Transmission and dynamics of mother-infant gut viruses during pregnancy and early life.

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life.

Diversity and Ecology of Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts.

The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts.

The degree of mu rhythm suppression in women is associated with presence of children as well as empathy and anxiety level.

In experiments on observing and performing social gestures, the level of mu rhythm suppression is associated with the activity of the mirror neuron system (MNS), which is responsible for the perception and understanding of nonverbal signals in social communication. In turn, while MNS activity may be associated primarily with empathy, it is also associated with other psychological and demographic factors affecting the effectiveness of cortical neural networks. In this study, we verified the influence of empathy, state and trait anxiety levels, presence and number of children, and age on the mu-suppression level in 40 women.

Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.

The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used.

ICTV Virus Taxonomy Profile: 2021.

The family comprises enveloped RNA viruses with a linear, positive-sense genome of approximately 12.7 to 15.7 kb.

Stability of the human gut virome and effect of gluten-free diet.

The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet.

Coronavirus replication-transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit.

RNA-dependent RNA polymerases (RdRps) of the (, , and 12 other families) are linked to an amino-terminal (N-terminal) domain, called NiRAN, in a nonstructural protein (nsp) that is released from polyprotein 1ab by the viral main protease (M). Previously, self-GMPylation/UMPylation activities were reported for an arterivirus NiRAN-RdRp nsp and suggested to generate a transient state primed for transferring nucleoside monophosphate (NMP) to (currently unknown) viral and/or cellular biopolymers. Here, we show that the coronavirus (human coronavirus [HCoV]-229E and severe acute respiratory syndrome coronavirus 2) nsp12 (NiRAN-RdRp) has Mn-dependent NMPylation activity that catalyzes the transfer of a single NMP to the cognate nsp9 by forming a phosphoramidate bond with the primary amine at the nsp9 N terminus (N3825) following M-mediated proteolytic release of nsp9 from N-terminally flanking nsps.

A nidovirus perspective on SARS-CoV-2.

Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales.

LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins.

Motivation: To facilitate accurate estimation of statistical significance of sequence similarity in profile-profile searches, queries should ideally correspond to protein domains. For multidomain proteins, using domains as queries depends on delineation of domain borders, which may be unknown. Thus, proteins are commonly used as queries that complicate establishing homology for similarities close to cutoff levels of statistical significance.

Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus.

Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CL), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CL structure (refined to 1.

A planarian nidovirus expands the limits of RNA genome size.

RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100-300 kb range.

PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands.

Background: Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for gastroenteritis while the novel HAstV are associated with cases of neurological disorders. Accurate detection of all known variants by (real-time) PCR is challenging because of the high intra- and intergroup genetic divergence of HAstV.

Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus.

Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.

Domain Organization and Evolution of the Highly Divergent 5' Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus.

In five experimentally characterized arterivirus species, the 5'-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5' rapid amplification of cDNA ends (RACE) protocol.

[CYTOKINES DURING THE HUMAN IMMUNODEFICIENCY VIRUS INFECTION TYPE 1(HIV-1)].

In this work the proinflammatory (IL-1β, IFN-γ, TNF-α, IL-2) and anti-inflammatory (IL-4, IL-10) plasma cytokine levels were evaluated in HIV-infected patients with or without antiretroviral treatment (ART). IFN-γ was detected in 94% samples with and without ART, TNF-α in 88% and IL-2 in 38% samples without ART, as well as in 12% and 30% samples with ART, respectively. Positive correlation was detected between viral RNA and IFN-γ levels (rs = 0.

[THE IMMUNOMODULATORY ACTIVITY OF PLASMA OF PATIENTS INFECTED WITH HUMAN HIV VIRUS].

The study was carried out to investigate impact of plasma of patients infected with human HIV virus receiving and not receiving highly active antiviral therapy on: expression of phenotypic markers of lymphocytes (CD3+, CD3+/CD4+, CD3+/CD8+, CD19+, CD3-/CD (16+56)+, CD3+/CD(16+56)+, CD3+/HLA-DR+, CD4+/CD62L+, CD8+/CD38+) in mononuclear cells of blood of donors and secretion of pro-inflammatory (interleukin-1β, interferon-γ, tumor necrosis factor-α, interleukin-4 and interleukin-10) cytokines. After 24 hours of activation of mononuclear cells with plasmas it was demonstrated that as compared with control groups, in of plasmas of patients with highly active antiviral therapy increasing of number of CD4+ T-cells and decreasing of CD8+ T-cells is observed. The plasmas of patients with highly active antiviral therapy activate in most instances CD4+ T-cells whereas plasmas of patients without treatment--CD8+ T-cells.

[The screening of donor blood on antibodies to nuclear antigen of hepatitis B virus as a tool of increasing of safety of transfusion for patients with diseases of blood system.].

Despite application of decreed modes of laboratory analysis of components of donors' blood, the risk of infection of recipients with hepatitis B virus continues to be actual. The isolated identification of HBsAg provides no control of all categories of persons infected with hepatitis B virus. The analysis of presence of antibodies to nuclear antigen of hepatitis B virus that are the first out of antiviral ones and are preserved for life, is an expedient technique of screening testing of donor's blood that permits implementing an additional selection of donors.

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses.

RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that catalyzes the synthesis of their RNA(s). In the case of positive-stranded RNA viruses belonging to the order Nidovirales, the RdRp resides in a replicase subunit that is unusually large. Bioinformatics analysis of this non-structural protein has now revealed a nidoviral signature domain (genetic marker) that is N-terminally adjacent to the RdRp and has no apparent homologs elsewhere.

Arterivirus nsp12 versus the coronavirus nsp16 2'-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins.

The 3'-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 2'-O-methyltransferase (2'-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 5' cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 5' cap although no candidate MTases have been identified thus far. To address this knowledge gap, we analysed the uncharacterized nsp12 of arteriviruses, which occupies the ORF1b position equivalent to that of the nidovirus 2'-O-MTase (coronavirus nsp16).

[Intramural chronotopography of depolarization of myocardium of heart ventricles of pig (Sus scrofa domesticus)].

Sequence of depolarization of myocardium of pig heart ventricles was studied by the method of multichannel synchronous cardioelectrotopography. There is established formation of areas of early depolarization in subendocardium of interventricular septum and in the base of left ventricle papillary muscles; of multiple foci--in the depth of walls; of areas of late depolarization--in subepicardium of the left ventricle dorsolateral side. As compared with other species of ungulate animals (reindeer and sheep, in pig heart ventricles, differences are revealed in locations of early and late depolarization, a breakdown of the excitation wave into subepicardium.

Morphology of moderator bands (septomarginal trabecula) in porcine heart ventricles.

The morphology of moderator bands in both heart ventricular cavities was examined on macro- and microscopic levels in 14 six-month-old Landrace pigs. One transverse moderator band, measuring 2.9 ± 0.