The role of influenza virus gene constellation and viral morphology on cytokine induction, pathogenesis, and viral virulence.

Key Messages 1. H5N1 viruses that cause severe disease in humans are potent inducers of proinflammatory cytokines in contrast to seasonal influenza viruses, and this may play a role in the mechanism of H5N1 pathogenesis. 2. H5N1 viruses are predominantly spherical in morphology. Virus morphology does not influence the ability to induce proinflammatory cytokines. 3. The NS1 viral protein may play a role in the potency of proinflammatory induction. 4. The H5N1 haemagglutinin and neuraminidase do not appear to transfer the high cytokine phenotype. 5. The ability to induce cytokines is a polygenic trait, involving a combination of different viral genes.published_or_final_versio

MOLECULAR PATHOGENESIS OF INFLUENZA IN SWINE AND ENGINEERING OF NOVEL RECOMBINANT INFLUENZA VIRUSES

Influenza A viruses (IAVs) belong to the family Orthomyxoviridae and represent major pathogens of both humans and animals. Swine influenza virus is an important pathogen that affects not only the swine industry, but also represents a constant threat to the turkey industry and is of particular concern to public health. In North America, H3N2 triple reassortant (TR) IAVs first emerged in 1998 and have since become endemic in swine populations. In the first part of this dissertation, we focused on the role of surface glycoproteins and PB1-F2 to unravel their roles in the virulence of TR IAVs in this important natural host. We found that surface glycoproteins are necessary and sufficient for the lung pathology, whereas the internal genes play a major role in the febrile response induced by TR H3N2 IAVs in swine. With respect to PB1-F2, we found that PB1-F2 exerts pleiotropic effects in the swine host, which are expressed in a strain-dependent manner. Pathogenicity studies in swine revealed that the presence of PB1-F2 leads the following effects in context of three TR strains tested: no effect in the context of sw/99 strain; increases the virulence of pH1N1; and decreases the virulence of ty/04. Next, we developed temperature-sensitive live attenuated influenza vaccines for use in swine and shown that these vaccines are safe and efficacious against aggressive intratracheal challenge with pH1N1. Lastly, we rearranged the genome of an avian H9N2 influenza virus to generate replication competent influenza virus vectors that provide a robust system for expression and delivery of foreign genes. As a proof-of-principle, we expressed the hemagglutinin from a prototypical highly pathogenic avian influenza virus (HPAIV) H5N1 and shown that this vectored H5 vaccine retained its safety properties in avian and mammalian species, and induced excellent protection against aggressive HPAIV H5N1 challenges in both mice and ferrets. Taken together, these studies have advanced our understanding of molecular basis of pathogenesis of influenza in the swine host and have contributed to the development of improved vaccines and influenza-based vectors with potential applications in both human and veterinary medicine

Influenza A virus Genomic Reassortment and Packaging

Influenza A viruses (IAV) are a major human and environmental pathogen. IAV successfully infects a diverse host range and adaptation of new viral strains to humans may cause pandemic events with high morbidity and mortality. As a member of the Orthomyxoviridae family, IAV inherently possesses a segmented genome, which enables a process of segment transmission between viruses following cellular co-infection, a process termed reassortment. The high rate of IAV mutation and continued co-circulation of diverse viral strains in divergent host species leads to the persistent prospect for emergence of new IAV with pandemic potential. Therefore, it is of great importance to understand the viral and host factors that restrict and promote the generation of emergent virus strains, their potential for pathogenesis, and discover novel mechanistic countermeasures against IAV, including improved vaccination and targeted therapeutic strategies. Human and avian IAV co-circulate and occasionally co-infect the same host, leading to the potential for generation of novel genome constellations following reassortment. The specific host and viral molecular determinants that allow replication of reassortant progeny virus are not well defined. Here, I show that the viral genetic context and host cell in which reassortment occurs determine the potential for genetic diversity derived from multiple distantly related strains. Importantly, we identify single gene reassortants between a North American avian strain and the 2009 pandemic H1N1 virus that are capable of causing disease in mammals and replicate in a human cell line as well as induce the production of several pro-inflammatory cytokines linked to severe disease outcomes. Additionally, utilizing a different viral genetic background, I show that the reassortment potential is regulated by species and cell type specific differences in viral replication due to augmented viral polymerase function dependent on the identity of a single amino acid in the PA protein. Together, these studies provide evidence that context- dependent compatibility between both viral and host factors determine the possibility for generation of novel reassortant genome constellations and regulate their potential for replication and transmission in new host species. Reassortment between IAV strains is likely dictated by the functional compatibility of vRNA segments bound by IAV nucleoprotein during genome packaging. I hypothesized that nucleoprotein (NP) scaffolds specific RNA elements that are required for genome packaging and interaction between viral RNA (vRNA) genome segments. Therefore, I sought to determine the functional consequences of genome architecture on genome packaging and for the first time determine the nucleotide-resolution landscape of NP-vRNA interactions in infected cells. We utilized Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) coupled to next-generation sequencing to determine the specific interaction sites of vRNA bound by NP. We then interrogated the functional importance of regions of vRNA bound or unbound by NP and identified a number of potentially structured RNA features required for efficient genome packaging and virus propagation. These studies provide a framework for understanding the multifactorial restrictions of IAV reassortment and potential for generation of novel genome constellations with pandemic potential. Finally, these studies expand our understanding of how viral and host determinants shape the possible evolutionary trajectories of IAV through reassortment and required genetic elements needed for genome assembly

Host adaptation and transmission of influenza A viruses in mammals

A wide range of influenza A viruses of pigs and birds have infected humans in the last decade, sometimes with severe clinical consequences. Each of these so-called zoonotic infections provides an opportunity for virus adaptation to the new host. Fortunately, most of these human infections do not yield viruses with the ability of sustained human-to-human transmission. However, animal influenza viruses have acquired the ability of sustained transmission between humans to cause pandemics on rare occasions in the past, and therefore, influenza virus zoonoses continue to represent threats to public health. Numerous recent studies have shed new light on the mechanisms of adaptation and transmission of avian and swine influenza A viruses in mammals. In particular, several studies provided insights into the genetic and phenotypic traits of

DIFFERENTIAL INNATE IMMUNE RESPONSES CORRELATE WITH THE CONTRASTING PATHOGENICITY OF THE EQUINE H7N7 INFLUENZA VIRUS DEMONSTRATED IN HORSES AND BALB/C MICE

Equine influenza virus causes a mild, self-limiting upper respiratory disease in its natural host. In stark contrast, equine influenza viruses of the H7N7 subtype produce lethal infection in BALB/c mice. This dissertation explored the mechanism underlying the differential pathogenicity of the equine H7N7 influenza virus observed in horses and BALB/c mice. Initially, a comparative study of the pathogenesis was conducted in BALB/c mice inoculated intranasally with a representative isolate of either H7N7 or H3N8 subtype equine influenza virus. All H3N8 virus-infected mice survived the infection whereas 100% mortality was documented for the mice receiving the H7N7 virus by day 8 post infection. Both viruses replicated to a similar degree in the lungs at the early stages of infection. However, after day 2 post infection until the death of the mice, the pulmonary viral loads of the H7N7 group were significantly higher than those of the control, whereas the H3N8 virus was eventually eradicated from the mice at day 7 p.i. Correspondingly, a vigorous pro-inflammatory cytokine response in the lung was induced by the H7N7 virus but not the H3N8 virus, which reflected a desperate attempt by the host immune responses to restrain the overwhelming infection. The H7N7 virus was poorly sensitive to the innate immune containment, resulting in a significant higher cumulative mortality rate than that of the control virus in chicken embryos aged 9 days and older. On the contrary, in horses, replication of the paired viruses was completely cleared by the host immune responses at day 7 p.i. and the infections produced an acute yet non-lethal illness, albeit the H3N8 virus induced generally more pronounced clinical manifestations than the H7N7 virus. The clinical severity correlated to the difference in cytokine-inducing capacity between the two viruses in horses, as evidenced by the finding that the H3N8 virus triggered significantly higher levels of gene transcription of multiple key inflammatory cytokines in the circulation than those seen for the H7N7 virus. In addition, equine peripheral monocyte-derived macrophages were found to be a target of equine influenza virus and can support the productive replication of the virus in vitro

Virology

Reconstruction of the 1918 influenza virus has facilitated considerable advancements in our understanding of this extraordinary pandemic virus. However, the benefits of virus reconstruction are not limited to this one strain. Here, we provide an overview of laboratory studies which have evaluated the reconstructed 1918 virus, and highlight key discoveries about determinants of virulence and transmissibility associated with this virus in mammals. We further discuss recent and current pandemic threats from avian and swine reservoirs, and provide specific examples of how reconstruction of the 1918 pandemic virus has improved our ability to contextualize research employing novel and emerging strains. As influenza viruses continue to evolve and pose a threat to human health, studying past pandemic viruses is key to future preparedness efforts.CC999999/ImCDC/Intramural CDC HHSUnited States/2022-04-25T00:00:00Z30142572PMC90365381148

Polymerase basic protein 1 (PB1) as a molecular determinant of fitness and adaptation in influenza a virus

Tese de doutoramento, Farmácia (Microbiologia), Universidade de Lisboa, Faculdade de Farmácia, 2017The World Health Organization and the National Institute of Allergy and Infectious Diseases reported growth deficits of influenza A(H1N1)pdm09 reverse genetic pandemic vaccine virus seeds. These have compromised the effective and timely distribution of vaccines in the 2009 pandemics and accentuated the need to improve the process of vaccine production. In pre-pandemic A(H5N1) research, seed viruses produced by reverse genetics have also been reported to present growth deficits. These deficits have been attributed to a putative sub-optimal protein interaction. The dynamics of the genetic evolution of influenza A viruses appears to suggest a gene segregation pattern between the Polymerase Basic protein 1 (PB1) and antigenic proteins Hemagglutinin (HA) and Neuraminidase (NA). In the reassortment events that lead to the emergence of the 1957 e 1968 pandemic viruses, the contemporary seasonal viruses acquired PB1 genomic segment together with antigenic glycoproteins originating from avian viruses. A similar pattern was identified in 1947, where a reassortment event between seasonal viruses, involving PB1 and antigenic proteins, has altered the epidemiology of the infection to a near-pandemic geographic dispersion. In both situations, viral fitness appears to have benefitted from acquiring a PB1 genomic segment homologous to antigenic proteins. Also, in retrospective studies on the genomic composition of high yield seasonal vaccine seeds produced by classical reassortment, PB1 is frequently co-incorporated with antigenic proteins HA and NA, further suggesting that the interaction between these proteins could have an impact in viral fitness. In this context, we proposed to address the question of PB1 genomic segment being a molecular determinant of fitness and adaptation in influenza A virus and, particularly, of the functional compatibility between PB1 and antigenic proteins being a driver of the overall viral fitness and putatively exploitable to improve seed virus production. The A(H1N1)pdm09 virus was used a model for this research because it is a product of viral reassortment with an unprecedented genomic composition of segments originating from avian, swine and human seasonal viruses. Additionally, the 2009 pandemic vaccine virus presented severe growth deficits and, since the A(H1N1)pdm09 persists in circulation with a seasonal epidemiologic profile, the demand for high yield A(H1N1)pdm09 vaccine seeds will be continuous and the need to adequate the immunogenic strain to the circulating viruses will be recurrent because of antigenic drifts. The objectives of this research were defined as 1) to evaluate the genetic evolution of PB1 in the zoonotic transmission of swine influenza virus and infer its putative contribution towards viral fitness and adaptation, and 2) to determine if the functional or structural compatibility between PB1 and antigenic proteins is a molecular determinant of the overall virus fitness in the reverse genetics A(H1N1)pdm09 vaccine seed model. The approach followed to accomplish objective 1 was to select a study sample of PB1 nucleotide sequences from swine virus that have infected the human host, to analyze phylogeny and mutation trends and to search for putative markers for viral adaptation on the basis of viral molecular epidemiology, genomic location of the polymorphisms and amino-acid properties. Our major findings were that the evolutionary history of PB1 is traceable in terms of lineage and host origin. Specific genomic markers in PB1 appear to putatively relate to the viral adaptation to mammalian hosts, 336I, 361R, 468K and 584Q, and to the viral adaptation to new genomic backgrounds possibly in the sequence of reassortment events, such as 638D and 618D. Residues 298I, 386K and 517V have been found to putatively relate to an enhanced compatibility between PB1 and HA of the H1 subtype, in the mammalian host. A subsequent in vitro investigation of the phenotypic impact of mutations L298I, R386K and I517V acquired by the A(H1N1)pdm09 during its evolutionary history, was performed by generating an A(H1N1)pdm09 recombinant virus and an A(H1N1)pdm09 reassortant in which the specific mutations have been reverted, by reverse genetics. This approach has resulted in two major findings. Acquiring these mutations has been found to putatively promote conformational changes in PB1 and enhance the span of complementary nucleotides possibly involved in PB1 interaction with HA at the RNA level and, on the other hand, has proven detrimental to viral growth kinetics in vitro. These findings have lead us to suggest that the interaction between genomic segments at the RNA level could be a determinant of co-segregation, concordant with a selective packaging model proposed by other authors, but that the mechanisms that drive this process are probably not dependent on a replicative advantage. Our approach to accomplishing objective 2) to determine if the functional or structural compatibility between PB1 and antigenic proteins is a molecular determinant of the overall virus fitness in the reverse genetic A(H1N1)pdm09 vaccine seed model, was to determine the genetic profile of A(H1N1)pdm09 strains circulating in Portugal during the pandemic period and select a prototype immunogenic strain, to generate reassortant viruses with the genomic composition of A(H1N1)pdm09 seed viruses prototypes bearing PB1 homologous and heterologous to antigenic proteins, and to evaluate viral growth and antigen yield in vitro. A sample of specimens collected from the pandemic period in Portugal were evaluated for genetic and phenotypic features and a strain similar to the consensus was selected as a prototype strain. Vaccine seed prototypes of the selected A(H1N1)pdm09 strain in an A/PuertoRico/08/34 backbone were generated by reverse genetics to present the genomic compositions of the 6:2 classical vaccine seed (PR8:HA,NA A(H1N1)pdm09) and a 5:3 seed prototype in which the PB1 segment from the immunogenic strain is co-incorporated with the antigenic proteins (PR8:HA,NA,PB1 A(H1N1)pdm09). Our major findings were that the presence of PB1 homologous to antigenic protein significantly increased viral replication, hemagglutination capacity and Neuraminidase activity. We have establishing proof of concept that, in the PR8:A(H1N1)pdm09 seed virus model, viral growth and antigen yield can be significantly improved by the inclusion of PB1 from the immunogenic strain when compared to the classical seed virus prototype. We consider that, additionally to the role of PB1 protein in viral replication, PB1 genomic segment may be a molecular determinant of the overall virus fitness and a determinant factor in the molecular epidemiology of the viruses by establishing interactions with other segments at the RNA level and by, apparently, being able to genetically change and adapt to improve these interactions. Further research is necessary to clarify the mechanisms of viral genome packaging, the role of interactions at the RNA level in establishing the co-segregation patterns and the specificities of this interactions at the subtype level. However, it becomes clear that the functional compatibility between PB1 and antigenic proteins is a driver of the overall viral fitness in the A(H1N1)pdm09 and is putatively exploitable to improve seed virus production. We also consider that exploring the concept of the compatibility between gene segments or proteins being a determinant factor in the overall viral fitness, can result in major improvements in the production of reverse genetics seed viruses of different influenza subtypes. Also, being aware of the fact that the genomic composition of influenza viruses can have a major phenotypic impact, and that consequently is a determinant of virulence even though the mechanisms that drive the selective packaging remain unclear, we consider that its inclusion in the risk assessment of influenza strains would be extremely relevant for seasonal and pandemic preparedness

Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus

Public health risks associated to infection by human coronaviruses remain considerable and vaccination is a key option for preventing the resurgence of severe acute respiratory syndrome coronavirus (SARS-CoV). We have previously reported that antibodies elicited by a SARS-CoV vaccine candidate based on recombinant, full-length SARS-CoV Spike-protein trimers, trigger infection of immune cell lines. These observations prompted us to investigate the molecular mechanisms and responses to antibody-mediated infection in human macrophages.published_or_final_versio

Role and Importance of NS1 Protein of Avian Influenza Virus to Grow in the Presence of Interferon and Evaluation of the NS1 Mutant Viruses as Potential DIVA Vaccines

A proper vaccination program can play a critical role in prevention and control of avian influenza (AI) in commercial poultry. Low pathogenic avian influenza viruses (LPAIV) of H5 and H7 AI subtypes cause serious economic losses to the poultry industry and have the potential to mutate to highly pathogenic AI (HPAI) strains. Due to trade implications, differentiation of infected from vaccinated animals (DIVA) is an important issue in the control of AI. Therefore, the development and characterization of vaccine candidates with DIVA properties is critical in improving vaccination programs. Keeping these aspects in mind, we investigated the role of an NS1 mutant virus as a potential live attenuated DIVA vaccine. The NS1 protein of influenza virus plays a major role in blocking the host's antiviral response. Using an eight-plasmid reverse genetics system, we recovered the low pathogenic parental (H5N3) and NS1 mutant (H5N3/NS1/144) viruses. H5N3/NS1/144 expresses only the first 144 amino acids of the NS1 protein compared to the 230 of the parental H5N3. The growth properties of H5N3 and H5N3/NS1/144 were compared in cell culture and in different age embryonated chicken eggs. Our results confirmed that NS1 is involved in down regulation of interferon as shown by IFN-beta mRNA expression analysis and by the inability of H5N3/NS1-144 to efficiently grow in older age, interferon competent, chicken embryos. However with regards to safety the virus reverted to virulence within five back passages in chickens and was therefore not a safe vaccine candidate. However the killed form of H5N3/NS1-144 was a safer alternative and it also induced antibody titers and protection not significantly different from the parental H5N3 as vaccine. To further understand the reversion of H5N3/NS1/144 to virulence, we carried out 3 independent serial passages of H5N3/NS1/144 in increasing age of embryonated chicken eggs and examined the NS1 gene for presence of mutations. RT-PCR and sequence analysis of the NS gene in all three lineages showed the presence of a 54 amino acid deletion resulting in the generation of a 87 amino acids long NS1 ORF with a point mutation (L80V) at the site of deletion. In addition, the NS1 ORF in lineages L2 and L3 presented two additional point mutations in the RNA binding domain (Q40R and T73M). To determine if these mutations played a role in increased virulence, recombinant viruses expressing these mutant NS1 proteins in the background of parental virus were generated by reverse genetics and their replication properties and pathogenicity was examined in vitro, in ovo and in vivo systems. Our results showed that the 87 amino acid long NS1 protein clearly increased virus replication and virulence specifically in interferon competent systems. In addition, the two point mutations in the RNA binding domain of NS1 ORF expressing 87 a protein slightly increased the virus virulence. Overall this study reinforces the role of NS1 in influenza virus pathogenicity and supports the use of killed inactivated NS1 mutant virus vaccines as potential DIVA vaccines

Investigating the mechanisms of influenza polymerase host adaptation

An avian virus can become adapted to humans by mutating or recombining with currently circulating human viruses. These viruses have the potential to cause pandemics in an immunologically naïve human population. Host restriction involves multiple determinants, however, influenza polymerase is considered to play an important role. The heterotrimeric polymerase complex (PA, PB1 and PB2) associates with viral RNA and nucleoprotein (NP) to form a ribonucleoprotein (RNP) complex responsible for viral replication and transcription. Host specific genetic signatures have been identified on all of the polymerase subunits and on NP, but the PB2 protein arguably carries the dominant determinants of host range. Avian-origin influenza polymerase activity can be dramatically increased in human cells with the PB2 E627K substitution. This has been suggested to stabilise the interaction between the NP and PB2 components of the vRNP complex in the nuclei of infected cells. However, we demonstrate that a variety of adaptive PB2 substitutions including E627K did not enhance the stability of the vRNP in human cells, but rather increased the amount of replicated RNA, and that resulted in more PB2-NP co-precipitation. The introduction of many adaptive PB2 mutations enhances avian influenza polymerase activity in an in vitro reconstituted polymerase assay. However, only some of these mutations have been detected in viruses that are found circulating in nature. We explored whether the polymerase assay truly predicts viral growth and investigated viral selection pressures that might favour some adaptive mutations over others. We used reverse genetics to create a series of viral variants carrying mutations in the PB2 gene and carried out virological assays and also analysed the effects of the mutations in vivo. Some mutations that increased in vitro polymerase activity led to attenuated virus replication and resulted in an increase in interferon activation. These data increase our understanding of the host range barrier and why certain adaptive mutations may or may not have emerged.Open Acces