1. Office of Infectious Diseases Computational Challenges for Infectious Diseases Michael Shaw, PhD OID/Office of the Director

2. 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

3. 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.

4. -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

5. Computational tools Next-Generation Sequencing Detection of epidemiological links 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.

6. Challenge: NGS error correction Challenge 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.

7. Challenge: Risk Assessment of an Emerging Pathogen, Influenza A (H7N9) Antigenic Site A Red Antigenic Site B Gold Antigenic Site C Magenta Antigenic Site D Cyan Antigenic Site E Green Receptor Binding Site Gray Hemagglutinin Structure RBS 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:e421895 Daniels et al. 1983, J Gen Virol 64:1657 Stray et al. 2012, Virol J 9:91

8. 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

9. 125: A / T / A / A Glycosylation site at position 123 in NL219 is not present in 2013 H7N9 217: L / Q / Q / I Equivalent to residue 226 in H3 numbering. Crucial for switching between α2-3 and α2-6 receptor specificity in H2/H3 HAs. H7 Receptor binding site Netherlands/219/2003 vs 2013 H7N9 177: V / G / G / V Point towards the RBS pocket. More hydrophobic in Anhui/1/2013 May reduce α2-3 interactions? 180: A / T / A / A Minimal impact, if any on the RBS. Assuming receptor binding is similar to published structural data, this should not directly interact with receptor 128: S A, conserved in other H7 HAs 212: T P, conserved in other H7 HAs

10. Glycans and influenza virus specificity  2-3 Avian-type receptors, found in human lower respiratory tract  2-6 Human-type receptors, found in human upper respiratory tract A/Netherlands/219/2003 (H7N7) Avian Receptor-binding Pattern A/Anhui/1/2013 (H7N9) A/New Caledonia/20/1999 (pre2009 H1N1) Seasonal Human Pattern

11. 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

12. Questions? Michael Shaw, Office of Infectious Diseases – MShaw1@cdc.gov MShaw1@cdc.gov Yuri Khudyakov, Division of Viral Hepatitis – YKhudyakov@cdc.gov YKhudyakov@cdc.gov