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Estimating Infection Prevalence in Wuhan City, China from Repatriation

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Estimating Infection Prevalence in Wuhan City, China from Repatriation Estimating infection prevalence in Wuhan City, China from repatriation flight data Hayley A Thompson1*, Natsuko Imai1, Amy B Dighe1, Kylie Ainslie1, Marc Baguelin1, Sangeeta Bhatia1, Samir Bhatt1, Adhiratha Boonyasiri1,2, Olivia Boyd1, Nicholas F Brazeau1, Lorenzo Cattarino1, Laura V Cooper1, Helen Coupland1, Zulma Cucunuba1, Gina Cuomo-Dannenburg1, Bimandra Djaafara1, Ilaria Dorigatti1, Sabine Leonore vanElsland1, Richard FitzJohn1, Han Fu1, Katy Gaythorpe1, Will Green1, Timothy Hallett1, Arran Hamlet1, David Haw1, Sarah Hayes1, Wes Hinsley1, Benjamin Jeffrey1, Edward Knock1, Daniel J Laydon1 , John Lees1, Tara D Mangal1, Thomas Mellan1, Swapnil Mishra1, Andria Mousa1, Gemma Nedjati-Gilani1, Pierre Nouvellet1,3, Lucy Okell1, Kris V Parag1, Manon Ragonnet-Cronin1, Steven Riley1, H. Juliette T Unwin1, Robert Verity1, Michaela Vollmer1, Erik Volz1, Patrick G T Walker1, Caroline Walters1, Haowei Wang1, Yuanrong Wang1, Oliver J Watson1, Charles Whittaker1, Lilith K Whittles1, Peter Winskill1, Xiaoyue Xi4, Christl A Donnelly1,5 & Neil M Ferguson1 Affiliations: 1. MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK 2. NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London 3. School of Life Sciences, University of Sussex, UK 4. Department of Mathematics, Imperial College London, London, UK 5. Department of Statistics, University of Oxford, Oxford, UK *Corresponding author: Ms Hayley Thompson, MRC Centre for Global Infectious Disease Analysis, Imperial College, Norfolk Place, London, W2 1NY. [email protected] (Submitted: 21 April 2020 – Published online: 23 April 2020) DISCLAIMER This paper was submitted to the Bulletin of the World Health Organization and was posted to the COVID-19 open site, according to the protocol for public health emergencies for international concern as described in Vasee Moorthy et al. (http://dx.doi.org/10.2471/BLT.20.251561). The information herein is available for unrestricted use, distribution and reproduction in any medium, provided that the original work is properly cited as indicated by the Creative Commons Attribution 3.0 Intergovernmental Organizations licence (CC BY IGO 3.0). RECOMMENDED CITATION Thompson HA, Imai N, Dighe AB, Ainslie K, Baguelin M, Bhatia S, et al. Estimating infection prevalence in Wuhan City, China from repatriation flight data. [Preprint]. Bull World Health Organ. E-pub: 23 April 2020. doi: http://dx.doi.org/10.2471/BLT.20.260307 Abstract Objective: To characterise the infection prevalence of SARS-CoV-2 over time from repatriates returning from Wuhan City, China between 29th January – 27th February 2020. Methods: We identified and tracked countries that were repatriating citizens on chartered flights departing Wuhan City between 29th January to the 27th February 2020. Data were curated from publicly available government or media sources, on the number of people repatriated, the number of people undergoing PCR testing and the symptomatic status of individuals being tested. We pooled these data and estimated the overall infection prevalence and a per-flight infection prevalence estimate over time. Findings: We identified 56 flights that repatriated a total of 8597 people to 55 different countries over the time period considered. Pooling the available data, we estimated overall infection prevalence to be 0.87% (95% CI: 0.32 – 1.89%) in Wuhan City, China. Infection prevalence was generally low across all flights with point estimates below 2% (range: 0 %– 1.9%). We observed a declining trend in infection prevalence over time; however, this was not statistically significant. Conclusion: Where population-level testing is not feasible during an outbreak, these repatriated cohorts provide snapshots of the infection prevalence over time in Wuhan City. Such early studies can be used to understand the potential scale of the epidemic and have subsequently helped to inform the ongoing global response and research into COVID-19. Introduction The outbreak of a novel coronavirus (coronavirus disease 2019 (COVID-19)), caused by the SARS-CoV-2 virus, was declared a global pandemic by the World Health Organization (WHO) on 11th March 2020 [1]. The virus was first detected in Wuhan City, China in late 2019 and has subsequently spread to over 200 countries states and territories across the globe [2]. China implemented strict travel and movement restrictions in Wuhan City following the detection of the outbreak which led to foreign governments chartering flights to repatriate citizens from the then epicentre of the outbreak. These flights began on 29th January 2020 and continued up to the point of our analysis on 27th February 2020. Repatriates underwent quarantine upon arrival in their home countries and many countries implemented PCR to test for infection regardless of symptoms. These repatriation flights therefore provide snapshots of infection prevalence over time and give us insights into the levels of transmission in Wuhan City where large-scale prevalence surveys were unfeasible given the scale of the outbreak and the response needed to contain it. We present an overview of these repatriation flights within this timeframe and estimate the infection prevalence over time. Methods Data Collection We identified countries that were scheduling repatriation flights through following international and local news outlets and the press releases of government departments including Ministries of Foreign Affairs and Ministries of Health. Once flights were identified we curated a list of key variables to track during the quarantine periods (Table 1). These variables included the total number of repatriates per flight and their final destinations, the number of those who were tested on arrival, during and before release from quarantine and the number who tested positive. In addition, we collected information on the number of people who tested positive while being asymptomatic or symptomatic. Statistical Analysis All analysis was performed using R Statistical Software version 3.6.3 [3]. The primary outcome was a confirmed PCR positive test result for SARS-CoV-2 infection. For the repatriation flights where all passengers were tested regardless of presence or absence of symptoms, we estimated the infection point prevalence as the number of positive test results divided by the total tested population and the corresponding exact 95% binomial confidence intervals [4]. To test for any association between date of repatriation flight and the level of infection prevalence we performed a logistic regression on the binomial count data over time. The dependent variable was confirmed SARS-CoV-2 infection (positive = 1, negative = 0) and the categorical predictor variable was the date of flight over the study period in question (29th January 2020 – 27th February 2020). Results A total of 8597 persons were repatriated over 56 flights from Wuhan City carrying citizens from 55 different countries (Table 1). Figure 1 highlights the countries (and the number of repatriation flights bycountry) where repatriates underwent their quarantine periods. As some flights were shared between two or more countries e.g. USA and Canada, the map shows the countries that chartered the primary flight out of Wuhan and therefore the destination of quarantine for the majority of passengers on-board. Quarantine periods were defined and carried out by governments following the arrival of the repatriation flights in country. Most countries implemented 14-day quarantine periods to reduce the risk of local onward transmission from this at- risk population. This follows WHO advice based on estimates that the maximum incubation period of the virus is around 14 days [5]. During this time the majority of countries tested for SARS-CoV-2 infection in symptomatic and asymptomatic repatriates, at multiple time points. The supplementary table outlines the testing procedures that have been made publicly available. While testing procedures varied, we identified 47 repatriation flights that tested for SARS-CoV-19 infection in their passengers resulting in a total tested population of 5,720 individuals. Of these passengers a total of 36 tested positive for SARS-CoV-2 infection resulting in an overall infection prevalence of 0.63% (95% CI: 0.44% - 0.87%). However, only 32 out of the 47 repatriation flights tested everyone regardless of symptoms (we include the first Japanese flight where 204 of 206 passengers were tested). Only considering these flights, the overall infection prevalence was 0.60% (95% CI: 0.41% -0.86%). Finally, repatriation flights had different testing protocols (Supplementary Table), and amongst the 47 flights that tested for SARS-CoV-2 infection, 20 tested upon arrival. Quarantine measures also differed slightly by country, with some individuals undergoing quarantine at home rather than in a designated facility. Accounting for the possibility individuals may have been infected on the flight itself and thus later test positive, to estimate a conservative point prevalence of infection, we estimated infection prevalence from flights that tested passengers immediately upon arrival. Of 2433 passengers tested immediately upon arrival, 13 individuals tested positive upon the initial test, giving an infection prevalence of 0.53% (95% CI: 0.28% - 0.91%). Over the 6 flights arriving between 30th January 2020 and
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