Genotype patterns of contemporary reassorted H3N2 virus in US swine

Kitikoon, Pravina; Nelson, Martha I.; Killian, Mary Lea; Anderson, Tavis K.; Koster, Leo; Culhane, Marie; Vincent, Amy L.

doi:10.1099/vir.0.051839-0

Cited by 65 publications

(56 citation statements)

References 24 publications

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“…In this study, we identified the genome patterns of H1N1 and H1N2 collected from swine in the United States from 2009 to 2016. Similar studies with H3N2 viruses from US swine populations have been previously reported [6,23], but a comprehensive analysis of H1 IAV was lacking. Among the 616 unique genome sets for H1N1 and H1N2 viruses, 74 whole-genome patterns and 47 NA+internal patterns were identified.…”

Section: Discussionsupporting

confidence: 48%

“…In the United States, the TRIG lineage was the predominant lineage prior to 2009. Recent records have shown that the H1N1pdm09 viruses have reassorted extensively with other co-circulating swine IAV in both H1 and H3 subtypes [9,22,23,26] and gradually replaced the dominant TRIG lineage internal genes, especially the pdm-lineage M gene [23,24,27]. All eight pdm-lineage genes were detected in our study in various combinations with TRIG-lineage genes.…”

Section: Discussionmentioning

confidence: 58%

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The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016

Gao

Anderson

Walia

et al. 2017

Journal of General Virology

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Transmission of influenza A virus (IAV) from humans to swine occurs with relative frequency and is a critical contributor to swine IAV diversity. Subsequent to the introduction of these human seasonal lineages, there is often reassortment with endemic viruses and antigenic drift. To address whether particular genome constellations contributed to viral persistence following the introduction of the 2009 H1N1 human pandemic virus to swine in the USA, we collated and analysed 616 whole genomes of swine H1 isolates. For each gene, sequences were aligned, the best-known maximum likelihood phylogeny was inferred, and each virus was assigned a clade based upon its evolutionary history. A time-scaled Bayesian approach was implemented for the haemagglutinin (HA) gene to determine the patterns of genetic diversity over time. From these analyses, we observed an increase in genome diversity across all H1 lineages and clades, with the H1-g and H1-d1 genetic clades containing the greatest number of unique genome patterns. We documented 74 genome patterns from 2009 to 2016, of which 3 genome patterns were consistently detected at a significantly higher level than others across the entire time period. Eight genome patterns increased significantly, while five genome patterns were shown to decline in detection over time. Viruses with genome patterns identified as persisting in the US swine population may possess a greater capacity to infect and transmit in swine. This study highlights the emerging genetic diversity of US swine IAV from 2009 to 2016, with implications for swine and public health and vaccine control efforts.

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Section: Discussionsupporting

confidence: 48%

Section: Discussionmentioning

confidence: 58%

The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016

Gao

Anderson

Walia

et al. 2017

Journal of General Virology

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“…The H3N2v virus was characterized as a reassortant (r) H3N2 in which seven genes originated from swine triple-reassortant IAV and the matrix (M) gene of pandemic (p) H1N1 origin (16). While numerous rH3N2p genome constellations have been identified in IAV isolated from pigs, this particular gene constellation is the only rH3N2p virus that has also been associated with zoonotic transmission to people to date (28).…”

Section: Discussionmentioning

confidence: 99%

Efficacy in Pigs of Inactivated and Live Attenuated Influenza Virus Vaccines against Infection and Transmission of an Emerging H3N2 Similar to the 2011-2012 H3N2v

Loving

Lager

Vincent

et al. 2013

J Virol

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cVaccines provide a primary means to limit disease but may not be effective at blocking infection and pathogen transmission. The objective of the present study was to evaluate the efficacy of commercial inactivated swine influenza A virus (IAV) vaccines and experimental live attenuated influenza virus (LAIV) vaccines against infection with H3N2 virus and subsequent indirect transmission to naive pigs. The H3N2 virus evaluated was similar to the H3N2v detected in humans during 2011-2012, which was associated with swine contact at agricultural fairs. One commercial vaccine provided partial protection measured by reduced nasal shedding; however, indirect contacts became infected, indicating that the reduction in nasal shedding did not prevent aerosol transmission. One LAIV vaccine provided complete protection, and none of the indirect-contact pigs became infected. Clinical disease was not observed in any group, including nonvaccinated animals, a consistent observation in pigs infected with contemporary reassortant H3N2 swine viruses. Serum hemagglutination inhibition antibody titers against the challenge virus were not predictive of efficacy; titers following vaccination with a LAIV that provided sterilizing immunity were below the level considered protective, yet titers in a commercial vaccine group that was not protected were above that level. While vaccination with currently approved commercial inactivated products did not fully prevent transmission, certain vaccines may provide a benefit by limitating shedding, transmission, and zoonotic spillover of antigenically similar H3N2 viruses at agriculture fairs when administered appropriately and used in conjunction with additional control measures.

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“…A swine-origin H1N1 IAV was responsible for the first pandemic of the twenty-first century (Rambaut & Holmes, 2009) and was associated with w200 000 human deaths (Simonsen et al, 2013). In recent decades, the genetic diversity of swine IAVs in North America has increased significantly due to the emergence of triple-reassortant H3N2 viruses in the late 1990s (Kitikoon et al, 2013), the numerous introductions of human-origin viruses in pigs including the 2009 pandemic virus (Nelson et al, 2012) and the large-scale movement of pigs between different US regions (Nelson et al, 2011). It is estimated that w90 % of swine herds in the mid-western US are infected with IAVs (Corzo et al, 2013) and that pigs can be exposed to different IAVs during their lifetime (Diaz et al, 2015;Ducatez et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…In pigs, H1N1, H1N2 and H3N2 are the most prevalent IAV subtypes (Torremorell et al, 2012). In North American swine there are six antigenically and phylogenetically distinct H1 groups (a, b, c1, c2, d1 and d2) (Anderson et al, 2015;Lorusso et al, 2011) and four H3 groups (I, II, III and IV) (Kitikoon et al, 2013). Multiple IAV subtypes can co-circulate in swine herds and persist at the population level for prolonged periods of time (Corzo et al, 2013;Diaz et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

Díaz

Enomoto

Romagosa

et al. 2015

Journal of General Virology

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To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n510). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.

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Genotype patterns of contemporary reassorted H3N2 virus in US swine

Cited by 65 publications

References 24 publications

The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016

The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016

Efficacy in Pigs of Inactivated and Live Attenuated Influenza Virus Vaccines against Infection and Transmission of an Emerging H3N2 Similar to the 2011-2012 H3N2v

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

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