Co-circulation of multiple influenza A variants in swine harboring genes from seasonal human and swine influenza viruses

AbstractSince the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018.In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Ten different swIAV subtypes were detected. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including novel reassortants and subtypes harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx viruses.The results provide essential data for the control of swIAV in pigs and for early detection of novel swIAV strains with zoonotic potential.

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Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses

eLife ◽

10.7554/elife.60940 ◽

2021 ◽

Vol 10 ◽

Author(s):

Pia Ryt-Hansen ◽

Jesper Schak Krog ◽

Solvej Østergaard Breum ◽

Charlotte Kristiane Hjulsager ◽

Anders Gorm Pedersen ◽

...

Keyword(s):

Influenza A ◽

Influenza Pandemic ◽

Swine Influenza ◽

Influenza Viruses ◽

Steady Increase ◽

Full Genome ◽

Potential Threat ◽

Antigenic Sites ◽

Hemagglutinin Protein ◽

Swine Influenza A Virus

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

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Variation in the HA antigenicity of A(H1N1)pdm09-related swine influenza viruses

Journal of General Virology ◽

10.1099/jgv.0.001569 ◽

2021 ◽

Author(s):

Ahmed Magdy Khalil ◽

Reiko Yoshida ◽

Tatsunori Masatani ◽

Ayato Takada ◽

Makoto Ozawa

Keyword(s):

Genetic Diversity ◽

Amino Acid ◽

Influenza A ◽

Influenza Pandemic ◽

Gene Segment ◽

Swine Influenza ◽

Influenza Viruses ◽

Single Amino Acid ◽

Ha Gene ◽

The Impact

Since the influenza pandemic in 2009, the causative agent ‘A(H1N1)pdm09 virus’, has been circulating in both human and swine populations. Although phylogenetic analyses of the haemagglutinin (HA) gene segment have revealed broader genetic diversity of A(H1N1)pdm09-related swine influenza A viruses (swIAVs) compared with human A(H1N1)pdm09 viruses, it remains unclear whether the genetic diversity reflects the antigenic differences in HA. To assess the impact of the diversity of the HA gene of A(H1N1)pdm09-related swIAVs on HA antigenicity, we characterized 12 swIAVs isolated in Japan from 2013 to 2018. We used a ferret antiserum and a panel of anti-HA mouse monoclonal antibodies (mAbs) raised against an early A(H1N1)pdm09 isolate. The neutralization assay with the ferret antiserum revealed that five of the 12 swIAVs were significantly different in their HA antigenicity from the early A(H1N1)pdm09 isolate. The mAbs also showed differential neutralization patterns depending on the swIAV strains. In addition, the single amino acid substitution at position 190 of HA, which was found in one of the five antigenically different swIAVs but not in human isolates, was shown to be one of the critical determinants for the antigenic difference of swIAV HAs. Two potential N-glycosylation sites at amino acid positions 185 and 276 of the HA molecule were identified in two antigenically different swIAVs. These results indicated that the genetic diversity of HA in the A(H1N1)pdm09-related swIAVs is associated with their HA antigenic variation. Our findings highlighted the need for surveillance to monitor the emergence of swIAV antigenic variants with public health importance.

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Infection Dynamics of Swine Influenza Virus in a Danish Pig Herd Reveals Recurrent Infections with Different Variants of the H1N2 Swine Influenza A Virus Subtype

Viruses ◽

10.3390/v12091013 ◽

2020 ◽

Vol 12 (9) ◽

pp. 1013

Author(s):

Tarka Bhatta ◽

Pia Ryt-Hansen ◽

Jens Nielsen ◽

Lars Larsen ◽

Inge Larsen ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Swine Influenza Virus ◽

Swine Influenza ◽

Respiratory Illness ◽

Antigenic Sites ◽

Infection Dynamics ◽

Next Generation Sequencing Ngs ◽

And Control ◽

Swine Influenza A Virus

Influenza A virus (IAV) in swine, so-called swine influenza A virus (swIAV), causes respiratory illness in pigs around the globe. In Danish pig herds, a H1N2 subtype named H1N2dk is one of the main circulating swIAV. In this cohort study, the infection dynamic of swIAV was evaluated in a Danish pig herd by sampling and PCR testing of pigs from two weeks of age until slaughter at 22 weeks of age. In addition, next generation sequencing (NGS) was used to identify and characterize the complete genome of swIAV circulating in the herd, and to examine the antigenic variability in the antigenic sites of the virus hemagglutinin (HA) and neuraminidase (NA) proteins. Overall, 76.6% of the pigs became PCR positive for swIAV during the study, with the highest prevalence at four weeks of age. Detailed analysis of the virus sequences obtained showed that the majority of mutations occurred at antigenic sites in the HA and NA proteins of the virus. At least two different H1N2 variants were found to be circulating in the herd; one H1N2 variant was circulating at the sow and nursery sites, while another H1N2 variant was circulating at the finisher site. Furthermore, it was demonstrated that individual pigs had recurrent swIAV infections with the two different H1N2 variants, but re-infection with the same H1N2 variant was also observed. Better understandings of the epidemiology, genetic and antigenic diversity of swIAV may help to design better health interventions for the prevention and control of swIAV infections in the herds.

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Identification and Characterization of Swine Influenza Virus H1N1 Variants Generated in Vaccinated and Nonvaccinated, Challenged Pigs

Viruses ◽

10.3390/v13102087 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2087

Author(s):

Álvaro López-Valiñas ◽

Marta Sisteré-Oró ◽

Sergi López-Serrano ◽

Laura Baioni ◽

Ayub Darji ◽

...

Keyword(s):

Influenza A ◽

Influenza Pandemic ◽

Viral Evolution ◽

Swine Influenza Virus ◽

Swine Influenza ◽

H1n1 Influenza ◽

Influenza Viruses ◽

Viral Fitness ◽

Ns1 Protein ◽

Trivalent Vaccine

Influenza viruses represent a continuous threat to both animal and human health. The 2009 H1N1 A influenza pandemic highlighted the importance of a swine host in the adaptation of influenza viruses to humans. Nowadays, one of the most extended strategies used to control swine influenza viruses (SIVs) is the trivalent vaccine application, whose formulation contains the most frequently circulating SIV subtypes H1N1, H1N2, and H3N2. These vaccines do not provide full protection against the virus, allowing its replication, evolution, and adaptation. To better understand the main mechanisms that shape viral evolution, here, the SIV intra-host diversity was analyzed in samples collected from both vaccinated and nonvaccinated animals challenged with the H1N1 influenza A virus. Twenty-eight whole SIV genomes were obtained by next-generation sequencing, and differences in nucleotide variants between groups were established. Substitutions were allocated along all influenza genetic segments, while the most relevant nonsynonymous substitutions were allocated in the NS1 protein on samples collected from vaccinated animals, suggesting that SIV is continuously evolving despite vaccine application. Moreover, new viral variants were found in both vaccinated and nonvaccinated pigs, showing relevant substitutions in the HA, NA, and NP proteins, which may increase viral fitness under field conditions.

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Swine influenza A virus subtypes circulating in Brazilian commercial pig herds from 2012 to 2019

Brazilian Journal of Microbiology ◽

10.1007/s42770-021-00550-y ◽

2021 ◽

Author(s):

Ana Luiza Soares Fraiha ◽

Ana Carolina Diniz Matos ◽

João Luis Reis Cunha ◽

Beatriz Senra Álvares da Silva Santos ◽

Maria Vitória Chaves Peixoto ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Swine Influenza ◽

Swine Influenza A Virus

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Prospective studies of swine influenza A virus epidemiology on swine farms, China

International Journal of Infectious Diseases ◽

10.1016/j.ijid.2020.09.1388 ◽

2020 ◽

Vol 101 ◽

pp. 535

Author(s):

G. Gray ◽

L.K. Borkenhagen ◽

G.-L. Wang ◽

M.-J. Ma

Keyword(s):

Influenza A Virus ◽

Prospective Studies ◽

Influenza A ◽

Swine Influenza ◽

Swine Farms ◽

Swine Influenza A Virus

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Swine influenza vaccines: current status and future perspectives

Animal Health Research Reviews ◽

10.1017/s146625231000006x ◽

2010 ◽

Vol 11 (1) ◽

pp. 81-96 ◽

Cited By ~ 41

Author(s):

Wenjun Ma ◽

Jürgen A. Richt

Keyword(s):

Influenza A ◽

Swine Influenza ◽

Influenza Viruses ◽

Current Status ◽

Economic Losses ◽

Influenza A Viruses ◽

Swine Industry ◽

Effective Strategies ◽

Swine Disease ◽

And Control

AbstractSwine influenza is an important contagious disease in pigs caused by influenza A viruses. Although only three subtypes of influenza A viruses, H1N1, H1N2 and H3N2, predominantly infect pigs worldwide, it is still a big challenge for vaccine manufacturers to produce efficacious vaccines for the prevention and control of swine influenza. Swine influenza viruses not only cause significant economic losses for the swine industry, but are also important zoonotic pathogens. Vaccination is still one of the most important and effective strategies to prevent and control influenza for both the animal and human population. In this review, we will discuss the current status of swine influenza worldwide as well as current and future options to control this economically important swine disease.

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Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018–2019

Viruses ◽

10.3390/v13060977 ◽

2021 ◽

Vol 13 (6) ◽

pp. 977

Author(s):

Kobporn Boonnak ◽

Chayasin Mansanguan ◽

Dennis Schuerch ◽

Usa Boonyuen ◽

Hatairat Lerdsamran ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Seasonal Influenza ◽

Influenza Viruses ◽

Surface Proteins ◽

Antigenic Drift ◽

Influenza B ◽

Receptor Binding Site ◽

Antigenic Sites ◽

Ha Protein

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.

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