Detection and Characterization of Swine Origin Influenza A(H1N1) Pandemic 2009 Viruses in Humans following Zoonotic Transmission

Abstract

Human-to-swine transmission of seasonal influenza viruses has led to sustained human-like influenza viruses circulating in the United States swine population. While some reverse zoonotic-origin viruses adapt and become enzootic in swine, nascent reverse zoonoses may result in virus detections that are difficult to classify as ‘swine-origin’ or ‘human-origin’ due to the genetic similarity of circulating viruses. This is the case for human-origin influenza A(H1N1) pandemic 2009 (pdm09) viruses detected in pigs following numerous reverse zoonosis events since the 2009 pandemic. We report the identification of two human infections with A(H1N1)pdm09 viruses originating from swine hosts and classify them as ‘swine-origin’ variant influenza viruses based on phylogenetic analysis and sequence comparison methods. Phylogenetic analyses of viral genomes from two cases revealed these viruses were reassortants containing A(H1N1)pdm09 HA and NA genes with genetic combinations derived from the triple reassortant internal gene cassette. Follow-up investigations determined that one individual had direct exposure to swine in the week preceding illness onset, while another did not report swine exposure. The swine-origin A(H1N1) variant cases were resolved by full genome sequence comparison of the variant viruses to swine influenza genomes. However, if reassortment does not result in the acquisition of swine-associated genes and swine virus genomic sequences are not available from the exposure source future cases may not be discernible. We have developed a pipeline that performs maximum likelihood analyses, a k-mer-based set difference algorithm, and random forest algorithms to identify swine-associated sequences in the hemagglutinin gene to differentiate between human-origin and swine-origin A(H1N1)pdm09 viruses. IMPORTANCE Influenza virus infects a wide range of hosts resulting in illnesses that vary from asymptomatic cases to severe pneumonia and death. Viral transfer can occur between human and non-human hosts resulting in human and non-human origin viruses circulating in novel hosts. In this work, we have identified the first case of a swine-origin influenza A(H1N1)pdm09 virus resulting in a human infection. This shows that as these viruses not only circulate in swine hosts, but are continuing to evolve and distinguish themselves from previously circulating human-origin influenza viruses. The development of techniques for distinguishing human-origin and swine-origin viruses are necessary for the continued surveillance of influenza viruses. We show that unique genetic signatures can differentiate circulating swine-associated strains from circulating human-associated strains of influenza A(H1N1)pdm09, and these signatures can be used to enhance surveillance of swine-origin influenza.

Pathogenesis and transmission of human seasonal and swine-origin A(H1) influenza viruses in the ferret model

“…Genotypic analysis revealed that both viruses had genes derived from A(H1N1)pdm09 virus; PA, NP, and MP in case of OH/24 and PB2, PB1, NP, and MP in case of Alberta/1 ( Figure 1 ). A/Michigan/288/2019 (MI/288) A(H1N1)v virus was previously phylogenetically classified as alpha lineage (1A.3.3.2) [ 15 ], while the HA and NA of this virus clustered with contemporary human A(H1N1)pdm09 viruses (clade 6B.1A) and swine IAVs from the USA; all of the internal protein coding vRNAs were similar to swine viruses circulating in the USA ( Figure 1 ). The PB1 and PA genes clustered with those of the A/swine/Texas/4199-2/1998 virus used in a commercial, live-attenuated swine vaccine in the USA.…”

“…Ferret immune sera were harvested 14 days post intranasal inoculation with 6 log 10 50% egg infectious dose (EID 50 ) of virus. Two-way hemagglutination inhibition (HI) assay was used to assess cross-reactivity between different virus strains and pooled human sera (with human subject research approval [ 14 ]) as previously described [ 15 ]. Briefly, each serum sample was treated at a 1:4 dilution with receptor-destroying enzyme (RDE, Denka Seiken) for 18 h at 37°C.…”

Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus Infection

“…Influenza A virus (IAV) infection causes severe respiratory symptoms and persistent morbidity as well as mortality during annual seasonal or pandemic outbreaks, resulting in a severe threat to public health and safety, and even huge economic burden (1). Over the past decade, influenza outbreaks and pandemics have been caused by different subtypes of IAV, including H1N1, H3N2, swine-origin H1N1, and highly pathogenic avian influenza viruses (2)(3)(4), suggesting that the deeper biologic and epidemiologic mechanisms should be revealed to confidently and accurately predict the next influenza outbreak. Accumulative evidence has shown that IAV is capable of eliciting cellular immune response thought changing the expression of multiple genes in diverse types of cells, which in turn inhibit IAV infection.…”

Influenza A Viruses and Zoonotic Events—Are We Creating Our Own Reservoirs?

“…Since the beginning of the 20th century, zoonotic spillover events have given rise to the generation of multiple, well-documented pandemic IAVs [3][4][5]. Intensification of animal husbandry, increasing encroachment into wildlife habitats for agricultural use, and increased connectivity of livestock populations through (transboundary) trade, created favorable conditions that are associated with the establishment of new IAV lineages in these reservoirs but also created new interfaces for human infections [6][7][8][9][10][11]. Some examples include the 2009 pandemic swine influenza virus [12] and an increasing number of reported zoonotic spillover infections with avian IAVs (AIVs) from poultry [13,14].…”