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countless pleasurable coffees, lunches or beers with) the students and postdocs in our lab group: Shirli Bar-David, Peter Baxter, Annaliese Beery, Allison Bidlack, Paul Cross, John Eppley, Alison Galvani, Kimber Gross, Eran Karmon, Karen Levy, Andy Lyons, Leo Polansky, Phil Starks, Jessica Redfern, Sadie Ryan, Maria Sanchez, Wendy Turner, Michael Westphal, Chris Wilmers, and George Wittemyer. I particularly thank Paul Cross, my partner on a series of enjoyable and fruitful projects and tireless wrangler of unruly field data (and buffalo). My classmates in Biophysics have provided a loose-knit but strongly-bonded community throughout my time here, and given me a glimpse of their diverse fields of study. I sadly acknowledge the loss of Eran Karmon, whose unexpected departure robbed me of a valued friend, respected colleague, intrepid ski buddy and all-around comic relief. We’re all poorer for his absence, and laugh less. Everything I’ve done is built on the foundation of unwavering support provided by my family. I am deeply grateful for this consistent encouragement, and for the taste for challenge and exploration that was instilled at an early age. I’m endebted to family and friends—old and new, local and distant—for their grounding influence and reliable injection of fun into a busy lifestyle. I thank Marc and Julie for opening their home to a stray foreigner and being steadfast friends ever since, and the McNamara and Henderson families for their warm welcome and inclusiveness. Finally I thank Katy for sharing her life with me: for joy and adventure when times are good, for comfort and strength when they’re bad, and for a broader, richer experience of the world through it all. I gratefully acknowledge financial support during my dissertation from a Berkeley Fellowship, a post-graduate fellowship from the Natural Sciences & iii
Engineering Research Council of Canada, and support from the National Science Foundation and National Institutes of Health. Funds for travel and collaborative work were provided by the South African Centre for Epidemiological Modelling and Analysis, the American Institute for Mathematical Sciences, the James S. McDonnell Foundation, and the U.C. Berkeley Graduate Division. iv
Page 1 and 2: Disease transmission in heterogeneo
Page 3 and 4: Abstract Disease transmission in he
Page 5 and 6: variation is quantified from outbre
Page 7: ACKNOWLEDGEMENTS I’ve been fortun
Page 11 and 12: Epidemic modelers face an essential
Page 13 and 14: casual contact (DCC), common usage
Page 15 and 16: HCW, and patient pools) and dynamic
Page 17 and 18: Hoffmann 2004; Shen et al. 2004)—
Page 19 and 20: Chapter Two Frequency-dependent inc
Page 21 and 22: principles and reach robust conclus
Page 23 and 24: partnership, disease and demographi
Page 25 and 26: transmission to incorporate this ph
Page 27 and 28: This result can be understood intui
Page 29 and 30: Garnett 2002). We simulated epidemi
Page 31 and 32: 4. Infection-induced changes in pai
Page 33 and 34: susceptible population (Diekmann an
Page 35 and 36: epidemics, since they bring R0 clos
Page 37 and 38: equired.) For slower-moving, chroni
Page 39 and 40: addressed here. Our treatment consi
Page 41 and 42: Table 1. Results for epidemics with
Page 43 and 44: (Equations 3 and A4); the lighter l
Page 45 and 46: Figure 2 A) B) Total proportion inf
Page 47 and 48: Appendix Derivation of SI pair dens
Page 49 and 50: As described in Section 2, our goal
Page 51 and 52: can be calculated as the product of
Page 53 and 54: Chapter Three Curtailing transmissi
Page 55 and 56: egions with on-going epidemics has
Page 57 and 58: transmission to the general communi
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and Ih), as well as from off-duty t
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ours—see Diekmann & Heesterbeek (
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In all cases (Figure 2C, 2D), we id
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Sensitivity to quarantining rate (s
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precautions in the hospital (η→1
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Preventing generalized community tr
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everywhere. These robust conclusion
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increasingly significant contributi
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hospitals or wards. Future work on
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Table 1. Summary of transmission an
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formulation of our model allows for
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Figure 3 (A) Increase in cumulative
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Figure 1 74
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Figure 3 (A) (B) (C) Cumulative num
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Appendix Sensitivity to population
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symptomatic HCWs is low. Indeed, th
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E I I I I m, i m, 1 m, 2 m , 3 m ,
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for a stochastic epidemic: the prob
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progress through the age sub-compar
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We therefore wish to characterize t
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Figure S4 Distribution of (A) incub
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Figure S2 (A) (C) 92 (B) (D)
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Figure S4 (A) (B) Proportion of cas
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1. Introduction During the global e
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quantity p0, the proportion of case
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model selection techniques, lending
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elatively mild variation in ν, sho
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cannot make inferences based on the
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low k extinction happens within the
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measured by the variance-to-mean ra
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succeed (Figure 3B). For a given re
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to lower infectiousness. Other rele
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observations for the diseases exami
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Pneumonic plague 6 outbreaks N=74 A
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s surveillance data. 90% CI: Bootst
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Figure captions Figure 1 Evidence f
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Figure 4 Impact of control measures
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Figure 2 Other Measles Influenza Ru
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Figure 4 C Reproductive number, R 1
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epresenting transmission yields a g
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We rescaled the AICc by subtracting
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for which the median of bootstrap e
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transmission due to the most infect
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an integer Z (99) such that FPoisso
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fv(u). Demographic stochasticity in
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original process is eliminated with
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For RA control, with a random propo
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∞ ( , ) ∫ ( ) ( ). k−1 −t w
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* and for ν < ν : ∞ ∫ ν C 1
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Contrib(control policy) = Pr(contai
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ange of the first disease generatio
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Figure S1 MLE estimates of k 10 1 0
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Figure S2 (cont) D E F k=inf k=4 k=
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Figure S4 Relative frequency 0.4 0.
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SARS (March 12) and the imposition
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Transmission was predominantly by i
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Monkeypox, Zaire 1980-1984 (Jezek e
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Rubella, Hawaii 1970 (Hattis et al.
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tracing, with the stated goal of de
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Table S1. Superspreading events in
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Measles 250 Dance party ?M First ar
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SARS 187+ Apartment block 26M Amoy
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SARS 33 Hospital 62W Undiagnosed: S
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SARS 24/2* Home, emergency room, IC
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Streptococcus group A (type 1) 100+
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References Abbot, P. and L. M. Dill
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Caswell, H. (2001) Matrix Populatio
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Evatt, B. L., W. R. Dowdle, M. John
Page 195 and 196:
Health Canada (2003) Summary of Sev
Page 197 and 198:
Kretzschmar, M. (2000). Sexual netw
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McCallum, H., N. Barlow and J. Hone
Page 201 and 202:
Taylor, H. M. and S. Karlin (1998).
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