Reconstructing the social network of viruses in wild ducks
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VReconstructing the social network
of viruses in wild ducks
Eric J. Ma, Runstadler Lab BATS 2013
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What’s the deal with influenza viruses in ducks?
How do we reconstruct and learn from a social network of viruses?
What’s up next?
Outline
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PB2 2.4 kb1
PB1 2.4 kb2
PA 2.2 kb3
HA 1.8 kb4
NP 1.6 kb5
NA 1.5 kb6
M1/M2 1.0 kb7
NS1/NS2 0.9 kb8
The flu virus has 8 (-) strand RNA segments in its genome.
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Because of its segmented nature, the flu virus is capable of genetic reassortment.
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Brooks Range
Alaska Range
Minto FlatsFairbanks
Yukon Delta
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Minto Flats, Alaska: Breeding ground for ducks along the Pacific flyways.
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DONALD
Duck flow = Virus flow
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Minto Flats
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15,083
Numbers
17520
2
ducks sampled
duck species in total
viruses isolated
years of sampling
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But what is the relationship between
these viruses?
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What’s the deal with influenza viruses in ducks?
How do we reconstruct and learn from a social network of viruses?
What’s up next?
Outline
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Segment Transmission Map= 1 virus= different subtypes
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Segment Transmission Map= 1 virus= different subtypes
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Cluster each segment by genetic similarity (PWI)
Segment Transmission Map= 1 virus= different subtypes
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Different clustering patterns for each segment
Segment Transmission Map= 1 virus= different subtypes
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Threshold = minimum in-cluster PWI
Segment Transmission Map= 1 virus= different subtypes
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Estimate transmission transmissions
segment-by-segment
Segment Transmission Map= 1 virus= different subtypes
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Segment 1
Segment Transmission Map= 1 virus= different subtypes
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Segment 2
Segment Transmission Map= 1 virus= different subtypes
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Segment 3
Segment Transmission Map= 1 virus= different subtypes
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Segment 4
Segment Transmission Map= 1 virus= different subtypes
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Segment 5
Segment Transmission Map= 1 virus= different subtypes
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Segment 6
Segment Transmission Map= 1 virus= different subtypes
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Segment 7
Segment Transmission Map= 1 virus= different subtypes
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Segment 8
Segment Transmission Map= 1 virus= different subtypes
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All hypothesized transmissions
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6
4
Segment Transmission Map= 1 virus= different subtypes
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Only full transmissions
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Segment Transmission Map= 1 virus= different subtypes
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Segment Transmission Map
Time
Order the isolates roughly in time.
= 1 virus= different subtypes
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Segment Transmission Map
Plot out the full transmissions
Time
= 1 virus= different subtypes
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Segment Transmission Map
In the Minto flats dataset, 460 out of 520 isolates were involved in 1096 full transmissions.
Time
= 1 virus= different subtypes
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Segment Transmission Map
Of 1096 transmissions, 974 were estimated as direct transmissions.
Time
= 1 virus= different subtypes
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Segment Transmission Map
Of 1096 transmissions, 49 were estimated as transmissions due to environmental persistence.
Time
= 1 virus= different subtypes
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Segment Transmission Map
Of 1096 transmissions, 73 were due to multiple isolations from the same bird.
Time
= 1 virus= different subtypes
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Segment Transmission Map
Of 1096 transmissions, 73 were due to multiple isolations from the same bird.
Time
= 1 virus= different subtypes
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Segment Transmission Map
What if we coloured the nodes by host species?
Time
= 1 virus= different subtypes
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Segment Transmission Map
What if we coloured isolates by host species?
Time
= 1 virus= different hosts
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Segment Transmission Map
We can estimate inter- and intra-species transmissions
Time
= 1 virus
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= different hosts inter intra
Segment Transmission Map
Time
= 1 virus
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= different hosts
379 inter-species transmissions644 intra-species transmissions
inter intra
Segment Transmission Map
Time
= 1 virus= different subtypes
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Let’s colour isolates by subtype again.
inter intra
Segment Transmission Map
In the Minto flats dataset, we have 92 subnetworks of full transmissions
Time
= 1 virus= different subtypes
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inter intra
Segment Transmission Map
Were there any reassortant viruses?
Time
= 1 virus= different subtypes
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inter intra reassort
Segment Transmission Map
In Minto Flats, we have putatively identified 52 reassortant viruses.
Time
= 1 virus= different subtypes
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inter intra reassort
Numbers520 viruses isolated
1096 full transmissions between 460 viruses
974 direct transmissions
49 environmental persisters
52 putative reassortants
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Segment Transmission Map
E.g. 1: Which viruses were really able to cross host species?
Time
= 1 virus= different subtypes
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inter intra reassort
Segment Transmission Map
E.g. 2: How many viruses carry over to the next year?
Time
= 1 virus= different subtypes
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2009 2010
inter intra reassort
Segment Transmission Map
E.g. 3: What factors allow cross-year viruses to persist?
Time
= 1 virus= different subtypes
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2009 2010
inter intra reassort
What’s the deal with influenza viruses in ducks?
How do we reconstruct and learn from a social network of viruses?
What’s up next?
Outline
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Q• How do host species barriers shape viral evolution?
• What is the relationship between Eurasian and N. American lineages of influenza?
• Is there a molecular basis for environmental persistence?
d3.js-based, web-ready !interactive data explorer
(prototype ready)
because some questions don’t show up until you see the data
Acknowledgments
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Jonathan Runstadler
The Awesome
Nichola Hill Brandt Meixell
who are amazing mentors & collaborators