ETIDIOH - NEW

  ABSTRACT Swine influenza A virus (swIAV) is an important zoonotic pathogen with the potential to cause human influenza pandemics . Swine are considered “ mixing vessels ” for generating novel reassortant influenza A viruses . In 2009, a swine-origin reassortant virus (2009 pandemic H1N1, pdm/09 H1N1 ) spilled over to humans , causing a global influenza pandemic . This virus soon spread back into swine herds and reassorted with the circulating swIAVs. We previously reported that the genotype 4 (G4) reassortant Eurasian avian-like (EA) H1N1 virus , which bore pdm/09- and triple reassortant (TR)-derived internal genes, had been predominant in swine populations of China since 2016, posing a threat to both the swine industry and public health . Here, our ongoing surveillance confirmed that G4 EA H1N1 viruses remained the predominant swIAVs in China from 2019 to 2023 and had reassorted with the co-circulating swIAVs, such as the H3N2 virus, to generate novel reassortant EA H1N2 viruses...

  Abstract In recent years, the four main swine influenza A virus (IAV-S) subtypes circulating in swine in the EU have been H1avN1, H1huN2, H1N1pdm09, and H3N2 . The latter emerged in 1984 from a reassortment event between a human seasonal H3N2 and H1avN1, and is currently detected at low prevalence in swine in Italy . Here, we describe nine H3N2 IAV-S isolates belonging to three novel genotypes , first detected in Italy in 2021 , likely resulting from reassortment events between swine and human IAVs. The first genotype was characterized by a hemagglutinin (H3 HA) of human seasonal origin , a neuraminidase (N2 NA) derived from H1huN2 strains circulating in Italian swine, and an avian-like internal gene cassette (IGC). The second genotype differed in its IGC constellation: PB2, PB1, PA and NP segments were of pandemic origin ( pdm09 ), while NS and M segments derived from the Eurasian avian-like lineage . The third genotype combined a human-derived H3, a Gent/84-derived N2, and a pd...

  ABSTRACT Influenza A virus (IAV) in swine in the U.S. is surveilled to monitor genetic evolution to inform intervention efforts and aid pandemic preparedness . We describe data from the U.S. Department of Agriculture National Surveillance Plan for Influenza A Virus in Pigs from 2009 to 2022. Clinical respiratory cases were subtyped, followed by sequencing of hemagglutinin (HA) and neuraminidase (NA), and a subset of viruses was whole genome sequenced . Phylogenetic analysis identified geographic and temporal IAV reassortment hotspots . Regions acting as IAV genomic diversity sources or sinks were quantified, and dissemination was qualified and modeled. The dominant IAV clades were H1N2 (1B.2.1), H3N2 (1990.4.a), and H1N1 (H1-1A.3.3.3-c3). Internal genes were classified as triple-reassortant (T) or pandemic 2009 (P), and three genome constellations represented 73.5% of detections across the last 2 years. In some years, the distribution of IAV diversity was so narrow that it presen...

  ABSTRACT Bats are the reservoir hosts of emerging coronaviruses (CoVs) affecting human and livestock health . We assessed the diversity, evolution, and geographic distribution of two alphacoronaviruses (subgenus Rhinacovirus ) with considerable potential for emergence : swine acute diarrhea syndrome coronavirus ( SADS-CoV ), which has caused large outbreaks in pigs in China and can infect primary human airway epithelial cells in vitro ; and the related Rhinolophus bat coronavirus HKU2 (HKU2-CoV). Phylogenetic analyses of 523 rhinacovirus sequences from bats in China and Southeast Asia suggest these viruses should be reclassified into at least two distinct CoV species representing two well-supported monophyletic clades. Stronger phylogenetic clustering by sampling location than by host species suggests infrequent long-distance transmission of rhinacoviruses in southern China. Ancestral state reconstruction analysis indicates that R. sinicus/thomasi and R. affinis have played an im...

Abstract Nipah virus (NiV) causes a severe neurological disease in humans . The first NiV outbreak, in Malaysia , involved pig-to-human transmission , that resulted in significant economic losses to the local pig industry. Despite the risk NiV poses to pig-dense regions, no licensed vaccines exist . This study therefore assessed three NiV vaccine candidates in pigs: (1) adjuvanted soluble NiV (s)G protein, (2) adjuvanted pre-fusion stabilised NiV (mcs)F protein, and (3) adenoviral vectored NiV G (ChAdOx1 NiV G). NiV sG induced the strongest neutralising antibody response , NiV mcsF induced antibodies best able to neutralise cell-cell fusion, whereas ChAdOx1 NiV G elicited CD8+ T-cell responses. Despite differences in immunogenicity, prime-boost immunisation with all candidates conferred a high degree of protection against NiV infection. Follow-up studies demonstrated longevity of immune responses and broadly comparable immune responses in Bangladeshi pigs under field conditions. These ...

Abstract The H1N1 swine influenza viruses CQ91 and CQ445, isolated from pigs in China, exhibited distinct virulence in mice despite sharing similar genomic constellations. CQ91 demonstrated higher pathogenicity (MLD50: 5.4 log10 EID50) and replication efficiency in mice compared to CQ445 (MLD50: 6.6 log10 EID50). Through reverse genetics, we found that the attenuation of CQ445 was due to a single substitution of glutamic acid (E) with lysine (K) at position 343 in the PB2 protein . Introducing the CQ445-PB2 (343K) into CQ91 significantly reduced viral replication and pathogenicity in mice, while replacing CQ445-PB2 with CQ91-PB2 (343E) restored virulence. In vitro studies showed that the K343E mutation impaired viral replication in MDCK and A549 cells and reduced polymerase activity in minigenome assays. Mechanistically, the amino acid at position 343 in the PB2 affects the transcription stage of the viral replication process . Structural modeling indicated that the charge reversal cau...

ABSTRACT H1 and H3 influenza A viruses (IAVs) circulating in European pigs are markedly distinct from those circulating in other global swine populations . These viruses exhibit significant genetic diversity , further expanded by periodic interspecies transmission of IAVs from humans into pigs , followed by sustained circulation. Several zoonotic IAV infections in humans in Europe have been associated with the 1C lineage of H1 IAVs . Given the predominance of H1 detections in pigs and their zoonotic potential, we quantified antigenic evolution of H1 viruses in European pigs using ferret and pig models and assessed diversity relative to swine IAV vaccine strains. Ferret and swine antisera comparisons revealed no significant differences in antibody responses . Viruses of the 1A.3.3.2 clade exhibited reduced cross-reactivity to human seasonal vaccine strains from 2009. Viruses of the 1B.1.2.2 clade showed no cross-reactivity to the 1978 human seasonal influenza viruses nor to candidate va...

Abstract The Eurasian avian-like swine (EA) H1N1 virus has been widely prevalent in the Chinese swine population and has caused infections in human . However, knowledge regarding its pathogenic mechanisms remains limited. In this study, we analyzed the pathogenic determinants of two G4 genotype EA H1N1 viruses (A/Swine/Guangdong/SS12/2017 and A/Swine/Jiangxi/1110/2017) with differing pathogenicity by constructing a series of reassortant and mutant viruses . The HA-G219A mutation was found to be determinant of pathogenicity in mice. Subsequent analyses revealed that this mutation enhances viral replication in human cells , improves thermal stability , reduces HA activation pH, and alters receptor-binding properties . Furthermore, HA-G219A mutation may be an adaptive mutation that facilitates influenza virus adaptation to swine , with its prevalence increasing in the swine population. This mutation may support cross-species transmission of EA H1N1 swine influenza viruses or genetic excha...

Abstract Since the first emergence of highly pathogenic avian influenza (HPAI) H5N1 viruses in dairy cattle , the virus has continued to spread, reaching at least 17 states and at least 950 dairy herds in the United States. Subsequently, spillovers of the virus from dairy cattle to humans have been reported. Pigs are an important reservoir in influenza ecology because they serve as a mixing vessel in which novel reassortant viruses with pandemic potential can be generated. Here, we show that oro-respiratory infection of pigs resulted in productive replication of a bovine-derived HPAI H5N1 B3.13 virus . Infectious virus was mainly identified in the lower respiratory tract of principal infected pigs, and sero-conversion was observed in most of the principal pigs at later time points, suggesting limited replication of the bovine-derived HPAI H5N1 B3.13 virus in pigs. In one animal, we detected the emergence of a mutation in hemagglutinin (HA) previously associated with increased affinity ...

Abstract Swine Influenza A Virus (IAV-S) poses a significant burden to both the pork industry and public health . Current vaccines against IAV-S are infrequently updated and induce strain-specific immunity. Computational platforms have recently emerged as a promising strategy to develop new-age vaccines. Here, we describe the Epigraph , a computationally derived and epitope optimized set of vaccine immunogens. When compared to wildtype immunogens (WT) and a commercial comparator (FluSure XP®), pigs immunized with Epigraph demonstrate significantly improved breadth and magnitude of antibody responses . Further, pigs immunized with Epigraph show more robust and a wider breadth of cross-reactive cell-mediated immune responses than pigs immunized with WT immunogens. In an experimental infection model , Epigraph immunized pigs demonstrate a significant reduction of clinical disease, lower shedding of infectious virus, reduction of lung lesions, and lower microscopic immunopathology compared...

Abstract Surveillance of influenza A viruses in pigs (SwIAV) is critical for identification of novel genetic groups that pose a risk to pig health and might have zoonotic potential . SwIAVs circulating in pigs in England between 2014 and 2021 were characterised using whole genome sequencing (WGS). Haemagglutinin (HA) and neuraminidase (NA) sequencing data from 82 of 368 influenza A positive samples (71 submissions) were determined, identifying H1N1 and H1N2 subtypes from the 1A classical swine and 1B human-seasonal lineages respectively. The 1B lineage viruses were predominant, accounting for 68.29% of sequenced viruses, with 1A lineage viruses comprising 31.71%, primarily from the 1A.3.3.2 clade (2009 H1N1 pandemic origin). This study characterised previously undefined diversity within the 1B lineage which led to the designation of new HA clades 1B.1.1.1, 1B.1.1.2 and 1B.1.1.3. Complete genome data were obtained from 64/82 viruses thereby updating the definition of genetic diversity t...

Abstract Educational farms provide students with hands-on experience in agricultural and animal practices . However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission , yet research on infectious diseases in such settings remains limited. This study investigates the ongoing spillovers of human-origin influenza A virus (IAV) into swine at an educational farm in central Chile , describing IAV prevalence, outbreak dynamics, and the genomic characterization of detected strains. The Menesianos educational farm, located in Melipilla, central Chile, houses approximately 40 swine alongside other domestic animals , such as horses and cows . As part of an active IAV surveillance project, monthly nasal swab samples were collected from pigs between June 2019 and September 2023 for IAV detection via RT-qPCR targeting the M gene, with positive samples subsequently sequenced. During the study period, monthly IAV prevalence ranged from ...

Abstract We detected influenza D virus in multiple swine herds in Northern Ireland . Whole-genome sequencing showed several circulating genotypes and novel mutations in the receptor-binding site and esterase domains of the hemagglutinin-esterase fusion protein. Transmission routes of influenza D virus to swine remain to be clarified but could be direct or indirect. Source: US Centers for Disease Control and Prevention,  https://wwwnc.cdc.gov/eid/article/31/5/24-1948_article ____

Abstract The spread of the highly pathogenic avian influenza (HPAI) H5N1 virus among dairy cattle illustrates the adaptability of influenza A viruses (IAV) to infect non-traditional species . While IAV-specific sialic acid (SA) receptors have been identified in the mammary glands of dairy cattle , their presence in pigs, sheep, goats, and alpacas has not been studied until now. The zoonotic transmission of HPAI H5N1 to dairy and poultry farm workers during outbreaks raises public health concerns . This study employed lectin histochemistry to examine the mammary glands of livestock and humans . We found that these tissues were rich in SA α2,6-Gal receptors, followed by SA α2,3-Gal receptors , essential for IAV binding . Notably, the A(H5N1) clade 2.3.4.4b virus could bind to mammary tissue from both cattle and pigs . These findings highlight the potential for HPAI H5N1 to infect and spread within the mammary glands of production animals and humans. Source: BioRxIV,  https://www.bior...

Highlights •  Scientific question :  Cross-species transmission of influenza A viruses from swine to humans occurs occasionally because their tracheal epitheliums possess both sialic acid α-2,6-Gal and α-2,3-Gal receptors . In 2011, the first human case of swine influenza virus infection in the mainland of China was detected in Jiangsu Province . Subsequently, the Eurasian avian-like H1N1 swine influenza virus (EAH1N1 SIV) had sporadically crossed the host barrier and infected humans, raising public concern for its pandemic potential. •  Evidence before this study :  A/Jiangsu/1/2011 (H1N1v) was first discovered in 2011 and belongs to the G1 genotype. The G4 and G5 genotypes that appeared successively in 2013 are recombinant H1N1 swine influenza viruses. The EAH1N1 SIVs from 2016 to the present are dominated by the G4 genotype, with hemagglutination (HA) and neuraminidase (NA) genes derived from the EAH1N1 SIVs, non-structural protein (NS) genes derived from the trip...

Highlights •  First isolation and molecular evidence of the subtype H3N2 in swine in Colombia . •  Swine H3N2 discovered is phylogenetically divergent from other viruses. •  Colombian H3N2 was originated from an independent human-to-swine spillover. •  Sequence-based analysis reveals this is a novel antigenic variant . •  Due to antigenic variation , Colombian H3N2 possess a relevant zoonotic risk. Abstract Influenza A virus (FLUAV) affects a wide range of hosts, including humans and animals, posing a threat to public health . In swine, H3N2 subtype is associated with human-to-swine spillovers of seasonal viruses . In Latin America , the molecular and antigenic characteristics of swine FLUAV H3N2, as well as its phylogenetic origin, are poorly understood. Therefore, the objective of this study was to characterize the first swine H3N2 detected in Colombia . The origin and lineage of the virus were estimated through phylogenetic and molecular clock analyses . Anti...

Abstract Since the first emergence of highly pathogenic avian influenza (HPAI) H5N1 viruses in dairy cattle , the virus has continued to spread, reaching at least 16 states and at least 950 dairy herds in the United States . Subsequently, spillovers of the virus from dairy cattle to humans have been reported. Pigs are an important reservoir in influenza ecology because they serve as a mixing vessel in which novel reassortant viruses with pandemic potential can be generated. Here, we show that oro-respiratory infection of pigs resulted in productive replication of a bovine-derived HPAI H5N1 B3.13 virus. Infectious viruses were mainly identified in the lower respiratory tract of principal infected pigs, and sero-conversion was observed in most of the principal pigs at later time points. In one animal, we detected the emergence of a mutation in hemagglutinin (HA) previously associated with increased affinity for mammalian-type alpha 2,6-linked sialic acid receptors , but this mutation did...

Abstract In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark . The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27% of swIAVs identified through the Danish passive swIAV surveillance program . Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an entire internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin . The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source , a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swi...

Abstract Vaccination is a common influenza A virus (IAV) control strategy for pigs. Vaccine efficacy depends on strain cross-protection and effective vaccination program implementation. We evaluated a multi-faceted IAV vaccination strategy which included (a) monthly surveillance of pigs at weaning , (b) selection of epidemiologically relevant strains from farms under surveillance, (c) updating IAV strains in custom-made vaccines, and (d) seasonal mass vaccination with custom-made vaccines given to sows in 35 farrow-to-wean farms within an integrated swine farm system. Reduction of IAV in pigs from vaccinated sows was determined by monthly monitoring of farms for 30 months by IAV rRT-PCR (PCR) testing of nasal wipes collected from litters of piglets at weaning. Hemagglutinin (HA) nucleotide and amino acid (AA) sequence homology of the circulating and vaccine strains was determined by pairwise alignment and AA comparison at antigenic sites. Of the 35 farms monitored, 28 (80%) tested posi...

Abstract Influenza A viruses (IAV) are likely candidates for pandemics . This report summarizes the results of the Swiss national program for surveillance of influenza viruses in pigs and transmissions to humans between 2010 and 2022. Challenges and optimization options in the program are discussed. Nasal swabs or lung tissue samples from pigs with influenza-like signs (e.g. fever, cough) were screened by real-time RT-PCR for swine influenza virus (SIV) genomes, including that of the 2009 pandemic strain A(H1N1)pdm09; positive samples were subtyped for H1, N1, H3 and N2 by RT-PCR and Sanger sequencing. In parallel, humans with influenza-like symptoms and recent contact to diseased pigs were asked to self-sample themselves with a nasal swab. Human swabs were tested for IAV and positive swabs further subtyped to identify potential cross-species transmission between swine and humans. In the pigs, SIV was detected in 375 of 674 farm visits . H1N1 is the only subtype detected in Swiss pigs ...