Recombination in RNA viruses

Transcription

1 Recombination in RNA viruses Dr Rowena Bull NHMRC Career Development Fellow School of Medical Sciences, University of New South Wales

2 Great diversity in viruses Arshan Nasir, and Gustavo Caetano-Anollés Sci Adv 2015;1:e

3 Mechanisms of viral diversity 3 main mechanisms that work in combination: Point mutations (frequent in RNA viruses ~1 mutation/10 virions - quasispecies) Recombination Reassortment

4 Recombination in RNA viruses Initially RNA viruses were thought to undergo limited recombination Frequency ranges from 10-8 to 10-4 per site per generation Can have a major impact on virus evolution, emergence and epidemiology. Eg. Expand host range, evade host immunity, resistance to antivirals Occurs in many RNA virus families.

5 Mechanism: template switch Requires dual infection + Replication Recombinant

6 Mechanisms of recombination In principle, recombination can occur in all RNA viruses (segmented and non-segmented) Factors influencing template switching include : RNA secondary structure, transcription kinetics and sequence identity between donor and recipient.

7 Recombination in RNA viruses Can have a major impact on virus evolution, emergence and epidemiology. Eg. Expand host range, evade host immunity, resistance to antivirals.

8 Recombination in Norovirus

9 Norovirus (NoV) Genome nm Non-enveloped virus 7,400 7,700 nucleotides ORF 1 ORF 2 ORF 3 5 NTPase Helicase VPg Protease Capsid Structural protein 3 RNA polymerase

10 Norovirus epidemics and pandemics

11 Norovirus epidemics in Sydney Farmington Hills virus (2002) 2006a virus (2006) 2006b virus (2007) 2009 virus 2012 virus US 95/96 virus ( ) Hunter virus (2004) 2008 virus 2010 virus

12 GII.11 GII GII.3 GII.8 GII.9 GII.7 GII.4 AY Limburg AJ Seacroft Sydney 4012/02S Sydney 1347/98S Sydney 1145/98S Sydney 755/97S Sydney 591/97S AB U17 Su2445/03O GII.10 Sydney 4264/01S AY Mc37* 85 AF Erfurt GII.5 AJ Hillingdon AF New Orleans 306 GII.2 X81879 Melksham GII.12 U70059 Snow Mountain 2 98 AF Schwerin U07611 Hawaii GII.1 69 Longbay/00O 91 AF Pt Canaveral Picton 037/03O 79 Picton 081/03O AY Picton 554/03O Sydney 715D/04S 70 C14-like 80 L23830 OTH25 recombinant U22498 Mexico U02030 Toronto Sydney 4360/02S Sydney 4136/01S AF Oberhausen Sydney 4337/02S C14-like Sydney 4480/02S recombinants Sydney 4384/02S Sydney 4209/01S Sydney 4134/01S AY C14/02O Sydney 2086/98S Sydney1696/98S Sydney 2113/98S 2212-like AY /98O recombinants Sydney 2145/98O AF Amsterdam AB U25 AY Mc24* AY0385 Virginia 207 AJ Leeds Sydney 4477/02S Sydney 4237/01S AY Mc17* U46500 Camberwell X86557 Lordsdale X76716 Bristol Turramurra 604J/04O Hunter 0O/04O Hunter 120A/04O Sydney 762I/04S Sydney 267J/04S Sydney 198N/04S Hunter 284E/04O Sydney 4228/04S Sydney 625K/04O Hunter 956S/04O Hunter 532D/04O Dulwich Hill 197P/04O Dulwich Hill 203D/04O Hunter 04 Dulwich Hill 190I/04O cluster Turramurra 597U/04O Dulwich Hill 194M/04O Manly Vale 098M/04O Jannali 670H/04O Kogarah 393H/04O Kogarah 4006/04O Jannali 611C/04O Hunter 504D/04O Hunter 273C/04O 75 Hunter 913K/04O Manly 388P/04O Ramsgate 336I/04O Sydney 4266/01S Sydney 4416/02S Sydney 812J/01O Farmington Sydney 917J/02O AY Germanton Hills cluster Sydney 198N/04S AY b4s6oxford AY Farmington Hills Sydney 4262/01S Sydney 348/97O Sydney 776/O Sydney 4288/02S AY Mora AF DOUG4770/00O US95/96 Sydney 284/97S cluster Sydney 642/97S AJ Grimsby AF Burwash Landing AF /96-US Phylogenetic tree of NoV GII capsid

13 Investigate Mechanisms of GII.4 Dominance Two mechanisms used to evolve: 1. Nucleotide substitution Antigenic Drift 2. Recombination Antigenic Shift - different regions of genome originate from different viruses

14 NoV Rate of Evolution 84 AB Apeldoorn AB OC AB Stockholm NSW 001P Nov08 GQ a NSW 956P Jul a VIC 595 Jul a WA 223N Jun07 EF Terneuzen EF Yerseke a 2006a WA 210Z Aug a NSW 023C Jan a NZ 327 Apr06 EF AY NL Hunter NSW 284E 2004 DQ AB Tilburg Hunter DQ MD AY Farmington Hills 2002 DQ Carlow 2002 AY ChippingNorton 2003 Farmington Hills AB Chiba AB Chiba DQ Guangzhou 2001 Asia EU Beijing b NSW 287R Nov07 GQ b NSW 544K Jan b NSW 3912 Nov b WA 145Y Jun b VIC 3863 Oct b NSW 4140 Oct b WA 145H Jan b NSW 696T Dec06 EF EU Kapuvar b b NSW 587V May07 EF DenHaag EU Duan b NSW 618P Aug b NSW 3639 Nov08 GQ EU Beijing Cairo NSW 505G Jul07 GQ EU Cairo Cairo 2007 FJ RIS 2006 FJ SSCS 2005 Osaka NSW 390I Jan08 GQ AB OC Osaka EU Cairo EU Cairo DQ Sydney AY Dresden AF Burwash Landing 15 AF Miami Beach US AB EmmenE AB Kaiso U45600 Camberwell X86557 Lordsdale 12 X76716 Bristol 13 AF UK Ancestral AY MD AY MD Number of changes plotted against time elapsed between that strains detection and the origin strain Evolution rate (substitutions/capsid gene/yr) is equivalent to the gradient of the line GII.4 = 6.30 ± 0.39, r2 = 0.84 GII.b = 4.03 ± 0.80, r2 = 0.68 GII.3 = 3.09 ± 0.95, r2 = 0.49 GII.7 = 3.82 ± 0.25, r2 = 0.

15 Evolution Hotspots in the Capsid Variation hotspots in the P2 domain Greater immune escape in GII.4 GII.7 GII.3 GII.4 Hutson, et al Trends Microbiol Bull, et al PLOS path.

16 Polymerase NoV recombination common 85 Vannes MOH White River 290 New Orleans 306 s63 Saitama U25 Virginia 207 Gwynedd Saitama U3 Baltimore Saitama U16 Melksham Sydney C14 Picton 398 Sydney Hawaii 77 Port Canaveral Richmond Mc37 Saitama U1 86 Lordsdale 76 Bristol Camberwell Farmington Miami Beach US95/96 Crete Snow Mountain OTH 25 Toronto New Orleans 279 Mexico Lionville oc98008 Saitama U201 Capsid GII.8 Saitama U25 95 GII.9 Virginia GII.7 Gwynedd Saitama U3 90 Baltimore GII.6 Saitama U16 s63 GII.5 MOH White River 290 New Orleans GII.10 Mc37 83 Melksham Snow Mountain GII.2 Crete 78 GII.12 Saitama U1 Hawaii Port Canaveral 95 GII.1 Richmond 78 Picton 398 Vannes Lordsdale Bristol 82 Camberwell GII.4 Farmington Miami Beach 326 US95/06 98 AF oc98008 Sydney Sydney C14 GII.3 L23830 OTH 25 U02030 Toronto U22498 Mexico New Orleans 279 Lionville Saitama U

17 Nucleotide Identity Simplot recombination tool Mc37 GII.4 prototype GII.10 prototype Genome Position ORF 1 ORF 2

18 Method of Analysis Recombination hotspot at ORF1/ORF2 overlap Chi Simplot ORF 1 ORF 1 Genomic Position (nt) Genomic Position (nt) ORF ORF ORF 3 5 NTPase Helicase VPg Protease RNA pol Capsid Structural protein 3

19 Does recombination have a role in the evolution of epidemic NoVs? 3 methods - chi square method - simplot - phylogenetic analysis

20 Maximum likelihood phylogenies of the NoV GII.4 genome. John-Sebastian Eden et al. J. Virol. 2013;87:

21 SimPlots for all putative NoV GII.4 recombinants analyzed in this study. John-Sebastian Eden et al. J. Virol. 2013;87:

22 Recombination breakpoints identified across the full-length genome in the NoV GII.4 lineage. John-Sebastian Eden et al. J. Virol. 2013;87:

23 Model for the emergence and origin of the NoV GII.4 variants. John-Sebastian Eden et al. J. Virol. 2013;87:

24 Recombination analysis in the NGS era

25 Hepatitis C Virus Major cause of hepatitis ~185 million chronic carriers world-wide (Hanafiah et al Hepatology). 2 million new infections/year (Hauri et al Int J STD AIDS). Most common reason for liver transplant (~50% in Australia and USA) Predominantly transmitted via intravenous drug use (IDU)

26 HCV Highly Diverse Genotypes - World View

27 HCV - Mixed infection cohort Inc 1M 2M 3M 6M 9 12M 18M 24M 30M 36M 42M 48M 54M 60M 66M 72M I / I I / I I I I I I I I I I I I I I I I I I I I I I I / / / / / / / / / / / / / / / / / / / / / / / / Subtype 2a Subtype 2b Second infection with same genotype / / / / / / Subtype 6a Subtype 1b Subtype 1a Subtype 3a Third infection with same genotype Negative timepoint

28 Coverage NGS powerful tool for detection of multiple infection,000 80,000 Coverage (GT1a) Coverage (GT3a) 60,000 40,000 20, HCV genome position (nt)

29 Multiple infection or recombination Reference aligned (against prototype) No. of nt/site De novo aligned No. of nt/site

30 Recombination in HCV Intergenotype recombination has been reported to occur within envelope region Unknown how frequent New antivirals delivered in combination on the market Recombination could facilitate antiviral resistance Multiple infection common but is recombination? New tools for analysing intrahost recombination needed.

31 Acknowledgments UNSW John-Sebastian Eden Peter White Fabio Luciani Auda Eltahla Andrew Lloyd Prince of Wales Hospital Dr Elise Tu Dr Chris McIver Prof Bill Rawlinson Funding UNSW Goldstar Award NHMRC ACH2