Theory versus Data: How to Calculate R0?

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Abstract
To predict the potential severity of outbreaks of infectious diseases such as SARS, HIV, TB and smallpox, a summary parameter, the basic reproduction number R0, is generally calculated from a population-level model. R0 specifies the average number of secondary infections caused by one infected individual during his/her entire infectious period at the start of an outbreak. R0 is used to assess the severity of the outbreak, as well as the strength of the medical and/or behavioral interventions necessary for control. Conventionally, it is assumed that if R0>1 the outbreak generates an epidemic, and if R00). Surprisingly, we find that this value of R0 calculated from the ILM is very different from the epidemic threshold calculated from the population-level model. This occurs because many different individual-level processes can generate the same incidence and prevalence patterns. We show that obtaining R0 from empirical contact tracing data collected by epidemiologists and using this R0 as a threshold parameter for a population-level model could produce extremely misleading estimates of the infectiousness of the pathogen, the severity of an outbreak, and the strength of the medical and/or behavioral interventions necessary for control.