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

Abstract

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.

Vaccination against swine influenza in pigs causes different drift evolutionary patterns upon swine influenza virus experimental infection and reduces the likelihood of genomic reassortments

“…On the other hand, for the endotracheal administration, animals were intubated. For both, a nose snare was used to restrain animals ( López-Valiñas et al., 2021 ). Experimentally inoculated animals were separated from the rest by a physical barrier.…”

“…To detect and quantify swine IAV RNA on each sample a RT-qPCR based on M segment amplification was performed in the Fast7500 equipment (Applied Biosystem) ( Spackman et al., 2002 ). Samples with a cycle threshold (Ct) value under 40 were considered positive whereas no fluorescence detection were considered negative ( Spackman et al., 2002 ; López-Valiñas et al., 2021 ).…”

“…It is known that swine IAV breakthrough infections are common in pigs because virus evolution favors the escape to the host immunity ( Murcia et al., 2012 ), this situation can promote the circulation of the virus in vaccinated pigs ( Chamba Pardo et al., 2018 ). Previous studies suggest that the application of the trivalent vaccine can influence on the evolutionary dynamics of swine IAV viral populations, being different in vaccinated and nonvaccinated animals ( López-Valiñas et al., 2021 ; López-Valiñas et al., 2022 ).Thus, the aim of the present study was to evaluate the evolutionary dynamics of swine IAV during a coinfection trial in pigs with EA swine H1N1 and “human-like” swine H3N2 strains in vaccinated and nonvaccinated pigs. Overall, our study retrieved by NGS 39 complete viral quasispecies collected from vaccinated and nonvaccinated pigs, finding different evolutionary patterns, and nonsynonymous substitutions that may play an important role in virulence and the evasion of the swine immune system.…”

H1N1 Influenza Virus-Infected Nasal Mucosal Epithelial Progenitor Cells Promote Dendritic Cell Recruitment and Maturation

“…About 90% of upper respiratory tract infections is caused by viruses. In recent years, some new types of highly pathogenic viruses that mainly cause respiratory tract infections have emerged, such as influenza A virus, which is a negative-sense enveloped RNA virus and hemagglutinin (HA) and neuraminidase (NA) are antigenic glycoproteins on the surface of the virus, and the pathogenicity of the virus is directly related ( 2 , 3 ). Influenza A virus H1N1 is one of the main viruses that cause acute upper respiratory tract infections in humans and animals, with high morbidity and mortality worldwide.…”

Identification of Single Amino Acid Changes in the Rift Valley Fever Virus Polymerase Core Domain Contributing to Virus Attenuation In Vivo

“…Finally, variants of each sample were noted in a variant calling file (VCF) generated with LoFreq software (v2.1.5) using default parameters ( Wilm et al., 2012 ). A variant was considered when following these requirements: mapping quality > 30, minimum coverage depth of 100, alternative base supported by at least 10 reads, and p value per change found <0.01 ( Lopez-Valinas et al., 2021 ). Finally, the nucleotide diversity (π) was calculated in each sample with SNPGenie software ( Nelson et al., 2015 ).…”