Novel coronavirus (nCoV) phylodynamics

Trevor Bedford (@trvrb)
10 Feb 2020
CMDI Seminar Series
Georgia Institute of Technology
 
Slides at: bedford.io/talks

Sequencing to reconstruct pathogen spread

Epidemic process

Sample some individuals

Sequence and determine phylogeny

Sequence and determine phylogeny

Nextstrain

Project to conduct real-time molecular epidemiology and evolutionary analysis of emerging epidemics

with Richard Neher, James Hadfield, Emma Hodcroft, Thomas Sibley, John Huddleston, Louise Moncla, Misja Ilcisin, Kairsten Fay, Jover Lee, Allison Black, Colin Megill, Sidney Bell, Barney Potter, Charlton Callender

Nextstrain architecture

All code open source at github.com/nextstrain

Two central aims: (1) rapid and flexible phylodynamic analysis and
(2) interactive visualization

Nextstrain is two things

• a bioinformatics toolkit and visualization app, which can be used for a broad range of datasets
• a collection of real-time pathogen analyses kept up-to-date on the website nextstrain.org

nextstrain.org

Novel coronavirus (nCoV)

Jan 11: Initial 5 nCoV genomes from Wuhan showed highly restricted genetic diversity

Initially thought clustering due to epi investigation of linked cases at Huanan seafood market

Jan 17: Additional 2 nCoV genomes from Thailand travel cases also lacked diversity

Jan 19: Additional 5 nCoV genomes from Wuhan still lacked diversity

😧

Single introduction into the human population between Nov 15 and Dec 15 and human-to-human epidemic spread from this point forward

Spent the week of Jan 20 alerting public health officials, and since then have aimed to keep nextstrain.org/ncov updated within ~1hr of new sequences being deposited

Data sharing through GISAID

• Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
• National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
• Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
• Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
• Department of Microbiology, Zhejiang Provincial CDC, Hangzhou, China
• Guangdong Provincial CDC, Guangzhou, China
• Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen, China
• Hangzhou Center for Disease and Control Microbiology Lab, Zhejiang, China
• National Institute of Health, Nonthaburi, Thailand

Data sharing through GISAID (continued)

• National Institute of Infectious Diseases, Tokyo, Japan
• Korea Centers for Disease Control & Prevention, Cheongju, Korea
• National Public Health Laboratory, Singapore
• US Centers for Disease Control and Prevention, Atlanta, USA
• Institut Pasteur, Paris, France
• Respiratory Virus Unit, Microbiology Services Colindale, Public Health England
• Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
• University of Melbourne, Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
• Victorian Infectious Disease Reference Laboratory, Melbourne, Australia

Almost real-time with many genomes shared within 3-6 days of sampling

Current state of nextstrain.org/ncov with 80 genomes as of Feb 10

Providing updated genomic situation reports at nextstrain.org/narratives/ncov/sit-rep/

Scientific communication surrounding outbreak has completely flipped with everything posted to bioRxiv, modeling groups posting live analyses and crowd-sourced line lists 🙌🏻

This communication between academics and public health officials has spilled over with huge interest from general public

This is having knock-on effects on science communication and spread of misinformation

Moving forward

• Epidemic spread still appears to be sustained with estimates of R0 between 1.5-3.5 and epidemic doubling time of ~6 days
• We have not yet had time to ascertain effects of intervention measures, but my hope for containment is slim
• Biggest question for me now surrounds infection-to-fatality ratio
• I expect genomic data to be most immediately useful to help pin down emerging community transmission

Acknowledgements

Bedford Lab: Alli Black, John Huddleston, James Hadfield, Katie Kistler, Louise Moncla, Maya Lewinsohn, Thomas Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Nicola Müller, Marlin Figgins

Data producers from all over the world, GISAID, Virological.org