Structural and functional impact by SARS-CoV-2 Omicron spike mutations

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein, but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.

PREPARATIVE ISOLATION OF SPECIFIC ANTIGENS OF FULL CELL LYSATE M. BOVIS

Bovine tuberculosis is a serious problem for agriculture all over the world and causes huge economic losses. At the same time, infections caused by Mycobacterium bovis not only affect animal husbandry and the food industry, but also pose a threat to public health, as M. bovis is often isolated as a pathogen of tuberculosis, especially in patients with various immune deficiencies. The situation is aggravated by the lack of simple and accessible methods for diagnosing tuberculosis in cattle, which significantly impedes the monitoring of infection and the application of appropriate preventive measures. Serological tests, due to their relatively cheap cost, rapidity, rather high sensitivity and specificity, are able to compete with the allergic test during mass examinations of cows. In the present study, we present the results on the study of the antigenic structure of mycobacteria and the isolation of the most specific antigenic components from the lysate of the M. Bovis cell wall destroyed on the Fast Prep 24 device. The developed method allows obtaining a serologically active antigenic fraction with a high degree of purity with a molecular weight of 28 kDa.

Dynamics of Salivary Adenosine Deaminase, Haptoglobin, and Cortisol in Lipopolysaccharide-Challenged Growing Pigs

Infectious and inflammatory conditions are common especially in growing pigs. Lipopolysaccharide (LPS) is an important antigenic structure of Gram-negative bacteria and can be used to induce inflammation experimentally. As pigs are usually group-housed in commercial conditions, it is difficult to detect sick individuals, particularly at an early stage of illness. Acute phase proteins such as haptoglobin (Hp) are known indicators of an activated innate immune system whereas adenosine deaminase (ADA) is a relatively novel inflammatory biomarker in pigs. Both parameters can be measured in saliva and could be used as indicators of inflammation. Compared with blood sampling, saliva sampling is a less stressful procedure that is rapid, non-invasive and easy to perform both at group and at individual level. In this blinded randomized clinical trial, 32 female pigs at their post-weaning phase were allocated to one of four treatments comprising two injections of the following substance combinations: saline-saline (SS), ketoprofen-saline (KS), saline-LPS (SL), and ketoprofen-LPS (KL). First, ketoprofen or saline was administered intramuscularly on average 1 h before either LPS or saline was given through an ear vein catheter. In all groups, saliva was collected prior to injections (baseline) and at 4, 24, 48, and 72 h post-injection for determination of ADA, Hp, and cortisol concentrations. A multivariate model was applied to describe the dynamics of each biomarker. Pairwise relationships between ADA, Hp, and cortisol responses from baseline to 4 h post-injection within the SL group were studied with Spearman correlations. A significant increase in the SL group was seen in all biomarkers 4 h post-injection compared to baseline and other time points (pairwise comparisons, p < 0.01 for all) and ketoprofen alleviated the LPS effect. We found a significant positive correlation between ADA and Hp within the SL group (r = 0.86, p < 0.05). The primary and novel findings of the present study are the response of ADA to LPS, its time course and alleviation by ketoprofen. Our results support the evidence that ADA and Hp can be used as inflammatory biomarkers in pigs. We suggest further studies to be conducted in commercial settings with larger sample sizes.

Two Cross-Protective Antigen Sites on Foot-and-Mouth Disease Virus Serotype O Structurally Revealed by Broadly Neutralizing Antibodies from Cattle

FMDV is the causative agent of foot-and-mouth disease (FMD), which is one of the most contagious and economically devastating diseases of domestic animals. The antigenic structure of FMDV serotype O is rather complicated, especially for those sites that can elicit a cross-protective neutralizing antibody response.

Serum antinuclear autoantibodies are associated with measures of oxidative stress and lifestyle factors - analysis of LIPIDOGRAM2015 and LIPIDOGEN2015 studies.

IntroductionOxidative stress is one of many factors suspected to promote antinuclear autoantibody (ANA) formation. Reactive oxygen species can induce changes in the antigenic structure of macromolecules, causing the immune system to treat them as “neo-antigens” and start production of autoantibodies. This study was designed to evaluate the relationship between oxidative stress markers, lifestyle factors and the detection of ANA.Material and methodsWe examined measures of oxidative stress indices of free-radical damage to lipids and proteins, such as total oxidant status (TOS), concentration of protein thiol groups (PSH), and malondialdehyde (MDA), activity of superoxide dismutase (SOD) in in 1731 serum samples. The parameters of the non-enzymatic antioxidant system, such as total antioxidant status (TAS) and uric acid concentration (UA), were also measured and the oxidative stress index (OSI -index) was calculated. All samples were tested for the presence of ANA using an indirect immunofluorescence assay (IIFA).ResultsThe presence of ANA in women was associated with lower physical activity (p=0.036), less frequent smoking (p=0.007) and drinking of alcohol (p=0.024) accompanied by significant changes in SOD isoenzymes activity (p<0.001) and a higher uric acid (UA) concentration (p<0.001). In ANA positive males we observed lower concentrations of PSH (p=0.046) and increased concentrations of MDA (p=0.047).ConclusionsThe results indicate that local oxidative stress may be associated with increased probability of ANA formation in a sex-specific manner.

PHENOMENON OF DEMIKHOV. In the Sklifosovsky Institute (1960–1986). Approaches to solving the problem of organ and tissue transplantation in the USSR and abroad (1967)

Analysis of the materials of the 2nd All-Union conference on the problem of tissue incompatibility, conservation and transplantation of tissues and organs (Odessa, 1967) showed that Soviet and foreign scientists had similar approaches to solving the problem of organ and tissue transplantation. Soviet scientists spoke about overcoming tissue incompatibility by hybridization of plants and chimerization of animals, about the effect of drug sleep on transplant immunity, about neurohumoral immunological shifts and the role of the central and peripheral nervous systems in the engraftment of grafts, about the influence of external factors on immunity. They also discussed the characterization of the antigenic structure of grafts, the role of DNA in immunity, the genetic transformation of homomaterial, the use of pharmacological agents to suppress immunogenesis, the cryopreservation of auto- and homo-organs and tissues with perfusion of their vascular bed, and the study of immunogenesis at the molecular level. A year earlier, the Americans discussed immunological paralysis, the effect on the recipient's immunity of the donor's blood transfused to him and its components, and biochemical studies of immunity. At the same time, without any ethical doubts, American scientists conducted experiments, including clinical ones, with multiple passages of homosexual skin, with exchange transfusion of blood to newborns and subsequent transplantation of homosexual donors to them, with irradiation of recipients with powerful doses of X-rays. It is shown that most of the trends that had been developed by V.P. Demikhov, were approved by the 2nd All-Union Conference. But what he lacked was close and comprehensive integration with morphologists, physiologists, immunologists, biochemists, pharmacologists and, sadly, with clinical surgeons. Based on the research conducted, an unambiguous conclusion can be drawn: Soviet scientists should not have criticized V.P. Demikhov for his "misunderstanding" of immunology, and to help him in every possible way, directing his energy in the right direction.

Chapter 2b: The molecular antigenic structure of the TBEV

TBEV-particles are assembled in an immature, noninfectious form in the endoplasmic reticulum by the envelopment of the viral core (containing the viral RNA) by a lipid membrane associated with two viral proteins, prM and E. Immature particles are transported through the cellular exocytic pathway and conformational changes induced by acidic pH in the trans-Golgi network allow the proteolytic cleavage of prM by furin, a cellular protease, resulting in the release of mature and infectious TBE-virions. The E protein controls cell entry by mediating attachment to as yet ill-defined receptors as well as by low-pH-triggered fusion of the viral and endosomal membrane after uptake by receptor-mediated endocytosis. Because of its key functions in cell entry, the E protein is the primary target of virus neutralizing antibodies, which inhibit these functions by different mechanisms. Although all flavivirus E proteins have a similar overall structure, divergence at the amino acid sequence level is up to 60 percent (e.g. between TBE and dengue viruses), and therefore cross-neutralization as well as (some degree of) cross-protection are limited to relatively closely related flaviviruses, such as those constituting the tick-borne encephalitis serocomplex.

Molecular-Genetic Monitoring of SARS-CoV-2 Genovariants in the Territory of the Volga Federal District of the Russian Federation. Communication 1

Emergence of various genovariants of the SARS-CoV-2 virus, which are characterized by a higher ability to spread and a more severe clinical manifestations compared to the initial variants, require molecular-genetic monitoring of strains circulating in the Russian Federation.The aim of the work was to identify the VOC SARS-CoV-2 genovariants in the territory of the Republics of Bashkortostan, Tatarstan, Udmurtia, and Samara, Penza, Saratov, Ulyanovsk, and Orenburg Regions.Materials and methods. The identification of genovariants and the determination of the type of mutations was carried out by the Sanger fragment sequencing method.Results and discussion. The study examined 298 samples of clinical material obtained from the Centers for Hygiene and Epidemiology in the Republics of Bashkortostan, Tatarstan, Udmurtia, Samara, Penza, Saratov, Ulyanovsk, and Orenburg Regions. In 17 % of cases, the variability of the SARS-CoV-2 virus was observed for one or more markers: in three samples, a new coronavirus of the B. 1.1.7 line (“British”) was detected; in a number of cases, only one mutation was detected in the virus found in samples – deletion Y144 or substitution D138Y, E484K, N501Y, and very rarely two mutations – deletion Y144 and substitution E484K. The presence of the L141-G142-V143 deletion localized in the recurrent deletion region RDR2 of the S-gene was shown in 10 % of the cases. The data obtained indicate the heterogeneity in macroorganism of the population of the new coronavirus with the deletion L141-G142-V143, which leads to a change in the antigenic structure of the virus, which probably allows the virus to evade the immune response.

Phage display identification of immunodominant epitopes and autoantibodies in autoimmune diseases

Phage display represents an invaluable tool to study autoimmune diseases. The side effects of immunosuppressive drugs for the treatment of autoimmune diseases raise awareness of the need to explore alternative therapeutic approaches such as antibodies and peptides. Therefore, phage display is an important technique for generating such molecules, so the purpose of this review is to determine the potential advantages of this technique in the research of autoimmune diseases. Many studies have also demonstrated the efficacy of phage display in identifying immunodominant epitopes of autoimmune diseases such as Goodpasture disease, immunologic thrombocytopenia, and systemic lupus erythematosus. Phage display peptide libraries have been screened with immunopurified autoantibodies from patients with autoimmune diseases. This makes it possible to more precisely locate the autoantibody binding sites, reveal a possible epitope sharing between the host and microbe, and identify a motif that mimics an antigenic structure such as that of dsDNA. Several studies have been conducted that have investigated the effectiveness of phage display in isolating autoantibody repertoires of autoantibodies against human epitopes. This allows the identification and design of antibody fragments (e.g., Fab, scFv, sdAb) that could block the binding of autoantibodies such as the deposition of IgG in the kidney and reduce the clinical signs of disease. In conclusion, phage display helps identify common epitopes and hotspot residues that can be potential therapeutic targets for the treatment of autoimmune diseases. This leads to a better understanding of the immunopathogenesis of autoimmune diseases and the development of more specific therapeutic strategies.