Phylogenetic analysis of the highly pathogenic avian influenza H5N8 outbreak in South Africa ANISE conference March 2018 - Drs. M. Romito, A ...
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Phylogenetic analysis of the highly
pathogenic avian influenza H5N8
outbreak in South Africa
ANISE conference March 2018
Drs. M. Romito, A. Lubisi, P. Moswa-Kato,
C. De Beer, A. van Schalkwyk and L. Rotherham
INTRODUCTION
• Avian influenza (AI) is a highly contagious
viral disease.
• Affects:
– Chickens, Turkeys, Quails, guinea fowl, pet birds,
wild birds
– Occasionally mammals, including humans
– Natural reservoirs of the virus include wild aquatic
birds such as Anseriformes (ducks and geese)
and Charadriiformes (gulls and shorebirds)
• Two main categories according to the severity
of the disease in poultry:
– low pathogenic (LPAI) strains, which typically
cause few or no clinical signs in poultry,
– and highly pathogenic (HPAI) strains, which
can cause severe clinical signs and potentially
high mortality rates among poultry.
AIV TESTING AT ARC-OVRI
• Molecular diagnostics:
- Nucleic acid-based detection assays
1. Real time RT-PCR: Influenza A serogroup
(matrix gene, + nucleocapsid gene).
2. RT-PCR (HA, H6, N1, N2, H5, and H7)
3. Real time RT-PCR: Subtype determination
(H5 and H7; HP/LP H5; N8 and H9)
4. Sanger sequencing of HA0 cleavage site
(Polybasic aa in HP : H5 & H7) *OIE
5. Full gene or genome sequencing:
Molecular epidemiological / evolution (Miseq)
AIV TESTING AT ARC-OVRI
• Other diagnostics:
– Large-scale screenings of chicken and ostrich
using serological
Multi-species Influenza A ELISA
HA and HI assays:
Subtype determinations
– Virus isolation (embryonated chicken eggs)
– In vivo pathogenicity testing
AI OUTBREAKS IN SA
2004 2006 2011 2012 2017 2018
LPAI H5N2
HPAI H5N2
LPAI H7N1
H9N2
HPAI H5N8
8000
* H6N2 ongoing infection in chickens 6000
4000
2000
0
2015 2016 2017 2018
Positives Negatives
2017/18 HPAI H5N8 OUTBREAK
IN SOUTHERN AFRICA
• 26 May 2017, positive case from Zimbabwe
• On 19 June 2017, the first case of HPAI was confirmed
in Mpumalanga.
• A number of other poultry and ostrich operations, as well
as wild bird species, have subsequently also been
infected with HPAI H5N8 since the index case.
• A total of 155 locations have tested positive for HPAI
H5N8 (up to 1 March 2018). Reported to the World
Organisation for Animal Health (OIE).
• Only one out of the nine provinces, (Northern Cape
Province), remains unaffected by HPAI H5N8
SAMPLES TESTED FOR AVIAN INFLUENZA IN 2017/ 2018
2000
1500
1000
500
0
Positive Negative
H5N8 HIGHLY PATHOGENIC AVIAN INFLUENZA OUTBREAK
IN SOUTH AFRICA (DATA UP TO FEBRUARY 2018)
2
Gauteng Limpopo
300
1
200
100
0
0
Mpumalanga
North West
15
60
10
40
5
20
0
0
Free state KwaZulu Natal
100 15
10
50
5
0 0
Western Cape Eastern Cape
6
1500
4
1000
2
500
0
0
Sept
July
Nov
Dec
Aug
Feb
Jan
Oct
1 2 3 4 5 6 7 8
H5N8 HIGHLY PATHOGENIC AVIAN INFLUENZA OUTBREAK
IN OTHER PROVINCES (DATA UP TO FEBRUARY 2018)
Initial AI (H5N8) cases per Bird group
30
25
Number of positive samples
20
15
10
5
0
Wild birds Hobby Ostriches Chickens
birds
Bird Grouping
H5N8 HIGHLY PATHOGENIC AVIAN INFLUENZA OUTBREAK
IN THE WESTERN CAPE (DATA UP TO FEBRUARY 2018)
Initial AI (H5N8) cases per Bird
group
30
Number of positive samples
25
20
15
10
5
0
Wild birds Hobby Ostriches Chickens
birds
Bird GroupingH5N8 REASSORTMENT Shesheny et al. 2017. Genesis of Influenza A(H5N8) viruses. Emerging Infectious Diseases (23): 1368 – 1371.
H5N8 (GROUP B) OUTBREAK Shesheny et al. 2017. Genesis of Influenza A(H5N8) viruses. Emerging Infectious Diseases (23): 1368 – 1371.
H5N8 outbreaks in
Sub-Saharan Africa
• From the phylogenetic tree the main
I ancestor for the HPAI H5N8 viruses is
Eastern China
• In South Africa we have four clusters,
all four share a recent common
ancestor with viruses from Egypt,
Korea and Siberia.
• The Zimbabwean isolate is genetically
similar to one of the South African
clusters.
II
III • Low genetic diversity: (mean = 0.005;
Lowest Percentage sequence identity
IV = 98.23%)
• Substitution rate: 2.6 X10-3
Egypt/Korea/SiberiaRussia / India / China
(2016) / Europe (2017)
Russia / India / Korea /
Egypt (2016) / SA (2017)
September
December
November
February
October
January
August
June
May
JulyCONCLUSIONS: • The Eastern China 2014 strain was the original strain (Group B of clade 2.3.4.4) that has since dispersed and caused outbreaks in many countries. • There have been several introductions of the virus into South Africa. • The exact origin of the viruses into southern Africa is still unknown. • While we continue to observe periodic spillover of both H5N1 and H7N9 avian flu strains into the human population, we currently seeing regional epidemics of H5N8 influenza in poultry and wild birds across the globe. • Species once assumed to be free of, or resistant to, influenza such as dogs and cows have now entered the ranks of the influenza-afflicted species of the world. • The question is not if circulating influenza strains will enter the human population, but only which ones and when.
ACKNOWLEDGMENTS • DAFF: Drs Maja, De Klerk, Gerstenberg, Strydom • Western Cape Provincial Veterinary Lab.: Dr Seutloli; R.Pieterse, B. Peyrot • Deltamune/Avimune: D. Rauff, E. van Zyl • GDARD: Dr P. Geertsma, Gauteng surveillance • Prof C. Abolnik: Veterinary Faculty, UP • Dr A. Olivier: ostrich practitioner, Oudtshoorn • Virology Lab, ARC-OVRI: H. Tshabala & M. Molefe
THANK YOU
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