted. Reducing this residual mobility should be a focus of efforts to reduce risk within the long-term care sector during the COVID-19 pandemic.


Subject(s)
COVID-19/prevention & control , Nursing Homes , Nursing Staff/organization & administration , Public Policy , Communicable Disease Control/organization & administration , Female , Humans , Male , Ontario , Pandemics , SARS-CoV-2
10.
Nat Commun ; 12(1): 311, 2021 01 12.
Article in English | MEDLINE | ID: covidwho-1026821

ABSTRACT

Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing imports from other cities. We provide a method, combining daily COVID-19 prevalence and flight passenger volume, to estimate importations from 18 Chinese cities to 43 international destinations, including 26 in Africa. Global case importations from China in early January came primarily from Wuhan, but the inferred source shifted to other cities in mid-February, especially for importations to African destinations. We estimate that 10.4 (6.2 - 27.1) COVID-19 cases were imported to these African destinations, which exhibited marked variation in their magnitude and main sources of importation. We estimate that 90% of imported cases arrived between 17 January and 7 February, prior to the first case detections. Our results highlight the dynamic role of source locations, which can help focus surveillance and response efforts.


Subject(s)
COVID-19/epidemiology , Pandemics , Travel , Africa/epidemiology , Aircraft , COVID-19/transmission , China/epidemiology , Humans , Models, Theoretical , Prevalence , SARS-CoV-2 , Travel/statistics & numerical data
11.
Remote Sensing ; 13(1):5, 2021.
Article in English | ScienceDirect | ID: covidwho-984853

ABSTRACT

The COVID-19 pandemic has infected almost 73 million people and is responsible for over 1.63 million fatalities worldwide since early December 2019, when it was first reported in Wuhan, China. In the early stages of the pandemic, social distancing measures, such as lockdown restrictions, were applied in a non-uniform way across the world to reduce the spread of the virus. While such restrictions contributed to flattening the curve in places like Italy, Germany, and South Korea, it plunged the economy in the United States to a level of recession not seen since WWII, while also improving air quality due to the reduced mobility. Using daily Earth observation data (Day/Night Band (DNB) from the National Oceanic and Atmospheric Administration Suomi-NPP and NO2 measurements from the TROPOspheric Monitoring Instrument TROPOMI) along with monthly averaged cell phone derived mobility data, we examined the economic and environmental impacts of lockdowns in Los Angeles, California;Chicago, Illinois;Washington DC from February to April 2020—encompassing the most profound shutdown measures taken in the U.S. The preliminary analysis revealed that the reduction in mobility involved two major observable impacts: (i) improved air quality (a reduction in NO2 and PM2.5 concentration), but (ii) reduced economic activity (a decrease in energy consumption as measured by the radiance from the DNB data) that impacted on gross domestic product, poverty levels, and the unemployment rate. With the continuing rise of COVID-19 cases and declining economic conditions, such knowledge can be combined with unemployment and demographic data to develop policies and strategies for the safe reopening of the economy while preserving our environment and protecting vulnerable populations susceptible to COVID-19 infection.

12.
Cell ; 181(5): 990-996.e5, 2020 05 28.
Article in English | MEDLINE | ID: covidwho-60444

ABSTRACT

The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/transmission , Pneumonia, Viral/transmission , Travel , Betacoronavirus/isolation & purification , COVID-19 , Connecticut/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Epidemiological Monitoring , Humans , Likelihood Functions , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , SARS-CoV-2 , Travel/legislation & jurisprudence , United States/epidemiology , Washington/epidemiology
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