the informatics crystal ball: mining the past to predict the species jump event

www.fludb.org

The Informatics Crystal Ball:Mining the Past to Predict

the Species Jump Event

19 April 2011

Richard H. Scheuermann, Ph.D.Department of Pathology

U.T. Southwestern Medical Center

www.fludb.org

Flu pandemics of the 20th and 21st centuries initiated by species jump events

• 1918 flu pandemic (Spanish flu)– subtype H1N1 (avian origin)– estimated to have claimed between 2.5% to 5.0% of the world’s population (20 > 100

million deaths)

• Asian flu (1957 – 1958)– subtype H2N2 (avian origin)– 1 - 1.5 million deaths

• Hong Kong flu (1968 – 1969)– subtype H3N2 (avian origin)– between 750,000 and 1 million deaths

• 2009 H1N1– subtype H1N1 (swine origin)– ~ 16,000 deaths as of March 2010

www.fludb.org2009 Pandemic species jump

www.fludb.orgPandemic stages

Adaptive drivers

www.fludb.orgBasic reproductive number (R0)

• Total number of secondary cases per case• Reasonable surrogate of fitness• Characteristics of pandemic viruses:

– R0H >1, and– In genetic neighborhood of viruses with R0R>1 and R0H<1

• Adaptive drivers

Pandemic Viruses(R0H >1)

Stuttering viruses(R0R>1 and R0H<1)

Reservoir virus(R0R>1 and R0H<<1)

A1 A2

www.fludb.orgAdaptive drivers

Pepin KM et al. (2010) “Identifying genetics markers of adaptation for surveillance of viral host jump” Nature Reviews Microbiology 8: 802-814.

www.fludb.orgStuttering transmission and adaptive drivers

• Stuttering transmission can reveal adaptive drivers by evidence of convergent evolution– Odds of finding the same neutral mutation by chance in multiple

species jumps is low– Therefore, finding same mutation in multiple independent species jump

events is strong evidence for adaptive driver

www.fludb.org

Genetic convergence during species jump

• Virus isolate groups from IRD– Avian H5N1 (PB2) from Southeast Asia* up to 2003 (260 records) –

reservoirs of source viruses– Human H5N1 (PB2) from Southeast Asia 2003-present (165 records) –

many examples of independent species jumps• Align amino acid sequence and calculate conservation score• Identify highly conserved positions in avian records (≤1/260

variants) (557positions/759) – functionally restricted in reservoir

• Select subset in which two or more human isolates contained the same sequence variant – either due to human-human transmission or convergent evolution

*China, Hong Kong, Indonesia, Thailand, Viet Nam

www.fludb.org

Strain Search – PB2 avian H5N1 Southeast Asia up to 2003

www.fludb.org260 PB2 records

www.fludb.orgSequence variation analysis

www.fludb.orgPosition order

www.fludb.orgOrder by conservation score

www.fludb.orgMy Workbench

www.fludb.orgConvergent evolution candidates

d

d

d

www.fludb.orgSurface exposed

PB2_A/MEXICO/INDRE4487/2009(H1N1)

Conservation scoreAll convergent evolution

candidates 586, 591, 627, 629

www.fludb.orgConvergent evolution candidates

www.fludb.orgE627K

www.fludb.orgE627K and species jump

www.fludb.orgK660R

www.fludb.orgSummary

• Human influenza pandemics are initiated by species jump events followed by sustained human to human transmission (R0H>1)

• Multiple independent occurrences of the same mutation during stuttering transmission is evidence of convergent evolution of adaptive drivers – hypotheses for experimental testing

• Surveillance for adaptive drivers in reservoir species could help anticipate the next pandemic

N01AI40041