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1.
Nat Commun ; 12(1): 311, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436574

RESUMEN

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.


Asunto(s)
/epidemiología , Pandemias , Viaje , África/epidemiología , Aeronaves , China/epidemiología , Humanos , Modelos Teóricos , Prevalencia , Viaje/estadística & datos numéricos
3.
J R Soc Interface ; 18(174): 20200657, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33404371

RESUMEN

COVID-19 is highly transmissible and containing outbreaks requires a rapid and effective response. Because infection may be spread by people who are pre-symptomatic or asymptomatic, substantial undetected transmission is likely to occur before clinical cases are diagnosed. Thus, when outbreaks occur there is a need to anticipate which populations and locations are at heightened risk of exposure. In this work, we evaluate the utility of aggregate human mobility data for estimating the geographical distribution of transmission risk. We present a simple procedure for producing spatial transmission risk assessments from near-real-time population mobility data. We validate our estimates against three well-documented COVID-19 outbreaks in Australia. Two of these were well-defined transmission clusters and one was a community transmission scenario. Our results indicate that mobility data can be a good predictor of geographical patterns of exposure risk from transmission centres, particularly in outbreaks involving workplaces or other environments associated with habitual travel patterns. For community transmission scenarios, our results demonstrate that mobility data add the most value to risk predictions when case counts are low and spatially clustered. Our method could assist health systems in the allocation of testing resources, and potentially guide the implementation of geographically targeted restrictions on movement and social interaction.


Asunto(s)
/epidemiología , Brotes de Enfermedades , Salud Pública , Viaje , Australia/epidemiología , Trazado de Contacto , Demografía , Brotes de Enfermedades/prevención & control , Brotes de Enfermedades/estadística & datos numéricos , Humanos , Modelos Biológicos , Medición de Riesgo
4.
5.
Int J Infect Dis ; 102: 455-459, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33035675

RESUMEN

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient's SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa.


Asunto(s)
/virología , Genoma Viral , /genética , Adulto , África , Humanos , Masculino , Filogenia , Viaje , Zambia
6.
Int J Infect Dis ; 102: 254-259, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33115683

RESUMEN

OBJECTIVE: The North American coronavirus disease-2019 (COVID-19) epidemic exhibited distinct early trajectories. In Canada, Quebec had the highest COVID-19 burden and its earlier March school break, taking place two weeks before those in other provinces, could have shaped early transmission dynamics. METHODS: We combined a semi-mechanistic model of SARS-CoV-2 transmission with detailed surveillance data from Quebec and Ontario (initially accounting for 85% of Canadian cases) to explore the impact of case importation and timing of control measures on cumulative hospitalizations. RESULTS: A total of 1544 and 1150 cases among returning travelers were laboratory-confirmed in Quebec and Ontario, respectively (symptoms onset ≤03-25-2020). Hospitalizations could have been reduced by 55% (95% CrI: 51%-59%) if no cases had been imported after Quebec's March break. However, if Quebec had experienced Ontario's number of introductions, hospitalizations would have only been reduced by 12% (95% CrI: 8%-16%). Early public health measures mitigated the epidemic spread as a one-week delay could have resulted in twice as many hospitalizations (95% CrI: 1.7-2.1). CONCLUSION: Beyond introductions, factors such as public health preparedness, responses and capacity could play a role in explaining interprovincial differences. In a context where regions are considering lifting travel restrictions, coordinated strategies and proactive measures are to be considered.


Asunto(s)
/transmisión , Viaje , Adulto , Anciano , Canadá/epidemiología , Humanos , Persona de Mediana Edad , Modelos Teóricos , Salud Pública
7.
Int J Infect Dis ; 102: 247-253, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33129965

RESUMEN

BACKGROUND: To evaluate and compare the effectiveness of four types of non-pharmaceutical interventions (NPIs) to contain the time-varying effective reproduction number (Rt) of coronavirus disease-2019 (COVID-19). METHODS: This study included 1,908,197 confirmed COVID-19 cases from 190 countries between 23 January and 13 April 2020. The implemented NPIs were categorised into four types: mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction (referred to as mandatory mask, quarantine, distancing and traffic hereafter, respectively). RESULTS: The implementations of mandatory mask, quarantine, distancing and traffic were associated with changes (95% confidence interval, CI) of -15.14% (from -21.79% to -7.93%), -11.40% (from -13.66% to -9.07%), -42.94% (from -44.24% to -41.60%) and -9.26% (from -11.46% to -7.01%) in the Rt of COVID-19 when compared with those without the implementation of the corresponding measures. Distancing and the simultaneous implementation of two or more types of NPIs seemed to be associated with a greater decrease in the Rt of COVID-19. CONCLUSION: Our study indicates that NPIs can significantly contain the COVID-19 pandemic. Distancing and the simultaneous implementation of two or more NPIs should be the strategic priorities for containing COVID-19.


Asunto(s)
/prevención & control , Humanos , Máscaras , Cuarentena , Factores de Tiempo , Viaje
8.
J Med Virol ; 93(2): 1158-1163, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-32761908

RESUMEN

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.


Asunto(s)
/virología , Variación Genética , Genoma Viral , Filogenia , /genética , Adulto , /transmisión , Colombia/epidemiología , Femenino , Geografía , Humanos , Masculino , Persona de Mediana Edad , ARN Viral/genética , Viaje
9.
Lancet Public Health ; 6(1): e12-e20, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33301722

RESUMEN

BACKGROUND: Countries have restricted international arrivals to delay the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These measures carry a high economic and social cost, and might have little effect on COVID-19 epidemics if there are many more cases resulting from local transmission compared with imported cases. Our study aims to investigate the extent to which imported cases contribute to local transmission under different epidemic conditions. METHODS: To inform decisions about international travel restrictions, we calculated the ratio of expected COVID-19 cases from international travel (assuming no travel restrictions) to expected cases arising from internal spread, expressed as a proportion, on an average day in May and September, 2020, in each country. COVID-19 prevalence and incidence were estimated using a modelling framework that adjusts reported cases for under-ascertainment and asymptomatic infections. We considered different travel scenarios for May and September, 2020: an upper bound with estimated travel volumes at the same levels as May and September, 2019, and a lower bound with estimated travel volumes adjusted downwards according to expected reductions in May and September, 2020. Results were interpreted in the context of local epidemic growth rates. FINDINGS: In May, 2020, imported cases are likely to have accounted for a high proportion of total incidence in many countries, contributing more than 10% of total incidence in 102 (95% credible interval 63-129) of 136 countries when assuming no reduction in travel volumes (ie, with 2019 travel volumes) and in 74 countries (33-114) when assuming estimated 2020 travel volumes. Imported cases in September, 2020, would have accounted for no more than 10% of total incidence in 106 (50-140) of 162 countries and less than 1% in 21 countries (4-71) when assuming no reductions in travel volumes. With estimated 2020 travel volumes, imported cases in September, 2020, accounted for no more than 10% of total incidence in 125 countries (65-162) and less than 1% in 44 countries (8-97). Of these 44 countries, 22 (2-61) had epidemic growth rates far from the tipping point of exponential growth, making them the least likely to benefit from travel restrictions. INTERPRETATION: Countries can expect travellers infected with SARS-CoV-2 to arrive in the absence of travel restrictions. Although such restrictions probably contribute to epidemic control in many countries, in others, imported cases are likely to contribute little to local COVID-19 epidemics. Stringent travel restrictions might have little impact on epidemic dynamics except in countries with low COVID-19 incidence and large numbers of arrivals from other countries, or where epidemics are close to tipping points for exponential growth. Countries should consider local COVID-19 incidence, local epidemic growth, and travel volumes before implementing such restrictions. FUNDING: Wellcome Trust, UK Foreign, Commonwealth & Development Office, European Commission, National Institute for Health Research, Medical Research Council, and Bill & Melinda Gates Foundation.


Asunto(s)
/epidemiología , Enfermedades Transmisibles Importadas/epidemiología , Epidemias , Internacionalidad , /prevención & control , Enfermedades Transmisibles Importadas/prevención & control , Humanos , Modelos Teóricos , Viaje/legislación & jurisprudencia
10.
Sci Total Environ ; 756: 143343, 2021 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-33302071

RESUMEN

A novel Coronavirus COVID-19 has caused high morbidity and mortality in China and worldwide. A few studies have explored the impact of climate change or human activity on the disease incidence in China or a city. The integrated study concerning environment impact on the emerging disease is rarely reported. Therefore, based on the two-stage modeling study, we investigate the effect of both natural and human environment on COVID-19 incidence at a city level. Besides, the interactive effect of different factors on COVID-19 incidence is analyzed using Geodetector; the impact of effective factors and interaction terms on COVID-19 is simulated with Geographically Weighted Regression (GWR) models. The results find that mean temperature (MeanT), destination proportion in population flow from Wuhan (WH), migration scale (MS), and WH*MeanT, are generally promoting for COVID-19 incidence before Wuhan's shutdown (T1); the WH and MeanT play a determinant role in the disease spread in T1. The effect of environment on COVID-19 incidence after Wuhan's shutdown (T2) includes more factors (including mean DEM, relative humidity, precipitation (Pre), travel intensity within a city (TC), and their interactive terms) than T1, and their effect shows distinct spatial heterogeneity. Interestingly, the dividing line of positive-negative effect of MeanT and Pre on COVID-19 incidence is 8.5°C and 1 mm, respectively. In T2, WH has weak impact, but the MS has the strongest effect. The COVID-19 incidence in T2 without quarantine is also modeled using the developed GWR model, and the modeled incidence shows an obvious increase for 75.6% cities compared with reported incidence in T2 especially for some mega cities. This evidences national quarantine and traffic control take determinant role in controlling the disease spread. The study indicates that both natural environment and human factors integratedly affect the spread pattern of COVID-19 in China.


Asunto(s)
China/epidemiología , Ciudades , Humanos , Viaje
11.
Clin Microbiol Infect ; 27(1): 130.e5-130.e8, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33007476

RESUMEN

OBJECTIVES: Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS: Metagenomic RNA-sequencing and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS: Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed us to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS: SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection clusters can provide further resolution on transmission events indistinguishable at a consensus sequence level.


Asunto(s)
/genética , /transmisión , Genoma Viral , Pandemias/prevención & control , /genética , Adulto , /biosíntesis , Trazado de Contacto/estadística & datos numéricos , Evolución Molecular , Femenino , Alemania/epidemiología , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Italia/epidemiología , Masculino , Familia de Multigenes , Filogenia , Polimorfismo de Nucleótido Simple , /patogenicidad , Viaje
14.
Nat Microbiol ; 6(1): 112-122, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33349681

RESUMEN

Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.


Asunto(s)
/epidemiología , /genética , Adulto , Anciano , Europa (Continente)/epidemiología , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Filogenia , España/epidemiología , Viaje/estadística & datos numéricos
15.
Epidemiology ; 32(1): 79-86, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33044319

RESUMEN

BACKGROUND: We hypothesize that comprehensive surveillance of COVID-19 in Singapore has facilitated early case detection and prompt contact tracing and, with community-based measures, contained spread. We assessed the effectiveness of containment measures by estimating transmissibility (effective reproduction number, (Equation is included in full-text article.)) over the course of the outbreak. METHODS: We used a Bayesian data augmentation framework to allocate infectors to infectees with no known infectors and determine serial interval distribution parameters via Markov chain Monte Carlo sampling. We fitted a smoothing spline to the number of secondary cases generated by each infector by respective onset dates to estimate (Equation is included in full-text article.)and evaluated increase in mean number of secondary cases per individual for each day's delay in starting isolation or quarantine. RESULTS: As of April 1, 2020, 1000 COVID-19 cases were reported in Singapore. We estimated a mean serial interval of 4.6 days [95% credible interval (CI) = 4.2, 5.1] with a SD of 3.5 days (95% CI = 3.1, 4.0). The posterior mean (Equation is included in full-text article.)was below one for most of the time, peaking at 1.1 (95% CI = 1.0, 1.3) on week 9 of 2020 due to a spreading event in one of the clusters. Eight hundred twenty-seven (82.7%) of cases infected less than one person on average. Over an interval of 7 days, the incremental mean number of cases generated per individual for each day's delay in starting isolation or quarantine was 0.03 cases (95% CI = 0.02, 0.05). CONCLUSIONS: We estimate that robust surveillance, active case detection, prompt contact tracing, and quarantine of close contacts kept (Equation is included in full-text article.)below one.


Asunto(s)
/prevención & control , Control de Enfermedades Transmisibles/métodos , Política de Salud , Número Básico de Reproducción , Teorema de Bayes , /transmisión , Enfermedades Transmisibles Importadas/epidemiología , Enfermedades Transmisibles Importadas/prevención & control , Enfermedades Transmisibles Importadas/transmisión , Trazado de Contacto , Diagnóstico Precoz , Monitoreo Epidemiológico , Humanos , Cadenas de Markov , Tamizaje Masivo , Método de Montecarlo , Singapur/epidemiología , Viaje
16.
Work ; 67(4): 779-782, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33325428

RESUMEN

BACKGROUND: The World Health Organization (WHO) has declared novel coronavirus (COVID-19) infection a global pandemic due to the fast transmission of this disease worldwide. To prevent and slow the transmission of this contagious illness, the public health officials of many affected countries scrambled to introduce measures aimed at controlling its spread. As a result, unprecedented interventions/measures, including strict contact tracing, quarantine of entire towns/cities, closing of borders and travel restrictions, have been implemented by most of the affected countries including the Kingdom of Saudi Arabia. OBJECTIVES: The aim of this paper is to share health care professionals' perspectives who are experiencing COVID19 firsthand in a foreign land. In addition, the role of the Saudi governance to combat the current situation is also discussed. DISCUSSION: Personal and previous experiences as related to Middle East respiratory syndrome coronavirus (MERS-CoV) by the authors has been compared to the current situation and how it affected our thoughts and management. A review of the evidence-based literature was conducted to investigate the demographics of the region; and to understand the awareness of the various tools that are available and how they were utilized in the present situation of pandemic. CONCLUSIONS: Saudi Arabia has been challenged during the pandemic as are other countries.


Asunto(s)
Actitud del Personal de Salud , Personal Profesional Extranjero/psicología , Pandemias/prevención & control , /transmisión , Trazado de Contacto , Odontólogos/psicología , Educación en Odontología , Educación a Distancia , Humanos , Cuarentena , Arabia Saudita/epidemiología , Viaje
17.
PLoS One ; 15(12): e0238200, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33326460

RESUMEN

With the rapid expansion of sensor technologies and wireless network infrastructure, research and development of traffic associated applications, such as real-time traffic maps, on-demand travel route reference and traffic forecasting are gaining much more attention than ever before. In this paper, we elaborate on our traffic prediction application, which is based on traffic data collected through Google Map API. Our application is a desktop-based application that predicts traffic congestion state using Estimated Time of Arrival (ETA). In addition to ETA, the prediction system takes into account various features such as weather, time period, special conditions, holidays, etc. The label of the classifier is identified as one of the five traffic states i.e. smooth, slightly congested, congested, highly congested or blockage. The results demonstrate that the random forest classification algorithm has the highest prediction accuracy of 92 percent followed by XGBoost and KNN respectively.


Asunto(s)
Conducción de Automóvil/estadística & datos numéricos , Viaje/estadística & datos numéricos , Accidentes de Tránsito/estadística & datos numéricos , Algoritmos , Aglomeración , Tiempo , Tiempo (Meteorología)
18.
Proc Natl Acad Sci U S A ; 117(52): 32883-32890, 2020 12 29.
Artículo en Inglés | MEDLINE | ID: mdl-33273120

RESUMEN

In the wake of the COVID-19 pandemic many countries implemented containment measures to reduce disease transmission. Studies using digital data sources show that the mobility of individuals was effectively reduced in multiple countries. However, it remains unclear whether these reductions caused deeper structural changes in mobility networks and how such changes may affect dynamic processes on the network. Here we use movement data of mobile phone users to show that mobility in Germany has not only been reduced considerably: Lockdown measures caused substantial and long-lasting structural changes in the mobility network. We find that long-distance travel was reduced disproportionately strongly. The trimming of long-range network connectivity leads to a more local, clustered network and a moderation of the "small-world" effect. We demonstrate that these structural changes have a considerable effect on epidemic spreading processes by "flattening" the epidemic curve and delaying the spread to geographically distant regions.


Asunto(s)
/prevención & control , Pandemias , Cuarentena , Análisis Espacial , Viaje/estadística & datos numéricos , Teléfono Celular , Alemania , Humanos
19.
Bull Math Biol ; 83(1): 2, 2020 Dec 14.
Artículo en Inglés | MEDLINE | ID: mdl-33315147

RESUMEN

It has long been known that epidemics can travel along communication lines, such as roads. In the current COVID-19 epidemic, it has been observed that major roads have enhanced its propagation in Italy. We propose a new simple model of propagation of epidemics which exhibits this effect and allows for a quantitative analysis. The model consists of a classical SIR model with diffusion, to which an additional compartment is added, formed by the infected individuals travelling on a line of fast diffusion. The line and the domain interact by constant exchanges of populations. A classical transformation allows us to reduce the proposed model to a system analogous to one we had previously introduced Berestycki et al. (J Math Biol 66:743-766, 2013) to describe the enhancement of biological invasions by lines of fast diffusion. We establish the existence of a minimal spreading speed, and we show that it may be quite large, even when the basic reproduction number [Formula: see text] is close to 1. We also prove here further qualitative features of the final state, showing the influence of the line.


Asunto(s)
/epidemiología , Epidemias , Número Básico de Reproducción , Simulación por Computador , Epidemias/estadística & datos numéricos , Humanos , Conceptos Matemáticos , Modelos Biológicos , Modelos Estadísticos , Viaje
20.
Isr Med Assoc J ; 22(12): 794-799, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33381955

RESUMEN

BACKGROUND: For most passengers, even those with respiratory disease, air travel is safe and comfortable. Some travelers may experience hypoxia at sea level but may not need supplemental oxygen during air travel in a hypobaric hypoxic environment. For some individuals compensatory pulmonary mechanisms may be inadequate, causing profound hypoxia. In addition, venous thromboembolism/pulmonary emboli may occur, especially during long haul flights. With adequate screening, patients at risk can be identified, therapeutic solutions can be proposed for the flight, and most can travel can continue safely with supplemental oxygen and other preventive measures.


Asunto(s)
Aeronaves , Enfermedades Respiratorias/etiología , Astenia/etiología , Bronquiectasia/etiología , Humanos , Enfermedad Pulmonar Obstructiva Crónica/etiología , Viaje
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