EU AI/ND Reference Laboratory Report

Response to the Work Programmes for 2018

adopted at the 2017 meeting

Required Functions of the EU Reference

Laboratory

Requirement 1

Characterise viruses submitted to the EU RL by EU

Member Countries and those included in Decisions

95/233/EC and 96/619/EC

KPIs for characterisation of viruses met

Viruses submitted to the Reference

Laboratory from all sources

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018

influenza 18 12 4 20 18 22 34 25 56 254 413 58 137 155 181 180 619 240 137 48 60 84 71 56 143 157 83 199 259

all viruses 113 154 198 285 411 605 284 227 285 357 704 316 333 464 426 387 831 366 428 218 236 333 212 245 196 177 141 524 295

0

100

200

300

400

500

600

700

800

900

Viruses/OAvV-1 submitted to the Reference

Laboratory from all sources

EU Member States and Non-EU countries

submitting viruses – thank you

AIAfghanistan

Bangladesh

Belgium

Bulgaria

Denmark

Croatia

Iraq

Israel

Italy

Republic of Ireland

Republic of Korea

South Africa

OAvVBangladesh

Belgium

Botswana

Cyprus

Denmark

France

Republic of Ireland

Sweden

Avian influenza viruses submitted to the

reference laboratory

* NA typing not confirmed; FTA cards

Virus identification Number* No HPAI No LPAI

Influenza A viruses 259

AI 3

AI/AAvV-1 1

H1N6 1

H2N6 1

H3N6 1

H4N2 1

H4N6 20

H5Nx 17 17

H5N1 3 3

H5N2 1 1

H5N3 1 1

H5N6 29 29

H5N8 53 53

H5N8 MIX 1 1

Total H5 103 2

H5 & H9 MIX 28

H6N2/AAvV-1 MIX 1

H9Nx 90

Awaiting typing 0

Negative samples 7

Paramyxoviruses submitted to the

Reference Laboratory

Virus identification Number

Orthoavulavirus Type 1 36

OAvV-1 received (from 8 cases) 30

NDV (virulent) cases

Orthoavulavirus (avirulent) cases

Pigeon OAvV-1 (PPMV-1)

716

Pathogenicity index tests

• One ICPI test was carried out in this period for

ND

• OAvV-1/chicken/Sweden/SVA171017SZ0661/17

= 0.90 indicating virulent avian orthoavulavirus

type 1 (XIII.1.1/ XIIIa) with virulent cleavage site

motif of RRQRRF

Required Functions of the EU Reference

Laboratory

Requirement 2

Maintain virus repository and distribute viruses and

reagents necessary for statutory virus characterisation

KPIs for deposition of viruses met

• This sub-activity included tasks to ensure the transfer of the activity

to the new laboratory at IZSVe, Padova, Italy appointed as EURL for

avian influenza as from 1 January 2019.

Required Functions of the EU Reference

Laboratory

Requirement 3Carry out work in relation to surveys for avian influenza in poultry and

wild birds implemented by Member States during 2017https://ec.europa.eu/food/sites/food/files/animals/docs/ad_control-measures_ai_surv-rslt_pltry-wld-brds_2017.pdf

Response

Emergency Situation reports of H5N6 HPAI

• 3 situation reports published in 2018

– https://science.vla.gov.uk/flu-lab-net/

• Contributed to EFSA working group on AI

Required Functions of the EU Reference

Laboratory

Requirement 5Liaise through EURL staff membership of the WHO/OFFLU networks and close contact with influenza laboratories in the public health sector including WHO collaborating centres and organisations such as ECDC

KPIs exceeded• The EURL also continued to collaborate with EFSA on the Standing

Working Group on Avian Influenza working to deliver quarterly overviews onAvian Influenza. This delivered 4 reports in 2018. In addition, the EURL alsoprovided substantial input into a new output on reporting Avian Influenzasurveillance that was published in November 2018.

• Supported ECDC and EFSA assessment of ongoing threat to the EU

• Tracked and monitored the continuing evolution and emergence of H5Nx

• Worked closely with Russian Federation and central Asia and China

Genotypic diversity amongst H5N6 HPAI

13

Required Functions of the EU Reference

Laboratory

Requirement 6

Prepare and distribute reagents for inter-laboratory comparison

tests for conventional methods

Response

• Reagents submitted to all putative attendees to Annual Meetings - 55 laboratories/42 countries

Results

• EU Labs – AI 100% (antigen)/ 98% (serology) outcome

• EU Labs – ND 86% (antigen)/98% serology outcome

KPIs exceeded

Required Functions of the EU Reference

Laboratory

Requirement 6

Prepare and distribute reagents for inter-laboratory

comparison tests for molecular methods

Response

• Reagents submitted to all putative attendees to Annual Meetings - 54 laboratories/42 countries

Results

• EU Labs – AI 93% (M gene)/100% H5/H7 outcomes

• EU Labs – ND 93% outcome

KPIs exceeded

AI conventional and molecular panel overall

results

ND conventional and molecular panel

overall results

Required Functions of the EU Reference

Laboratory

Requirement 9

Consultation by National Laboratories/commission on

problems in diagnosis

KPIs met

EU RL staff were consulted on an ad hoc basis.

• Requests for information: 3.9 calendar days turnaround based on

126 pieces of correspondence

• Flu-Lab-Net threads – 18 info on current outbreaks, epi reports and

sharing of sequencing data

• Working with Bulgaria to carry out full analysis of H5N8 HPAI,

scientific report prepared and shared with the Commission and the

Bulgarian competent authority.

Required Functions of the EU Reference

Laboratory

Requirement 10

Support NLs and commission with advice and technical support

during epidemics including problems areas in diagnosis

• Staff of the EU RL were consulted on numerous occasions by other

National Laboratories, representatives of member states, the Commission,

ECDC, FVO, WHO, EFSA and representatives of trading partners.

• Technical support and advice for emergency preparedness and response

to HPAI H5

• EURL outreach programme to gain a better understanding of disease

threats close to the ‘EU border’

• Emerging threat in BE – ND genotype VII.2 (VIIi/5a)

Required Functions of the EU Reference

Laboratory

Requirement 11

Maintain close awareness of developments in diagnostic methodology and report and advise, as relevant, to Annual Meeting of National AI & ND Laboratories

KPIs exceeded • Development of real-time RT-PCR assays for specific detection of

contemporary avian influenza subtype N2, N3, N4, N5, N6, N7, N8 and N9 viruses

• Further validation of simultaneous detection and pathotyping of HPAI by real time RT-PCR

• Assessment of standard rapid passage virus isolation

• Annual training workshop at EURL

• Fitness for purpose testing

Required Functions of the EU Reference

Laboratory

Requirement 11Maintain close awareness of developments in diagnostic methodology and report and advise, as relevant, to Annual Meeting of National AI & ND Laboratories

KPIs exceeded • Evaluation of MGBII L-gene Real-Time RT-PCR assay on pigeon

samples submitted for statutory testing

• Evaluation and Development of Full Fusion Gene Sequencing

• Evaluation of AAvV-1 pathotyping assays

• Annual training workshop at EURL

• Fitness for purpose testing

Required Functions of the EU Reference

Laboratory

Requirement 15

Facilitate rapid and urgent genetic data analyses and sharing

• Number of phylogenetic trees shared on Flu-Lab-Net - 2

International working group on APMV1

New unified taxonomy (Dimitrov et al 2019)

Sub/lineage

Aldous et al., 2003

Sub/genotype

Diel et al., 2012New system

Class II

1

I a I.1.1

I b I.2.

I c I.1.2.1

I d I.1.2.2

2 II II

3a, 3f III III

3b IV IV

3c

V b V; V.1

V c V.2

V d V

4bii eVI a

VI.2.1.1.1VI n

4b, 4bi, VI b VI.1.1

4bii d

VI e VI.1.2.2.2

VI f VI.1.2.2.1

VI h VI.1.2.1.2

4bii fVI j VI.2.1.1.2.1

VI k VI.2.1.1.2.2

4c - -

5a VII a – one sequence VII.2

5d

VII b

VII.1.1VII b

VII j

VII l

5cVII e VII.1.1

VII f VII.1.2

- VII g (RF) -

- VII h

VII.25a VII i*

- VII k

5e VII VII, VII.2 3000 sequences condensed into backbone tree

Required Functions of the EU Reference

Laboratory

Requirement 16

In the light of the occurrence of influenza in birds and other animals keep under review the possible zoonotic impact arising from the risk of reassortment between influenza viruses

• All emergent viruses received were analysed for markers

of increased zoonotic risk

• Information rapidly disseminated to key stakeholders

Required Functions of the EU Reference

Laboratory

Requirement 18

Where appropriate develop collaborative programmes of investigation with NRLs to address laboratory issues as relevant to this work programme including moderation of the FLULABNET network.

KPIs exceeded• Gathering and sharing lab data in response to emergence of

H5N6

• A project was undertaken in collaboration with several NRL’s to formally use methodology developed by our colleagues in the German NRL to apply real-time PCR to immediate and rapid pathotyping of LPAI/HPAI. The tools had satisfactory results but only for a defined subset of H5 or H7 viruses.

• A moderator continued to maintain and monitor the FLULABNET website. Continued usage, thank you to all

Required Functions of the EU Reference

Laboratory

Requirement 19

Prepare and publish articles and reports associated with work of EURL

KPIs exceeded

• See papers in Proceedings of Annual Meeting.

• A total of 16 published papers on influenza/51conference abstracts/3 internet publications

• 1 published paper on ND /9 conference abstracts on ND/4 internet/1 book chapter

• Internet

– Authorship on Defra RA ‘s for incursion risk of AI or ND

– APHA Internet/FLN for protocols - upgraded

APHA peer reviewed publications on Avian

Influenza

AI Outbreak Activity

Thank you for your support over the yearsIt has been a privilege to serve in the role as EURL.

We look forward to continued strong scientific interaction with the network.

New website domain to be launched soon

FLU-GLOBAL-NETContact us AIWRL@apha.gov.uk