The use of microarrays for the identification of the origin of genes of avian influenza viruses in wild birds

Forty-two strains of avian influenza viruses were isolated from the wild waterfowls’ feces in the city of Moscow. These viruses, as well as reference strains and some experimental reassortants, were analyzed by microarrays. The microarrays contained 176 probes to the different segments of influenza virus genome. The microarray helps to determine 1) the hemagglutinin and neuraminidase proteins subtype; 2) the primary structure of the C-terminal sequence of the viral NS1 protein, which serves as a ligand for the PDZ domain; 3) the presence of stop codons in the reading frame of PB1-F2 as well as the N66S substitution in the PB1-F2 viral protein; 4) the presence of the polybasic site for hemagglutinin cleavage. The viruses of the H3N1, H3N6, H3N8, H4N6, H1N1, H5N3, and H11N9 subtypes were identified from the group of wild birds’ isolates. All isolates contained the ESEV sequence at the C-terminus of the NS1 protein and the full-length reading frame for the PB1-F2 protein. The replacement of N66S in PB1-F2 was found in six strains. However, the presence of the ESEV sequence (ligand of PDZ domain) in the NS1 virus protein and the N66S substitution in PB1-F2 did not lead to the pathogenicity of these viruses for mice. All isolates demonstrated high yield growth in chicken embryos and were infectious and immunogenic for mice, but did not induce any clinical symptoms.Forty-two strains of avian influenza viruses were isolated from the wild waterfowls’ feces in the city of Moscow. These viruses, as well as reference strains and some experimental reassortants, were analyzed by microarrays. The microarrays contained 176 probes to the different segments of influenza virus genome. The microarray helps to determine 1) the hemagglutinin and neuraminidase proteins subtype; 2) the primary structure of the C-terminal sequence of the viral NS1 protein, which serves as a ligand for the PDZ domain; 3) the presence of stop codons in the reading frame of PB1-F2 as well as the N66S substitution in the PB1-F2 viral protein; 4) the presence of the polybasic site for hemagglutinin cleavage. The viruses of the H3N1, H3N6, H3N8, H4N6, H1N1, H5N3, and H11N9 subtypes were identified from the group of wild birds’ isolates. All isolates contained the ESEV sequence at the C-terminus of the NS1 protein and the full-length reading frame for the PB1-F2 protein. The replacement of N66S in PB1-F2 was found in six strains. However, the presence of the ESEV sequence (ligand of PDZ domain) in the NS1 virus protein and the N66S substitution in PB1-F2 did not lead to the pathogenicity of these viruses for mice. All isolates demonstrated high yield growth in chicken embryos and were infectious and immunogenic for mice, but did not induce any clinical symptoms

Interaction and Cooperative Nucleation of InAsSbP Quantum Dots and Pits on InAs(100) Substrate

An example of InAsSbP quaternary quantum dots (QDs), pits and dots–pits cooperative structures’ growth on InAs(100) substrates by liquid phase epitaxy (LPE) is reported. The interaction and surface morphology of the dots–pits combinations are investigated by the high-resolution scanning electron microscope. Bimodal growth mechanism for the both QDs and pits nucleation is observed. Cooperative structures consist of the QDs banded by pits, as well as the “large” pits banded by the quantum wires are detected. The composition of the islands and the pits edges is found to be quaternary, enriched by antimony and phosphorus, respectively. This repartition is caused by dissociation of the wetting layer, followed by migration (surface diffusion) of the Sb and P atoms in opposite directions. The “small” QDs average density ranges from 0.8 to 2 × 109 cm−2, with heights and widths dimensions from 2 to 20 nm and 5 to 45 nm, respectively. The average density of the “small” pits is equal to (6–10) × 109 cm−2 with dimensions of 5–40 nm in width and depth. Lifshits–Slezov-like distribution for the amount and surface density of both “small” QDs and pits versus their average diameter is experimentally detected. A displacement of the absorption edge toward the long wavelength region and enlargement toward the short wavelength region is detected by the Fourier transform infrared spectrometry

Adiabatic description of nonspherical quantum dot models

Within the effective mass approximation an adiabatic description of spheroidal and dumbbell quantum dot models in the regime of strong dimensional quantization is presented using the expansion of the wave function in appropriate sets of single-parameter basis functions. The comparison is given and the peculiarities are considered for spectral and optical characteristics of the models with axially symmetric confining potentials depending on their geometric size making use of the total sets of exact and adiabatic quantum numbers in appropriate analytic approximations

Glycans as receptors for influenza pathogenesis

Influenza A viruses, members of the Orthomyxoviridae family, are responsible for annual seasonal influenza epidemics and occasional global pandemics. The binding of viral coat glycoprotein hemagglutinin (HA) to sialylated glycan receptors on host epithelial cells is the critical initial step in the infection and transmission of these viruses. Scientists believe that a switch in the binding specificity of HA from Neu5Acα2-3Gal linked (α2-3) to Neu5Acα2-6Gal linked (α2-6) glycans is essential for the crossover of the viruses from avian to human hosts. However, studies have shown that the classification of glycan binding preference of HA based on sialic acid linkage alone is insufficient to establish a correlation between receptor specificity of HA and the efficient transmission of influenza A viruses. A recent study reported extensive diversity in the structure and composition of α2-6 glycans (which goes beyond the sialic acid linkage) in human upper respiratory epithelia and identified different glycan structural topologies. Biochemical examination of the multivalent HA binding to these diverse sialylated glycan structures also demonstrated that high affinity binding of HA to α2-6 glycans with a characteristic umbrella-like structural topology is critical for efficient human adaptation and human-human transmission of influenza A viruses. This review summarizes studies which suggest a new paradigm for understanding the role of the structure of sialylated glycan receptors in influenza virus pathogenesis.National Institute of General Medical Sciences (U.S.) (Glue Grant U54 GM62116)National Institutes of Health (U.S.) (Grant GM57073)Singapore-MIT Alliance for Research and Technolog

Molecular identification of Newcastle disease virus isolated on the poultry farm of the Moscow Oblast in summer of 2022

In August 2022, a sudden death in backyard chickens was reported in the Moscow Oblast (urban district Chernogolovka, settlement Starki). As a result, within just a few days 45 chickens on this farm died or fell ill with the following signs – gray mucus discharge from nostrils and beak, coughing, gasping and rales. On day 1–3 after the onset of symptoms, the chicken died. The Newcastle disease virus, which is a representative of the Paramyxoviruses family, was isolated from the dead poultry. We determined the nucleotide sequences of fragments in F gene (encodes the fusion surface protein) and in NP gene (encodes the nucleocapsid protein). The motif of 109SGGRRQKRFIG119 proteolysis site, typical for the velogenic pathotype, was determined for the F gene, and a phylogenetic analysis was carried out to demonstrate that the isolate belonged to Subgenotype VII, Class II of the subfamily Avulavirinae. The Basic Local Alignment Search Tool revealed that they are most genetically related with isolates from Iran. It was found that the average death time of developing chicken embryos, infected with a minimum infectious dose, was 52 hours, which is typical for the velogenic pathotype. The virus caused 100% death in six-week-old chickens after oral infection and 100% death in all contact chickens, including those kept in cages at a distance, which proves the high level of pathogenicity and contagiousness of the recovered isolate and its ability to transmit both via fecal-oral and aerosols–borne routes. No death cases were reported in mice after intranasal infection with high doses

The pattern of influenza virus attachment varies among wild bird species

The ability to attach to host cells is one of the main determinants of the host range of influenza A viruses. By using virus histochemistry, we investigate the pattern of virus attachment of both a human and an avian influenza virus in colon and trachea sections from 12 wild bird species. We show that significant variations exist, even between closely related avian species, which suggests that the ability of wild birds to serve as hosts for influenza viruses strongly varies among species. These results will prove valuable to assess the possibilities of interspecies transmission of influenza viruses in natural environments and better understand the ecology of influenza

1918 Influenza Pandemic and Highly Conserved Viruses with Two Receptor-Binding Variants

The “Spanish influenza pandemic swept the globe in the autumn and winter of 1918–19, and resulted in the deaths of approximately 40 million people. Clinically, epidemiologically, and pathologically, the disease was remarkably uniform, which suggests that similar viruses were causing disease around the world. To assess the homogeneity of the 1918 pandemic influenza virus, partial hemagglutinin gene sequences have been determined for five cases, including two newly identified samples from London, United Kingdom. The strains show 98.9% to 99.8% nucleotide sequence identity. One of the few differences between the strains maps to the receptor-binding site of hemagglutinin, suggesting that two receptor-binding configurations were co-circulating during the pandemic. The results suggest that in the early stages of an influenza A pandemic, mutations that occur during replication do not become fixed so that a uniform “consensus” strain circulates for some time

Growth of large-area single- and bi-layer graphene by controlled carbon precipitation on polycrystalline Ni surfaces

We report graphene films composed mostly of one or two layers of graphene grown by controlled carbon precipitation on the surface of polycrystalline Ni thin films during atmospheric chemical vapor deposition(CVD). Controlling both the methane concentration during CVD and the substrate cooling rate during graphene growth can significantly improve the thickness uniformity. As a result, one- or two- layer graphene regions occupy up to 87% of the film area. Single layer coverage accounts for 5-11% of the overall film. These regions expand across multiple grain boundaries of the underlying polycrystalline Ni film. The number density of sites with multilayer graphene/graphite (>2 layers) is reduced as the cooling rate decreases. These films can also be transferred to other substrates and their sizes are only limited by the sizes of the Ni film and the CVD chamber. Here, we demonstrate the formation of films as large as 1 in2. These findings represent an important step towards the fabrication of large-scale high-quality graphene samples

Human-Like Receptor Specificity Does Not Affect the Neuraminidase-Inhibitor Susceptibility of H5N1 Influenza Viruses

If highly pathogenic H5N1 influenza viruses acquire affinity for human rather than avian respiratory epithelium, will their susceptibility to neuraminidase (NA) inhibitors (the likely first line of defense against an influenza pandemic) change as well? Adequate pandemic preparedness requires that this question be answered. We generated and tested 31 recombinants of A/Vietnam/1203/04 (H5N1) influenza virus carrying single, double, or triple mutations located within or near the receptor binding site in the hemagglutinin (HA) glycoprotein that alter H5 HA binding affinity or specificity. To gain insight into how combinations of HA and NA mutations can affect the sensitivity of H5N1 virus to NA inhibitors, we also rescued viruses carrying the HA changes together with the H274Y NA substitution, which was reported to confer resistance to the NA inhibitor oseltamivir. Twenty viruses were genetically stable. The triple N158S/Q226L/N248D HA mutation (which eliminates a glycosylation site at position 158) caused a switch from avian to human receptor specificity. In cultures of differentiated human airway epithelial (NHBE) cells, which provide an ex vivo model that recapitulates the receptors in the human respiratory tract, none of the HA-mutant recombinants showed reduced susceptibility to antiviral drugs (oseltamivir or zanamivir). This finding was consistent with the results of NA enzyme inhibition assay, which appears to predict influenza virus susceptibility in vivo. Therefore, acquisition of human-like receptor specificity does not affect susceptibility to NA inhibitors. Sequence analysis of the NA gene alone, rather than analysis of both the NA and HA genes, and phenotypic assays in NHBE cells are likely to adequately identify drug-resistant H5N1 variants isolated from humans during an outbreak