Search Results (7)

This study explores Mpox transmission dynamics using a mathematical and data-driven epidemiological model that incorporates two viral strains, Clade I and Clade II. The model includes transmission pathways between humans and mammals and divides the human population into susceptible, exposed, infectious, hospitalized, and recovered groups. Weekly data from the WHO for Spain, Italy, Nigeria, and the DRC from 2022 to 2024 are used for model validation via non-linear least-squares fitting, with model performance assessed by Root Mean Squared Error (RMSE). We conduct time-series analysis to detect trends and anomalies in Mpox cases, with scenario simulations examining strain-specific transmission and the basic reproduction number (${\mathcal{R}}_0)$. The mathematical model fit is compared with two statistical model fits to emphasize the importance of developing a model that incorporates Mpox strain. Mathematical analysis confirms the model’s key properties, including positivity, boundedness, and equilibrium stability. Results underscore the importance of strain-specific dynamics and varying infection proportions for ${\mathcal{R}}_0$. This study combines mathematical rigor with empirical data to provide valuable insights into Mpox transmission and offers a framework for understanding multi-strain pathogens in diverse populations. Results from the simulation indicate that an increase in the effective contact rate leads to the dominance of the prevalent Mpox Clades in each country. Based on these findings, we recommend the implementation of strategies aimed at reducing the effective contact rate to control the spread of the virus strains. Full article

It is unclear if piglets benefit from vaccination of sows against influenza. For the first time, methods of evidence-based medicine were applied to answer the question: “Does vaccine-induced maternally-derived immunity (MDI) protect swine offspring against influenza A viruses?”. Challenge trials were reviewed that were published from 1990 to April 2021 and measured at least one of six outcomes in MDI-positive versus MDI-negative offspring (hemagglutination inhibition (HI) titers, virus titers, time to begin and time to stop shedding, risk of infection, average daily gain (ADG), and coughing) (n = 15). Screening and extraction of study characteristics was conducted in duplicate by two reviewers, with data extraction and assessment for risk of bias performed by one. Homology was defined by the antigenic match of vaccine and challenge virus hemagglutinin epitopes. Results: Homologous, but not heterologous MDI, reduced virus titers in piglets. There was no difference, calculated as relative risks (RR), in infection incidence risk over the entire study period; however, infection hazard (instantaneous risk) was decreased in pigs with MDI (log HR = −0.64, 95% CI: −1.13, −0.15). Overall, pigs with MDI took about a ½ day longer to begin shedding virus post-challenge (MD = 0.51, 95% CI: 0.03, 0.99) but the hazard of infected pigs ceasing to shed was not different (log HR = 0.32, 95% CI: −0.29, 0.93). HI titers were synthesized qualitatively and although data on ADG and coughing was extracted, details were insufficient for conducting meta-analyses. Conclusion: Homology of vaccine strains with challenge viruses is an important consideration when assessing vaccine effectiveness. Herd viral dynamics are complex and may include concurrent or sequential exposures in the field. The practical significance of reduced weaned pig virus titers is, therefore, not known and evidence from challenge trials is insufficient to make inferences on the effects of MDI on incidence risk, time to begin or to cease shedding virus, coughing, and ADG. The applicability of evidence from single-strain challenge trials to field practices is limited. Despite the synthesis of six outcomes, challenge trial evidence does not support or refute vaccination of sows against influenza to protect piglets. Additional research is needed; controlled trials with multi-strain concurrent or sequential heterologous challenges have not been conducted, and sequential homologous exposure trials were rare. Consensus is also warranted on (1) the selection of core outcomes, (2) the sizing of trial populations to be reflective of field populations, (3) the reporting of antigenic characterization of vaccines, challenge viruses, and sow exposure history, and (4) on the collection of non-aggregated individual pig data. Full article

Plants can be infected with multiple viruses. High-throughput sequencing tools have enabled numerous discoveries of multi-strain infections, when more than one viral strain or divergent genomic variant infects a single plant. Here, we investigated small interfering RNAs (siRNAs) in a single strawberry plant co-infected with several strains of strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). A range of plants infected with subsets of the initial viral species and strains that were obtained by aphid-mediated transmission were also evaluated. Using high-throughput sequencing, we characterized the small RNA fractions associated with different genotypes of these three viruses and determined small RNA hotspot regions in viral genomes. A comparison of virus-specific siRNA (vsiRNA) abundance with relative viral concentrations did not reveal any consistent agreement. Strawberry mottle virus strains exhibiting considerable variations in concentrations were found to be associated with comparable quantities of vsiRNAs. Additionally, by estimating the specificity of siRNAs to different viral strains, we observed that a substantial pool of vsiRNAs could target all SMoV strains, while strain-specific vsiRNAs predominantly targeted rhabdoviruses, SCV and StrV-1. This highlights the intricate nature and potential interference of the antiviral response within a single infected plant when multiple viruses are present. Full article

The emergence of SARS-CoV-2 virus mutations is a pressing concern in the context of the COVID-19 pandemic. In this paper, a Susceptible–Infected–Recovered (SIR) compartmental model has been formulated in terms of cellular automata and ordinary differential equations to simulate the transmission dynamics of a virus. This model accounts for the potential of new virus mutations to create additional infections of a multi-strain disease while also considering the impact of vaccination on disease control within a population. The basic reproduction number of the disease is derived, and the effect of virus mutations and vaccination rates is evaluated on a population over five years. The results of numerical simulations demonstrate the significant role of maintaining high vaccination rates in controlling the spread of the virus, even when assuming that all variants have similar illness characteristics and that a single shot of vaccine provides complete and lifelong protection against all strains. The findings underscore the necessity for countries to implement a consistent and high-level vaccination plan as soon as vaccines become available in order to mitigate the impact of a pandemic effectively. In conclusion, this study highlights the importance of taking into account the potential impact of virus mutations for controlling the COVID-19 pandemic. Furthermore, it emphasizes the critical role of vaccination in limiting the spread of the virus, and emphasizes the need to implement and maintain high vaccination rates as part of a comprehensive approach to managing the ongoing pandemic. Full article

SARS-CoV-2 continues to upend human life by posing novel threats related to disease spread and mutations. Current models for the disease burden of SARS-CoV-2 consider the aggregate nature of the virus without differentiating between the potency of its multiple strains. Hence, there is a need to create a fundamental modeling framework for multi-strain viruses that considers the competing viral pathogenic pathways. Alongside the consideration that other viral pathogens may coexist, there is also a need for a generalizable modeling framework to account for multiple epidemics (i.e., multi-demics) scenarios, such as influenza and COVID-19 occurring simultaneously. We present a fundamental network thermodynamics approach for assessing, determining, and predicting viral outbreak severity, which extends well-known standard epidemiological models. In particular, we use historical data from New York City’s 2011–2019 influenza seasons and SARS-CoV-2 spread to identify the model parameters. In our model-based analysis, we employ a standard susceptible–infected–recovered (SIR) model with pertinent generalizations to account for multi-strain and multi-demics scenarios. We show that the reaction affinities underpinning the formation processes of our model can be used to categorize the severity of infectious or deceased populations. The spontaneity of occurrence captured by the change in Gibbs free energy of reaction ($∆G$) in the system suggests the stability of forward occurring population transfers. The magnitude of $∆G$ is used to examine past influenza outbreaks and infer epidemiological factors, such as mortality and case burden. This method can be extrapolated for wide-ranging utility in computational epidemiology. The risk of overlapping multi-demics seasons between influenza and SARS-CoV-2 will persist as a significant threat in forthcoming years. Further, the possibility of mutating strains requires novel ways of analyzing the network of competing infection pathways. The approach outlined in this study allows for the identification of new stable strains and the potential increase in disease burden from a complex systems perspective, thereby allowing for a potential response to the significant question: are the effects of a multi-demic greater than the sum of its individual viral epidemics? Full article

Advances in high-throughput sequencing methods have boosted the discovery of multistrain viral infections in diverse plant systems. This phenomenon appears to be pervasive for certain viral species. However, our knowledge of the transmission aspects leading to the establishment of such mixed infections is limited. Recently, we reported a mixed infection of a single strawberry plant with strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). While SCV and StrV-1 are represented by two and three molecular variants, respectively, SmoV has three different RNA1 and RNA2 segments. In this study, we focus on virus acquisition by individual adult aphids of the Aphis gossypii, Aphis forbesi and Chaetosiphon fragaefolii species. Single-aphid transmission trials are performed under experimental conditions. Both different viruses and individual virus strains show varying performances in single aphid acquisition. The obtained data suggests that numerous individual transmission events lead to the establishment of multistrain infections. These data will be important for the development of epidemiological models in plant virology. Full article

Background: Gut microbiota has metabolic activity which influences mucosal homeostasis, local and systemic immune responses, and other anatomical systems (i.e., brain). The effects of dysbiosis are still poorly studied in Human Immunodeficiency Virus-1 (HIV-1) positive subjects and insufficient data are available on the impairment of the gut-brain axis, despite neurocognitive disorders being commonly diagnosed in these patients. This study evaluated the impact of a probiotic supplementation strategy on intrathecal immune activation and cognitive performance in combined antiretroviral therapy (cART) treated HIV-1 infected subjects. Methods: Thirty-five HIV-1 infected individuals were included in this study. At baseline (T0) a battery of tests was administered, to evaluate neurocognitive function and a lumbar puncture was performed to determine neopterin concentration in cerebrospinal fluid (CSF), as a marker of Central Nervous System (CNS) immune activation. Subsequently, a subgroup of participants underwent a 6-month course of multi-strain probiotics supplementation; this intervention group was evaluated, after probiotic treatment, with a second lumbar puncture and with repeated neurocognitive tests. Results: At T0, all participants showed impaired results in at least one neurocognitive test and elevated neopterin concentrations in CSF. After supplementation with probiotics (T6), the interventional group presented a significant decrease in neopterin concentration and a significant improvement in several neurocognitive tests. In contrast, no significant modifications were observed in the neurocognitive performance of controls between T0 and T6. The CNS Penetration Effectiveness Score of antiretroviral therapy did not show an influence from any of the investigated variables. Conclusions: Multi-strain probiotic supplementation seems to exert a positive effect on neuroinflammation and neurocognitive impairment in HIV-1 infected subjects, but large trials are needed to support the concept that modulation of the gut microbiota can provide specific neurological benefits in these patients. Full article