Office of Infectious Diseases Computational Challenges for Infectious Diseases Michael Shaw, PhD OID/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 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):

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 BMC bioinformatics. 2012, 13(Suppl 10):S6.

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:e Daniels 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 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 / 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

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

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 – Yuri Khudyakov, Division of Viral Hepatitis –