New coronaviruses. Common genetics and pathobiological features

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1 New coronaviruses Common genetics and pathobiological features Summer Conference 2014 : Zoonoses 30 June 3 July 2014 The Grand Hotel, Brighton, UK Astrid Vabret University Hospital of Caen, Department of Virology National Reference Lab for Measles and paramyxoviridae EA4655, Unité de Recherche Risques Microbiens University of Caen Lower Normandy

2 Coronavirus and publications 5489 = number of CoV sequences submitted to Genbank 460 HCoVs and 390 Bat CoVs Difficulties to obtain HCoV and BatCoV isolates Multiple ways of sampling Importance of CoVs in veterinary medecine (livestock farming and pets) Drexler et al., Antiviral Research 2013

3 816 nt RdRp Chiropterra (1 100 species) Natural reservoir of alpha- and betacoronaviruses? 4 of 6 HCoVs have a zoonotic origin, 3 of them from chiroptera reservoir (SARS-CoV, MERS-CoV, NL63) Drexler et al., Antiviral Research 2013

4 Nidovirales order : 4 families 31 kb «Large-size» «Intermediate -size» 20 kb «small-size» Current Opinion in Microbiology 12,7 kb

5 Nidovirales : monophyletic group of envelopped viruses with single strand, positive sense RNA genome from12.7 to 31 kb Genomic organization Gradual increase of the genome size due to gene acquisition: optimization of adaptation Lauber C et al., PLOS Pathogens 2013

6 Coronavirus : the largest RNA genome ExoN (RNA 3 5 exo-ribonuclease (acquisition during evolution from a common ancestor) allowing for proof reading during the replication cycle and genome maintenance «Eigen paradox», triangular relationship Fidelity Size Complexity Nga Pt et al., PLOS Pathogens, 2011

7 Coronavirus : 4 genera alpha-, beta-, gamma-, et delta- Beta Coronavirus Phylogenetic trees constructed from 42 full genome coronavirus sequences Kin N et al., en préparation

8 Coronavirus : a wide host spectrum γ β OC HKU OC43 DrCoV MERS-CoV 2012 α SARS-CoV E 1966 NL Corman WN et al., 2014 Woo PC et al., J. Virol Woo PC., EID 2014

9 Coronavirus Hosts : the absents

10 Particles of coronavirus M = matrix protein E = small enveloppe protein N = nucleocapsid protein Single strand, linear, positive sense RNA genome S : spike protein Type 1 fusion protein 2 sub-units S1 ans S2 + envelopped protein HE, present only in betacoronaviruses clade A

11 Genomic and sub-genomic RNAs 5 Replication complex: 16 nsp HE S NS E M N 3 L ORF 1a ORF 1b Transcription Regulatory Intergenic Sequence TRS Discontinuous transcription with synhesis of 7 or 8 sub genomic mrnas of decreasing size and having all the same end 3 polya, Evolution : mutations and recombinaisons

12 RdRp RNA / nsp14 Mutations Quasispecies Persistant infections Coronaviruses: design to emerge Deletions Insertions RNA genome Size 30 kb Positive sense Discontinuons transcription Recombinations ++ High adaptive potential+ Crossing barrier species Emergential success

13 Examples of successful emergence 1980s : TGEV: Transmissible Gastro-Enteritis Virus PRCV: Porcine Respiratory Coronavirus «natural attenuated vaccine?» Deletion 750 nt in spike protein S May 2013: Porcine Epidemic Diarrhea Virus emergence in US The virus was originally identified in the UK in 1971 and caused epidemics in the EU in the following decade High pathogenic PEDV strain circulated in China since 2010 It affects all pigs but is especially virulent in suckling piglets (80-100% die once infected)

14 Since 2013, 8 millions pigs have been lost in 30 states in US PEDV in US

15 Circulating genotype strains PEDV in China. Bootscan analysis: multiple recombination events between different PEDV lineages G2 Wuagn YW et al., mbio 2014

16 Severe Acute Respiratory Syndrome: SARS - CoV

17 SARS- pandemic Natural reservoir bats SARS-CoV H2H transmission R0 > 1 + Superspreader events Intermediate reservoir: paguma larvata Civet cats In market places

18 Superspreader event SARS-CoV diffusion

19 MERS- CoV

20 MERS-CoV : History of emergence Recent emergence (2012) due to the infection of human with a new virus Contact Human Animal reservoir Severe respiratory disease Emergence in a limited geographical area in the Middle East Cross barrier species Probable zoonotic disease Animal reservoir? On going The virus is a coronavirus: All of the knowledge acquired during the SARS pandemic in provides an important aid to understanding the biology of these viruses. Human to human transmission R0 > 1 Adaptation Variant selection

21 MERS-CoV : year 2012 June: index case Saoudi Arabia April May June July August Sept. Oct. Nov. Dec. 20 september 2012 : a new coronavirus is identified (Online PubMed, Dr Zaki) First identification: Pan-coronavirus RT-PCR From the cell culture supernatants

22 Index patient Published in october 2012 Index patient: 60 year old man, without significant medical history Hospitalized in Djedda, June 13, 2012 Severe respiratory disease and renal failure Death D+11 Admission D+2

23 MERS-CoV : year 2012 June: index case Saoudi Arabia September 27, 2012 : first molecular diagnostic tests available April May June July August Sept. Oct. Nov. Dec. 20 september 2012 : a new coronavirus is identified (Online PubMed, Dr Zaki) September 26, 2012 : Ron Fouchier team submits the full genome sequence to GenBank : betacoronavirus 2c EMC/2012 Corman VM et al., Eurosurveillance.org

24 Diagnostic tests: screening and confirmation. Virus level 3 5 L ORF 1a ORF 1b HE S NS E M N 3 M Le Gouil, JC Manuguerra, 2013 Corman VM et al, Eurosurveillance / Eurosurveillance ; Muller et al., mbio, 2012, Raj et al., Nature 2013

25 MERS-CoV can replicate on bat, primates, pig, civet, rabbit, and human cells Low barrier agains cross host-transmission? MERS-CoV receptor = DPP4 Implications for pathogenesis and transmission in vivo? NO DATA FROM AUTOPSY SAMPLES OR SURGICAL SPECIMENS Gallahet T et al., Nature 2014; Corman et al. Eurosurv, 2012

26 MERS-CoV : year 2012 June: index case Saoudi Arabia September 27, 2012 : first molecular diagnostic tests available April May June July Aug Sept. Oct. Nov. Dec. 20 september 2012 : a new coronavirus is identified (Online PubMed, Dr Zaki) September 26, 2012 : Ron Fouchier team submits the full genome sequence to GenBank : betacoronavirus 2c EMC/2012 September 22, 2012 : the UK Health Protection Agency confirms a new case: ncov Corman VM et al., Eurosurveillance.org

27 MERS-CoV : year 2012 December 2012 : WHO encourages coronavirus infection surveillance and investigation of suspected cases April May June July August Sept. Oct. Nov. Dec. April, 2012 : cluster of 13 pneumonia without microbiological diagnosis in Amman, Jordan. Retrospective tests in November 2012 : MERS-CoV for 2 fatal cases

28 MERS-CoV : November 3, 2013 : 150 cases, 63 deaths. Mortality 42% Alert Influenza A H7N9 Nature, Butler D., 19 septembre 2013

29 Mortality risk factors in MERS-CoV: sex, age, comorbidities 64% man Median age= 47 ans (<1 94 years) 45% Co morbidities Source: ECDC June 5, 2014

30 June : Saudi Arabia: 708 confirmed cases and 292 deaths (Mortality rate 41%) WHO: 815 confirmed cases and 313 deaths (Mortality rate 38%) All cases have either occurred in the Middle East or have direct links to a primary case infected in the Middle East 29% mild ou asymptomatic 62% severe cases 25% health workers Bialek SR et al.mmwr, Source ECDC June 2014

31 Epicenter of the emergence: Saudi Arabia Middle East: United Arab Emirates, Qatar, Jordan, Oman, Koweit, Egypt, Yemen, Lebanon Europe: Germany, France, UK, Greece, Netherlands Africa: Tunisia, Algeria Asia: Malaysia, Philippines USA Bialek SR et al.mmwr, 2014

32 Cotten M. et al., Mbio February 2014 Circulation of several clades: genetic diversity The study concludes that there is a limited human to human transmission and a serial cross species from a source not yet known 65 MERS-CoV sequences tmrca = March2012 R0 < 1

33 Distribution of different clades in time and in space Limited persistence of clades in time: limited H2H transmission Little selection pressure on spike protein (small number of adaptive mutations)

34 Phylogenetic analysis has identified a close relationship between MERS-CoV in Humans and various bat species. However, the MERS-CoV has not been confirmed in any bat Reusken CB et al., 2010, Vector Borne Zoonotic Dis Emerging Infectious Diseases : Memish ZA et al., 2013, Vol 19, Number 11 MERS-CoV in Bats, Saudi Arabia

35 Dromedary camels : Animal reservoir? Middle East: Dromadaries : major sources of milk and meat Stables racing camels MERS-CoV like antibodies have been identified in dromadery camels from Oman and Spain MERS-CoV RNA has been identified in respiratory tract of dromadery camels Genetic diversity of MERS-CoV detected in dromadery camels versus MERS-CoV isolated from Humans A new betacoronavirus has been identified in feces sampled from young dromadery camels in EAU : DcCoV-HKU23, closed to bovine coronavirus Reusken CB et al., Lancet Infect Dis Pereira RA et al., Euro Surveil, Haagmans BL et al., Lancet Infectious Dis Woo PC et al., EID Briese et al., Mbio, 2014

36 M. Le Gouil

37 MERS-CoV : a remake of SARS- CoV? Unanswered questions of the MERS-CoV emergence Why the infection is still ongoing in humans? What is the source of ongoing transmission to humans? Only camels? H2H transmission is demonstrated in some nosocomial or familial clusters, but does not appear frequent in general population No evidence of superspreader events Mild or asymptomatic cases has been identified, but serological study failed to demonstrated that MERS-CoV circulate widely in humans, in the study region in Saudi Arabia 2012 (Aburizaiza et al., 2013) Lack of epidemic sparked during mass gatherings in Saudi Arabia in 2012 and The dynamic of the MERS-CoV emergence remains a mystery to this day It does not seem to obey pre-established patterns

38 Consortium EPICOREM, ANR project Eco-epidemiology of coronaviruses from wildlife to humans Université de Caen Basse-Normandie EA4655 Astrid Vabret Fabien Miszczak Nathalie Kin UMR1161 ANSES, ENVA, INRA Sophie Le Poder Stéphan Zientara Institut Pasteur Paris Meriadeg Ar Gouilh Jean-Claude Manuguerra Hervé Bourrhy Valérie Caro ANSES Nancy Elodie Montchatre Franck Boué François Moutou ANSES Ploufragan Nicolas Eteradossi Paul Brown Ecole Vétérinaire Toulouse Jean-Luc Guérin Mariette Ducatez Christine Legall-Reculé

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