Replication Rate Research Articles

Emergence and competition of virus variants in respiratory viral infections.

The emergence of new variants of concern (VOCs) of the SARS-CoV-2 infection is one of the main factors of epidemic progression. Their development can be characterized by three critical stages: virus mutation leading to the appearance of new viable variants; the competition of different variants leading to the production of a sufficiently large number of copies; and infection transmission between individuals and its spreading in the population. The first two stages take place at the individual level (infected individual), while the third one takes place at the population level with possible competition between different variants. This work is devoted to the mathematical modeling of the first two stages of this process: the emergence of new variants and their progression in the epithelial tissue with a possible competition between them. The emergence of new virus variants is modeled with non-local reaction-diffusion equations describing virus evolution and immune escape in the space of genotypes. The conditions of the emergence of new virus variants are determined by the mutation rate, the cross-reactivity of the immune response, and the rates of virus replication and death. Once different variants emerge, they spread in the infected tissue with a certain speed and viral load that can be determined through the parameters of the model. The competition of different variants for uninfected cells leads to the emergence of a single dominant variant and the elimination of the others due to competitive exclusion. The dominant variant is the one with the maximal individual spreading speed. Thus, the emergence of new variants at the individual level is determined by the immune escape and by the virus spreading speed in the infected tissue.

Impact of Laboratory-Adapted Intracellular Trypanosoma cruzi Strains on the Activity Profiles of Compounds with Anti-T. cruzi Activity.

Chagas disease is caused by infection with the protozoan parasite, Trypanosoma cruzi. The disease causes ~12,000 deaths annually and is one of the world's 20 neglected tropical diseases, as defined by the World Health Organisation. The drug discovery pipeline for Chagas disease currently has few new clinical candidates, with high attrition rates an ongoing issue. To determine if the Trypanosoma cruzi strain utilised to assess in vitro compound activity impacts activity, a comparison of laboratory-adapted T. cruzi strains from differing geographical locations was undertaken for a selection of compounds with anti-T. cruzi activity. To minimise the possible effect of differences in experimental methodology, the same host cell and multiplicity of infection were utilised. To determine whether the compound exposure time influenced results, activity was determined following exposure for 48 and 72 h of incubation. To ascertain whether replication rates affected outcomes, comparative rates of replication of the T. cruzi strains were investigated, using the nucleoside analogue, 5-ethynyl-2'-deoxyuridine. Minimal differences in the in vitro activity of compounds between strains were observed following 48 h incubation, whereas significant differences were observed following 72 h incubation, in particular for the cytochrome P450 inhibitors tested and the cell cycle inhibitor, camptothecin. Thus, the use of panels of laboratory adapted strains in vitro may be dependent on the speed of action that is prioritised. For the identification of fast-acting compounds, an initial shorter duration assay using a single strain may be used. A longer incubation to identify compound activity may alternatively require profiling of compounds against multiple T. cruzi strains.

How did life become cellular?

How did life become cellular?

Infection burdens and virulence under heat stress: ecological and evolutionary considerations.

As a result of global change, hosts and parasites (including pathogens) are experiencing shifts in their thermal environment. Despite the importance of heat stress tolerance for host population persistence, infection by parasites can impair a host's ability to cope with heat. Host-parasite eco-evolutionary dynamics will be affected if infection reduces host performance during heating. Theory predicts that within-host parasite burden (replication rate or number of infecting parasites per host), a key component of parasite fitness, should correlate positively with virulence-the harm caused to hosts during infection. Surprisingly, however, the relationship between within-host parasite burden and virulence during heating is often weak. Here, we describe the current evidence for the link between within-host parasite burden and host heat stress tolerance. We consider the biology of host-parasite systems that may explain the weak or absent link between these two important host and parasite traits during hot conditions. The processes that mediate the relationship between parasite burden and host fitness will be fundamental in ecological and evolutionary responses of host and parasites in a warming world. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Infectious disease ecology and evolution in a changing world.

Infectious disease ecology and evolution in a changing world.

A hybrid individual-based mathematical model to study bladder infections

IntroductionBladder infections are common, affecting millions each year, and are often recurrent problems.MethodsWe have developed a spatial mathematical framework consisting of a hybrid individual-based model to simulate these infections in order to understand more about the bacterial mechanisms and immune dynamics. We integrate a varying bacterial replication rate and model bacterial shedding as an immune mechanism.ResultsWe investigate the effect that varying the initial bacterial load has on infection outcome, where we find that higher bacterial burden leads to poorer outcomes, but also find that only a single bacterium is needed to establish infection in some cases. We also simulate an immunocompromised environment, confirming the intuitive result that bacterial spread typically progresses at a higher rate.ConclusionsWith future model developments, this framework is capable of providing new clinical insight into bladder infections.

Coronavirus infection in chemosensory cells.

Clinical manifestations of human coronavirus (HCoV)-related diseases are mostly related to the respiratory system, although secondary complications such as headache, anosmia, ageusia, and myalgia have been reported. HCoV infection and replication in chemosensory cells associated with ageusia and anosmia is poorly understood. Here, we characterized HCoV-OC43 and SARS-CoV-2 infection in two types of chemosensory cells, olfactory and taste cells, with their unique molecular and histological characteristics. We first assessed HCoV-OC43 infection in in vitro cultured human olfactory epithelial cells (hOECs) and fungiform taste papilla (HBO) cells. Interestingly, while both cell types were susceptible to HCoV-OC43 infection, viral replication rates were significantly reduced in HBO cells compared to hOECs. More interestingly, while culture media from hOECs was able to produce secondary infection in Vero cells, there was very limited secondary infection from HBO cells, suggesting that HBO cells may not be able to release infectious virus. On the other hand, unlike HCoV-OC43, SARS-CoV-2 showed comparable levels of viral infection rates in both hOECs and HBO cells. Furthermore, our RT-qPCR-based gene array studies revealed that several key genes involved in taste and olfactory functions were significantly altered by SARS-CoV-2 infection. These results may suggest a possible mechanism associated with chemosensory symptoms, such as anosmia and ageusia in patients infected with SARS-CoV-2.

A discipline-wide investigation of the replicability of Psychology papers over the past two decades

Conjecture about the weak replicability in social sciences has made scholars eager to quantify the scale and scope of replication failure for a discipline. Yet small-scale manual replication methods alone are ill-suited to deal with this big data problem. Here, we conduct a discipline-wide replication census in science. Our sample (N = 14,126 papers) covers nearly all papers published in the six top-tier Psychology journals over the past 20 y. Using a validated machine learning model that estimates a paper's likelihood of replication, we found evidence that both supports and refutes speculations drawn from a relatively small sample of manual replications. First, we find that a single overall replication rate of Psychology poorly captures the varying degree of replicability among subfields. Second, we find that replication rates are strongly correlated with research methods in all subfields. Experiments replicate at a significantly lower rate than do non-experimental studies. Third, we find that authors' cumulative publication number and citation impact are positively related to the likelihood of replication, while other proxies of research quality and rigor, such as an author's university prestige and a paper's citations, are unrelated to replicability. Finally, contrary to the ideal that media attention should cover replicable research, we find that media attention is positively related to the likelihood of replication failure. Our assessments of the scale and scope of replicability are important next steps toward broadly resolving issues of replicability.

Long-term passaging of pseudo-typed SARS-CoV-2 reveals the breadth of monoclonal and bispecific antibody cocktails.

The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses challenges to the effectiveness of neutralizing antibodies. Rational design of antibody cocktails is a realizable approach addressing viral immune evasion. However, evaluating the breadth of antibody cocktails is essential for understanding the development potential. Here, based on a replication competent vesicular stomatitis virus model that incorporates the spike of SARS-CoV-2 (VSV-SARS-CoV-2), we evaluated the breadth of a number of antibody cocktails consisting of monoclonal antibodies and bispecific antibodies by long-term passaging the virus in the presence of the cocktails. Results from over two-month passaging of the virus showed that 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 from these cocktails were highly resistant to random mutation, and there was no breakthrough after 30 rounds of passaging. As a control, antibody REGN10933 was broken through in the third passage. Next generation sequencing was performed and several critical mutations related to viral evasion were identified. These mutations caused a decrease in neutralization efficiency, but the reduced replication rate and ACE2 susceptibility of the mutant virus suggested that they might not have the potential to become epidemic strains. The 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 cocktails that picked from the VSV-SARS-CoV-2 system efficiently neutralized all current variants of concern and variants of interest including the most recent variants Delta and Omicron, as well as SARS-CoV-1. Our results highlight the feasibility of using the VSV-SARS-CoV-2 system to develop SARS-CoV-2 antibody cocktails and provide a reference for the clinical selection of therapeutic strategies to address the mutational escape of SARS-CoV-2.

Differential Gene Expression Pattern of Importin β3 and NS5 in C6/36 Cells Acutely and Persistently Infected with Dengue Virus 2.

The establishment of persistent dengue virus infection within the cells of the mosquito vector is an essential requirement for viral transmission to a new human host. The mechanisms involved in the establishment and maintenance of persistent infection are not well understood, but it has been suggested that both viral and cellular factors might play an important role. In the present work, we evaluated differential gene expression in Aedes albopictus cells acutely (C6/36-HT) and persistently infected (C6-L) with Dengue virus 2 by cDNA-AFLP. We observed that importin β3 was upregulated in noninfected cells compared with C6-L cells. Using RT-qPCR and plaque assays, we observed that Dengue virus levels in C6-L cells essentially do not vary over time, and peak viral titers in acutely infected cells are observed at 72 and 120 h postinfection. The expression level of importin β3 was higher in acutely infected cells than in persistently infected cells; this correlates with higher levels of NS5 in the nucleus of the cell. The differential pattern of importin β3 expression between acute and persistent infection with Dengue virus 2 could be a mechanism to maintain viral infection over time, reducing the antiviral response of the cell and the viral replicative rate.

Environmental water in Kolkata is suitable for the survival of Vibrio cholerae O1

Many patients with cholera emerge in Kolkata, India throughout the year. Such emergency indicates that cholera toxin-producing Vibrio cholerae O1 (toxigenic V. cholerae O1) are widespread in Kolkata. This suggests that the suitable conditions for replication of toxigenic V. cholerae O1 is provided in Kolkata. In previous studies, we found that the replication rate of toxigenic V. cholerae O1 is low in the low ionic aqueous solution. Then we measured the ion concentration in the environmental water of Kolkata. As a control, we measured them in Japanese environmental water. The ion concentration in the environmental water of Kolkata was significantly high. Then, we examined the survival of toxigenic V. cholerae O1 in groundwater from Kolkata and found that V. cholerae O1 survive for long time in the solution but not in the solution diluted with Milli Q water. In addition, we found that V. cholerae O1 proliferated in environmental water of Kolkata to which a small amount of nutrient was added, but did not grow in the environmental water diluted with water to which the same amount of nutrient was added. These results indicate that the environmental water from Kolkata is suitable for survival of V. cholerae O1.

Climate change and its extensions in infectious diseases: South-Eastern Europe under focus

Climate change is a result of natural processes and human-made activities influencing the atmosphere. Many infectious diseases are climate-sensitive and their nature and epidemiology are changing in parallel with the change in climatic conditions and global warming. Increased replication rates of pathogens at higher temperatures, extended transmission seasons, migration of vectors or human populations are some outcomes of the changing climate, to trigger new concerns including new epidemics with old or new pathogens. Climate change is presenting itself today as an urgent global health threat and it requires immediate international action with high priority. Infectious diseases in relation to changing climatic conditions are reviewed with predominating current examples, keeping a focus on Europe with particular emphasis on South-Eastern European and Eurasian regions.

Selecting for infectivity across metapopulations can increase virulence in the social microbe Bacillus thuringiensis.

Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, for many invertebrate pathogens, passage has been applied naively without a full theoretical understanding of how best to select for increased virulence and this has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. In this study, we tested how varying mutation supply and selection for infectivity or pathogen yield (population size in hosts) affected the evolution of virulence against resistant hosts in the specialist insect pathogen Bacillus thuringiensis, aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between subpopulations in a metapopulation prevents social cheating, acts to retain key virulence plasmids, and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and possible loss of function in putative regulatory genes but not with altered expression of the primary virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life-history traits such as faster replication or larger population sizes can reduce virulence in social microbes.

Association of Torquetenovirus Viremia with Physical Frailty and Cognitive Impairment in Three Independent European Cohorts

Introduction: Immunosenescence and inflammaging have been implicated in the pathophysiology of frailty. Torquetenovirus (TTV), a single-stranded DNA anellovirus, the major component of the human blood virome, shows an increased replication rate with advancing age. An elevated TTV viremia has been associated with an impaired immune function and an increased risk of mortality in the older population. The objective of this study was to analyze the relation between TTV viremia, physical frailty, and cognitive impairment. Methods: TTV viremia was measured in 1,131 nonfrail, 45 physically frail, and 113 cognitively impaired older adults recruited in the MARK-AGE study (overall mean age 64.7 ± 5.9 years), and then the results were checked in two other independent cohorts from Spain and Portugal, including 126 frail, 252 prefrail, and 141 nonfrail individuals (overall mean age: 77.5 ± 8.3 years). Results: TTV viremia ≥4log was associated with physical frailty (OR: 4.69; 95% CI: 2.06–10.67, p < 0.0001) and cognitive impairment (OR: 3.49, 95% CI: 2.14–5.69, p < 0.0001) in the MARK-AGE population. The association between TTV DNA load and frailty status was confirmed in the Spanish cohort, while a slight association with cognitive impairment was observed (OR: 1.33; 95% CI: 1.000–1.773), only in the unadjusted model. No association between TTV load and frailty or cognitive impairment was found in the Portuguese sample, although a negative association between TTV viremia and MMSE score was observed in Spanish and Portuguese females. Conclusions: These findings demonstrate an association between TTV viremia and physical frailty, while the association with cognitive impairment was observed only in the younger population from the MARK-AGE study. Further research is necessary to clarify TTV’s clinical relevance in the onset and progression of frailty and cognitive decline in older individuals.

Liposomal Delivery of Saquinavir to Macrophages Overcomes Cathepsin Blockade by Mycobacterium tuberculosis and Helps Control the Phagosomal Replicative Niches.

Mycobacterium tuberculosis is able to establish a chronic colonization of lung macrophages in a controlled replication manner, giving rise to a so-called latent infection. Conversely, when intracellular bacteria undergo actively uncontrolled replication rates, they provide the switch for the active infection called tuberculosis to occur. Our group found that the pathogen is able to manipulate the activity of endolysosomal enzymes, cathepsins, directly at the level of gene expression or indirectly by regulating their natural inhibitors, cystatins. To provide evidence for the crucial role of cathepsin manipulation for the success of tuberculosis bacilli in their intracellular survival, we used liposomal delivery of saquinavir. This protease inhibitor was previously found to be able to increase cathepsin proteolytic activity, overcoming the pathogen induced blockade. In this study, we demonstrate that incorporation in liposomes was able to increase the efficiency of saquinavir internalization in macrophages, reducing cytotoxicity at higher concentrations. Consequently, our results show a significant impact on the intracellular killing not only to reference and clinical strains susceptible to current antibiotic therapy but also to multidrug- and extensively drug-resistant (XDR) Mtb strains. Altogether, this indicates the manipulation of cathepsins as a fine-tuning strategy used by the pathogen to survive and replicate in host cells.

Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses.

Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.

СОЦИАЛЬНО-ЭКОНОМИЧЕСКИЕ АСПЕКТЫ ИЗМЕНЕНИЯ ПИЩЕВЫХ ПРИВЫЧЕК ВСЛЕДСТВИЕ ПАНДЕМИИ COVID-19

Severe consequences of the COVID-19 pandemic, both in demographic and socio-economic aspects, have predetermined many scientific studies. The scientific community in the field of medicine has increased interest in the role of vitamin Д in the development of acute respiratory infections. Vitamin Д is believed to be responsible for modulating the immune response. The mechanism of its action is associated with a decrease in the rate of replication of the virus, an increase in the concentration of anti-inflammatory cytokines, thereby reducing pro-inflammatory cytokines that cause pneumonia and lung damage. At the same time, the scientific community in the field of economics and sociology has deepened the factor analysis of the impact of the COVID-19 pandemic on changes in consumer behavior due to changes in dietary habits associated with vitamin Д enrichment. Non-medical attention to vitamin Д in terms of its protective characteristics for the human body against acute respiratory infections, which include coronavirus, as well as an increased emphasis on information that the absence of vitamin Д deficiency reduces the likelihood of complications (such as “cytokine storm”) and death from COVID-19, led to increased the demand for food fortified with vitamin D, as well as dietary supplements.

Development of a nomogram for predicting pathological complete response in luminal breast cancer patients following neoadjuvant chemotherapy

Given the low chance of response to neoadjuvant chemotherapy (NACT) in luminal breast cancer (LBC), the identification of predictive factors of pathological complete response (pCR) represents a challenge. A multicenter retrospective analysis was performed to develop and validate a predictive nomogram for pCR, based on pre-treatment clinicopathological features. Clinicopathological data from stage I-III LBC patients undergone NACT and surgery were retrospectively collected. Descriptive statistics was adopted. A multivariate model was used to identify independent predictors of pCR. The obtained log-odds ratios (ORs) were adopted to derive weighting factors for the predictive nomogram. The receiver operating characteristic analysis was applied to determine the nomogram accuracy. The model was internally and externally validated. In the training set, data from 539 patients were gathered: pCR rate was 11.3% [95% confidence interval (CI): 8.6-13.9] (luminal A-like: 5.3%, 95% CI: 1.5-9.1, and luminal B-like: 13.1%, 95% CI: 9.8-13.4). The optimal Ki67 cutoff to predict pCR was 44% (area under the curve (AUC): 0.69; p < 0.001). Clinical stage I-II (OR: 3.67, 95% CI: 1.75-7.71, p = 0.001), Ki67 ⩾44% (OR: 3.00, 95% CI: 1.59-5.65, p = 0.001), and progesterone receptor (PR) <1% (OR: 2.49, 95% CI: 1.15-5.38, p = 0.019) were independent predictors of pCR, with high replication rates at internal validation (100%, 98%, and 87%, respectively). According to the nomogram, the probability of pCR ranged from 3.4% for clinical stage III, PR > 1%, and Ki67 <44% to 53.3% for clinical stage I-II, PR < 1%, and Ki67 ⩾44% (accuracy: AUC, 0.73; p < 0.0001). In the validation set (248 patients), the predictive performance of the model was confirmed (AUC: 0.7; p < 0.0001). The combination of commonly available clinicopathological pre-NACT factors allows to develop a nomogram which appears to reliably predict pCR in LBC.

Repurposed drug molecules targeting NSP12 protein of SARS-CoV-2: An in-silico study

&lt;abstract&gt; &lt;p&gt;The emergence of SARS-CoV-2 created a havoc worldwide, causing high morbidity, serious complications and mortality. The ORF1ab of SARS-CoV-2 has 16 non-structural proteins which are required for genome replication and transcription. All of these are druggable targets, of which NSP12 (RNA-dependent RNA polymerase), was selected as a potential target for drug molecules. Remdesivir is a recommended drug for SARS-CoV-2 and it targets the RdRp protein. Although Remdesivir was given to COVID-19 patients based on their clinical manifestations, yet the transmission and spread of the virus continued and to add to its pandemicity, new variants emerged from time to time. This necessitates the need for molecular modification of existing antiviral drugs so that more precise targets for halting viral replication can be selected. For this, the approach used was repurposing of the existing drugs. In the present study, ten FDA-approved drugs were chosen on the basis of their properties of inhibiting the RdRp protein. These drugs were subjected for checking the docking score with the target protein. Of these, Remdesivir, Ribavirin, Favipiravir and Baloxavir were taken for further analysis on the basis of their best scores. These drugs were then modified to check the efficiency to inhibit the RdRp and to stop the replication rate of the virus. We docked the modified drugs with the macrodomain of RdRp by using the CB-Dock web server and checked the binding affinity and amino acid contact residues. The modified drugs were also checked for bioactivity in the Molinspiration cheminformatics online tool. Our results showed increased affinity for RdRp of SARS-CoV-2 when compared to the original compound. We also checked the synthetic accessibility of the drugs using the SwissADME tool. The study showed promising results when modified. The findings reported need further confirmation through wet lab studies.&lt;/p&gt; &lt;/abstract&gt;

The effects of medium nutritional profile on Bacillus sp. Par 3 plant-growth promoting and biocontrol activity against Botrytis cinerea

Substantial agricultural losses resulting from plant diseases caused by different plant pathogens are one of the worldwide challenges today. Among these, Botrytis cinerea, responsible for gray mold disease, stands out for its capacity to devastate significant quantities of diverse valuable crops. Utilization of biocontrol agents for suppressing phytopathogens has become imperative, and bacteria from the genus Bacillus hold an immense potential due to their rapid replication rate, resistance to adverse environmental conditions, enhanced effectiveness in promoting plant growth and broad-spectrum activity. The objective of this study was to determine the best sources of carbon, nitrogen and phosphorus in cultivation media with the aim of maximizing both antimicrobial activity against B. cinerea and plantgrowth-promoting (PGP) potential during the early stages of cucumber plant development, exhibited by Bacillus sp. isolate Par 3. Antimicrobial activity was tested using the well diffusion method. The influence of Bacillus sp. isolate Par 3 on plant germination was tested on cucumber seeds. The largest inhibition zones were achieved in two cases, with 1) sucrose as carbon source, ammonium nitrate as nitrogen source, and diammonium hydrogen phosphate as phosphorus source and 2) glycerol as carbon source, ammonium nitrate as nitrogen source and dipotassium hydrogen phosphate as phosphorus source. Seeds treated with a culture liquid of Bacillus sp. isolate Par 3 using the optimized medium exhibited the best results in terms of cucumber germination percentage (100%), root length (53.09 mm) and shoot length (13.26 mm). Bacillus sp. Par 3 isolate was identified as Bacillus subtilis using 16S rRNA gene sequencing. The results of this study underscore the significance of media optimization for the production of biocontrol agents, taking into account both antimicrobial efficacy and PGP characteristics.