Laboratory Diagnosis of Arboviruses ESCMID

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Laboratory Diagnosis of Arboviruses

ESCMID - Bukarest, Romania March 2018

Chantal Reusken [email protected] Distribution of vector-borne diseases

Arboviruses with public health impact have a global and ever changing distribution.

Notifications of vector-borne diseases in 2016 on Healthmap.org Syndromes of arboviral diseases

1) Febrile syndrome: . Fever & Malaise . Headache & retro-orbital pain . Myalgia

2) Neurological syndrome: . Meningitis, encephalitis & myelitis . Convulsions & coma . Paralysis

3) Hemorrhagic syndrome: . Low platelet count, liver enlargement . Petechiae . Spontaneous or persistent bleeding . Shock

4) Arthralgia, Arthritis and Rash: . Exanthema or maculopapular rash . Polyarthralgia & polyarthritis Human arboviruses: 6 main virus families

Family Genus Species examples

Flaviviridae flavivirus Dengue 1-5 (DENV) West Nile virus (WNV) Yellow fever virus (YFV) Zika virus (ZIKV) Tick-borne encephalitis virus (TBEV) Togaviridae alphavirus Chikungunya virus (CHIKV) O’Nyong Nyong virus (ONNV) Mayaro virus (MAYV) Sindbis virus (SINV) Ross River virus (RRV) Barmah forest virus (BFV) Bunyaviridae nairo-, phlebo-, orthobunyavirus Crimean-Congo heamoragic fever Nairoviridae, (CCHFV) Peribunyaviridae, Sandfly fever virus (SFV, TOSV) Phenuiviridae Rift Valley fever virus (RVFV) Oropouche virus (OROV) Reoviridae orbi- en coltivirus Colorado tick-borne fever (CTFV) Overview of spread & syndromes of vector-borne diseases Many diseases display overlapping symptoms and geographical distribution

Europe AR NS HS WNV* TBEV* DENV^ East Asia North America DENV^ WNV* CCHFV AR NS HS AR NS HS TAHV LIV DENV^* JEV* DENV^* WNV* CEV/LCV* DENV^ SINV* TOSV* §SFV* WNV TBEV OHFV DENV^ WNV* CHIKV BATV CHIKV* WNV SFTSV CHIKV POWV TAHV SLEV TAHV BANV CCHFV EEEV West and Central Asia TAHV WEEV AR NS HS CTFV DENV^* CHIKV* RVFV* North Africa WNV* WNV* CCHFV AR NS HS TAHV TBEV DENV^* Caribbean and Central America DENV^* TOSV* RVFV* SINV BANV OHFV South and Southeast Asia AR NS HS WNV* RVFV* CCHFV* TAHV AHFV AR NS HS DENV^* OROV* DENV^* CHIKV* TAHV YFV* §SFV* RVFV* DENV^* JEV* DENV^* WNV WEEV SINV DENV^* WNV* WNV* KFDV ZIKV* EEEV TAHV §SFV* ZIKV* TBEV SFTSV OROV* VEEV BUNV TBEV BANV CCHFV CHIKV* ILHV Sub-Saharan Africa CHIKV* TAHV WNV AR NS HS TAHV SLEV DENV^* WNV* DENV^* Flaviridea WNV* RVFV* RVFV* YFV* BUNV NRIV Togaviridae South America ZIKV TAHV ILEV CHIKV* BWA CCHFV AR NS HS SINV BUNV Bunyaviridae DENV^* OROV* DENV^* ONNV ILEV ZIKV* WEEV YFV BWA Reoviridae / Seadornaviridae WNV EEEV Oceania TAHV CHIKV* VEEV AR NS HS ILEV MAYV* SLEV RRV* MEV* DENV^ TATV §WSBV OROV* WNV BFV* JEV NRIV ILHV CHIKV WNV ROCV SINV WNV DENV^ ZIKV

Fig 1. Geographical distribution of medically important arboviruses that cause febrile disease in humans.

All arboviruses cause febrile symptoms, but symptoms more specific to certain viruses are represented in three columns: 1) Arthralgia-Rash (AR); 2) Neurological symptoms (NS), and 3) Hemorrhagic symptoms (HS). Virus name is written in the color of its corresponding (and potentially cross-reactive) family. Arboviruses not known to cause more than febrile symptoms are preceded with a §-sign. Arboviruses more likely to be diagnosed in travelers are followed by *.

AKHV = Alkhurma hemorrhagic fever virus; BANV = Banna virus; BFV = Barmah Forest virus; BWAV = Bwamba virus; BUNV = Bunyamwera virus; CEV = California encephalitis virus; CHIKV = Chikungunya virus; CTFV = Colorado tick fever virus; CCHFV = Crimean-Congo hemorrhagic fever; DENV = Dengue virus; EEEV = Eastern equine encephalitis virus; GROV = Guaroa virus; ILEV = Ilesha virus; ILHV = Ilheus virus; JEV = Japanese encephalitis virus; KFDV = Kyasanur Forest disease virus; LCV = La cross virus; LIV = Louping Ill virus; MAYV = Mayaro virus; MURV = Murray Valley virus; NRIV = Ngari virus; OHFV = Omsk hemorrhagic fever virus; ONNV = O’Nyong Nyong virus; OROV = Oropouche virus; RVFV = Rift Valley fever virus; ROCV = Rocio virus; RRV = Ross river virus; SFV = Sandfly fever (Naples / Sicilian / other); SFTS V = Severe Fever with Thrombocytopenia Syndrome Virus; SINV = Sindbis virus; SLEV = St. Louis encephalitis virus; TAHV = Tahyna virus; TATV = Tataguine virus; TBEV = Tick-borne encephalitis virus; TOSV = Toscana virus; VEEV = Venezuelan equine encephalitis virus; WEEV = Western equine encephalitis virus; WNV = West Nile virus; YFV = Yellow fever virus; ZIKV = Zika virus. Cleton et al 2012 Journal of Clinical virology & Cleton et al 2015 PNTD Testing algorithm

Selection based on

. Travel history

. Clinical symptoms

. Potential cross-reactivity / vaccination

. Virus kinetics (Days post onset symptoms)

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. Exposure history

. Risk factors

Cleton et al., 2016, 2017 Testing algorithm and available information

Information provided to LIMS at Erasmus MC 75%

42% ?

0.5%

0.5% Cleton et al., 2016, 2017 Sample possibilities

. Serum / plasma => Virus detection / Antibodies

. CSF => Virus detection / Antibodies

. Urine (WNV, DENV, ZIKV, YFV) => Virus detection

. Tissues (post mortem) => Virus detection Testing method options

. Viral detection . Virus isolation => Vero cells => BSL3/4!!!!

. Detection of viral genome => RT-PCR / IHC

. Detection of viral antigen => DENV NS1 Testing method options

Antibody detection . IgG/IgM

. Seroconversion

. IgG/IgM 4x titer increase =>2 samples needed with 14 day interval

. IgM in liquor in case of neurological disease => confirmative

ELISA

Immuno flourenscence Plaque reduction Neutrilization

Haemagglutination inhibition Test selection dependent on disease kinetics

Humans are often dead-end hosts in these cases . West Nile virus . Japanese encephalitis virus . Tick-borne encephalitis virus . Sandfly fever virus

Onset of NS symptoms

L. Peterson, proceedings on Arboviral Management 2012 WNV, TBEV, TOSV - sensitivity type of tests

Sensitivity Molecular Serology

0-3 days POS Fever => 56% in serum Fever => 54% in serum NS => 10% serum / 55% CSF NS => 75% serum/CSF

4-7 days POS Fever => 56% in serum Fever => 98% in serum NS => 10% serum / 55% CSF NS => 100% serum/CSF

>7 days POS Fever => 4% in serum Fever => 98% in serum NS => 1% serum / 10% CSF NS => 100% serum/CSF

POS = Post Onset Symptoms NS = Neurological symptoms CHIKV, ZIKV, DENV – disease kinetics

Barbara Johnson, Branch of Vector-borne diseases, CDC, Meeting CARPHA, 2015 DENV, ZIKV, CHIKV - sensitivity type of tests

Sensitivity Molecular/NS1 Serology

0-3 days POS Fever => 50% in serum Fever => 50% in serum

4-7 days POS Fever => 50% in serum Fever => 75% in serum

>7 days POS Fever => <10% in serum Fever => 100% in serum

POS = Post Onset Symptoms NS = Neurological symptoms Disease kinetics CCHFV

Ergonul, LID 2006 CCHFV - sensitivity type of tests

Virus isolation Molecular Serology

0-3 days POS 67% serum 0% serum

4-7 days POS 71% serum 65% serum

>7 days POS 61% serum up to 98% serum 16 days POS

POS = Post Onset Symptoms Interpretation of serological results

Results dependent health status of patient

. Vaccination history: Cross-reactivity in serological tests due to flavivirus vaccines . Yellow fever virus (South Americas, Africa) . Japanese encephalitis virus (Asia) . Tick-brone encephalitis virus (Central and Eastern Europe) . Dengue virus (only available in a few countries)

. Young, Old, Pregnant, Immunosuppressed => low or no immune response

. Previous infections => antigenic sin

29 maart 2018 Antigenic sin

. Memory B-cells developed against epitopes of primary pathogen

. Secondary infection with closely related pathogen (Influenza, Dengue, HIV, Cowpox)

. Memory B-cells activated to primary pathogen

. Reducing production of b-cells to secondary pathogen

http://nfs.unipv.it/nfs/minf/dispense/immunology/lectures Interpretation of arbovirus diagnostic results

Acute sample

Antigen- Virus isolation IgM IgG PCR capture Pos Pos Pos Pos Neg Neg Pos Neg No Vaccination Neg in CSF? history? IHC Pos Yes No Neg Pos interpretation interpretation interpretation ID Virus not possible not possible ID Virus not possible

Convalescent serum sample with 2wk interval needed

Seroconversion or 4-fold titre increase Pos Neg

ID Virus No diagnosis Interpretation of arbovirus diagnostic results

Acute sample

Convalescent serum sample with 2wk interval needed

Seroconversion or 4-fold titre increase Pos Neg

ID Virus No diagnosis Interpretation of results dependent on test specifics

. Sensitivity / Specificity provided by manufacturer

. Analytical sens/spec dependent on: . cross-reactivity . lab variation . robustness test

. Diagnostic sens/spec dependent on: . Sampling day post onset disease => viral kinetics

. Comparison method used (how solid is the Gold Standard?)

. Background samples used (predictive value): . Endemic / sporadic / disease free area . Healthy / disease population . Vaccination status / previous exposure Important terms in interpretation of (all!) diagnostic tests

Bayesian Clinical Diagnostic Model

True presence of disease

Total positive for Total negative for Total population disease (a+c) disease (b+d)

Positive predictive value Predicted positive True positive (a) False positive (b) = for diseases (a+b) True positive (a) Predicted positive (a+b) Test outcome Negative predicitive value Predicted negative False negative (c) True negative (d) = for disease (c+d) True negative (d) Predicted negative (c+d) Sensitivity Specificty = = True positive (a) True negative (d) Prevalence =? total positive (a+c) total negative (b+d) The influence of selected testing population

Low prevelance population (1%) High sensitivity (99%) High specificity (99%)

Usefullness of a diagnostic test for prediciting disease (>1) or predicting absennce of disease (<1)

= the probability of a person who has the disease testing positive the probability of a person who does not have the disease testing positive

https://kennis-research.shinyapps.io/Bayes-App/ The influence of selected testing population

High prevelance population (10%) High sensitivity (99%) High specificity (99%)

https://kennis-research.shinyapps.io/Bayes-App/ Development in multiplex techniques

Virus detection Antibody detection • Multi-plex PCR • Luminex • Microarrays • Microarrays • Multiplex IFA (commercial) Interactive session Case 1

Patient: -28 years old -Travelled to Amazon basis, Iquitos, Peru -Rash and Fever