Epidemiological and molecular information on avian influenza from India and the SAARC sub-region
S. Nagarajan, C. Tosh and V. P. Singh ICAR-National Institute of High Security Animal Diseases (OIE Ref Lab for Avian Influenza) Bhopal (MP), India
OIE expert group meeting Sapporo, Japan 03-05 Oct, 2017 H5 and H7 AIV in SAARC region
• Afghanistan: H5N1 – 2006 • Bangladesh: H5N1 – 2007; H7N9, H5N2 – 2016 • Bhutan: H5N1 – 2010 • India: H5N1 – 2006; H5N8 - 2016 • Myanmar: H5N6 – 2017; H5N1 - 2006 • Nepal: H5N1 – 2009; H5N8 – 2017 • Pakistan: H5N1- 2006; H7N3 – 1995 • Sri Lanka: H5N2 – 2012 Cumulative number of human cases for AI (H5N1) reported to WHO, 2003-17 Genetic and Antigenic divergence of H5N1 virus
Multiple genetic clades (0-9) Map and timeline of H5 subtype of Avian influenza outbreaks in South Asia
• Outbreaks: 22 • H5N1 236 • H5N8 51 1 21 • H5N2 • H5N6 123 124 32 552 1 Afghanistan India Myanmar BangladeshBhutan Nepal India India Nepal (H5N1) (H5N1) (H5N1) (H5N1 (H5N1) (H5N8) (H5N8) 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
Bangladesh India Bangladesh Nepal Bhutan Sri Lanka Myanmar (H5N1) Pakistan (H5N1) (H5N1) (Feb) (H5N2) (H5N6) (H5N1) 1 Phylogenetic relationship of HA genes of H5N1 viruses isolated in South Asia
Genetic clades: • Afghanistan - 2.2 • Bangladesh - 2.2, 2.3.4, 2.3.2.1a (H5N1), • Bhutan- 2.2, 2.3.2.1a (H5N1) • Nepal - 2.2, 2.3.2.1a, 2.3.2.1c (H5N1), • India - 2.2, 2.3.2.1a, 2.3.2.1c (H5N1), 2.3.4.4 (H5N8) • Pakistan - 2.2 • Myanmar - 2.3.2, 2.3.4, 7 Bangladesh Bhutan India Myanmar Nepal Pakistan Bangladesh Bhutan India Myanmar Nepal Pakistan • From 2011, a new genotype of H5N1 viruses with PB1 gene of H9N2 virus circulated in Indo- gangetic plains.
• In June 2015, a new genotype of H5N1 viruses, clade 2.3.2.1a identified in Bangladesh with the HA, NA and M genes of circulating 2.3.2.1a H5N1 viruses and five other genes of LPAIVs (Eurasian-lineage).
• In India, similar viruses were isolated in 2006 and caused recent outbreaks in 2016-2017 except in the state of Karnataka in May, 2016. Antigenic divergence of H5N1 viruses
2.3.2.1a 2..2.2.1
2..2 2.3.2.1c Antigenic cartography • Cross hemagglutination inhibition data indicated antigenic divergence (6-21 fold reduction in cross-reactivity) between the two recently emerged H5N1 clades 2.3.2.1a and 2.3.2.1c.
• These two clades are highly divergent (21-128 fold reduction in HI titre) from the earlier clades 2.2 /2.2.2.1 isolated in India. Bhat et al., (2017) Arch. Virol. 162(2):487-494 H5N8 Outbreaks (2016-17)
• India – 32 outbreaks (Oct to Dec, 2016) • Zoological Parks - Delhi, Madhya Pradesh, Karnataka • Wetlands and lakes - Haryana, Punjab, Gujarat • Domestic poultry - Karnataka & Kerala • Species: Chicken, duck, crow, goose, Pelican, Painted stork, Black-necked stork, Heron, Grey legged goose
• Nepal – One outbreak (Mar, 2017) in Koshi Species: Chickens (Layers) H5N8 outbreaks, India (2016)
A/migratory bird/India/10CA01/2016(delhi) A/duck/India/11CA23/2016(Delhi) A/duck/India/10CA01/2016(H5N8) A/chicken/India/11TI03/2016(Karnataka) 95 A/crane/India/11CA01/2016(Haryana) A/duck/India/11CA22/2016(Haryana) A/duck/India/10TI07/2016(Punjab) A/mute swan/Croatia/85/2016(H5N8) A/tufted duck/Germany-SH/R8446/2016(H5N8) A/great crested grebe/Uvs-Nuur Lake/341/2016(H5N8) A/Bar-headed Goose/Qinghai/BTY17-LU/2016(H5N8) 95 A/painted stork/India/10CA03/2016(H5N8) A/chicken/India/11CA01/2016-Kerala icB A/goose/India/12TI01/2016(Gujarat) A/wild bird/India/12TI01/2016(Mysore zoo) 94 A/duck/India/10CA07/2016(Kerala) A/crow/India/11CA01/2016-Kerala A/duck/India/10TI06/2016(Kerala Ramankary) A/wild bird/India/10CA03/2016(delhi) A/Black-Necked Stark/India/12CA01/2016(BNS Delhi) A/duck/India/11Ca25/2016-Delhi 91 • Phylogenetic analysis - Group B of A/black-headed gull/Tyva/41/2016(H5N8) A/duck/Eastern China/S1109/2014(H5N8) genetic clade 2.3.4.4 A/goose/Zhejiang/925037/2014(H5N8) A/breeder duck/Korea/Gochang1/2014(H5N8) A/duck/Jiangsu/k1203/2010(H5N8) • Related to H5N8 viruses isolated A/duck/Eastern China/L0611/2011(H5N8) A/duck/Eastern China/L1021/2012(H5N8) from wild birds in May, 2016 in A/duck/England/36254/14(H5N8) A/domestic duck/Hungary/7341/2015(H5N8) A/turkey/Germany/AR2485-86-L00899/2014(H5N8) A1 Russian Federation (UVS-Nuur A/eurasian wigeon/Netherlands/2/2014(H5N8) A/duck/Chiba/26-372-48/2014(H5N8) Lake, Tyva Republic) and China A/wigeon/Sakha/1/2014(H5N8) A/chicken/Saga/1-1/2015(H5N8) A/mandarin duck/Gifu/2112D001/2014(H5N8) A3 (Qinghai Lake). 99 99 A/mallard/Korea/KU3-2/2015(H5N8) A/Chicken/Miyazaki/7/2014(H5N8) A/baikal teal/Korea/1449/2014(H5N8) A/Coot/Korea/H81/2014(H5N8) icA A/broiler duck/Korea/Buan2/2014(H5N8) A/broiler duck/Korea/H65/2014(H5N8) A/baikal teal/Korea/1456/2014(H5N8) A/bean goose/Korea/H328/2014(H5N8) A/white-fronted goose/Korea/H231/2014(H5N8) A/chicken/kumamoto/1-7/2014(H5N8) A/goose/Taiwan/01026/2015(H5N8) A/crane/Kagoshima/KU1/2014(H5N8) A/chicken/California/15-004912/2015(H5N8) A2 A/turkey/California/K1500169-1.2/2015(H5N8) A/American wigeon/Oregon/AH0012525/2015(H5N8)
0.01 HA gene phylogeny A/crow/India/11CA01/2016(Kerala) A/duck/India/10CA01/2016(H5N8) A/duck/India/10CA072016 kerala Agoose/India/10CA01/2016-Delhi A/Black-Necked Stark/India/12CA01/2016(BNS Delhi) 98 Amigratory bird/India/10CA01/2016-Delhi A/painted stork/India/10CA03/2016(H5N8) MP A/chicken/India/11CA01/2016(Kerala) Aduck/India/10CA08/2016-Delhi A/gadwall/Chany/97/2016(H5N8) A/duck/India/11CA23/2016-Delhi A/domestic duck/Siberia/50K/2016(H5N8) A/duck/India/11CA22/2016-Haryana A/turkey/Italy/17VIR538-1/2017(H5N8) 95 Aduck/India/10TI07/2016-Punjab A/heron/India/10CA03/2016-Delhi A/chicken/India/11TI03/2016-Karnataka A/goose/India/11TI01/2016-Gujarat 99 A/duck/India/11CA25/2016-Delhi 99 A/crane/India/11CA01/2016-Haryana 99 A/duck/India/10TI06/2016-Kerala Ramankary A/Bar-headed Goose/Qinghai/BTY9-LU/2016(H5N8) 80 A/chicken/India/11TI03/2016(Karnataka) 77 94 A/black-headed gull/Tyva/41/2016(H5N8) 82 100 A/crane/India/11CA01/2016(Haryana) A/great crested grebe/Uvs-Nuur Lake/341/2016(H5N8) A/pigeon/Egypt/S10409A/2014(H9N2) 78 99 A/duck/Mongolia/996/2015(H3N8) A/Anas platyrhynchos/Belgium/17330cls42/2013(H5N2) A/mallard/Republic of Georgia/3/2010(H7N3) 75 A/duck/Mongolia/118/2015(H4N6) 90 A/duck/Vietnam/LBM300/2012(H10N2) A/muscovy duck/Vietnam/LBM529/2013(H3N8) 98 A/duck/Mongolia/167/2015(H3N8) 70 A/duck/Mongolia/141/2015(H10N2) 72 70 A/wild waterfowl/Dongting/C2383/2012(H1N2) A/mallard/Republic of Georgia/1/2010(H10N7)) DUOR15 A/northern shoveler/Georgia/1/2010(H2N3) 99 A/duck/India/10TI07/2016(Punjab) 81 A/duck/India/11CA22/2016(Haryana) A/mallard/Czech Republic/13438-29K/2010(H11N9) 100 A/Brown-headed Gull/Qinghai/ZTO5-K/2016(H5N8) 70 A/wild waterfowl/Dongting/C2383/2012(H1N2) A/great crested grebe/Uvs-Nuur Lake/341/2016(H5N8) 99 A/duck/Sichuan/S4202/2011(H4N2) A/black-headed gull/Tyva/41/2016(H5N8) A/duck/India/10TI06/2016-Kerala ramankary A/Caspian seal/Russia/T1/2012(H4N6) A/common eider/Netherlands/1/2006(H3N8) A/migraory bird/India/12CA01/2016-Delhi BNS A/common Teal/Republic of Georgia/1/2011(H3N8) 99 A/turkey/Italy/17VIR538-1/2017(H5N8) 100 A/mallard duck/Netherlands/23/2012(H11N9) A/common teal/Korea/W550/2016(H5N8) A/mallard/Czech Republic/14333-1K/2011(H3N8) 95 A/mallard duck/Korea/WA137/2017(H5N8) A/mallard duck/Netherlands/15/2011(H6N8) 89 A/chicken/Korea/H903/2017(H5N8) A/greater white-fronted goose/Netherlands/6/2011(H6N8) A/Italy/3/2013(H7N7) A/crow/India/11CA01/2016-Kerala A/chicken/England/474-016250/2014(H4N6) A/duck/India/10CA07/2016-kerala 94 B314 A/heron/India/10CA03/2016-Delhi A/mallard/Republic of Georgia/13/2011(H6N2) A/painted stork/India/10CA03/2016(H5N8) A/gadwall/Kurgan/2442/2016(H5N8) 88 A/duck/India/11CA25/2016 Delhi 100 A/wild duck/Tatarstan/3059/2016(H5N8) A/chicken/Voronezh/20/2017(H5N8) A/goose/India/12TI01/2016-Gujarat A/duck/India/10CA08/2016-delhi A/gadwall/Chany/97/2016(H5N8) 90 A/duck/India/11CA23/2016-Delhi A/domestic duck/Siberia/103/2016(H5N8) 97 100 A/duck/India/10CA01/2016(H5N8) delhi A/domestic duck/Siberia/50K/2016(H5N8) A/goose/India/10CA01/2016-Delhi 99 icB A/migratory bird/India/10CA01/2016-Delhi 97 99 icA icB 99 100 icA 100 NP gene phylogeny 0.01 PA gene phylogeny Species affected
• H5N1 virus: chickens, ducks, quail, goose, pigeon, crow, water coot, wild birds (Species not known),
• H5N8 virus: chickens, ducks, goose, Crane, Painted stork, Black-necked stork, Pelican, Heron, crow, Grey legged goose
• H5N2 virus: Chickens
• H5N6 virus: Chickens (Myanmar) Other than H5 and H7 in SAARC region
• Afghanistan: H9N2 - 2008 • Bangladesh: • H9N2 – 2006 • H11N3, H4N6, H1N1, H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H6N1 and H6N7 - 2016 • India: • H9N2 - 2003. Sequence of H9 haemagglutinin subtype in duck – 1986 • H6N2 – 2014; H4N6 – 2009-2011; H11N9 – 2011; H3N8 - 2014 • Myanmar: H9N2 - 2014 • Nepal: H9N2 – Seropositivity, 2008 • Pakistan: H9N2 - 1998 • Sri Lanka: H6 and H9 – Seropositivity, 2007 ML phylogenetic tree for the HA gene segment of H9N2 avian influenza viruses from the Middle East and Asia.
• Purple for Iran • Green for Israel • Red for Saudi Arabia • Gray for the UAE, • Yellow for Afghanistan • Orange for Pakistan • Blue for Jordan • Light blue for Iraq
Alice Fusaro et al. J. Virol. 2011;85:8413-8421 H9N2 AIV - India
• All Indian H9N2 viruses belong to G1 sub-lineage of Eurasian lineage
• Form four distinct phylogenetic groups (2003-2016) G1-lineage
• Reassortant (Polymerase and India NS genes from unknown origin). H9N2 AIV - Bangladesh
• The Bangladeshi H9N2 viruses (2009-2013) clustered with the H9N2 viruses isolated from India, Pakistan and the Middle East. • In the HA tree, all of the H9N2 viruses formed a well- supported monophyletic cluster (99% bootstrap value) in the Mideast B sublineage.
Shanmuganatham et al. (2014). Emerging Microbes and Infections 3, e88 H9N2 AIV - Pakistan
• The HA gene of H9N2 viruses identified in Pakistan from 2004 to 2015 belonged to Middle East group B • Sublineage B1 -viruses collected from 2004 to 2008 and clustered with other Middle East viruses • Sublineage B2 - viruses collected from 2008 to 2015 and clustered with viruses identified from the Indian subcontinent.
Dong-Hun Lee et al. Vet Rec Open. 2016; 3(1): e000171 Wild birds and avian influenza outbreaks
• Cluster analysis showed that H5N1 was introduced in West Bengal at least 3 times between 2008 and 2010, and role of wild birds are suspected (Pandit et al., 2013).
• H5N8 viruses isolated from wild birds and poultry in India during Oct-Dec, 2016 are related to Uvs-Nuur lake-like virus (isolated in May 2016) and coincides with winter migration of birds indicating role of wild birds in the dispersal of virus (Nagarajan et al.,2017, Sims et al., 2016). Central Asian Flyway
FAO https://commons.wikimedia.org/w/index.php?curid=1387483 • Eight Bird flyways – across the world • Central Asian flyway (extends between Arctic and Indian ocean- 29 countries • Movement of wild waterfowls was suspected in intercontinental spread of AI as the outbreaks coincided with bird migration routes
Bird Life International Migratory flyways and H5N8 outbreak
20th July, 2017 ICAR-NIHSAD, Bhopal Shesheny et al., 2017 Winter season in Northern Hemisphere increases the risk of avian influenza
Oct 16- Mar 17
Apr - Sep, 2016 Avian influenza H5Nx outbreaks and Rearing system
Country H5Nx outbreaks in various rearing system Backyard Farm Crow Zoo Livestock /village market Afghanistan 20 2 - - Bangladesh 510 42 2 - - Bhutan 18 3 - - - India 116 26 8 5 - Myanmar 4 120 - - 1 Nepal 28 205 3 1 Pakistan 2 47 1 1 - Sri Lanka - 1 (LPAI,H5N2) - - - Conclusion • HPAI H5Nx virus is a regional problem and only country specific control measures will not be effective.
• The H5N1 and H9N2 viruses are evolving continuously in the SAARC region.
• Cultural and economic factors lead to close interaction of human and poultry in this region and hence there is a need for targeted and coordinated active surveillance .
• Strengthening surveillance of avian influenza in poultry, wild birds and other hosts is important to assess their impact on animal health.
• Creating awareness about biosecurity and its implementation is essential. However, cost of such measures need to he kept in mind while advocating the same. Thank you for kind attention