Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs

Powell, Joshua D.; Abente, Eugenio J.; Chang, Jennifer; Souza, Carine K.; Rajão, Daniela S.; Anderson, Tavis K.; Zeller, Michael A.; Gauger, Phillip C.; Lewis, Nicola S.; Vincent, Amy L.

doi:10.1016/j.virol.2020.11.006

Cited by 19 publications

(23 citation statements)

References 37 publications

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“…In addition, the 2WF10:6pH1N1 virus was also able to transmit by airborne route, although with delayed replication kinetics, whereas no evidence of airborne transmission with 1WF10:7pH1N1 was observed, suggesting that compatibility and balance between the HA and NA is also important (Figure 2B). It is tempting to speculate that the pH1N1 backbone is more flexible to accept reassortment with diverse surface genes and does provide a replicative advantage in mammals, as has been observed in multiple examples of reassortant H1N1 and H3N2 viruses in swine [127][128][129][130]. Sequencing information showed a S261N mutation in PB1 and V104A in HA in the viruses isolated from respiratory contact animals (Table 1); however, the role of those positions in airborne transmission remains unknown [88].…”

Section: Experimental Infections/transmission Of H9n2 Iav In Mammalian Modelsmentioning

confidence: 94%

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals

Cáceres

Rajão

Pérez

2021

Viruses

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Influenza A viruses (IAV) are widespread viruses affecting avian and mammalian species worldwide. IAVs from avian species can be transmitted to mammals including humans and, thus, they are of inherent pandemic concern. Most of the efforts to understand the pathogenicity and transmission of avian origin IAVs have been focused on H5 and H7 subtypes due to their highly pathogenic phenotype in poultry. However, IAV of the H9 subtype, which circulate endemically in poultry flocks in some regions of the world, have also been associated with cases of zoonotic infections. In this review, we discuss the mammalian transmission of H9N2 and the molecular factors that are thought relevant for this spillover, focusing on the HA segment. Additionally, we discuss factors that have been associated with the ability of these viruses to transmit through the respiratory route in mammalian species. The summarized information shows that minimal amino acid changes in the HA and/or the combination of H9N2 surface genes with internal genes of human influenza viruses are enough for the generation of H9N2 viruses with the ability to transmit via aerosol.

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Section: Experimental Infections/transmission Of H9n2 Iav In Mammalian Modelsmentioning

confidence: 94%

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals

Cáceres

Rajão

Pérez

2021

Viruses

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“…In addition, the 2WF10:6pH1N1 virus was also able to transmit by airborne route, although with delayed replication kinetics, whereas no evidence of airborne transmission with 1WF10:7pH1N1 was observed, suggesting that compatibility and balance between the HA and NA is also important (Fig 2B). It is tempting to speculate that the pH1N1 backbone is more flexible to accept reassortment with diverse surface genes and does provide a replicative advantage in mammals, as has been observed in multiple examples of reassortant H1N1 and H3N2 viruses in swine (Everett et al 2020, Powell et al 2021, Ryt-Hansen et al 2020, Zell et al 2020). Sequencing information showed a S261N mutation in PB1 and V104A in HA in the viruses isolated from respiratory contact animals (Table 1); however, the role of those positions in airborne transmission remains unknown (Kimble et al 2011).…”

Section: Experimental Infections/transmission Of H9n2 Iav In Mammalian Modelsmentioning

confidence: 96%

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses

Cáceres¹,

Rajão²,

Pérez³

2021

Preprint

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Influenza A viruses (IAV) are widespread viruses affecting avian and mammalian species worldwide. Outbreaks of IAV in poultry are usually associated with substantial morbidity and mortality, significantly affecting the poultry industry and food security. IAVs from avian species can be transmitted to mammals including humans and, thus, they are of inherent pandemic concern. Most of the efforts to understand the pathogenicity and transmission of avian origin IAVs have been focused on H5 and H7 subtypes due to their highly pathogenic phenotype in poultry. However, IAV of the H9 subtype that circulate endemically in poultry flocks in some regions of the world have also been associated with cases of zoonotic infections. As a result, the World Health Organization includes avian origin H9N2 IAV among the top in the list of IAVs of pandemic concern. In this review, we discuss the interspecies transmission of H9N2 between avian and mammalian species and the molecular factors that are thought relevant for this spillover. Additionally, we discuss factors that have been associated with the ability of these viruses to transmit through the respiratory route in mammalian species.

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“…Though there is little experimental work in swine IAV (but see examples in human IAV White and Lowen, 2018; White et al ., 2019 and review by Lowen, 2017), there is observational evidence that certain gene combinations provide fitness advantages and disadvantages. This is evident from the presence of extensive reassortment of IAV in swine (Gao et al ., 2017; Rajão et al ., 2017; Diaz et al ., 2017; Henritzi et al ., 2020) with more than 100 distinct genome constellations, but only a small fraction of these constellations are frequently detected, suggesting that the majority of these reassorted viruses may have little epidemiological relevance (Powell et al ., 2020).…”

Section: Empirical Studymentioning

confidence: 99%

“…In this empirical example, we focus on an H3.2010.1 swine IAV lineage derived from a human-seasonal H3 introduction to swine (Anderson et al ., 2020; Rajão et al ., 2015). Generally, human IAV infection in swine results in low replication and rare pig-to-pig transmission, but some human-origin IAV become endemic, and this is typically associated with genetic differences from the precursor strain (Lewis et al ., 2016; Rajão et al ., 2018; Powell et al ., 2020), or reassortment with endemic host-adapted viruses. The H3.2010.1 lineage follows this paradigm, and assessing reassortment in this lineage allows us to generate testable hypotheses on how expansion in the genomic diversity of IAV in swine populations may facilitate IAV capable of spillover from swine to humans.…”

Section: Empirical Studymentioning

confidence: 99%

“…The second reassortment event resulted in viruses where the human N2-NA was replaced by a classical swine N1-NA. The third major reassortment event involved the exchange of the N1-NA to an N2-NA derived from endemic swine 2002 N2 genes, the inclusion of the Matrix (M) gene from H1N1pdm09, with the remaining internal genes associated with the endemic swine triple reas-sortant internal gene (TRIG) constellation (Powell et al ., 2020). Given the known minimum number of reassortment events in this IAV lineage, our method adequately recreates its evolutionary history.…”

Section: Empirical Studymentioning

confidence: 99%

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RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks

Markin

Wagle

Anderson

et al. 2021

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Motivation: A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g., hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results: Here we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. Additionally, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical influenza A virus evolutionary analyses. Availability: RF-Net 2 is available at https://github.com/flu-crew/rf-net-2.

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Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs

Cited by 19 publications

References 37 publications

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses

RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks

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