Measurably evolving pathogens in the genomic era




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Supplementary Material

Measurably evolving pathogens in the genomic era

Roman Biek1,2, Oliver G Pybus3, James O Lloyd-Smith2,4, Xavier Didelot5



1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK

2 Fogarty International Center, National Institutes of Health, Bethesda MD, USA

3 Department of Zoology, University of Oxford, Oxford, UK


4 Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA

5 Department of Infectious Disease Epidemiology, Imperial College London, UK

Table S1 – Evolutionary rate estimates for viral and bacterial pathogen genomes



Pathogen

Group

Genome size (bp)

Evolutionary rate (site-1 year-1)

Evolutionary rate (genome-1 year-1)

Host scale

Date range (yrs)

Source

Clostridium difficile

Bacteria

4300000

3.20E-07

1.38

within

1

[S1]

Clostridium difficile

Bacteria

430000

1.15E-10

5E-4

among

1,100,000

[S2]

Helicobacter pylori

Bacteria

1600000

2.60E-07

0.42

among

70,000

[S3]

Helicobacter pylori

Bacteria

1600000

1.90E-05

40.00

among

3

[S4]

Helicobacter pylori

Bacteria

1600000

1.38E-05

22.00

among

15

[S5]

Mycobacterium bovis

Bacteria

4300000

3.40E-08

0.15

among

12

[S6]

Mycobacterium leprae

Bacteria

3200000

6.10E-09

0.02

among

1,000

[S7]

Mycobacterium tuberculosis

Bacteria

4400000

1.00E-07

0.44

within

1

[S8]

Mycobacterium tuberculosis

Bacteria

4400000

6.80E-08

0.30

among

10

[S9]

Mycobacterium tuberculosis

Bacteria

4400000

1.10E-07

0.48

within

1

[S10]

Mycobacterium tuberculosis

Bacteria

4400000

2.58E-9

0.01

among

70,000

[S11]

Salmonella enterica Agona

Bacteria

4200000

9.30E-08

0.39

among

60

[S12]

Staphylococcus aureus (ST239)

Bacteria

2900000

3.30E-06

9.57

among

25

[S13]

Staphylococcus aureus (ST239)

Bacteria

2900001

2.70E-06

7.83

within

1

[S14]

Streptococcus pneumoniae (PMEN1)

Bacteria

2200000

1.60E-06

3.52

among

25

[S15]

Vibrio cholerae

Bacteria

4000000

8.30E-07

3.32

among

60

[S16]

Yersinia pestis

Bacteria

4500000

8.60E-09

0.04

among

70

[S17]

Human polyomavirus (BK)

dsDNA virus

5000

3.00E-05

0.15

among

30

[S18]

Myxoma virus

dsDNA virus

162000

9.60E-06

1.56

among

46

[S19]

Smallpox virus

dsDNA virus

200000

9.00E-06

1.80

among

31

[S18]

Hep C virus (1b)

RNA virus

9000

1.00E-03

9.00

among

35

[S20]

HIV-M

RNA virus

10000

3.30E-03

33.00

among

50

[S21]

Influenza A virus (H1N1, 2009)

RNA virus

13600

3.60E-03

48.96

among

1

[S22]

Influenza A virus (H1N1, seasonal)

RNA virus

13600

2.00E-03

27.20

among

60

[S23]

Rabies virus

RNA virus

12000

2.00E-04

2.40

among

22

[S24], Biek, unpubl.

West Nile virus

RNA virus

11000

5.60E-04

6.16

among

13

[S25]

Feline panleukopenia virus/Canine parvovirus

ssDNA virus

5000

1.00E-04 a

0.50

among

42

[26]

a based on partial genome data only

Supplementary References

S1 Didelot, X. et al. (2012) Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol 13, R118

S2 He, M. et al. (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. U. S. A. 107, 7527–7532

S3 Moodley, Y. et al. (2009) The peopling of the Pacific from a bacterial perspective. Science 323, 527–530

S4 Kennemann, L. et al. (2011) Helicobacter pylori genome evolution during human infection. Proc. Natl. Acad. Sci. U. S. A. 108, 5033–5038

S5 Didelot, X. et al. (2013) Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc. Natl. Acad. Sci. U. S. A. 110, 13880–13885

S6 Biek, R. et al. (2012) Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations. PLoS Pathog. 8, e1003008

S7 Schuenemann, V.J. et al. (2013) Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 341, 179–183

S8 Ford, C.B. et al. (2011) Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet. 43, 482–486

S9 Bryant, J.M. et al. (2013) Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: A retrospective observational study. Lancet Respir. Med. 1, 786–792

S10 Walker, T.M. et al. (2013) Contact investigations for outbreaks of Mycobacterium tuberculosis: Advances through whole genome sequencing. Clin. Microbiol. Inf., 19. , 796–802

S11 Comas, I. et al. (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 45, 1176–1182

S12 Zhou, Z. et al. (2013) Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona. PLoS Genet. 9, e1003471

S13 Harris, S.R.R. et al. (2010) Evolution of MRSA During Hospital Transmission and Intercontinental Spread. Science 327, 469–474

S14 Young, B.C. et al. (2012) Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc. Natl. Acad. Sci. U. S. A. 109 , 4550–4555

S15 Croucher, N.J. et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430–434

S16 Mutreja, A. et al. (2011) Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465

S17 Morelli, G. et al. (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat. Genet. 42, 1140–1143

S18 Firth, C. et al. (2010) Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol. Biol. Evol. 27, 2038–2051

S19 Kerr, P.J. et al. (2012) Evolutionary History and Attenuation of Myxoma Virus on Two Continents. PLoS Pathog. 8, e1002950

S20 Gray, R.R. et al. (2011) The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol. Biol. 11, 131

S21 Faria, N.R. et al. (2014) HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 346, 56–61

S22 Fraser, C. et al. (2009) Pandemic potential of a strain of influenza A (H1N1): early findings. Science 324, 1557–1561

S23 Worobey, M. et al. (2014) Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus. Proc. Natl. Acad. Sci. U. S. A. 111, 8107–8112

S24 Biek, R. et al. (2007) A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proc. Natl. Acad. Sci. U. S. A. 104, 7993–7998

S25 Pybus, O.G. et al. (2012) Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proc. Natl. Acad. Sci. U. S. A 109, 15066–15071



S26 Shackelton, L.A. et al. (2005) High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc. Natl. Acad. Sci. U. S. A 102, 379–384


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