Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals

Influenza A virus coinfection dynamics are shaped by distinct virus-virus interactions within and between cells

When multiple viral populations propagate within the same host environment, they often shape each other's dynamics. These interactions can be positive or negative and can occur at multiple scales, from coinfection of a cell to co-circulation at a global population level. For influenza A viruses (IAVs), the delivery of multiple viral genomes to a cell substantially increases burst size. However, despite its relevance for IAV evolution through reassortment, the implications of this positive density dependence for coinfection between distinct IAVs has not been explored. Furthermore, the extent to which these interactions within the cell shape viral dynamics at the level of the host remains unclear. Here we show that, within cells, diverse coinfecting IAVs strongly augment the replication of a focal strain, irrespective of their homology to the focal strain. Coinfecting viruses with a low intrinsic reliance on multiple infection offer the greatest benefit. Nevertheless, virus-virus interactions at the level of the whole host are antagonistic. This antagonism is recapitulated in cell culture when the coinfecting virus is introduced several hours prior to the focal strain or under conditions conducive to multiple rounds of viral replication. Together, these data suggest that beneficial virus-virus interactions within cells are counterbalanced by competition for susceptible cells during viral propagation through a tissue. The integration of virus-virus interactions across scales is critical in defining the outcomes of viral coinfection.

Influenza A virus reassortment is strain dependent

RNA viruses can exchange genetic material during coinfection, an interaction that creates novel strains with implications for viral evolution and public health. Influenza A viral genetic exchange can occur when genome segments from distinct strains reassort in coinfected cells. Predicting potential genomic reassortment between influenza strains has been a long-standing goal. Experimental coinfection studies have shed light on factors that limit or promote reassortment. However, determining the reassortment potential between diverse Influenza A strains has remained elusive. To address this challenge, we developed a high throughput genotyping approach to quantify reassortment among a diverse panel of human influenza virus strains encompassing two pandemics (swine and avian origin), three specific epidemics, and both circulating human subtypes A/H1N1 and A/H3N2. We found that reassortment frequency (the proportion of reassortants generated) is an emergent property of specific pairs of strains where strain identity is a predictor of reassortment frequency. We detect little evidence that antigenic subtype drives reassortment as intersubtype (H1N1xH3N2) and intrasubtype reassortment frequencies were, on average, similar. Instead, our data suggest that certain strains bias the reassortment frequency up or down, independently of the coinfecting partner. We observe that viral productivity is also an emergent property of coinfections, but uncorrelated to reassortment frequency; thus viral productivity is a separate factor affecting the total number of reassortants produced. Assortment of individual segments among progeny and pairwise segment combinations within progeny generally favored homologous combinations. These outcomes were not related to strain similarity or shared subtype but reassortment frequency was closely correlated to the proportion of both unique genotypes and of progeny with heterologous pairwise segment combinations. We provide experimental evidence that viral genetic exchange is potentially an individual social trait subject to natural selection, which implies the propensity for reassortment is not evenly shared among strains. This study highlights the need for research incorporating diverse strains to discover the traits that shift the reassortment potential to realize the goal of predicting influenza virus evolution resulting from segment exchange.

Pathogenicity, transmissibility and immunogenicity of recombinant H9N2 avian influenza viruses based on representative viruses of Southeast China

H9N2 is currently the main subtype of avian influenza in China. In order to use reverse genetics to rapid preparation of seed strains for vaccine production, and intend to prevent and control the H9N2 subtype epidemic strains of avian influenza virus (AIV). In this study, we successfully rescued 2 H9N2 recombinant viruses based on the representative viruses of Southeast China and confirmed by RT-PCR and sequencing. Genetic stability, pathogenicity, transmissibility, and antigenicity of 2 recombinant viruses were evaluated. Compared to the FZ1, the growth kinetics of H9N2(HA+NA)/PR8 showed no significant difference, H9N2(HA+NA+M+PB1)/PR8 was slightly lower. Our study also confirmed 2 recombinant viruses had good genetic stability after 10 passages but possessed lower pathogenicity than FZ1. Although both recombinant viruses led to seroconversion in all inoculated birds on 14 dpi, they complete loss of viral transmission of the virus to contact birds. In addition, birds were immunized via hypodermic route by inactivated vaccines of H9N2(HA+NA)/PR8, H9N2(HA+NA+M+PB1)/PR8 and wild-type virus with a single dose, and the results showed that the hemagglutination inhibition titers on 21 dpv were 10.5, 9.6, and 10.5 log2, respectively. And recombinant viruses both provided a certain protection against wild-type virus challenge. In conclusion, these data indicated that 2 recombinant viruses will be expected to be used as inactivated vaccines to controlling the spread of H9N2 subtype AIV even have potential application for attenuated viral vaccines, which provides a reference for the prevention and control of influenza virus pandemics.

Influenza A virus reassortment in mammals gives rise to genetically distinct within-host subpopulations

Influenza A virus (IAV) genetic exchange through reassortment has the potential to accelerate viral evolution and has played a critical role in the generation of multiple pandemic strains. For reassortment to occur, distinct viruses must co-infect the same cell. The spatio-temporal dynamics of viral dissemination within an infected host therefore define opportunity for reassortment. Here, we used wild type and synonymously barcoded variant viruses of a pandemic H1N1 strain to examine the within-host viral dynamics that govern reassortment in guinea pigs, ferrets and swine. The first two species are well-established models of human influenza, while swine are a natural host and a frequent conduit for cross-species transmission and reassortment. Our results show reassortment to be pervasive in all three hosts but less frequent in swine than in ferrets and guinea pigs. In ferrets, tissue-specific differences in the opportunity for reassortment are also evident, with more reassortants detected in the nasal tract than the lower respiratory tract. While temporal trends in viral diversity are limited, spatial patterns are clear, with heterogeneity in the viral genotypes detected at distinct anatomical sites revealing extensive compartmentalization of reassortment and replication. Our data indicate that the dynamics of viral replication in mammals allow diversification through reassortment but that the spatial compartmentalization of variants likely shapes their evolution and onward transmission.

Synthesizing the connections between environmental disturbances and zoonotic spillover

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.

Beneficial effects of cellular coinfection resolve inefficiency in influenza A virus transcription

For diverse viruses, cellular infection with single vs. multiple virions can yield distinct biological outcomes. We previously found that influenza A/guinea fowl/Hong Kong/WF10/99 (H9N2) virus (GFHK99) displays a particularly high reliance on multiple infection in mammalian cells. Here, we sought to uncover the viral processes underlying this phenotype. We found that the need for multiple infection maps to amino acid 26K of the viral PA protein. PA 26K suppresses endonuclease activity and viral transcription, specifically within cells infected at low multiplicity. In the context of the higher functioning PA 26E, inhibition of PA using baloxavir acid augments reliance on multiple infection. Together, these data suggest a model in which sub-optimal activity of the GFHK99 endonuclease results in inefficient priming of viral transcription, an insufficiency which can be overcome with the introduction of additional viral ribonucleoprotein templates to the cell. More broadly, the finding that deficiency in a core viral function is ameliorated through multiple infection suggests that the fitness effects of many viral mutations are likely to be modulated by multiplicity of infection, such that the shape of fitness landscapes varies with viral densities.

First detection of avian influenza subtype H4N6 in Israel in a wild mallard (Anas platyrhynchos)

Avian influenza viruses (AIV) are a worldwide threat to animal and human health. As wild waterfowl circulate and spread these viruses around the world, investigations of AIV prevalence in wild populations are critical for understanding pathogen transmission, as well as predicting disease outbreaks in domestic animals and humans. Surveillance efforts in this study have isolated H4N6 for the first time in Israel from a faecal sample of a wild mallard (Anas platyrhynchos). Phylogenetic analyses of the HA and NA genes revealed that this strain is closely related to isolates from Europe and Asia. This Eurasian origin, together with Israel serving as an important migratory bottleneck of the mid Palearctic-African flyway, suggests a potential introduction of this strain by migratory birds. Additional phylogenetic analysis of the isolate's internal genes (PB1, PB2, PA, NP, M and NS) revealed high levels of phylogenetic relatedness with other AIV subtypes, indicating previous reassortment events. High reassortment rates are characteristic for H4N6 viruses, which, together with this subtype's ability to infect pigs and adaptability to the human receptor binding domain, raises the concern that it would potentially become zoonotic in the future. These results emphasize the importance of continuous AIV monitoring in migratory birds.

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

Background

Large poultry die-offs happened in Kazakhstan during autumn of 2020. The birds' disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia.

Methods

Samples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions.

Results

Phylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan's viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan's viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds.

Conclusion

The findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination.

Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail

Influenza A viruses (IAVs) are constantly evolving. Crucial steps in the infection cycle, such as sialic acid (SA) receptor binding on the host cell surface, can either promote or hamper the emergence of new variants. We previously assessed the relative fitness in Japanese quail of H9N2 variant viruses differing at a single amino acid position, residue 216 in the hemagglutinin (HA) viral surface protein. This site is known to modulate SA recognition. Our prior study generated a valuable set of longitudinal samples from quail transmission groups where the inoculum comprised different mixed populations of HA 216 variant viruses. Here, we leveraged these samples to examine the evolutionary dynamics of viral populations within and between inoculated and naïve contact quails. We found that positive selection dominated HA gene evolution, but fixation of the fittest variant depended on the competition mixture. Analysis of the whole genome revealed further evidence of positive selection acting both within and between hosts. Positive selection drove fixation of variants in non-HA segments within inoculated and contact quails. Importantly, transmission bottlenecks were modulated by the molecular signature at HA 216, revealing viral receptor usage as a determinant of transmitted diversity. Overall, we show that selection strongly shaped the evolutionary dynamics within and between quails. These findings support the notion that selective processes act effectively on IAV populations in poultry hosts, facilitating rapid viral evolution in this ecological niche.

Knowledge, Attitudes, and Risk Perception Toward Avian Influenza Virus Exposure Among Cuban Hunters

A critical step for decreasing zoonotic disease threats is to have a good understanding of the associated risks. Hunters frequently handle potentially infected birds, so they are more at risk of being exposed to zoonotic avian pathogens, including avian influenza viruses (AIVs). The objective of the current study was to gain a better understanding of Cuban hunters' general hunting practices, focusing on their knowledge and risk perception on avian influenza. An anonymous and voluntary semi-structured questionnaire was designed and applied to 398 hunters. Multiple correspondence analyses found relationships with potential exposure of AIVs to people and domestic animals. The main associated risks factors identified were not taking the annual flu vaccine (60.1%) and not cleaning hunting knives (26.3%); Direct contact with water (32.1%), cleaning wild birds at home (33.2%); receiving assistance during bird cleaning (41.9%), keeping poultry at home (56.5%) and feeding domestic animals with wild bird leftovers (30.3%) were also identified as significant risk factors. The lack of use of some protective measures reported by hunters had no relationship with their awareness on avian influenza, which may imply a lack of such knowledge. The results evidenced that more effective risk communication strategies about the consequences of AIVs infecting human or other animals, and the importance of reducing such risks, are urgently needed.