Genetic and evolutionary dynamics of avian influenza A virus in wild birds

Influenza A virus (IAV) is the prototype of the family Orthomyxoviridae, a group of segmented, negative-sense, single-stranded RNA viruses. The virus circulates in wild bird species but does not usually cause severe disease in these hosts. However, highly pathogenic forms exist and have caused numerous deaths in wild and farmed birds. The eastern coast of Canada represents an interesting location for the study of IAVs in their natural reservoir as it has a large number of bird breeding colonies and migratory bird connections with the mainland of North America and Eurasia. Previous research on IAV ecology and transmission has shown that migratory birds in this region move the virus around the globe and contribute an important facet to IAV dynamics. My thesis focuses on the study of the virus genetics and evolutionary dynamics in different wild bird species. By applying high-throughput next-generation sequencing technologies, I characterized complete IAV genomes from different wild bird species from Newfoundland and Labrador and conducted in-depth analyses of the virus genomic structure. My study revealed that the structure of the virus genome is conserved among similar avian hosts. I also demonstrated though experimental mutation studies that a change of host can causes major changes in the viral genome. I also explored evolutionary patterns in the viral genomic non-coding regions (NCRs), and found that variation in the NCR sequences is correlated with the original host species and geographic origin. Finally, I analyzed IAVs from Laridae family hosts (gulls and terns) and demonstrated that these hosts are important for the transmission of IAVs around the globe and to other hosts and participate in the generation of pandemic viruses. Overall, my results contribute to give a better understanding on the evolution and geographic patterns of influenza A viruses in their natural hosts

Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from a Fish Farm in Scotland

The aquatic virus, infectious pancreatic necrosis virus (IPNV), is known to infect various farmed fish, in particular salmonids, and is responsible for large economic losses in the aquaculture industry. Common practices to detect the virus include qPCR tests based on specific primers and serum neutralization tests for virus serotyping. Following the potential presence of IPNV viruses in a fish farm in Scotland containing vaccinated and IPNV-resistant fish, the common serotyping of the IPNV isolates was not made possible. This led us to determine the complete genome of the new IPNV isolates in order to investigate the cause of the serotyping discrepancy. Next-generation sequencing using the Illumina technology along with the sequence-independent single primer amplification (SISPA) approach was conducted to fully characterize the new Scottish isolates. With this approach, the full genome of two isolates, V1810–4 and V1810–6, was determined and analyzed. The potential origin of the virus isolates was investigated by phylogenetic analyses along with tridimensional and secondary protein structure analyses. These revealed the emergence of a new variant from one of the main virus serotypes, probably caused by the presence of selective pressure exerted by the vaccinated IPNV-resistant farmed fish

Impact of genetic diversity on biological characteristics of Usutu virus strains in Africa

Usutu virus (USUV) previously restricted to Africa where it caused mild infections, emerged in 2001 in Europe and caused more severe infections among birds and humans with neurological forms, suggesting an adaptation and increasing virulence. This evolution suggests the need to better understand USUV transmission patterns for assessing risks and to develop control strategies. Phylogenetic analysis conducted in Africa showed low genetic diversity of African USUV strains except for one human and the USUV subtype (USUVsub) strains, which exhibited a deletion in the 3′UTR and nucleotide substitutions throughout the genome. Here we analyzed their viral replication in vitro in mosquito and mammalian cells, and vector competence of Culex quinquefasciatus, compared to a reference strain. Growth kinetics of the different strains showed comparable replication rates however variations in replication and translation efficiency were observed. Vector competence analysis showed that all strains were able to infect Culex quinquefasciatus the main peridomestic Culex species in Africa, with detection of USUV viral genomes and infectious particles. Dissemination and transmission were observed only for USUVsub, but infectious particles were not detected in Culex quinquefasciatus saliva. Our findings suggest that genetic variability can affect USUV in vitro replication in a cell type-dependent manner and in vivo in mosquitoes. In addition, the results show that Culex quinquefasciatus is not competent for the USUV strains analyzed here and also suggest an aborted transmission process for the USUVsub, which requires further investigations

Emerging complexities of APOBEC3G action on immunity and viral fitness during HIV infection and treatment

<p>Abstract</p> <p>The enzyme APOBEC3G (A3G) mutates the human immunodeficiency virus (HIV) genome by converting deoxycytidine (dC) to deoxyuridine (dU) on minus strand viral DNA during reverse transcription. A3G restricts viral propagation by degrading or incapacitating the coding ability of the HIV genome. Thus, this enzyme has been perceived as an innate immune barrier to viral replication whilst adaptive immunity responses escalate to effective levels. The discovery of A3G less than a decade ago led to the promise of new anti-viral therapies based on manipulation of its cellular expression and/or activity. The rationale for therapeutic approaches has been solidified by demonstration of the effectiveness of A3G in diminishing viral replication in cell culture systems of HIV infection, reports of its mutational footprint in virions from patients, and recognition of its unusually robust enzymatic potential in biochemical studies in vitro. Despite its effectiveness in various experimental systems, numerous recent studies have shown that the ability of A3G to combat HIV in the physiological setting is severely limited. In fact, it has become apparent that its mutational activity may actually enhance viral fitness by accelerating HIV evolution towards the evasion of both anti-viral drugs and the immune system. This body of work suggests that the role of A3G in HIV infection is more complex than heretofore appreciated and supports the hypothesis that HIV has evolved to exploit the action of this host factor. Here we present an overview of recent data that bring to light historical overestimation of A3G’s standing as a strictly anti-viral agent. We discuss the limitations of experimental systems used to assess its activities as well as caveats in data interpretation.</p

Analysis of the Variability in the Non-Coding Regions of Influenza A Viruses

The genomes of influenza A viruses (IAVs) comprise eight negative-sense single-stranded RNA segments. In addition to the protein-coding region, each segment possesses 5&prime; and 3&prime; non-coding regions (NCR) that are important for transcription, replication and packaging. The NCRs contain both conserved and segment-specific sequences, and the impacts of variability in the NCRs are not completely understood. Full NCRs have been determined from some viruses, but a detailed analysis of potential variability in these regions among viruses from different host groups and locations has not been performed. To evaluate the degree of conservation in NCRs among different viruses, we sequenced the NCRs of IAVs isolated from different wild bird host groups (ducks, gulls and seabirds). We then extended our study to include NCRs available from the National Center for Biotechnology Information (NCBI) Influenza Virus Database, which allowed us to analyze a wider variety of host species and more HA and NA subtypes. We found that the amount of variability within the NCRs varies among segments, with the greatest variation found in the HA and NA and the least in the M and NS segments. Overall, variability in NCR sequences was correlated with the coding region phylogeny, suggesting vertical coevolution of the (coding sequence) CDS and NCR regions

Analysis of influenza A viruses from gulls: An evaluation of inter-regional movements and interactions with other avian and mammalian influenza A viruses

<p>Birds, including members of the families Anatidae (waterfowl) and Laridae (gulls and terns), serve as the major reservoir of influenza A viruses (IAVs). The ecogeographic contributions of gulls to global IAV dynamics, in terms of geographic scale and virus movements, are important and are distinct from those of waterfowl. Gulls primarily carry the H13 and H16 subtypes, yet can be infected by additional subtypes. Also, gulls are frequently infected by IAVs that contain mixtures of genes from different geographic phylogenetic lineages (e.g. North American and Eurasian). The present analysis examines a variety of viruses isolated from gulls and terns across the world that exhibit particularly high phylogenetic affinities to viruses found in other hosts. This illustrates the potential for gulls to act as highly pathogenic virus carriers, disseminators of viruses over long distances, and contributors in the genesis of pandemic strains. The historical evolution of an entirely Eurasian gull virus isolated in North America was also traced and indicates the Caspian Sea, in southwestern Asia, was an important area for the generation of this virus, and analysis of IAVs from terns also points to this region as relevant for the generation of novel strains.</p

Structural Insights into the HIV-1 Minus-strand Strong-stop DNA

Close view of a façade, depicting windows with semi-circular fan lights; Much of the architecture has not changed in style for hundreds of years and some old building techniques survive. The urgent need for restoration work is recognized and some has been undertaken. The State together with UNESCO launched a campaign in 1984 to preserve the old city of San'a; a similar campaign was introduced for the town of Shibam in Wadi Hadramawt. The most distinctive buildings [in San'a] are tower houses, of between four and nine storeys, intended for one family. Built of mud-brick or stone or a combination, depending on the region, they typically contain small rooms, thick outer walls and at the top a large reception room (mafraj). The tower houses in the old city in San'a are of natural stone for the ground floor, with fired brick for the upper storeys. Walls are decorated with bands of geometric patterns formed by protruding bricks, which may be whitewashed annually. The bands surround the windows or mark the different storeys. Arched or semicircular fanlights contain coloured glass in geometric or floral patterns. Source: Grove Art Online; http://www.groveart.com/ (accessed 1/28/2008