Computational Challenges for
Infectious Diseases
Michael Shaw, PhD
OID/Office of the Director
Office of Infectious Diseases
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.
Challenge: Hepatitis C virus (HCV) exists in infected host as a
large population of genetically related intra-host variants
-
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
Detection of HCV transmissions using NGS
Clinical
Institution
HCV cases
Detection of
epidemiological links
Surveillance
Next-Generation
Sequencing
Computational
tools
Not linked
Most probable
source
Network of
transmissions
Transmission
cluster
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 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.
Challenge: Risk Assessment of an Emerging Pathogen,
Influenza A (H7N9)
Hemagglutinin Structure
RBS
AS-B
AS-A
AS-D
AS-E
AS-C
Antigenic Site A Red
Antigenic Site B Gold
Antigenic Site C Magenta
Antigenic Site D Cyan
Antigenic Site E Green
Receptor Binding Site Gray
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
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
H7 Receptor binding site
Netherlands/219/2003 vs 2013 H7N9
Minimal impact, if any on
the RBS. Assuming receptor
binding is similar to
published structural data,
this should not directly
interact with receptor
177: V / G / G / V
Point towards the RBS
pocket. More hydrophobic
in Anhui/1/2013 May
reduce α2-3 interactions?
212: T
125: A / T / A / A
P, conserved in
other H7 HAs
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.
180: A / T / A / A
128: S
A, conserved in
other H7 HAs
Glycans and influenza virus specificity
A/Netherlands/219/2003 (H7N7)
Avian Receptor-binding
Pattern
A/Anhui/1/2013 (H7N9)
A/New Caledonia/20/1999
(pre2009 H1N1)
Seasonal Human Pattern
a2-3 Avian-type receptors, found in human lower respiratory tract
a2-6 Human-type receptors, found in human upper respiratory tract
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