scholarly journals Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

2020 ◽  
Author(s):  
Ana da Silva Filipe ◽  
James Shepherd ◽  
Thomas Williams ◽  
Joseph Hughes ◽  
Elihu Aranday-Cortes ◽  
...  
Keyword(s):  
Real Time ◽  
Hospital Admissions ◽  
International Travel ◽  
European Countries ◽  
Added Value ◽  
Contact Tracing ◽  
Genomic Epidemiology ◽  
First Case ◽  
Travel Restrictions ◽  
Community Transmission

AbstractSARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks.We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland.From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions.The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.FundingMRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/ZResearch in contextEvidence before this studyCoronavirus disease-2019 (COVID-19) was first diagnosed in Scotland on the 1st of March 2020 following the emergence of the causative severe acute respiratory system coronavirus 2 (SARS-CoV-2) virus in China in December 2019. During the first month of the outbreak in Scotland, 2310 positive cases of COVID-19 were detected, associated with 1832 hospital admissions, 207 intensive care admissions and 126 deaths. The number of introductions into Scotland and the source of those introductions was not known prior to this study.Added value of this studyUsing a combined phylogenetic and epidemiological approach following real-time next generation sequencing of 452 SARS-CoV-2 samples, it was estimated that the virus was introduced to Scotland on at least 113 occasions, mostly from other European countries, including Italy, Austria and Spain. Localised outbreaks occurred in the community across multiple Scottish health boards, within healthcare facilities and an international conference and community transmission was established rapidly, before local and international lockdown measures were introduced.

scholarly journals Estimating COVID Risk During a Period of Pandemic Decline

2021 ◽  
Vol 9 ◽  
Author(s):  
Timothy J. J. Inglis ◽  
Benjamin McFadden ◽  
Anthony Macali
Keyword(s):  
Public Health ◽  
Real Time ◽  
Health Resources ◽  
Risk Estimate ◽  
Contact Tracing ◽  
Business Continuity ◽  
Risk Monitoring ◽  
Open Source Data ◽  
Travel Restrictions ◽  
Community Transmission

Background: Many parts of the world that succeeded in suppressing epidemic coronavirus spread in 2020 have been caught out by recent changes in the transmission dynamics of SARS-CoV-2. Australia's early success in suppressing COVID-19 resulted in lengthy periods without community transmission. However, a slow vaccine rollout leaves this geographically isolated population vulnerable to leakage of new variants from quarantine, which requires internal travel restrictions, disruptive lockdowns, contact tracing and testing surges.Methods: To assist long term sustainment of limited public health resources, we sought a method of continuous, real-time COVID-19 risk monitoring that could be used to alert non-specialists to the level of epidemic risk on a sub-national scale. After an exploratory data assessment, we selected four COVID-19 metrics used by public health in their periodic threat assessments, applied a business continuity matrix and derived a numeric indicator; the COVID-19 Risk Estimate (CRE), to generate a daily spot CRE, a 3 day net rise and a seven day rolling average. We used open source data updated daily from all Australian states and territories to monitor the CRE for over a year.Results: Upper and lower CRE thresholds were established for the CRE seven day rolling average, corresponding to risk of sustained and potential outbreak propagation, respectively. These CRE thresholds were used in a real-time map of Australian COVID-19 risk estimate distribution by state and territory.Conclusions: The CRE toolkit we developed complements other COVID-19 risk management techniques and provides an early indication of emerging threats to business continuity.

scholarly journals Uncovering two phases of early intercontinental COVID-19 transmission dynamics

2020 ◽  
Vol 27 (8) ◽  
Author(s):  
Jing Yang ◽  
Juan Li ◽  
Shengjie Lai ◽  
Corrine W Ruktanonchai ◽  
Weijia Xing ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
International Travel ◽  
Contact Tracing ◽  
Genetic Sequencing ◽  
Response Strategies ◽  
The World ◽  
Containment Measures ◽  
The Usa ◽  
Community Transmission ◽  
Two Phases

Abstract Background The COVID-19 pandemic has posed an ongoing global crisis, but how the virus spread across the world remains poorly understood. This is of vital importance for informing current and future pandemic response strategies. Methods We performed two independent analyses, travel network-based epidemiological modelling and Bayesian phylogeographic inference, to investigate the intercontinental spread of COVID-19. Results Both approaches revealed two distinct phases of COVID-19 spread by the end of March 2020. In the first phase, COVID-19 largely circulated in China during mid-to-late January 2020 and was interrupted by containment measures in China. In the second and predominant phase extending from late February to mid-March, unrestricted movements between countries outside of China facilitated intercontinental spread, with Europe as a major source. Phylogenetic analyses also revealed that the dominant strains circulating in the USA were introduced from Europe. However, stringent restrictions on international travel across the world since late March have substantially reduced intercontinental transmission. Conclusions Our analyses highlight that heterogeneities in international travel have shaped the spatiotemporal characteristics of the pandemic. Unrestricted travel caused a large number of COVID-19 exportations from Europe to other continents between late February and mid-March, which facilitated the COVID-19 pandemic. Targeted restrictions on international travel from countries with widespread community transmission, together with improved capacity in testing, genetic sequencing and contact tracing, can inform timely strategies for mitigating and containing ongoing and future waves of COVID-19 pandemic.

scholarly journals The first 100 days of SARS-CoV-2 control in Vietnam

2020 ◽  
Author(s):  
Thai Quang Pham ◽  
Maia Rabaa ◽  
Luong Huy Duong ◽  
Tan Quang Dang ◽  
Quang Dai Tran ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Severe Disease ◽  
Steering Committee ◽  
International Travel ◽  
Control Measures ◽  
Contact Tracing ◽  
Population Mobility ◽  
Early Introduction ◽  
Mobility Data ◽  
Travel Restrictions

Background: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23rd, 270 cases have been confirmed, with no deaths. We describe the control measures used and their relationship with imported and domestically-acquired case numbers. Methods: Data on the first 270 SARS-CoV-2 infected cases and the timing and nature of control measures were captured by Vietnam's National Steering Committee for COVID-19 response. Apple and Google mobility data provided population movement proxies. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. Results: After the first confirmed case on January 23rd, the Vietnamese Government initiated mass communications measures, contact tracing, mandatory 14-day quarantine, school and university closures, and progressive flight restrictions. A national lockdown was implemented between April 1st and 22nd. Around 200,000 people were quarantined and 266,122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections were asymptomatic. 21 developed severe disease, with no deaths. The serial interval was 3.24 days, and 27.5% (95% confidence interval, 15.7%-40.0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1.15 (95% confidence interval, 0.37-2.36). No community transmission has been detected since April 15th. Conclusions: Vietnam has controlled SARS-CoV-2 spread through the early introduction of communication, contact-tracing, quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic cases and imported cases, and evidence for substantial pre-symptomatic transmission.

scholarly journals Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

2020 ◽  
Author(s):  
Joseph R. Fauver ◽  
Mary E. Petrone ◽  
Emma B. Hodcroft ◽  
Kayoko Shioda ◽  
Hanna Y. Ehrlich ◽  
...  
Keyword(s):  
United States ◽  
Pacific Northwest ◽  
The United States ◽  
International Travel ◽  
Viral Genomes ◽  
Genomic Epidemiology ◽  
The Pacific ◽  
Travel Restrictions ◽  
Novel Coronavirus ◽  
The U.S

SummarySince its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus 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 U.S., 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 impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.

scholarly journals A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

2020 ◽  
Author(s):  
Xianding Deng ◽  
Wei Gu ◽  
Scot Federman ◽  
Louis du Plessis ◽  
Oliver G. Pybus ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
The United States ◽  
Contact Tracing ◽  
Northern California ◽  
Cruise Ship ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
The Usa ◽  
Community Transmission ◽  
Virus Genomes

AbstractThe COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

scholarly journals Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island

2020 ◽  
Author(s):  
D. C. Nuckchady
Keyword(s):  
Stochastic Model ◽  
Population Surveillance ◽  
Health Interventions ◽  
Contact Tracing ◽  
Point Of Entry ◽  
Highly Sensitive ◽  
Travel Restrictions ◽  
Community Transmission ◽  
The Impact ◽  
Key Interventions

AbstractA stochastic model was created to simulate the impact of various healthcare measures on the COVID-19 epidemic. Travel restrictions and point of entry or exit screening help to delay the onset of the outbreak by a few weeks. Population surveillance is critical to detect the start of community transmission early and to avoid a surge in cases. Contact reduction and contact tracing are key interventions that can help to control the outbreak. To promptly curb the number of new cases, countries should diagnose patients using a highly sensitive test.

scholarly journals An integrated analysis of contact tracing and genomics to assess the efficacy of travel restrictions on SARS-CoV-2 introduction and transmission in England from June to September, 2020

2021 ◽  
Author(s):  
Dinesh Aggarwal ◽  
Andrew J Page ◽  
Ulf Schaefer ◽  
George M Savva ◽  
Richard Myers ◽  
...  
Keyword(s):  
Rate Ratio ◽  
Negative Binomial ◽  
Negative Binomial Regression ◽  
Median Number ◽  
International Travel ◽  
Contact Tracing ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Travel Restrictions ◽  
Travel Restriction

Background: Mitigation of SARS-CoV-2 transmission from international travel is a priority. Travellers from countries with travel restrictions (closed travel-corridors) were required to quarantine for 14 days over Summer 2020 in England. We describe the genomic epidemiology of travel-related cases in England and evaluate the effectiveness of this travel policy. Methods: Between 27/05/2020 and 13/09/2020, probable travel-related SARS-CoV-2 cases and their contacts were identified and combined with UK SARS-CoV-2 sequencing data. The epidemiology and demographics of cases was identified, and the number of contacts per case modelled using negative binomial regression to estimate the effect of travel restriction, and any variation by age, sex and calendar date. Unique travel-related SARS-CoV-2 genomes in the COG-UK dataset were identified to estimate the effect travel restrictions on cluster size generated from these. The Polecat Clustering Tool was used to identify a travel-related SARS-CoV-2 cluster of infection. Findings: 4,207 travel-related SARS-CoV-2 cases are identified. 51.2% (2155/4207) of cases reported travel to one of three countries; 21.0% (882) Greece, 16.3% (685) Croatia and 14.0% (589) Spain. Median number of contacts per case was 3 (IQR 1-5), and greatest for the 16-20 age-group (9.0, 95% C.I.=5.6-14.5), which saw the largest attenuation by travel restriction. Travel restriction was associated with a 40% (rate ratio=0.60, 95% C.I.=0.37-0.95) lower rate of contacts. 827/4207 (19.7%) of cases had high-quality SARS-CoV-2 genomes available. Fewer genomically-linked cases were observed for index cases related to countries with travel restrictions compared to cases from non-travel restriction countries (rate ratio=0.17, 95% C.I.=0.05-0.52). A large travel-related cluster dispersed across England is identified through genomics, confirmed with contact-tracing data. Interpretation: This study demonstrates the efficacy of travel restriction policy in reducing the onward transmission of imported cases. Funding: Wellcome Trust, Biotechnology and Biological Sciences Research Council, UK Research & Innovation, National Institute of Health Research, Wellcome Sanger Institute.

scholarly journals Demand for Self-Managed Online Telemedicine Abortion in Eight European Countries During the COVID-19 Pandemic: A Regression Discontinuity Analysis

2020 ◽  
Author(s):  
Abigail R.A. Aiken ◽  
Jennifer E Starling ◽  
Rebecca Gomperts ◽  
James G Scott ◽  
Catherine Aiken
Keyword(s):  
Great Britain ◽  
Regression Discontinuity ◽  
International Travel ◽  
European Countries ◽  
Telemedicine Service ◽  
Medication Abortion ◽  
Healthcare Settings ◽  
Economic Support ◽  
Travel Restrictions ◽  
Before And After

Objectives: In most European countries, patients seeking medication abortion during the COVID-19 pandemic are still expected to attend healthcare settings in person despite lockdown measures and infection risk. We assessed whether demand for self-managed medication abortion provided by a fully remote online telemedicine service increased following the emergence of COVID-19. Design: We used regression discontinuity to compare the number of requests to online telemedicine service Women on Web in eight European countries before and after they implemented lockdown measures to slow COVID-19 transmission. We examined the number deaths due to COVID-19, the degree of government-provided economic support, the severity of lockdown travel restrictions, and the medication abortion service provision model in countries with and without significant changes in requests. Setting: Eight European countries served by Women on Web. Participants: 3,915 people who made requests for self-managed abortion to Women on Web between January 1st, 2019 and June 1st, 2020. Main Outcome Measures: Percent change in requests to Women on Web before and after the emergence of COVID-19 and associated lockdown measures. Results: Five countries showed significant increases in requests, ranging from 28% in Northern Ireland (p=0.001) to 139% in Portugal (p<0.001). Two countries showed no significant change in requests, and one country, Great Britain, showed an 88% decrease in requests (p<0.001). Countries with significant increases in requests were either countries where abortion services are mainly provided in hospitals or where no abortion services are available and international travel was prohibited during lockdown. By contrast, Great Britain authorized teleconsultation for medication abortion and provision of medications by mail during the pandemic. Conclusion: These marked changes in requests for self-managed medication abortion during COVID-19 demonstrate demand for fully remote models of abortion care and an urgent need for policymakers to expand access to medication abortion by telemedicine.

scholarly journals COVID-19: Recent updates on SARS-CoV-2 and Preventing its Community Transmission in India by 21 Days Lockdown

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 921-929
Author(s):  
Satyajeet K. Pawar ◽  
Shivaji T. Mohite
Keyword(s):  
Hubei Province ◽  
Hand Washing ◽  
Contact Tracing ◽  
Wuhan City ◽  
Social Distancing ◽  
First Case ◽  
Rapid Spread ◽  
Community Transmission ◽  
Almost All

The current pandemic of COVID-19 has caused havoc all over world since its emergence and rapid spread. Within three months the virus SARS-CoV-2 which was isolated from pneumonia cases in Wuhan City, Hubei Province, China in late December 2019, has affected almost all countries. India reported its first case of COVID-19 from state of Kerala on January 30, 2020, a student returned from city of Wuhan. Till date in India the disease had affected 12759 patients with 420 deaths. With every passing day the mysterious virus is been uncovered with its unique characteristics enabling the researcher to unfold the various methods including hand washing and social distancing to curtail the pandemic. Measures like 21 days lockdown to certain extent are effective but considering asymptomatic spreaders, extended measured lockdowns will be useful in the long term war against COVID-19. Till the vaccine and therapeutic solutions are derived, answer to pandemic and SARS-CoV-2 lies in lockdown, social distancing, contact tracing and containment.

scholarly journals THE RIPPLE EFFECT OF COVID-19 PANDEMIC IN HEALTHCARE

2020 ◽  
Vol 8 (12) ◽  
pp. 30-35
Author(s):  
Aaminah Najmus Sahar
Keyword(s):  
Working Conditions ◽  
Hospital Admissions ◽  
Healthcare Systems ◽  
Ripple Effect ◽  
Limited Information ◽  
Frontline Workers ◽  
The Past ◽  
First Case ◽  
Travel Restrictions ◽  
Diagnosis Of Diseases

The COVID-19 Pandemic has disrupted life and changed what we knew as normal, for the past 9 months. Although the first case of COVID-19 was identified in Wuhan, China in mid-December 2019, it was coined as a Pandemic by WHO in March 2020. The COVID-19 Pandemic has impacted each and everyone and caused a ripple effect in all areas of life, the healthcare is no exception. With its novel nature, limited information, lack of resources, risky working conditions, and high spikes in cases, it has caused a massive overload on the healthcare systems. It has caused mental health disturbances not just in the frontline workers and COVID-19 survivors but also in the general public owing to uncertainty, isolation, fear, anxiety, andmisinformation. In addition to this, there has also been an increase in the prescription of antibiotics which stems from the inability to examine the patient physically and obtain samples for cultures as consultations are scheduled through telemedicine. Antimicrobial resistance(AMR) is considered to be further potentiated during the Pandemic as Antimicrobial stewardship programs (ASP) have been disrupted and there is an increase in hospital admissions and intubations of patients. Measures like lockdown and travel restrictions placed to curb the spread of the virus have negatively impacted individuals with addictions and substance use disorders (SUD’s) due to inability to access de-addiction centers, increased isolation, and inability to obtain toxicants which lead to the use of adulterated substances and in some cases withdrawal symptoms. The lockdown has also caused delays in the treatment of chronic and co-morbid diseases like Diabetes, Cardiovascular diseases, Cancer, Dialysis leading to poor disease management and progression of the disease. It has also impacted regular vaccination schedules and periodic health checkups leading to late diagnosis of diseases.

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