Office of Infectious Diseases

Computational Challenges for Infectious Diseases

Michael Shaw, PhDOID/Office of the Director

CDC’s Scientific Agenda for AMD:

To use modern laboratory and computing technologies to enhance public health

surveillance, response to outbreaks, and the control and prevention of infectious

diseases

Pathogen Detection and Characterization Applications.

Molecular detection as a replacement for traditional methods such as culture/isolation or visualization of antigens/antibodies:

Allows more laboratories to detect pathogens and thus increases the amount of surveillance data.

Allows surveillance of more pathogens.

Makes true Molecular Epidemiology possible.

- A single sequence cannot adequately represent the intra-host viral population- It is important to sample numerous intra-host viral variants for many molecular epidemiological

applications: - - detection of transmission networks

- drug resistance- vaccine escape- disease severity

Challenge: Hepatitis C virus (HCV) exists in infected host as a large population of genetically related intra-host variants

Computational tools

Next-Generation Sequencing

Detection of epidemiological links

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Clinical Institution HCV cases

Surveillance

Detection of HCV transmissions using NGS

Not linked

Transmission cluster

Most probable source Network of

transmissions

Ganova-Raeva, L. et al. Detection of hepatitis C virus transmission using mass spectrometry. Journal of Infectious Diseases. 207(6):999-1006.

Challenge: NGS error correctionChallenge

• Distinguishing viral variants from NGS errors• Extremely large data sets

- Blue dot represents the only real variant - Yellow dots are NGS errors

Solution

• Error correction algorithms

Skums, P. Et al. Efficient Error Correction of High-throughput Viral Sequencing. 2011. BMC bioinformatics. 2012, 13(Suppl 10):S6.

Challenge: Risk Assessment of an Emerging Pathogen, Influenza A (H7N9)

Antigenic Site A RedAntigenic Site B GoldAntigenic Site C MagentaAntigenic Site D CyanAntigenic Site E GreenReceptor Binding Site Gray

Hemagglutinin StructureRBS

AS-A

AS-B

AS-C

AS-D

AS-E

Equivalent sites to H3N2 viruses:Wiley et al. 1981, Nature 289:373 Popova et al. 2012, PLoS One 7:e421895Daniels et al. 1983, J Gen Virol 64:1657 Stray et al. 2012, Virol J 9:91

H7N9: Genetic Markers Characteristic of Host Adaptation or Virulence

• NA stalk deletion aa 69-73 characteristic of poultry adaptation

• M1 protein: N30D and T215A – increased virulence in mice• PB2:

• 89V – enhanced polymerase activity and increased virulence in mice

• 627K - enhanced polymerase activity and increased virulence in mice (most human isolates; absent in avian or environmental virus sequences)

• PB1:• H99Y and I368V – H5 transmissibility in ferrets; not

present in all• NS1

• P42S – increased virulence in mice

125: A / T / A / AGlycosylation site at position 123 in NL219 is not present in 2013 H7N9

217: L / Q / Q / IEquivalent to residue 226 in H3 numbering. Crucial for switching between α2-3 and α2-6 receptor specificity in H2/H3 HAs.

H7 Receptor binding siteNetherlands/219/2003 vs 2013 H7N9

177: V / G / G / VPoint towards the RBS pocket. More hydrophobic in Anhui/1/2013 May reduce α2-3 interactions?

180: A / T / A / AMinimal impact, if any on the RBS. Assuming receptor binding is similar to published structural data, this should not directly interact with receptor

128: SA, conserved in other H7 HAs

212: T P, conserved in other H7 HAs

Glycans and influenza virus specificity

a2-3 Avian-type receptors, found in human lower respiratory tract

a2-6 Human-type receptors, found in human upper respiratory tract

A/Netherlands/219/2003 (H7N7)Avian Receptor-binding

PatternA/Anhui/1/2013 (H7N9)

A/New Caledonia/20/1999(pre2009 H1N1)

Seasonal Human Pattern

Outbreak Response

• Detection of etiologic agent– Identification of previously unknown pathogens

• SARS and MERS CoV

– Distinguish from background of commensals– Increasing reliance on PCR and sequencing

• Characterization of etiologic agent– Tissue tropism and host range

• Clinical recognition and management• Non human reservoir identification (important for control

efforts)

– Diagnostics development– Susceptibility to antimicrobial therapeutics– Vaccine development and use

Questions?

• Michael Shaw, Office of Infectious Diseases– MShaw1@cdc.gov

• Yuri Khudyakov, Division of Viral Hepatitis– YKhudyakov@cdc.gov