SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic.

BACKGROUND: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. METHODS: We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. RESULTS: We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. CONCLUSIONS: COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.

The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.

Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.

No transmitted drug resistance to HIV integrase strand-transfer inhibitors after their scale-up in Estonia in 2017.

OBJECTIVES: In Eastern Europe, HIV-1 transmitted drug resistance (TDR) data, especially in the integrase (IN) region, are limited. In Estonia, INSTI (integrase strand transfer inhibitors) TDR has been studied only prior to the INSTI scale-up in late 2010s. The current study aimed to determine the levels of protease (PR), reverse transcriptase (RT) and IN surveillance drug resistance mutations (SDRMs) among newly diagnosed patients in Estonia in 2017. METHODS: The study included 216 newly diagnosed HIV-1 individuals from 1 January until 31 December 2017 in Estonia. Demographic and clinical data were obtained from the Estonian Health Board, the Estonian HIV Cohort Study (E-HIV) and clinical laboratories' databases. The PR-RT and IN regions were sequenced and analysed for SDRMs and subtype determination. RESULTS: Seventy-one percent (151/213) of available HIV-positive samples were successfully sequenced. The overall level of TDR was 7.9% (12/151; 95% CI 4.4%-13.8%); no dual or triple class resistance was detected. No major INSTI mutations were found. The distribution of SDRMs for NNRTI, NRTI and PI was 5.9% (9/151), 1.3% (2/151) and 0.7% (1/151), respectively. The predominant NNRTI mutation was K103N. CRF06_cpx was the predominant variant (59%) in the Estonian HIV-1 population, followed by subtype A (9%) and subtype B (8%). CONCLUSION: Although no major INSTI mutations were found, close monitoring of INSTI SDRMs is needed considering the extensive use of the first- and second-generation INSTIs. PR-RT TDR is slowly rising in Estonia, indicating the need for continuous surveillance in the future. Low genetic barrier NNRTIs should be avoided in the treatment regimens.

A field-wide assessment of differential expression profiling by high-throughput sequencing reveals widespread bias.

We assess inferential quality in the field of differential expression profiling by high-throughput sequencing (HT-seq) based on analysis of datasets submitted from 2008 to 2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p-values, the distribution of which can indicate the validity of assumptions behind the test. From a well-behaved p-value set π0, the fraction of genes that are not differentially expressed can be estimated. We found that only 25% of experiments resulted in theoretically expected p-value histogram shapes, although there is a marked improvement over time. Uniform p-value histogram shapes, indicative of <100 actual effects, were extremely few. Furthermore, although many HT-seq workflows assume that most genes are not differentially expressed, 37% of experiments have π0-s of less than 0.5, as if most genes changed their expression level. Most HT-seq experiments have very small sample sizes and are expected to be underpowered. Nevertheless, the estimated π0-s do not have the expected association with N, suggesting widespread problems of experiments with controlling false discovery rate (FDR). Both the fractions of different p-value histogram types and the π0 values are strongly associated with the differential expression analysis program used by the original authors. While we could double the proportion of theoretically expected p-value distributions by removing low-count features from the analysis, this treatment did not remove the association with the analysis program. Taken together, our results indicate widespread bias in the differential expression profiling field and the unreliability of statistical methods used to analyze HT-seq data.

SARS-CoV-2 dual infection with Delta and Omicron variants in an immunocompetent host: a case report.

Despite the high number of SARS-CoV-2 infections, only a few cases of dual infection have been reported. Here, we describe a case of COVID-19 caused simultaneously by Delta and Omicron variants in an immunocompetent individual during the early emergence of Omicron variant. A 73-year-old man was hospitalized with suspected acute coronary syndrome and a positive test result for SARS-CoV-2 RNA was received during routine testing at the hospital. He experienced mild symptoms of COVID-19 and was discharged on the ninth day. We sequenced the SARS-CoV-2 whole genome from the sample obtained on admission. The viral sequence was classified as PANGO lineage B.1.1.10 by the Galaxy pipeline; however, on detailed manual analysis, we identified the presence of both Delta and Omicron variants. After excluding the possibilities of a recombinant virus or contamination in the sample, we confirmed the presence of dual infection in this patient. We highlight that dual infections with SARS-CoV-2 may be more common than expected but are difficult to detect during the waves of one dominant variant.

The therapeutic effect of Värska mud and Värska mineral water baths on the overuse pain and muscle tension syndromes in the working age population.

The effects of bath therapy are complex and result from a unique interaction between the aquatic environment and the human body functions. The effect of bath therapy depends on both water temperature and chemical additives (mineral substances and humic substances). Värska Resort Centre, in south-eastern Estonia, uses for the balneotherapy the local curative mud and mineral water. The aim of the study was to evaluate and compare the effects of Värska's local mud bath and mineral water bath on moderate musculoskeletal pains in working-age people. The study involved 64 working-age subjects: within two weeks, 32 of them received five general mineral water baths, and another 32 received five general curative mud baths. Pain was assessed with the Nordic Musculosceletal Questionnaire, and muscle tension was measured with a myotonometer in m. erector spinae and m. trapezius. Measurements were performed three times: before the start of the study, immediately after the last procedure, and 2-3 weeks after the last procedure. Both the Värska curative mud bath and the Värska mineral water bath showed a positive effect on musculoskeletal pain and muscle tension. Both procedures can be recommended as drug-free interventions for mild to moderate musculoskeletal pain syndrome and muscle tensions, in both prevention and treatment.

Purification, characterization and plasma half-life of PEGylated soluble recombinant non-HA-binding CD44.

BACKGROUND AND OBJECTIVES: The aim of this study was to increase the serum half-life of recombinant CD44 hyaluronan (HA) binding domain by PEGylation. We have previously found that recombinant soluble CD44 HA binding domain (CD44HABD) and its non-HA-binding triple mutant CD44HABD(R41AY78SY79S) (CD44-3MUT) inhibits angiogenesis and subcutaneous tumor growth. However, this ~12 kDa recombinant protein displays a high serum clearance rate. METHODS: Here, we report the purification of monomeric CD44-3MUT from urea solubilized inclusion bodies using weak anion exchange chromatography and gel filtration. To increase the serum residence time of CD44-3MUT we PEGylated the resulting protein using 20 kDa methoxy-PEG-propionaldehyde. RESULTS: PEGylation of CD44-3MUT prolonged its in vivo serum half-life about 70-fold from 0.03 to 1.8 hours. Along with extended plasma residence time, PEGylation also increased the systemic exposure. By cell impedance assay we confirmed that PEGylated CD44-3MUT maintained its in vitro function. The results from the impedance assay additionally demonstrate that the CD44-3MUT effect on endothelial cells is mediated by vimentin. CONCLUSIONS: In summary, we have developed a purification protocol for large-scale production of CD44-3MUT and generated a PEGylated form of CD44-3MUT. HA binding domain of CD44(CD44HABD) and its modified non-HA binding form (CD44-3MUT) inhibit angiogenesis and tumor growth in vivo without disturbing HA-binding functions. CD44-3MUT has been PEGylated for use as a new type of anti-angiogenic human drug. PEGylation of CD44-3MUT improved pharmacokinetic properties but retains its functional activity.

Soluble CD44 interacts with intermediate filament protein vimentin on endothelial cell surface.

CD44 is a cell surface glycoprotein that functions as hyaluronan receptor. Mouse and human serum contain substantial amounts of soluble CD44, generated either by shedding or alternative splicing. During inflammation and in cancer patients serum levels of soluble CD44 are significantly increased. Experimentally, soluble CD44 overexpression blocks cancer cell adhesion to HA. We have previously found that recombinant CD44 hyaluronan binding domain (CD44HABD) and its non-HA-binding mutant inhibited tumor xenograft growth, angiogenesis, and endothelial cell proliferation. These data suggested an additional target other than HA for CD44HABD. By using non-HA-binding CD44HABD Arg41Ala, Arg78Ser, and Tyr79Ser-triple mutant (CD443MUT) we have identified intermediate filament protein vimentin as a novel interaction partner of CD44. We found that vimentin is expressed on the cell surface of human umbilical vein endothelial cells (HUVEC). Endogenous CD44 and vimentin coprecipitate from HUVECs, and when overexpressed in vimentin-negative MCF-7 cells. By using deletion mutants, we found that CD44HABD and CD443MUT bind vimentin N-terminal head domain. CD443MUT binds vimentin in solution with a Kd in range of 12-37 nM, and immobilised vimentin with Kd of 74 nM. CD443MUT binds to HUVEC and recombinant vimentin displaces CD443MUT from its binding sites. CD44HABD and CD443MUT were internalized by wild-type endothelial cells, but not by lung endothelial cells isolated from vimentin knock-out mice. Together, these data suggest that vimentin provides a specific binding site for soluble CD44 on endothelial cells.

Recombinant CD44-HABD is a novel and potent direct angiogenesis inhibitor enforcing endothelial cell-specific growth inhibition independently of hyaluronic acid binding.

CD44 is the main cellular receptor for hyaluronic acid (HA). We previously found that overexpression of CD44 inhibited tumor growth of mouse fibrosarcoma cells in mice. Here, we show that soluble recombinant CD44 HA-binding domain (CD44-HABD) acts directly onto endothelial cells by inhibiting endothelial cell proliferation in a cell-specific manner. Consequently, soluble recombinant CD44-HABD also blocked angiogenesis in vivo in chick and mouse, and thereby inhibited tumor growth of various origins at very low doses (0.25 mg/kg x day). The antiangiogenic effect of CD44 is independent of its HA-binding capacity, since mutants deficient in HA binding still maintain their antiangiogenic and antiproliferative properties. Recombinant CD44-HABD represents a novel class of angiogenesis inhibitors based on a cell-surface receptor.