Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020

Zhang, Jiahao; Li, Xudong; Wang, Xiaomin; HeJia, Ye; Li, Bo; Chen, Yiqun; Chen, Junhong; Zhang, Tao; Qiu, Ziwen; Li, Huanan; Jia, Weixin; Liao, Ming; Qi, Wenbao

doi:10.1093/ve/veab046

Cited by 20 publications

(14 citation statements)

References 37 publications

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“…The viruses from Pakistan are distantly related to A/Astrakhan/3212/2020, responsible for the first human A(H5N8) infection in Russia in late December 2020, clustering in subgroup 8 that contains clade 2.3.4.4b A(H5N8) viruses which circulated in domestic and wild birds across Europe during May 2020-February 2021 (Figure 2c). The mean estimated TMRCA of the HA-H5 virus of subgroup 8 was estimated in early December 2019 (95% HPD: May 2019-March 2020), consistent with previous observation [56]. The H5-HA phylogeny shows that the human strain (A/Astrakhan/3212/2020) is most closely related to two chicken A(H5N8) clade 2.3.4.4b viruses with an estimated TMRCA in late November 2020 (green dotted arrow in Figure 2c, 95% HPD: October 2020-December 2020), indicative of direct transmission from domestic poultry.…”

Section: Molecular Characterizations Of Pakistan A(h5n8) Virusessupporting

confidence: 90%

Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N8) Virus in Pakistani Live Bird Markets Reveals Rapid Diversification of Clade 2.3.4.4b Viruses

Ali

Yaqub

Shahid

et al. 2021

Viruses

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The highly pathogenic (HPAI) avian influenza A(H5N1) viruses have undergone reassortment with multiple non-N1-subtype neuraminidase genes since 2008, leading to the emergence of H5Nx viruses. H5Nx viruses established themselves quickly in birds and disseminated from China to Africa, the Middle East, Europe and North America. Multiple genetic clades have successively evolved through frequent mutations and reassortment, posing a continuous threat to domestic poultry and causing substantial economic losses. Live bird markets are recognized as major sources of avian-to-human infection and for the emergence of zoonotic influenza. In Pakistan, the A(H5N1) virus was first reported in domestic birds in 2007; however, avian influenza surveillance is limited and there is a lack of knowledge on the evolution and transmission of the A(H5) virus in the country. We collected oropharyngeal swabs from domestic poultry and environmental samples from six different live bird markets during 2018–2019. We detected and sequenced HPAI A(H5N8) viruses from two chickens, one quail and one environmental sample in two markets. Temporal phylogenetics indicated that all novel HPAI A(H5N8) viruses belonged to clade 2.3.4.4b, with all eight genes of Pakistan A(H5N8) viruses most closely related to 2017 Saudi Arabia A(H5N8) viruses, which were likely introduced via cross-border transmission from neighboring regions approximately three months prior to virus detection into domestic poultry. Our data further revealed that clade 2.3.4.4b viruses underwent rapid lineage expansion in 2017 and acquired significant amino acid mutations, including mutations associated with increased haemagglutinin affinity to human α-2,6 receptors, prior to the first human A(H5N8) infection in Russian poultry workers in 2020. These results highlight the need for systematic avian influenza surveillance in live bird markets in Pakistan to monitor for potential A(H5Nx) variants that may arise from poultry populations.

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Section: Molecular Characterizations Of Pakistan A(h5n8) Virusessupporting

confidence: 90%

Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N8) Virus in Pakistani Live Bird Markets Reveals Rapid Diversification of Clade 2.3.4.4b Viruses

Ali

Yaqub

Shahid

et al. 2021

Viruses

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“…In addition, a study on seroprevalence showed that H6 subtype viruses had seropositivity among occupational contact workers in 19 provinces in China [21]. For our part, we recently demonstrated that reassorting human-and bird-origin H5N6 viruses all harbored a segment of H6 origin [22,23]. Altogether, those findings indicated that H6 subtype viruses pose a significant threat to public health.…”

Section: Introductionmentioning

confidence: 61%

The Genomic Evolution and the Transmission Dynamics of H6N2 Avian Influenza A Viruses in Southern China

Yuan

Zhou

Zhang

et al. 2022

Viruses

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In China, the broad prevalence of H6 subtype influenza viruses, increasingly detected in aquatic birds, promotes their exchange materials with other highly pathogenic human-infecting H5N1, H5N6, and H7N9 influenza viruses. Strikingly, some H6 subtype viruses can infect pigs, dogs, and humans, posing risks to public health. In this study, 9 H6N2 viruses recovered from waterfowl species in the Guangdong province of China in 2018 were isolated and sequenced. Phylogenetic analysis revealed that the genome sequences of these H6N2 viruses belonged to Group I, except for the NP gene in Group III. Coalescent analyses demonstrated that the reassortment of NA and NS genes have occurred in two independent clusters, suggesting H6 subtype viruses had been undergoing a complex reassortant. To examine the evolutionary dynamics and the dissemination of the H6 subtype viruses, a Bayesian stochastic search variable selection was performed for results showing higher viral migration rates between closer provinces, including Guangdong, Jiangxi, Guangxi, and Fujian. Notably, the transmission routes of the H6 subtype viruses were concentrated in Jiangxi Province, the most frequent location for input and output transmission and a region containing Poyang Lake, a well-known wintering site for migration birds. We also found that the aquatic birds, especially ducks, were the most common input source of the viral transmission. In addition, we also found that eight positively selected amino acid sites were identified in HA protein. Given their continuous dissemination and the broad prevalence of the H6 subtype influenza viruses, continued surveillance is warranted in the future.

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“…There remains an important question to answer regarding whether these H5N8 viruses could become the dominant subtype in domestic poultry in China. Our previous study showed that these 2.3.4.4b H5N8 viruses were antigenically distinct from the commercial vaccine strains in China (Zhang et al, 2021). In China, vaccination of chickens can be a major strategy for controlling the spread of AIVs in poultry.…”

Section: Discussionmentioning

confidence: 98%

“…Frequent contact between wild birds and poultry were regarded as the most probable cause of viral introduction into domestic poultry (Zhang et al, 2020a(Zhang et al, , 2021. It is noteworthy that the circulating 2.3.4.4b viruses were antigenically distinct from the clade 2.3.4.4h and 2.3.2.1b vaccine strains in China (Zhang et al, 2021), highlighting the update of H5 subtype vaccine in poultry. The poultry-to-human interface may remain elevated due to possible dissemination of the H5N8 viruses among poultry and wild birds.…”

Section: Introductionmentioning

confidence: 99%

Divergent Reassortment and Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Virus in Birds of China During 2021

Zhang

Sang

et al. 2022

Front. Microbiol.

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Highly pathogenic influenza A(H5N8) viruses had caused several outbreaks among wild bird and poultry populations across the globe, and strikingly, caused human infection, posing serious public health concerns. In this study, we conducted influenza surveillance in China during 2021 to monitor the evolution of influenza viruses in poultry. A total of 35 influenza viruses were obtained in chickens, ducks, and geese, of which 30 H5N8 viruses, 3 H5N1 viruses, and 2 H5N6 viruses. Phylogenetic analysis suggested all of H5N1, H5N6, and H5N8 isolates were derived from clade 2.3.4.4b H5N8 viruses during 2020/21 season, and notably, the internal genes of H5N1 and H5N6 viruses shared different genetic heterogeneity with H5N8 viruses and had been reassorted with wild bird-origin H5N1 viruses from Europe. By contrast, almost all H5N8 viruses exhibited only one phylogenic cluster with wild bird-origin H5N8 viruses in China and Korea, indicating that H5N8 viruses in China were more stable. Besides, we found that Korea is the main output geographic location in the spread of these H5N8 viruses to northern and eastern China, and especially, the co-circulation of H5N8 viruses occurred within China, with central China acted as a seeding population during the H5N8 epidemic. The statistical support was strong for viral migration from wild birds to chickens and ducks, indicating that 2.3.4.4b poultry-origin H5N8 viruses during 2020–2021 were originated from wild birds. Our findings provide novel insights into evolution and transmission dynamics of H5 subtype influenza viruses among poultry after novel H5N8 viruses invaded China for nearly one year.

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Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020

Cited by 20 publications

References 37 publications

Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N8) Virus in Pakistani Live Bird Markets Reveals Rapid Diversification of Clade 2.3.4.4b Viruses

Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N8) Virus in Pakistani Live Bird Markets Reveals Rapid Diversification of Clade 2.3.4.4b Viruses

The Genomic Evolution and the Transmission Dynamics of H6N2 Avian Influenza A Viruses in Southern China

Divergent Reassortment and Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Virus in Birds of China During 2021

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