Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken

The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host–virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.

Avian Influenza H7N9 Virus Adaptation to Human Hosts

Avian influenza virus A (H7N9), after circulating in avian hosts for decades, was identified as a human pathogen in 2013. Herein, amino acid substitutions possibly essential for human adaptation were identified by comparing the 4706 aligned overlapping nonamer position sequences (1–9, 2–10, etc.) of the reported 2014 and 2017 avian and human H7N9 datasets. The initial set of virus sequences (as of year 2014) exhibited a total of 109 avian-to-human (A2H) signature amino acid substitutions. Each represented the most prevalent substitution at a given avian virus nonamer position that was selectively adapted as the corresponding index (most prevalent sequence) of the human viruses. The majority of these avian substitutions were long-standing in the evolution of H7N9, and only 17 were first detected in 2013 as possibly essential for the initial human adaptation. Strikingly, continued evolution of the avian H7N9 virus has resulted in avian and human protein sequences that are almost identical. This rapid and continued adaptation of the avian H7N9 virus to the human host, with near identity of the avian and human viruses, is associated with increased human infection and a predicted greater risk of human-to-human transmission.

Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 16 million infections and more than 600,000 deaths worldwide. There is an urgent need to develop a safe and effective vaccine against SARS-CoV-2. Currently, several strategies are being pursued to develop a safe and effective SARS-CoV-2 vaccine. However, each vaccine strategy has distinct advantages and disadvantages. Therefore, it is important to evaluate multiple vaccine platforms to select the most efficient vaccine platform for SARS-CoV-2. In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Here, we elaborate on the idea of considering NDV as a vaccine vector for SARS-CoV-2.

Avian Bornaviral Ganglioneuritis: Current Debates and Unanswered Questions

Avian bornaviral ganglioneuritis, often referred to as parrot wasting disease, is associated with a newly discovered avian virus from the taxonomic family Bornaviridae. Research regarding the pathogenesis and treatment for this disease is ongoing, with implications for understanding other emerging human and nonhuman diseases, as well as the health and ecology of wildlife. At this time, numerous questions remain unanswered regarding the transmission of the disease, best practices for diagnostic sampling and testing, and whether currently used drug therapies are effective or harmful for afflicted birds. The pathogenesis of the disease also remains unclear with many birds showing resistance to the effects of the virus and being able to remain clinically unaffected for years, while other birds succumb to its effects. New research findings regarding avian bornaviral ganglioneuritis are discussed and important as yet unanswered questions are identified.

Identification of a Divergent Avian Influenza H3N2 Virus from Domestic Ducks in France

An avian influenza H3N2 virus was isolated from domestic ducks in France in 2016. Although this French H3N2 virus possesses traits of an avian virus, the genetic distances observed for hemagglutinin (HA) and neuraminidase (NA) show that these two genes most likely evolved independently from other avian influenza sequences.

Influenza A virus avian-derived PB1 gene has evolved to match its codon usage to interferon-altered human tRNA pools

Influenza A viruses cause an annual highly contagious respiratory disease in humans, and are responsible for periodic human pandemics that have high mortality rates. Pandemic influenza A viruses can result from reassortment of one or more gene segments between a human and an avian virus. These avian virus gene segments need to adapt to humans post introduction. The role of synonymous mutations in this adaptation is not known. Here we focus on the human adaptation of the synonymous codons of the avian virus PB1 gene of the 1968 H3N2 pandemic virus. We generate recombinant H3N2 viruses differing only in codon usage of PB1 mRNA, and demonstrate that the codon usage of recent virus isolates enhances replication in interferon-treated human cells rather than in untreated cells, thereby partially alleviating the interferon-induced antiviral state. High-throughput sequencing of tRNA pools explains this virus phenotype: the levels of some tRNAs differ between interferon-treated and untreated human cells; and the codon usage of H3N2 PB1 mRNA has been evolving over time to match the tRNA pools in interferon-treated human cells. Consequently, our results identify a previously unknown mechanism by which influenza A virus counteracts the host interferon-induced antiviral response and highlight the important role of tRNA pools in the regulation of gene expression.

Influenza A virus avian-derived PB1 gene has evolved to match its codon usage to interferon-altered human tRNA pools

Influenza A viruses cause an annual highly contagious respiratory disease in humans, and are responsible for periodic human pandemics that have high mortality rates. Pandemic influenza A viruses can result from reassortment of one or more gene segments between a human and an avian virus. These avian virus gene segments need to adapt to humans post introduction. The role of synonymous mutations in this adaptation is not known. Here we focus on the human adaptation of the synonymous codons of the avian virus PB1 gene of the 1968 H3N2 pandemic virus. We generate recombinant H3N2 viruses differing only in codon usage of PB1 mRNA, and demonstrate that the codon usage of recent virus isolates enhances replication in interferon-treated human cells rather than in untreated cells, thereby partially alleviating the interferon-induced antiviral state. High-throughput sequencing of tRNA pools explains this virus phenotype: the levels of some tRNAs differ between interferon-treated and untreated human cells; and the codon usage of H3N2 PB1 mRNA has been evolving over time to match the tRNA pools in interferon-treated human cells. Consequently, our results identify a previously unknown mechanism by which influenza A virus counteracts the host interferon-induced antiviral response and highlight the important role of tRNA pools in the regulation of gene expression.

Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity

ABSTRACTTwo alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types. Exemplar reassortant viruses also replicated to similar titers in mice, although mice infected with viruses with the avian virus-derived segment 8s had reduced weight loss compared to that achieved in mice infected with the A/Puerto Rico/8/1934 (H1N1) parent.In vitro, the viruses coped similarly with type I interferons. Temporal proteomics analysis of cellular responses to infection showed that the avian virus-derived NS segments provoked lower levels of expression of interferon-stimulated genes in cells than wild type-derived NS segments. Thus, neither the A nor the B allele of avian virus-derived NS segments necessarily attenuates virus replication in a mammalian host, although the alleles can attenuate disease. Phylogenetic analyses identified 32 independent incursions of an avian virus-derived A allele into mammals, whereas 6 introductions of a B allele were identified. However, A-allele isolates from birds outnumbered B-allele isolates, and the relative rates ofAves-to-Mammaliatransmission were not significantly different. We conclude that while the introduction of an avian virus segment 8 into mammals is a relatively rare event, the dogma of the B allele being especially restricted is misleading, with implications in the assessment of the pandemic potential of avian influenza viruses.IMPORTANCEInfluenza A virus (IAV) can adapt to poultry and mammalian species, inflicting a great socioeconomic burden on farming and health care sectors. Host adaptation likely involves multiple viral factors. Here, we investigated the role of IAV segment 8. Segment 8 has evolved into two distinct clades: the A and B alleles. The B-allele genes have previously been suggested to be restricted to avian virus species. We introduced a selection of avian virus A- and B-allele segment 8s into human H1N1 and H3N2 virus backgrounds and found that these reassortant viruses were fully competent in mammalian host systems. We also analyzed the currently available public data on the segment 8 gene distribution and found surprisingly little evidence for specific avian host restriction of the B-clade segment. We conclude that B-allele segment 8 genes are, in fact, capable of supporting infection in mammals and that they should be considered during the assessment of the pandemic risk of zoonotic influenza A viruses.