Galina V. Klink

The role of escape from the cytotoxic T cell (CTL) response in Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the human leukocyte antigen (HLA) class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and 39% of all subsequent viral mutations, facilitate escape of viral epitopes from presentation. Mutations allowing escape from more common HLA alleles reach higher frequencies, particularly in those countries where these HLA alleles are more frequent, indicating that escape is selected by the local genetic composition of the human host population. We also show that viral mutations that accumulated in general-population transmission chains matched population HLA class I allele frequencies as well as, or better than, mutations acquired during persistent infections, suggesting that selection in favor of escape mutations is not limited to immunocompromised individuals. Together, these data reveal CTL escape as a facet of selection, a driver of evolution, and an epidemiological concern for SARS-CoV-2.

Tick-borne encephalitis virus (TBEV) causes tick-borne encephalitis (TBE), a severe disease of the human central nervous system. Currently, the data on the genetic variants of TBEV in Kyrgyzstan are practically absent. Therefore, the aim of this study was to analyze and describe the genetic diversity of TBEV in this region. The complete genome sequences of seven TBEV strains from the collection of the Scientific Centre for Family Health and Human Reproduction Problems (Irkutsk, Russia) were determined. These strains, isolated from Ixodes persulcatus ticks from Kyrgyzstan, were sequenced using the next generation sequencing approach on a MiSeq high-performance sequencer (Illumina, San Diego, CA, USA). A molecular genetic analysis of the obtained sequences, along with sequences of two previously isolated TBEV strains from Kyrgyzstan available in the GenBank database, demonstrated that the Siberian subtype of three genetic lineages (Zausaev, Vasilchenko and Bosnia) is predominantly distributed in Kyrgyzstan. The Far Eastern subtype of TBEV is also present. To date, this location probably represents the southernmost boundary of these TBEV subtypes’ ranges.

Tick-borne encephalitis virus (TBEV) causes tick-borne encephalitis (TBE), a severe disease of the human central nervous system. Currently, the data on the genetic variants of TBEV in Kyrgyzstan is practically absent, so the aim of this study was to analyze and describe the genetic diversity of TBEV in Kyrgyzstan. The complete genome sequences of seven TBEV strains from the collection of the Scientific Сentre for Family Health and Human Reproduction Problems, Irkutsk, Russia isolated from Ixodes persulcatus ticks from Kyrgyzstan were determined by next generation sequencing approach with high-performance sequencer MiSeq (Illumina, USA). A molecular genetic analysis of the obtained sequences and sequences of two TBEV strains isolated previously in Kyrgyzstan from the GenBank database demonstrated that the Siberian subtype of three genetic lineages (Zausaev, Vasilchenko and Bosnia) is predominantly distributed in Kyrgyzstan, and TBEV of the Far Eastern subtype is also present. To date, this is probably southernmost range boundary for these TBEV subtypes.

Background: Although COVID-19 is primarily an acute disease, there are cases of persistent infection, primarily in immunocompromised patients. It is hypothesized that at least some variants of concern (VOCs) have arisen in such persistent cases, with the virus “spilling over” into the general population after accumulating intra-host mutations. Additionally, a growing body of evidence hints at the gastrointestinal (GI) tract as a reservoir of long-term infection, at least in some cases.Results: We report the genomic analysis of a highly divergent SARS-CoV-2 sample obtained in October 2022 from an HIV+ patient with presumably long-term COVID-19 infection. Phylogenetic analysis indicates that the sample is characterized by a gain of 89 mutations since divergence from its nearest sequenced neighbor, which had been collected in September 2020 and belongs to the B.1.1 lineage, largely extinct by 2022. Of these mutations, 33 were nonsynonymous and occurred in the Spike protein. Of these, 17 are lineage-defining in some VOCs or are at sites where another mutation is lineage-defining in a VOC, and/or have been shown to be involved in antibody evasion, and/or have been detected in other cases of persistent COVID-19; these include some “usual suspects,” such as Spike:L452R, E484Q, K417T, Y453F, and N460K. Molecular clock analysis indicates that mutations in this lineage accumulated at an increased rate compared with the ancestral B.1.1 strain. This increase is driven by the accumulation of non-synonymous mutations, with an average dN/dS value of 2.2, indicating strong positive selection during within-patient evolution. Additionally, the presence of mutations that are rare in the general population samples but common in samples from wastewater suggests that the virus had persisted for at least some time in the GI tract.Conclusions: Our analysis adds to the growing body of evidence that the evolution of SARS-CoV-2 in chronically infected patients can be a major source of novel epidemiologically important variants and points to the potential role of the GI tract in long-term infection.

The state of meadow vegetation in areas with different ages of experimental spring burnout (from 1 to 12 years ago) was studied in the Tomsk region for 3 years. On experimental plots of 1 m² and 100 m² (small- and middle-scale levels, respectively), the dynamics of species richness, total projective cover of vegetation, and aboveground phytomass reserves were characterized, and the structure of communities was analyzed. It was revealed that a single fire in the spring significantly reduces species richness for small-scale plots and increases the total projective cover for middle-scale plots. Structural differences from control plots can be traced from 1 to 4 years for different characteristics. The effects of fire are more prominent for small-scale plots. To suppress tree growth and maintain the existence of meadows, grass fires seem to be a less effective practice than mowing. At the same time, the results obtained potentially allow us to consider prescribed burning as a tool for maintaining the stability of meadow plant communities in the south of Western Siberia, preventing them from becoming overgrown with tree undergrowth, in cases with a controlled frequency of burning and the use of appropriate fire safety measures.

Understanding the rate and direction of pyrogenic succession in arid ecosystems, which depends on many factors, including the intensity of grazing and the frequency of pyrogenic expo-sure, will allow for more accurate predictions of the consequences of fire onplant communities, and will assist with better fire management. We studied the vegetation on 55 sites in and near the “Chernye Zemli” Natural Biosphere Reserve that burned at different times or were not affected by fires over the past 35 years and characterized the changes in vegetation cover associated with the impact of wildfire and grazing. The descriptions were grouped into chronological stages according to the time elapsed since the last fire, or into groups according to the frequency of fires. In pairwise comparison of the projective cover of plant species between chronological stages, it correlated most strongly between successive initial stages (for stages 1 and 2, p = 0.003, r = 0.73; for stages 2 and 3, p < 0.001, r = 0.78). Species with an initially higher projective cover were more likely to grow on plots in the first year after the fire: p < 0.03. Plots with rare and frequent fires had similar projective cover of individual species (r = 0.64, p < 0.001). We conclude that in the course of pyrogenic succession, communities are gradually replaced over at least ten years. At the same time, the composition of a plant community at the initial point of succession depends on the prevalence of species in the community before the fire. No fundamental effect of the frequency of fires on the composition of plant communities has been revealed.

Variability of acidity, electrical conductivity, and redox potential depends on processes affecting the soil quality. The study of these properties is important in planning and analyzing the results of ecological and geochemical monitoring. The purpose of the work is to assess the intrahorizontal variability of acidity, electrical conductivity and redox potential within different depths of automorphic sandy soils of the Smolenskoye Poozerye National Park. Variability of pH values, electrical conductivity of water extract, and redox potential were studied in each horizon of the postagrogenic Entic Rustic Podzol under a birchoak-spruce forest and the Katogleyic Albic Carbic Podzol under pine-spruce forest located at the Smolenskoye Poozerye National Park (55°32′ N, 31°24′ E). Entic Rustic Podzol was sampled at seven depths in five repetitions. Samples were taken from the Katogleyic Albic Carbic Podzol from nine depths in triplicate. The pH values, electrical conductivity, and redox potential of the samples from Entic Rustic Podzol were measured five times in aqueous suspension within one day after sampling and once in Katogleyic Albic Carbic Podzol. The variability of the physicochemical properties of soils in each data set was estimated using the three groups of coefficients of variation. In the Entic Rustic Podzol, Cv1 was a measurement variability calculated for five repeated measurements of the same suspension, Cv1av was averaged Cv1; Cv2 was calculated for averaged values of five samples which suspension was measured five times. Cv for Katogleyic Albic Carbic Podzol was calculated from three samples from nine depths and for Entic Rustic Podzol from the first measurement of five in each of five suspensions from seven depths. Variability of properties of all studied soils was at a low level: Cv < 50%. In comparing with the coefficients of variation calculated for pH and electrical conductivity in different soil horizons, the averaged coefficients of variation of the same properties, which were calculated for the whole data set characterizing Entic Rustic Podzol variability, were generally lower. The variability of the electrical conductivity was the highest among all the parameters studied, and the variability of the redox potential was the lowest. In the Katogleyic Albic Carbic Podzol, acidity variability increased in the Bs horizon. The variability of the redox potential was increased in the uppermost part of the humus horizon. The variability of electrical conductivity was maximum in the middle part of the profile and it was present in an extremely small amount in lacustrine sands with an uneven distribution of electrolytes. In the Entic Rustic Podzol, the variability of acidity increased in the middle part of the profile due to accumulation of Fe and Al fulvates. The variability of electrical conductivity varied slightly along the Entic Rustic Podzol profile. The variability of the redox potential was maximum in the forest litter, since the values of this parameter depend on the variability of moisture and microbiological activity.

Amino acid preferences at a protein site depend on the role of this site in protein function and structure as well as on external constraints. All these factors can change in the course of evolution, making amino acid propensities of a site time-dependent. When viral subtypes divergently evolve in different host subpopulations, such changes may depend on genetic, medical, and sociocultural differences between these subpopulations. Here, using our previously developed phylogenetic approach, we describe sixty-nine amino acid sites of the Gag protein of human immunodeficiency virus type 1 (HIV-1) where amino acids have different impact on viral fitness in six major subtypes of the type M. These changes in preferences trigger adaptive evolution; indeed, 32 (46 per cent) of these sites experienced strong positive selection at least in one of the subtypes. At some of the sites, changes in amino acid preferences may be associated with differences in immune escape between subtypes. The prevalence of an amino acid in a protein site within a subtype is only a poor predictor for whether this amino acid is preferred in this subtype according to the phylogenetic analysis. Therefore, attempts to identify the factors of viral evolution from comparative genomics data should integrate across multiple sources of information.

The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, another closely related midge was discovered, Polypedilum pembai, which is able not only to tolerate desiccation but also to survive multiple desiccation–rehydration cycles. To investigate the evolution of anhydrobiosis in these species, we sequenced and assembled the genome of P. pembai and compared it with P. vanderplanki and also performed a population genomics analysis of several populations of P. vanderplanki and one population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including its amplification in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with postduplication adaptation in the former. Overall, our results suggest an extensive relatively recent and likely ongoing adaptation of the mechanisms of anhydrobiosis.