#Human-Origin #Influenza A(#H3N2) #Reassortant Viruses in #Swine, Southeast #Mexico (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 4—April 2019 / Research

Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico

Martha I. Nelson  , Carine Souza, Nídia S. Trovão, Andres Diaz, Ignacio Mena, Albert Rovira, Amy L. Vincent, Montserrat Torremorell, Douglas Marthaler1, and Marie R. Culhane

Author affiliations: National Institutes of Health, Bethesda, Maryland, USA (M.I. Nelson, N.S. Trovão); National Animal Disease Center, Ames, Iowa, USA (C. Souza, A.L. Vincent); Icahn School of Medicine at Mount Sinai, New York, New York, USA (N.S. Trovão, I. Mena); University of Minnesota, Saint Paul, Minnesota, USA (A. Diaz, A. Rovira, M. Torremorell, D. Marthaler, M.R. Culhane)



The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.

Keywords: Seasonal Influenza; Swine Influenza; Reassortant Strain; Pigs; Human; H1N1pdm09; H3N2; Mexico.



#Origins of the 1918 #Pandemic: Revisiting the #Swine “Mixing Vessel” #Hypothesis (Am J Epidemiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Am J Epidemiol. 2018 Dec 1;187(12):2498-2502. doi: 10.1093/aje/kwy150.

Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis.

Nelson MI1, Worobey M2.

Author information: 1 Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland. 2 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.



How influenza A viruses host-jump from animal reservoir species to humans, which can initiate global pandemics, is a central question in pathogen evolution. The zoonotic and spatial origins of the influenza virus associated with the “Spanish flu” pandemic of 1918 have been debated for decades. Outbreaks of respiratory disease in US swine occurred concurrently with disease in humans, raising the possibility that the 1918 virus originated in pigs. Swine also were proposed as “mixing vessel” intermediary hosts between birds and humans during the 1957 Asian and 1968 Hong Kong pandemics. Swine have presented an attractive explanation for how avian viruses overcome the substantial evolutionary barriers presented by different cellular environments in humans and birds. However, key assumptions underpinning the swine mixing-vessel model of pandemic emergence have been challenged in light of new evidence. Increased surveillance in swine has revealed that human-to-swine transmission actually occurs far more frequently than the reverse, and there is no empirical evidence that swine played a role in the emergence of human influenza in 1918, 1957, or 1968. Swine-to-human transmission occurs periodically and can trigger pandemics, as in 2009. But swine are not necessary to mediate the establishment of avian viruses in humans, which invites new perspectives on the evolutionary processes underlying pandemic emergence.

PMID: 30508193 DOI: 10.1093/aje/kwy150

Keywords: Avian Influenza; Swine Influenza; Influenza A; Pandemic Influenza; H1N1; Spanish Flu; Pigs; Reassortant strain.


#Tissue #tropisms opt for transmissible #reassortants during #avian and #swine #influenza A virus co-infection in swine (PLoS Pathogens, abstract)

[Source: PLoS Pathogens, full page: (LINK). Abstract, edited.]


Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine

Xiaojian Zhang , Hailiang Sun , Fred L. Cunningham , Lei Li , Katie Hanson-Dorr, Matthew W. Hopken, Jim Cooley, Li-Ping Long, John A. Baroch, Tao Li, Brandon S. Schmit, Xiaoxu Lin, Alicia K. Olivier,  [ … ], Xiu-Feng Wan

Published: December 3, 2018 / DOI: https://doi.org/10.1371/journal.ppat.1007417 / This is an uncorrected proof.



Genetic reassortment between influenza A viruses (IAVs) facilitate emergence of pandemic strains, and swine are proposed as a “mixing vessel” for generating reassortants of avian and mammalian IAVs that could be of risk to mammals, including humans. However, how a transmissible reassortant emerges in swine are not well understood. Genomic analyses of 571 isolates recovered from nasal wash samples and respiratory tract tissues of a group of co-housed pigs (influenza-seronegative, avian H1N1 IAV–infected, and swine H3N2 IAV–infected pigs) identified 30 distinct genotypes of reassortants. Viruses recovered from lower respiratory tract tissues had the largest genomic diversity, and those recovered from turbinates and nasal wash fluids had the least. Reassortants from lower respiratory tracts had the largest variations in growth kinetics in respiratory tract epithelial cells, and the cold temperature in swine nasal cells seemed to select the type of reassortant viruses shed by the pigs. One reassortant in nasal wash samples was consistently identified in upper, middle, and lower respiratory tract tissues, and it was confirmed to be transmitted efficiently between pigs. Study findings suggest that, during mixed infections of avian and swine IAVs, genetic reassortments are likely to occur in the lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant.


Author summary

Genetic reassortments between avian and swine influenza viruses are likely to occur in the swine lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant; determination of tissue tropisms for potential reassortants between contemporary avian and swine influenza viruses would help identify transmissible reassortants with public health risks.


Citation: Zhang X, Sun H, Cunningham FL, Li L, Hanson-Dorr K, Hopken MW, et al. (2018) Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine. PLoS Pathog 14(12): e1007417. https://doi.org/10.1371/journal.ppat.1007417

Editor: Anice C. Lowen, Emory University School of Medicine, UNITED STATES

Received: July 24, 2018; Accepted: October 18, 2018; Published: December 3, 2018

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: The sequence of A/swine/Texas/A01104013/2012 (H3N2) and A/mallard/Wisconsin/A00751454/2009 (H1N1) viruses are available from Genbank under the accession numbers JX280447 to JX280454 and MH879773 to MH879780. All other relevant data are included in the main text of this paper or the Supporting Information files associated with this paper.

Funding: This study was supported by the U.S. Department of Agriculture and the National Institutes of Health (NIH) [grant number R21AI135820]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Avian Influenza; Swine Influenza; Influenza A; H1N1; H3N2 Pigs; Reassortant strain.


#Eurasian #avian-like #swine #influenza A viruses escape human MxA restriction by distinct #mutations in their nucleoprotein (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Eurasian avian-like swine influenza A viruses escape human MxA restriction by distinct mutations in their nucleoprotein

ominik Dornfeld, Philipp P. Petric, Ebrahim Hassan, Roland Zell, Martin Schwemmle

DOI: 10.1128/JVI.00997-18



To cross the human species barrier, influenza A viruses (IAV) of avian origin have to overcome the interferon-induced host restriction factor MxA by acquiring distinct mutations in their nucleoprotein (NP). We recently demonstrated that North American classical swine IAV are able to escape MxA restriction partially. Here, we investigated whether the Eurasian avian-like swine IAV lineage currently circulating in European swine would likewise evade restriction by human MxA. We found that the NP of the isolate A/swine/Belzig/2/2001 (Belzig) exerts increased MxA escape similar in extent to human IAV NPs. Mutational analysis revealed that the MxA escape mutations in Belzig-NP differ from the known MxA resistance cluster of the North American classical swine lineage and human-derived IAV NPs. A mouse-adapted avian IAV of the H7N7 subtype encoding Belzig-NP showed significantly enhanced viral growth in both MxA-expressing cells and MxA-transgenic mice compared to control viruses lacking the MxA escape mutations. Similarly, growth of recombinant Belzig virus was only marginally affected in MxA-expressing cells and MxA-transgenic mice compared to Belzig mutant viruses lacking MxA escape mutations in NP. Phylogenetic analysis of the Eurasian avian-like swine IAV revealed that the NP amino acids required for MxA escape were acquired successively and were maintained after their introduction. Our results suggest that circulation of IAV in the swine population can result in the selection of NP variants with a high degree of MxA resistance, thereby increasing the zoonotic potential of these viruses.



The human MxA protein efficiently blocks replication of IAV from non-human species. In rare cases, however, these IAV overcome the species barrier and become pandemic. All known pandemic viruses have acquired and maintained MxA escape mutations in the viral NP and are thus not efficiently controlled by MxA. Intriguingly, partial MxA resistance can also be acquired in other hosts that express antivirally active Mx proteins such as swine. To perform a risk assessment of IAV circulating in the European swine population, we analyzed the degree of MxA resistance of Eurasian avian-like swine IAV. Our data demonstrate that these viruses carry yet undescribed Mx resistance mutations in NP that mediate efficient escape from human MxA. We conclude that Eurasian avian-like swine IAV possess a substantial zoonotic potential.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Influenza A; Avian Influenza; Swine Influenza; H7N7; Animal Models.


Plasticity of #aminoacid residue 145 near the #receptor binding site of #H3 #swine #influenza A viruses and its impact on receptor binding and #antibody recognition (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Plasticity of amino acid residue 145 near the receptor binding site of H3 swine influenza A viruses and its impact on receptor binding and antibody recognition.

Jefferson J. S. Santos, Eugenio J. Abente, Adebimpe O. Obadan, Andrew J. Thompson, Lucas Ferreri, Ginger Geiger, Ana S. Gonzalez-Reiche, Nicola S. Lewis, David F. Burke,Daniela S. Rajão, James C. Paulson, Amy L. Vincent, Daniel R. Perez

DOI: 10.1128/JVI.01413-18



The hemagglutinin (HA), a glycoprotein on the surface of influenza A virus (IAV), initiates the virus life cycle by binding to terminal sialic acid (SA) residues on host cells. The HA gradually accumulates amino acid (aa) substitutions that allow IAV to escape immunity through a mechanism known as antigenic drift. We recently confirmed that a small set of aa residues are largely responsible for driving antigenic drift in swine-origin H3 IAV. All identified residues are located adjacent to the HA receptor binding site (RBS), suggesting that substitutions associated with antigenic drift may also influence receptor binding. Among those substitutions, residue 145 was shown to be a major determinant of antigenic evolution. To determine whether there are functional constraints to substitutions near the RBS and their impact on receptor binding and antigenic properties, we carried out site-directed mutagenesis experiments at the single aa level. We generated a panel of viruses carrying substitutions at residue 145 representing all 20 amino acids. Despite limited amino acid usage in nature, most substitutions at residue 145 were well tolerated without major impact on virus replication in vitro. All substitutions retained receptor binding specificity, but frequently led to decreased receptor binding. Glycan microarray analysis showed that substitutions at residue 145 modulate binding to a broad range of glycans. Furthermore, antigenic characterization identified specific substitutions at residue 145 that altered antibody recognition. This work provides a better understanding of the functional effects of aa substitutions near the RBS and the interplay between receptor binding and antigenic drift.



The complex and continuous antigenic evolution of IAVs remains a major hurdle for vaccine selection and effective vaccination. On the virus’ hemagglutinin (HA) of the H3N2 IAVs, the aa substitution N145K causes significant antigenic changes. We show that aa 145 displays remarkable amino acid plasticity in vitro tolerating multiple aa substitutions, many of which have not yet been observed in nature. Mutant viruses carrying substitutions at residue 145 showed no major impairment on virus replication in the presence of lower receptor binding avidity. However, their antigenic characterization confirmed the impact of the 145K substitution in antibody immunodominance. We provide a better understanding of the functional effects of aa substitutions implicated in antigenic drift and its consequences on receptor binding and antigenicity. The mutation analyses presented in this report represent a significant dataset to aid and test computational approaches’ ability to predict binding of glycans and in antigenic cartography analyses.

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Keywords: Influenza A; Swine Influenza; A/H3.


Spatio-temporal #distribution and #evolution of the A #H1N1pdm09 virus in #pigs in #France from 2009 to 2017: identification of a potential swine-specific lineage (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Spatio-temporal distribution and evolution of the A/H1N1 2009 pandemic virus in pigs in France from 2009 to 2017: identification of a potential swine-specific lineage

Amélie Chastagner, Séverine Hervé, Emilie Bonin, Stéphane Quéguiner, Edouard Hirchaud, Dinah Henritzi, Véronique Béven, Stéphane Gorin, Nicolas Barbier, Yannick Blanchard,Gaëlle Simon

DOI: 10.1128/JVI.00988-18



The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated to pig density. From these isolates, 17 whole genome sequences were obtained as well as 6 additional HA/NA sequences, in order to perform spatial and temporal analyses of the genetic diversity, and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains. Following mutation accumulation and fixation over time, phylogenetic analyses revealed for the first time the divergence of a swine-specific genogroup within the H1N1pdm lineage. The divergence is thought to have occurred around 2011, although this was only demonstrated through strains isolated in 2015-2016 in the southern half of France. To date, these H1N1pdm swine strains have not been related to any increased virulence in swine herds and have not exhibited any antigenic drift as compared to seasonal human strains. However, further monitoring is encouraged as diverging evolutionary patterns in these two species, i.e. swine and humans, may lead to the emergence of viruses with a potentially higher risk for both animal and human health.



Pigs are a ‘mixing vessel’ for influenza A viruses (IAVs) because of their ability to be infected by avian and human IAVs, and their propensity to facilitate viral genomic reassortment events. Also, as IAVs may evolve differently in swine and humans, pigs can become a reservoir for old human strains against which the human population has become immunologically naïve. Thus, viruses from the novel swine-specific H1N1pdm genogroup may continue to diverge from seasonal H1N1pdm strains and/or from other H1N1pdm viruses infecting pigs and lead to the emergence of viruses that would not be covered by human vaccines and/or swine vaccines based on antigens closely related to the original H1N1pdm virus. This discovery confirms the importance of encouraging swine IAV monitoring because H1N1pdm swine viruses could carry an increased risk for both human and swine health in the future, as a whole H1N1pdm or gene provider in subsequent reassortant viruses.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Seasonal Influenza; Pandemic Influenza; Swine Influenza; H1N1pdm09; Pigs; France.


Comparison of adjuvanted-whole inactivated virus and live-attenuated virus #vaccines against challenge with contemporary, antigenically distinct #swine #H3N2 #influenza A viruses (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Comparison of adjuvanted-whole inactivated virus and live-attenuated virus vaccines against challenge with contemporary, antigenically distinct swine H3N2 influenza A viruses

Eugenio J. Abente, Daniela S. Rajao, Jefferson Santos, Bryan S. Kaplan, Tracy L. Nicholson, Susan L. Brockmeier, Phillip C. Gauger, Daniel R. Perez, Amy L. Vincent

DOI: 10.1128/JVI.01323-18



Influenza A virus in swine (IAV-S) circulating in the United States of America are phylogenetically and antigenically distinct. A human H3 hemagglutinin (HA) was introduced in the IAV-S gene pool in the late 1990s, sustained continued circulation, and evolved into five monophyletic genetic clades after 2009, H3 IVA-E. Across these phylogenetic clades, distinct antigenic clusters were identified, with three clusters (cyan, red and green) among the most frequently detected antigenic phenotypes. Although it was demonstrated that antigenic diversity of H3N2 IAV-S was associated with changes at a few amino acid positions in the head of the HA, the implications of this diversity on vaccine efficacy was not tested. Using antigenically representative H3N2 viruses, we compared whole inactivated virus (WIV) and live attenuated influenza vaccine (LAIV) vaccines for protection against challenge with antigenically distinct H3N2 viruses in pigs. WIV provided partial protection against antigenically distinct viruses, but did not prevent virus replication in the upper respiratory tract. In contrast, LAIV provided complete protection from disease and virus was not detected after challenge with antigenically distinct viruses.



Due to the rapid evolution of the influenza A virus, vaccines require continuous strain updates. Additionally, the platform used to deliver the vaccine can have an impact on the breadth of protection. Currently, there are various vaccine platforms available to prevent influenza A virus infection in swine, and we experimentally tested two: adjuvanted-whole inactivated virus and live attenuated virus. When challenged with an antigenically distinct virus, adjuvanted-whole inactivated virus provided partial protection while live attenuated virus provided effective protection. Additional strategies are required to broaden the protective properties of inactivated virus vaccines given the dynamic antigenic landscape of co-circulating strains in North America, whereas live attenuated vaccines may require less frequent strain updates based on demonstrated cross-protection. Enhancing vaccine efficacy to control influenza infections in swine will help reduce the impact it has on swine production and reduce the risk of swine-to-human transmission.



#Corresponding author: Amy L. Vincent, Virus and Prion Diseases of Livestock Research Unit, NADC, USDA-ARS, 1920 Dayton Avenue, PO Box 70, Ames, IA 50010, USA, Phone: +1 515 337 7557, Email address: amy.vincent@ars.usda.gov

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Keywords: Influenza A; Swine Influenza; H3N2; Pigs; Vaccines.