reconstructing the social network of viruses in wild ducks

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

8

6

4

Segment Transmission Map= 1 virus= different subtypes

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Only full transmissions

8

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