Search Results (264)

We discuss the spread of epidemics caused by two viruses which cannot infect the same individual at the same time. The mathematical modeling of this epidemic leads to a kind of SIIRR model with two groups of infected individuals and two groups of recovered individuals. An additional assumption is that after recovering from one of the viruses, the individual cannot be infected by the other virus. The mathematical model consists of five equations which can be reduced to a system of three differential equations for the susceptible and for the recovered individuals. This system has analytical solutions for the case when one of the viruses infects many more individuals than the other virus. Cases which are more complicated than this one can be studied numerically. The theory is applied to the study of waves of popularity of an individual/groups of individuals or of an idea/group of ideas in the case of the presence of two opposite opinions about the popularity of the corresponding individual/group of individuals or idea/group of ideas. We consider two cases for the initial values of the infected individuals: (a) the initial value of the individuals infected with one of the viruses is much larger than the initial values of the individuals infected by the second virus, and (b) the two initial values of the infected individuals are the same. The following effects connected to the evolution of the numbers of infected individuals are observed: 1. arising of bell-shaped profiles of the numbers of infected individuals; 2. suppression of popularity; 3. faster increase–faster decrease effect for the peaks of the bell-shaped profiles; 4. peak shift in the time; 5. effect of forgetting; 6. window of dominance; 7. short-term win–long-term loss effect; 8. effect of the single peak. The proposed SIIRR model is used to build a mathematical theory of popularity waves where a person or idea can have positive and negative popularity at the same time and these popularities evolve with time. Full article

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underwent significant mutations, resulting in the Omicron variant. Methods: In this study, we analyzed blood samples from 98 patients with acute coronavirus disease 19 (COVID-19) hospitalized during the initial SARS-CoV-2 wave and the onset of Omicron in 2021. High-resolution melting (HRM) analysis of PCR products was used to analyze RNA extracted from clinical samples collected in July and November 2021 from patients infected with SARS-CoV-2. Results: HRM analysis revealed a characteristic deletion in the N protein RNA of the virus isolated in November 2021, associated with the Omicron variant. Elevated levels of inflammatory markers and interleukin-6 (IL-6) were observed in both waves of COVID-19. Complement levels and IgG and IgM antibodies to SARS-CoV-2 were detected more often during the second wave. An increase in hemagglutinin-inhibiting (HI) antibodies against influenza viruses was observed in paired blood specimens from moderate to severe COVID-19 patients during both outbreaks. Conclusions: Patients admitted during both waves of COVID-19 showed a significant rise in inflammatory markers, suggesting that Omicron triggers inflammatory responses. The rapid formation of IgM and IgG in Omicron may indicate a faster immune response. Seasonal flu may negatively impact the clinical course of coronavirus infections. Full article

Rotavirus is an enteric virus that leads to 200,000 deaths worldwide every year. The live-cell imaging evaluating rotavirus infection of MA104 cells revealed that rotavirus replication and spread occurs in a spatially controlled manner. Specifically, following initial rotavirus infection, the infected cells die, and the second round of infection occurs in the restricted area surrounding the initially infected cell. Interestingly, we found that the time required to establish the secondary infection is shorter compared to the time required for the initial infection. To determine if this increase in the kinetic of secondary infection was due to the early release of viruses or priming of the cells that are infected during the secondary infection, we used a combination of live-cell microscopy, trypsin neutralization assays, and the pharmacological inhibition of calcium signaling. Together, our results show that the second round of infection required rotavirus to be released and accessible to extracellular proteases. In addition, we found that the calcium wave induced upon rotavirus infection was critical for initial infection but did not play a role in the establishment of a secondary infection. Finally, we uncovered that high viral titers released from the initial infection were sufficient to accelerate the rate of the secondary infection. Full article

Background: The wave of wartime migration from Ukraine has raised a number of concerns about infectious diseases, the prevalence of which is higher in Ukraine than in host countries, with hepatitis C virus (HCV) infection being one of them. Our analysis aimed to assess the percentage of HCV-infected Ukrainian refugees under care in Polish centers providing antiviral diagnosis and therapy, to evaluate their characteristics and the effectiveness of treatment with direct-acting antiviral drugs (DAAs). Methods: The analysis included patients of Polish and Ukrainian nationality treated for HCV infection between 2022 and 2024 in Polish hepatology centers. Data were collected retrospectively and completed online. Results: In the population of 3911 patients with chronic hepatitis C treated with DAAs in 16 Polish centers in 2022–2024, there were 429 war refugees from Ukraine, accounting for 11% of the total treated. The Ukrainian population was significantly younger (45.7 vs. 51 years, p < 0.001) and had a higher percentage of women (50.3% vs. 45.3%, p = 0.048) compared to Polish patients. Patients of Ukrainian origin had less advanced liver disease and were significantly less likely to have comorbidities and the need for comedications. Coinfection with human immunodeficiency virus was significantly more common in Ukrainians than in Polish patients, 16.1% vs. 5.9% (p < 0.001). The distribution of HCV genotypes (GTs) also differed; although GT1b predominated in both populations, its frequency was significantly higher in the Polish population (62.3% vs. 44.5%, p < 0.001), while the second most common GT3 was significantly more common in Ukrainian patients (30.5% vs. 16.2%, p < 0.001). Conclusions: Documented differences in patient characteristics did not affect the effectiveness of antiviral therapy, which exceeded 97% in both populations, but there was a higher rate of those lost to follow-up among Ukrainian patients. Full article

The development of Long COVID is a complex disease process that may be partially driven by neuroinflammation. Antipsychotics have been shown to exert neuroprotective effects under certain conditions. Our study aimed to determine if veterans treated with antipsychotics and/or selective serotonin reuptake inhibitors (SSRIs) for a psychiatric condition had a reduced risk of developing long-term COVID. We conducted a retrospective cohort study with two cohorts of patients based on the COVID-19 wave in which the patient’s initial infection occurred (Cohort 1: alpha/beta waves, and Cohort 2: delta/omicron waves) with stratification by age. A multivariate logistic regression model was used to evaluate the association between the use of antipsychotics and Long COVID diagnosis. In Cohort 1, antipsychotic use was associated with 43% and 34% reductions in the odds of developing Long COVID in patients aged <65 and >65 years, respectively. This association was reduced in the second cohort to 11% in patients aged <65 years and without an association over 65 years of age. SSRIs showed no benefit in either age group or cohort. Our results show that antipsychotic use for the treatment of a mental health condition was associated with a reduction in the risk of developing Long COVID, and the magnitude of this reduction varied between COVID-19 cohorts. Full article

Since the first reported case of COVID-19 in December 2019, several SARS-CoV-2 variants have evolved, and some of them have shown higher transmissibility, becoming the prevalent strains. Genomic epidemiological investigations into strains from different time points, including the early stages of the pandemic, are very crucial for understanding the evolution and transmission patterns. Using whole-genome sequences, our study describes the early landscape of SARS-CoV-2 variants in central India retrospectively (including the first known occurrence of SARS-CoV-2 in Madhya Pradesh). We performed amplicon-based whole-genome sequencing of randomly selected SARS-CoV-2 isolates (n = 38) collected between 2020 and 2022 at state level VRDL, ICMR-NIRTH, Jabalpur, from 11899 RT-qPCR-positive samples. We observed the presence of five lineages, namely B.1, B.1.1, B.1.36.8, B.1.195, and B.6, in 19 genomes from the first wave cases and variants of concern (VOCs) lineages, i.e., B.1.617.2 (Delta) and BA.2.10 (Omicron) in the second wave cases. There was a shift in mutational pattern in the spike protein coding region of SRAS-CoV-2 strains from the second wave in contrast to the first wave. In the first wave of infections, we observed variations in the ORF1Ab region, and with the emergence of Delta lineages, the D614G mutation associated with an increase in infectivity became a prominent change. We have identified five immune escape variants in the S gene, P681R, P681H, L452R, Q57H, and N501Y, in the isolates collected during the second wave. Furthermore, these genomes were compared with 2160 complete genome sequences reported from central India that encompass 109 different SARS-CoV-2 lineages. Among them, VOC lineages Delta (28.93%) and Omicron (56.11%) were circulating predominantly in this region. This study provides useful insights into the genetic diversity of SARS-CoV-2 strains over the initial course of the COVID-19 pandemic in central India. Full article

This study analyzes immune responses to SARS-CoV-2 vaccination and infection, including asymptomatic cases, focusing on infection risks during the Omicron wave, particularly among high-risk healthcare workers. In the KoCo-Impf study, we monitored 6088 vaccinated participants in Munich aged 18 and above. From 13 May to 31 July 2022, 2351 participants were follow-uped. Logistic regression models evaluated primary, secondary, and breakthrough infections (BTIs). Roche Elecsys^® Anti-SARS-CoV-2 assays detected prior infections (via anti-Nucleocapsid antibodies) and assessed vaccination/infection impact (via anti-Spike antibodies) using dried blood spots. Our findings revealed an anti-Nucleocapsid seroprevalence of 44.1%. BTIs occurred in 38.8% of participants, with reinfections in 48.0%. Follow-up participation was inversely associated with current smoking and non-vaccination, while significantly increasing with age and receipt of three vaccine doses. Larger household sizes and younger age increased infection risks, whereas multiple vaccinations and older age reduced them. Household size and specific institutional subgroups were risk factors for BTIs. The anti-Nucleocapsid value prior to the second infection was significantly associated with reinfection risk. Institutional subgroups influenced all models, underscoring the importance of tailored outbreak responses. The KoCo-Impf study underscores the importance of vaccination, demographic factors, and institutional settings in understanding SARS-CoV-2 infection risks during the Omicron wave. Full article

Objective: This cross-sectional study aimed to identify potential predictors of poor mental health outcomes among healthcare workers in two different waves of the COVID-19 emergency in Italy. Methods: An online survey collected data from N = 557 healthcare workers (21–77 years). The study predictors were sociodemographic characteristics, occupational status, factors related to the work environment, COVID-19-related adverse events, and lifetime traumatic events. The poor mental health outcomes that were considered were depersonalization/derealization, anxiety, depression, and somatization symptoms. Results: The main predictors of poor mental health outcomes were sleeping less than six hours per night, inadequate protective equipment measures, female gender, personal and familiar infection, living alone, working as a nurse, and working in a COVID-19 ward. Healthcare workers in 2021 reported experiencing more serious accidents and stressful events than those of the first wave. Depressive symptoms and COVID-19-related adverse events were higher in the second pandemic outbreak than in the first. Conclusions: Preventive strategies against poor mental health outcomes should be particularly focused on female nurses who live alone, work in areas with high infection rates, and have experienced the COVID-19 infection personally or who are close to people that have experienced the infection. Full article

The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease’s severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments. Full article

Plasma technology, relatively new in the fields of biomedicine, agriculture, and ecology, is the subject of intensive research as a prospective means of decontamination of various microorganisms (bacteria, viruses, and fungi). The objectives of the present study were to follow the effect of cold atmospheric plasma (CAP) treatment on in vitro grown plum plants (Prunus domestica L. ‘Kyustendilska sinya’ cv.) and the possibility of eradicating or inactivating plum pox virus (PPV) causing Sharka disease by CAP. The source tree is naturally co-infected by PPV (both M and D strains). In the experiments, two different plasma sources were used. First, a surface-wave-sustained Argon plasma torch and second, an underwater diaphragm discharge. For the treatments, nodal segments (10 mm in length) from in vitro cultured plum plants with or without one leaf were prepared. Apical shoots from treated plants (PPV-positive and negative clones as well non-treated controls) were cultivated in vitro for four passages. Then they were rooted and acclimatized to ex vitro conditions, and their virus status was observed periodically for more than 3 years after treatment for the appearance of Sharka symptoms. All plants, acclimatized to ex vitro conditions, were tested for PPV by immune capture–reverse transcription–polymerase chain reaction (IC-RT-PCR). As a first step in understanding the plasma treatment of living plants, a plasma treatment variant causing no damage must be established; this has been done in our previous works. Treatment of plants by plasma with parameters that have been carefully selected leads to better development than the non-treated plants. In the treated in vitro plants, no significant differences were found in the number and length of shoots compared to the control plantlets. In ex vitro acclimated plants, greater stem length was reported, but no differences in leaf number were observed. No significant differences in growth were recorded between the control and plants that were treated twice or three times. At this stage, 3 years after ex vitro cultivation in a greenhouse, Sharka symptoms were not registered on treated in vitro negative PPV plants, and the virus was not detected by IC-RT-PCR. Very mild symptoms were showing in CAP-treated PPV-positive plants. Development of typical Sharka symptoms on non-treated controls were observed. Full article

Background: Severe coagulation abnormalities are common in patients with COVID-19 infection. We aimed to investigate the relationship between pro-inflammatory cytokines and coagulation parameters concerning socio-demographic, clinical, and laboratory characteristics. Methods: Our study included patients hospitalized during the second wave of COVID-19 in the Republic of Serbia. We collected socio-demographic, clinical, and blood-sample data for all patients. Cytokine levels were measured using flow cytometry. Results: We analyzed data from 113 COVID-19 patients with an average age of 58.15 years, of whom 79 (69.9%) were male. Longer duration of COVID-19 symptoms before hospitalization (B = 69.672; p = 0.002) and use of meropenem (B = 1237.220; p = 0.014) were predictive of higher D-dimer values. Among cytokines, higher IL-5 values significantly predicted higher INR values (B = 0.152; p = 0.040) and longer prothrombin times (B = 0.412; p = 0.043), and higher IL-6 (B = 0.137; p = 0.003) predicted longer prothrombin times. Lower IL-17F concentrations at admission (B = 0.024; p = 0.050) were predictive of higher INR values, and lower IFN-γ values (B = −0.306; p = 0.017) were predictive of higher aPTT values. Conclusions: Our findings indicate a significant correlation between pro-inflammatory cytokines and coagulation-related parameters. Factors such as the patient’s level of education, gender, oxygen-therapy use, symptom duration before hospitalization, meropenem use, and serum concentrations of IL-5, IL-6, IL-17F, and IFN-γ were associated with worse coagulation-related parameters. Full article

During the COVID-19 pandemic, several vaccines were developed to limit the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, due to SARS-CoV-2 mutations and uneven vaccination coverage among populations, a series of COVID-19 waves have been caused by different variants of concern (VOCs). Despite the updated vaccine formulations for the new VOC, the benefits of additional COVID-19 vaccine doses have raised many doubts, even among high-risk groups such as healthcare workers (HCWs). We examined the factors underlying hesitancy to receive COVID-19 booster vaccine doses and analysed the anti-SARS-CoV-2 IgG antibody response after booster vaccination among HCWs. Our study found that 42% of the HCWs were hesitant about the second booster dose, while 7% reported no intent to get vaccinated with any additional doses. As reasons for not vaccinating, participants most frequently highlighted lack of time, negative experiences with previous vaccinations, and immunity conferred by past infections. In addition, we found the lowest post-vaccination antibody titres among HCWs who did not receive any vaccine booster dose and the highest among HCWs vaccinated with two booster doses. Full article

Patients hospitalized in ICUs with severe COVID-19 are at risk for developing hospital-acquired infections, especially infections caused by Pseudomonas aeruginosa. We aimed to describe the evolution of P. aeruginosa infections in ICUs at CHRU-Nancy (France) in patients with severe COVID-19 during the three initial waves of COVID-19. The second aims were to analyze P. aeruginosa resistance and to describe the antibiotic treatments. We conducted a retrospective cohort study among adult patients who were hospitalized for acute respiratory distress syndrome due to COVID-19 and who developed a hospital-acquired infection caused by P. aeruginosa during their ICU stay. Among the 51 patients included, most were male (90%) with comorbidities (77%), and the first identification of P. aeruginosa infection occurred after a median ICU stay of 11 days. Several patients acquired infections with MDR (27%) and XDR (8%) P. aeruginosa strains. The agents that strains most commonly exhibited resistance to were penicillin + β-lactamase inhibitors (59%), cephalosporins (42%), monobactams (32%), and carbapenems (27%). Probabilistic antibiotic treatment was prescribed for 49 patients (96%) and was subsequently adapted for 51% of patients after antibiogram and for 33% of patients after noncompliant antibiotic plasma concentration. Hospital-acquired infection is a common and life-threatening complication in critically ill patients. Efforts to minimize the occurrence and improve the treatment of such infections, including infections caused by resistant strains, must be pursued. Full article

COVID-19 breakthrough infection (BTI) can occur despite vaccination. Using a multi-centre, prospective, observational Canadian cohort of people with HIV (PWH) receiving ≥2 COVID-19 vaccines, we compared the SARS-CoV-2 spike (S) and receptor-binding domain (RBD)-specific IgG levels 3 and 6 months post second dose, as well as 1 month post third dose, in PWH with and without BTI. BTI was defined as positivity based on self-report measures (data up to last study visit) or IgG data (up to 1 month post dose 3). The self-report measures were based on their symptoms and either a positive PCR or rapid antigen test. The analysis was restricted to persons without previous COVID-19 infection. Persons without BTI remained COVID-19-naïve until ≥3 months following the third dose. Of 289 participants, 92 developed BTI (31.5 infections per 100 person-years). The median days between last vaccination and BTI was 128 (IQR 67, 176), with the most cases occurring between the third and fourth dose (n = 59), corresponding to the Omicron wave. In analyses adjusted for age, sex, race, multimorbidity, hypertension, chronic kidney disease, diabetes and obesity, a lower IgG S/RBD (log10 BAU/mL) at 1 month post dose 3 was significantly associated with BTI, suggesting that a lower IgG level at this time point may predict BTI in this cohort of PWH. Full article

Coxiella (C.) burnetii, a zoonotic bacterium, is prevalent in dairy farms. Some cows develop a persistent infection and shed C. burnetii into milk and occasionally by amniotic fluid at calving. Serological diagnosis of Q fever in humans is performed by phase (Ph)-specific antibody tests; PhII antibodies usually indicate an acute infection, while the development of a chronic infection is characterised by elevated PhI antibody titres. Phase-specific tests have now been established for diagnosis of coxiellosis in cattle. Additionally, an interferon-γ (IFN-γ) recall assay has been implemented to assess cellular immunity to C. burnetii in cattle. Milk samples from all lactating cows (n = 2718) of 49 Bavarian dairy farms were collected through a convenience sample and analysed for phase-specific antibodies. Antibody profiles were evaluated by age. Based on the seropositivity of first-lactation cows, three distinct herd profiles were observed: an ‘acute’ state of herd infection was characterised by a PhI⁻/PhII⁺ pattern. The detection of PhI antibodies (PhI⁺/PhII⁺) characterised the ‘chronic’ state, and seronegative results defined the ‘silent’ state of herd infection. If antibodies had not been detected in multiparous cows, the herd was considered as probably free of coxiellosis. The analysed cattle herds were noted to have an ‘acute’ (n = 12, 24.5%), ‘chronic’ (n = 18, 36.8%), or ‘silent’ state of herd infection (n = 16, 32.6%). Only three farms (6.1%) were classified as ‘free’ of C. burnetii. The detection of these herd states over a time period of 4 years in one farm indicated that the described states occur in a cyclical manner. Frequently, a wave-like profile was seen, i.e., a circumscribed seronegative age group was flanked by seropositive age groups. In seronegative animals, IFN-γ reactivity was demonstrated. Seroconversion after vaccination was observed by day 7 post-vaccination in chronically infected herds, whereas in the case of silent infection, it started by day 14. These data indicated a pre-existing immunity in seronegative animals in chronically infected herds. Additionally, IFN-γ reactivity was detected in seronegative calves (>3 months) and heifers from chronically infected farms compared to a negative farm. An infection prior to 3 months of age resulted in cellular immunity in the absence of detectable antibodies. An infection around calving would explain this. The aforementioned circumscribed seronegative age groups are, therefore, explained by an infection early in life during active shedding at calving. Based on these results, an endemic cycle of coxiellosis is proposed: Susceptible young heifers get infected by persistently infected cows. Subsequently, shedding of C. burnetii at calving results in infection and then in cellular immunity in offspring. When these calves enter the cow herd two years later, a maximum of herd immunity is achieved, shedding ceases, and new susceptible animals are raised. In an acutely infected dairy farm, the PhI⁺/PhII⁺ serological pattern prevailed in second-lactation cows. In this study, stored sera collected since birth were analysed retrospectively. From the earliest seroconversion, the peak of seroconversion took about 33 months. These data suggested a slow spread of infection within herds. The classification of dairy cow herds is a promising basis for further analysis of the clinical impact of coxiellosis. Full article