Matthew Cotten Department of Viroscience Erasmus Medical Center Useful data analysis for clinical applications of viral next generation sequencing

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1 Matthew Cotten Department of Viroscience Erasmus Medical Center Useful data analysis for clinical applications of viral next generation sequencing

2 Challenges of clinical applications of viral NGS 1. Standardized and accredited methods (e.g. PCR diagnostics) Sample handling (integrity, contamination, chain of custody) Extraction and amplification methods 2. Robust and accessible computational methods. 3. Some of the virology questions we can answer using NGS: Is this a new virus? Where does it come from? How does it spread?

3 Next Generation Sequencing (NGS) NGS comprises new, rapid methods of sequencing RNA or DNA from minimum amounts of biological material All viral pathogens are encoded by RNA or DNA Their sequences (AGCT...) provide a specific signature to identify and track pathogens A virus genome evolves at a defined rate The virus genome sequence can reveal close virus ancestors and potential sources of the infection

4 The probability of no changes in a pair of viruses sampled at different times

5 Full genomes add resolution RSV G region only RSV Full genomes At the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation. Charles Agoti et al. Virus Evol Mar 11;3(1):vex006 Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

6 Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016 Full genome phylogenetics support conclusion that child s virus was most closely related to virus from the swine herd visited Euro Surveill Dec 1; 21(48): Pieter L A Fraaij, Enno D Wildschut, Robert J Houmes, Corien M Swaan, Christian J Hoebe, H C C de Jonge, Paulien Tolsma, Isme de Kleer, Suzan D Pas, Bas B Oude Munnink, My V T Phan,Theo M Bestebroer, R Shanty Roosenhoff, Jeroen J A van Kampen, Matthew Cotten, Nancy Beerens, Ron A M Fouchier, Johannes H van den Kerkhof, Aura Timen, and Marion P Koopmans

7 All segments cluster, support conclusion of close link between child and herd viruses

8 Chimeric reads Discontinuous sequences artificially linked by ligation or PCR during the sequencing process

9 Ebola virus, Ion Torrent, amplicon Chimeric content greater with higher viral load

10 Chimeric reads detected with uchime Chimeras resolved used python script

11 De novo assembly before and after resolution of Chimeric reads

12 Identify sequences in metagenomic samples SLIM GenBank contigs/reads ublast + output taxon ID virus_1_protein_database virus_2_protein_database virus_3_protein_database virus_4_protein_database 1. fasta files, contigs sorted, labeled, correct orientation etc. 2. simple summary: hit, length, ID etc. 3. alignment file 12

13 Blastn against local NT database SLIM 43 virus family protein database 1.25 contigs/sec contigs/sec

14 Accuracy of Blastn vs SLIM 54 samples, (1,015,342 contigs) de novo assembled contigs Identification at virus family level BLASTN BLASTN+SLIM SLIM

15 Could we detect an emerging or re-emerging virus using SLIM? Virus MERS-CoV Discovery 2012, Saudi Arabia Database Virus Family Coronaviridae Exclude MERS coronavirus (species) Nipah 1999, Malaysia Paramyxoviridae Henipavirus (genus) Lassa virus 1969, Nigeria Arenaviridae Lassa mammarenavirus (species EBOLA virus 1977, Zaire (DRC) Filoviridae Zaire Ebola virus (species ) SARS 2003, Asia Coronaviridae SARS-related coronavirus (species) ZIKA virus 1947, Uganda Flaviviridae ZIKA virus (species)

16 Prepare Databases, nt for BLASTN, aa for BLASTX, SLIM All Coronaviridae sequences Gamma Bafini Unclassified MERS Beta Delta Alpha Toro All Coronaviridae MINUS MERS-CoV Unclassified Gamma Bafini Beta Delta Toro Alpha Mimic data available before MERS-CoV discovered

17 Computationally generate MERS-CoV 1000 fragments nt in length

18 Classification of random virus fragments if virus Genus sequences are removed from virus Family databases. Virus Fragmented genome 1 Database 2 BLASTN BLASTN % 3 time 4 BLASTX BLASTX % 3 time 4 SLIM % 3 SLIM time 4 MERS- CoV KF MERS-CoV Al-Hasa_1_2013 Coronaviridae not MERS-CoV

19 Classification of random virus fragments if virus Genus sequences are removed from virus Family databases. Virus Fragmented genome 1 Database 2 BLASTN BLASTN % 3 time 4 BLASTX BLASTX % 3 time 4 SLIM % 3 SLIM time 4 MERS- CoV KF MERS-CoV Al-Hasa_1_2013 Coronaviridae not MERS-CoV Nipah NC_ Nipah_virus Paramyxoviridae not Henipa Lassa virus NC_ Lassa virus segment L Arenaviridae not Lassa EBOLA virus KJ Zaire_ebolavirus Kissidougou C15 Filoviridae not Zaire Ebolavirus SARS NC_ SARS coronavirus Coronaviridae not SARS ZIKA NC_ Zika virus Flaviviridae not Zika

20 Conclusions Could we detect an emerging virus using SLIM? Probably yes, if virus family sequences available How well? SPEED BLASTN >> SLIM > BLASTX SENSITIVITY SLIM > BLASTX >>BLASTN

21 Agnostic sequencing methods Fecal sample DNase centrifugation

22 Clean viral material Convert to dsdna Random primers (non-rrna) High coverage Illumina (2x250nt reads) de novo assembly etc. Full viral genomes

23 Agnostic method detects additional distant viruses Yield of viral specific contigs >1000nt Human Pig

24 Full Calicivirus/Norovirus genomes ML tree, full genomes black: reference genomes colors: New caliciviruses from study Agnostic sequencing yields 26 Calicivirus genomes Specific GII norovirus primers would amplify only 5 viruses

25 KNOWN viruses Rotavirus: Phan et al., 2016 Caliciviridae: Phan et al., in preparation Astroviridae: Oude Munnink et al., in preparation Novel viruses Novel Picornavirus (Posavirus): Oude Munnink et al., 2016, 2017, in preparation Novel Bunyaviruses: Oude Munnink et al., 2016 Novel Polyomavirus: Hill et al Novel virus family between Astrovirus/HepatitisE virus: Oude Munnink et al., 2015, 2017 Unexpected viruses Unexpected Rhinovirus: Agoti et al., 2016 Unexpected Measles: Oude Munnink et al., 2016 Unexpected Poliovirus: unpublished, Vietnam, Kenya

26 Utility of these viral sequences Improve diagnostic ability to detect local virus variants Reveal unexpected viral agents Contribute to GenBank and other public databases Useful for surveillance Identify agents associated with diseases of unknown origin

27 Acknowledgements Erasmus Medical Center Marion Koopmans, My Phan, Bas Oude Munnink, Suzan D. Pas, Peter Fraaij, Ron Fouchier Wellcome Trust Sanger Institute Paul Kellam Kenya Medical Research Institute (KEMRI), Kilifi, Kenya Charles Nyaigoti, Patrick Munyoki, James Nokes Wellcome Trust VIZIONS Consortium