Avian influenza in the Greater Mekong Subregion, 2003–2018

Suttie, Annika; Karlsson, Erik A.; Deng, Yi‐Mo; Hurt, Aeron C.; Greenhill, Andrew R.; Barr, Ian G.; Dussart, Philippe; Horwood, Paul F.

doi:10.1016/j.meegid.2019.103920

Cited by 21 publications

(23 citation statements)

References 163 publications

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“…As part of ongoing diagnostic and surveillance effort, the Institut Pasteur du Cambodge collects and confirms samples from AIV-infected poultry during routine market surveillance, and from human cases and poultry during AIV outbreaks. Since H5N1 was first detected in Cambodia in 2004, 56 human cases and 58 poultry outbreaks have been confirmed and many more have gone undetected [21]. Here we analyze previously generated deep sequence data [22] from 8 infected humans and 5 infected domestic ducks collected in Cambodia between 2010 and 2014.…”

Section: Introductionmentioning

confidence: 99%

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

et al. 2020

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Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying hostadaptation in other zoonotic viruses.

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Section: Introductionmentioning

confidence: 99%

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

et al. 2020

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“…Finally, the South African H6N2-endemic status of poultry is entirely different from the East Asian situation. East Asian poultry production is characterized by inter-species mingling in live bird markets, frequent contact between domestic poultry and wild aquatic birds, and the resulting co-circulation of a great diversity of IAV subtypes that continuously undergo reassortment [12,21]. South Africa's is a less dense and more geographically isolated system, with few live bird markets to facilitate interspecies mixing, geophysical separation of the major ostrich and chicken-producing areas, very little direct contact between wild aquatic birds and chickens; duck farming is minor and turkey farming is absent.…”

Section: Resultsmentioning

confidence: 99%

“…However, since 2001 H6N2 circulated in meat turkey flocks in Germany [3], H6N1 infected meat turkeys in France [4], H6N2 caused sustained outbreaks among domestic poultry in the USA from 2000 to 2005 [5][6], and H6 IAVs have been one of the predominant subtypes circulating since the 1970's in live bird markets in southern China and later South Korea, Vietnam, Cambodia, Thailand and Laos. In this sub-region, H6N1, H6N2, H6N5, H6N6, H6N8 and H6N9 co-circulate in chicken and duck populations, undergoing frequent reassortment with other subtypes [7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Continuing evolution of H6N2 influenza A virus in South African chickens and the implications for diagnosis and control

Abolnik¹,

Strydom

Rauff

et al. 2019

Preprint

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Background: The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of twelve H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests. Results: Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that these antigens are likely to miss H6N2 field infections. More concerning, sub-lineage I H6N2 viruses have acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 have acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF. Conclusions: The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.

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“…H6 IAVs have been one of the predominant subtypes circulating since the 1970's in live bird markets in southern China and later South Korea, Vietnam, Cambodia, Thailand and Laos. In the East Asian sub-region, H6N1, H6N2, H6N5, H6N6, H6N8 and H6N9 co-circulate in chicken and duck populations, undergoing frequent reassortment with other subtypes [7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Continuing evolution of H6N2 influenza A virus in South African chickens and the implications for diagnosis and control

Abolnik¹,

Strydom

Rauff

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of twelve H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests. Results: Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for routine hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that H6N2 field infections are likely to be missed. More concerning, sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF. Conclusions: The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.

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Avian influenza in the Greater Mekong Subregion, 2003–2018

Cited by 21 publications

References 163 publications

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

Continuing evolution of H6N2 influenza A virus in South African chickens and the implications for diagnosis and control

Continuing evolution of H6N2 influenza A virus in South African chickens and the implications for diagnosis and control

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