In outbreak analysis, the most significant moments aren’t the ones where we’re right. It’s those moments when we realise we’ve been wrong. When something doesn’t look quite right: a pattern catches our eye, an exception breaks what we thought was the rule. Whether we want an innovation to take off or an infection to decline, these are the moments we need to reach as early as possible. The moments that allow us to unravel chains of transmission, searching for weak links, missing links, and unusual links. The moments that let us look back, to work out how outbreaks really happened in the past. Then look forward, to change how they happen in future.
Notes
Introduction
1. Original tweet, which had 49,090 impressions in total. Unsurprisingly, several users would subsequently ‘unretweet’ it: https://twitter.com/AdamJKucharski/status/885799460206510080 (Of course, a large number of impressions does not necessarily mean that users read the tweet, as we shall see in Chapter 5.)
2. Background on 1918 pandemic: Barry J.M., ‘The site of origin of the 1918 influenza pandemic and its public health implications’ Journal of Translational Medicine, 2004; Johnson N.P.A.S. and Mueller J., ‘Updating the Accounts: Global Mortality of the 1918–1920 “Spanish” Influenza Pandemic’ Bulletin of the History of Medicine, 2002; World War One casualty and death tables. PBS, Oct 2016. https://www.uwosh.edu/faculty_staff/henson/188/WWI_Casualties%20and%20Deaths%20%20PBS.html. Note that there have recently been other theories about the source of the 1918 flu pandemic, with some arguing that the introduction was much earlier than previously thought e.g. Branswell H., ‘A shot-in-the-dark email leads to a century-old family treasure – and hope of cracking a deadly flu’s secret’, STAT News, 2018.
3. Examples of quote in media: Gerstel J., ‘Uncertainty over H1N1 warranted, experts say’ Toronto Star, 9 October 2009; Osterholm M.T., ‘Making sense of the H1N1 pandemic: What’s going on?’ Center for Infectious Disease Research and Policy, 2009.
4. Eames K.T.D. et al., ‘Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza’, PLOS Computational Biology, 2012; Health Protection Agency, ‘Epidemiological report of pandemic (H1N1) 2009 in the UK’, 2010.
5. Other groups reached similar conclusions, e.g. WHO Ebola Response Team, ‘Ebola Virus Disease in West Africa – The First 9 Months of the Epidemic and Forward Projections’, The New England Journal of Medicine (NEJM), 2014.
6. ‘Ransomware cyber-attack: Who has been hardest hit?’, BBC News Online, 15 May 2017; ‘What you need to know about the WannaCry Ransomware’, Symantec Blogs, 23 October 2017. Exploit attempts increased from 2000 to 80000 in 7 hours, implying doubling time = 7/log2(80000/2000) = 1.32 hours.
7. Media Metrics #6: The Video Revolution. The Progress & Freedom Foundation Blog, 2 March 2008. http://blog.pff.org/archives/2008/03/print/005037.html. Adoption went from 2.2% of homes in 1981 to 18% homes in 1985, implying doubling time = 365 × 4/log2(0.18/0.02) = 481 days.
8. Etymologia: influenza. Emerging Infectious Diseases 12(1):179, 2006.
1. A theory of happenings
1. Dumas A., The Count of Monte Cristo (1844–46), Chapter 117.
2. Kucharski A.J. et al., ‘Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji’, eLIFE, 2018.
3. Pastula D.M. et al., ‘Investigation of a Guillain-Barré syndrome cluster in the Republic of Fiji’, Journal of the Neurological Sciences, 2017; Musso D. et al., ‘Rapid spread of emerging Zika virus in the Pacific area’, Clinical Microbiology and Infection, 2014; Sejvar J.J. et al., ‘Population incidence of Guillain-Barré syndrome: a systematic review and meta-analysis’, Neuroepidemiology, 2011.
4. Willison H.J. et al., ‘Guillain-Barré syndrome’, The Lancet, 2016.
5. Kron J., ‘In a Remote Ugandan Lab, Encounters With the Zika Virus and Mosquitoes Decades Ago’, New York Times, 5 April 2016.
6. Amorim M. and Melo A.N., ‘Revisiting head circumference of Brazilian newborns in public and private maternity hospitals’, Arquivos de Neuro-Psiquiatria, 2017.
7. World Health Organization, ‘WHO statement on the first meeting of the International Health Regulations (2005) (IHR 2005) Emergency Committee on Zika virus and observed increase in neurological disorders and neonatal malformations’, 2016.
8. Rasmussen S.A. et al., ‘Zika Virus and Birth Defects – Reviewing the Evidence for Causality’, NEJM, 2016.
9. Rodrigues L.C., ‘Microcephaly and Zika virus infection’, The Lancet, 2016.
10. Unless otherwise stated, background information is from: Ross R., The Prevention of Malaria (New York, 1910); Ross R., Memoirs, With a Full Account of the Great Malaria Problem and its Solution (London, 1923).
11. Barnes J., The Beginnings Of The Cinema In England, 1894–1901: Volume 1: 1894–1896 (University of Exeter Press, 2015).
12. Joy D.A. et al., ‘Early origin and recent expansion of Plasmodium falciparum’, Science, 2003.
13. Mason-Bahr P., ‘The Jubilee of Sir Patrick Manson: A Tribute to his Work on the Malaria Problem’, Postgraduate Medical Journal, 1938.
14. To K.W.K. and Yuen K-Y., ‘In memory of Patrick Manson, founding father of tropical medicine and the discovery of vector-borne infections’ Emerging Microbes and Infections, 2012.
15. Burton R., First Footsteps in East Africa (London, 1856).
16. Hsu E., ‘Reflections on the “discovery” of the antimalarial qinghao’, British Journal of Clinical Pharmacololgy, 2006.
17. Sallares R., Malaria and Rome: A History of Malaria in Ancient Italy (Oxford University Press, 2002).
18. Ross claimed that the participants had been told what was involved, and that risks of the experiments were justified: ‘I think myself justified in making this experiment because of the vast importance a positive result would have and because I have a specific in quinine always at hand.’ (source: Ross, 1923). However, it is not clear how fully the risks were actually explained to participants; quinine is not as effective as the treatments used in modern studies of malaria (source: Achan J. et al., ‘Quinine, an old anti-malarial drug in a modern world: role in the treatment of malaria’ Malaria Journal, 2011.) We will look at the ethics of human experiments in more detail in Chapter 7.
19. Bhattacharya S. et al., ‘Ronald Ross: Known scientist, unknown man’, Science and Culture, 2010.
20. Chernin E., ‘Sir Ronald Ross vs. Sir Patrick Manson: A Matter of Libel’, Journal of the History of Medicine and Allied Sciences, 1988.
21. Manson-Bahr P., History Of The School Of Tropical Medicine In London, 1899–1949, (London, 1956).
22. Reiter P., ‘From Shakespeare to Defoe: Malaria in England in the Little Ice Age’, Emerging Infectious
