Changing Contact Patterns Over Disease Progression: Nipah Virus as a Case Study.
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ABSTRACT:
SUBMITTER: Lee KH
PROVIDER: S-EPMC7336571 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Codon usage bias (CUB) is the unequal usage of synonymous codons of an amino acid in which some codons are used more often than others and is widely used in understanding molecular biology, genetics, and functional regulation of gene expression. Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes fatal disease in both humans and animals. NiV was first identified during an outbreak of a disease in Malaysia in 1998 and then occurred periodically since 2001 in India, Bangladesh, and the Philippines. We used bioinformatics tools to analyze the codon usage patterns in a genome-wide manner among 11 genomes of NiV as no work was reported yet. The compositional properties revealed that the overall GC and AT contents were 41.96 and 58.04%, respectively i.e. Nipah virus genes were AT-rich. Correlation analysis between overall nucleotide composition and its 3rd codon position suggested that both mutation pressure and natural selection might influence the CUB across Nipah genomes. Neutrality plot revealed natural selection might have played a major role while mutation pressure had a minor role in shaping the codon usage bias in NiV genomes.
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Project description:Changing patterns in aerosol concentrations over the Asian region is well documented with a concurrent increase over India and a marked reduction over China. However, aerosol vertical distribution in the changing climate is not fully understood. By combining long-term satellite observations from MODIS and CALIOP, here we show rapid changes in the aerosol vertical distribution over the South and East Asia covering India and China. A statistically significant decreasing (increasing) trend in the boundary layer (free troposphere) aerosol concentrations is noticed over India. ERA-Interim reanalysis model suggests that this increase in free tropospheric aerosol concentrations are due to the lifting of boundary layer pollutants through an increase in convection (and vertical velocity) in a changing climate. In contrast, a consistent decreasing trend is observed over China irrespective of the altitude. Interestingly, a decreasing trend in Aerosol Optical Depth is observed over the northwest India and we relate this to an observed increase in precipitation leading to increase in the vegetation. It is also found that long-term oscillations like QBO, ENSO and solar cycle significantly affect the aerosol concentrations. Thus, it is prudent to conclude that background meteorology and dynamics play an important role in changing patterns of aerosol vertical distribution.
| S-EPMC7801640 | biostudies-literature
Project description:Driven by factors such as an increased reliance on genetically modified crops, government policies, and market forces, the crop mix in South Dakota and elsewhere in the United States has become less diverse and moved toward the production of corn and soybeans as the most predominant cash crops over the past two decades. Coinciding with a reduced complexity of crop rotation practices, the prevalence of mono-cropping has increased and crop chemical usage has changed as well. Overall, the reduced reliance on traditional crop rotation practices for mitigating pests corresponds with an increase in crop acres treated with insecticides, expressed as a proportion of total cropland acres, and referred to in the literature as the extensive usage of insecticides. In this paper, we identify how changing cropping patterns in South Dakota have affected the extensive usage of insecticides, an aspect often overlooked by producers and policy makers. Results indicate that increased corn production has contributed to an increase in the share of cropland acres treated with insecticides at the county level in eastern South Dakota.
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Project description:ObjectivesTuberculosis (TB) is a major public health concern worldwide. Social contact patterns can affect the epidemiology and risk of airborne diseases such as TB. This study was designed to investigate the social contact patterns associated with TB.MethodsIn this case-control study, groups of participants with and without TB were matched by age and sex. Participants reported the nature, location, frequency, and average duration of social contacts over 1 month. The duration and number of social and spatial contacts were compared between groups using the chi-square test and the t-test. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to quantify the relationship between social contact time and TB status. Data were analyzed using Stata version 11 statistical software. A p-value of <0.05 was considered to indicate statistical significance.ResultsIn this study, 80 patients with TB and 172 control participants were included, and a total of 3545 social contacts were registered. Social contact with family members (OR, 1.72; 95% CI, 1.10 to 2.40), contact with a person with TB (OR, 1.53; 95% CI, 1.16 to 2.01), and contact at the participant's home (OR, 1.42; 95% CI, 1.19 to 1.82) were significantly associated with TB status.ConclusionsThe duration of long-term social contact, rather than the number of contacts, may be the main contact-related factor associated with TB transmission in this population. The focus of contact-tracing efforts should be on finding and treating both family members and long-term contacts in non-household settings.
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Project description:Surveillance for Nipah virus (NV) was conducted in Thailand's bat population. Immunoglobulin G antibodies to NV were detected with enzyme immunoassay in 82 of 1,304 bats. NV RNA was found in bat saliva and urine. These data suggest the persistence of NV infection in Thai bats.
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Project description:The addition of cetuximab (CTX) to perioperative chemotherapy (CT) for operable colorectal liver metastases resulted in a shorter progression-free survival. Details of disease progression are described to further inform the primary study outcome.A total of 257 KRAS wild-type patients were randomised to CT alone or CT with CTX. Data regarding sites and treatment of progressive disease were obtained for the 109 (CT n=48, CT and CTX n=61) patients with progressive disease at the cut-off date for analysis of November 2012.The liver was the most frequent site of progression (CT 67% (32/48); CT and CTX 66% (40/61)). A higher proportion of patients in the CT and group had multiple sites of progressive disease (CT 8%, 4/48; CT and CTX 23%, 14/61 P=0.04). Further treatment for progressive disease is known for 84 patients of whom 69 received further CT, most frequently irinotecan based. Twenty-two patients, 11 in each arm, received CTX as a further line agent.Both the distribution of progressive disease and further treatment are as expected for such a cohort. The pattern of disease progression seen is consistent with failure of systemic micrometastatic disease control rather than failure of local disease control following liver surgery.
| S-EPMC4985352 | biostudies-other
Project description:Human-to-human contact plays a leading role in the transmission of infectious diseases, and the contact pattern between individuals has an important influence on the intensity and trend of disease transmission. In this paper, we define regular contacts and random contacts. Then, taking the COVID-19 outbreak in Yangzhou City, China as an example, we consider age heterogeneity, household structure and two contact patterns to establish discrete dynamic models with switching between daytime and nighttime to depict the transmission mechanism of COVID-19 in population. We studied the changes in the reproduction number with different age groups and household sizes at different stages. The effects of the proportion of two contacts patterns on reproduction number were also studied. Furthermore, taking the final size, the peak value of infected individuals in community and the peak value of quarantine infected individuals and nucleic acid test positive individuals as indicators, we evaluate the impact of the number of random contacts, the duration of the free transmission stage and summer vacation on the spread of the disease. The results show that a series of prevention and control measures taken by the Chinese government in response to the epidemic situation are reasonable and effective, and the young and middle-aged adults (aged 18-59) with household size of 6 have the strongest transmission ability. In addition, the results also indicate that increasing the proportion of random contact is beneficial to the control of the infectious disease in the phase with interventions. This work enriches the content of infectious disease modeling and provides theoretical guidance for the prevention and control of follow-up major infectious diseases.
| S-EPMC11008907 | biostudies-literature
Project description:Abstract We analyse the transmission factors shaping the spatial distribution of COVID‐19 infections during the distinct phases of the pandemic’s first wave in Madrid, Spain, by fitting a spatial regression model capturing neighbourhood effects between municipalities. Our findings highlight that factors such as population, mobility, and tourism were instrumental in the days before the national lockdown. As a result, already in the early part of the lockdown phase, a geographical pattern emerged in the spread of the disease, along with the positive (negative) impact of age (wealth) on virus transmission. Thereafter, spatial links between municipalities weakened, as the influences of mobility and tourism were eroded by mass quarantine. However, in the de‐escalation phase, mobility reappeared, reinforcing the geographical pattern, an issue that policymakers must pay heed to. Indeed, a counterfactual analysis shows that the number of infections without the lockdown would have been around 170% higher. Explanatory factors of the spread of the pandemic in Madrid changed according to the phase of national lockdown. As for the effectiveness of social distance measures, a counterfactual analysis shows that the number of infections without the lockdown would have been around 170% higher.
| S-EPMC8652501 | biostudies-literature
Project description:UNLABELLED:Nipah virus (NiV) is a highly lethal paramyxovirus that recently emerged as a causative agent of febrile encephalitis and severe respiratory disease in humans. The ferret model has emerged as the preferred small-animal model with which to study NiV disease, but much is still unknown about the viral determinants of NiV pathogenesis, including the contribution of the C protein in ferrets. Additionally, studies have yet to examine the synergistic effects of the various P gene products on pathogenesis in animal models. Using recombinant NiVs (rNiVs), we examine the sole contribution of the NiV C protein and the combined contributions of the C and W proteins in the ferret model of NiV pathogenesis. We show that an rNiV void of C expression resulted in 100% mortality, though with limited respiratory disease, like our previously reported rNiV void of W expression; this finding is in stark contrast to the attenuated phenotype observed in previous hamster studies utilizing rNiVs void of C expression. We also observed that an rNiV void of both C and W expression resulted in limited respiratory disease; however, there was severe neurological disease leading to 60% mortality, and the surviving ferrets demonstrated sequelae similar to those for human survivors of NiV encephalitis. IMPORTANCE:Nipah virus (NiV) is a human pathogen capable of causing lethal respiratory and neurological disease. Many human survivors have long-lasting neurological impairment. Using a ferret model, this study demonstrated the roles of the NiV C and W proteins in pathogenesis, where lack of either the C or the W protein independently decreased the severity of clinical respiratory disease but did not decrease lethality. Abolishing both C and W expression, however, dramatically decreased the severity of respiratory disease and the level of destruction of splenic germinal centers. These ferrets still suffered severe neurological disease: 60% succumbed to disease, and the survivors experienced long-term neurological impairment, such as that seen in human survivors. This new ferret NiV C and W knockout model may allow, for the first time, the examination of interventions to prevent or mitigate the neurological damage and sequelae experienced by human survivors.
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Project description:The viral determinants that contribute to Nipah virus (NiV)-mediated disease are poorly understood compared with other paramyxoviruses. Here we use recombinant NiVs (rNiVs) to examine the contributions of the NiV V and W proteins to NiV pathogenesis in a ferret model. We show that a V-deficient rNiV is susceptible to the innate immune response in vitro and behaves as a replicating non-lethal virus in vivo. Remarkably, rNiV lacking W expression results in a delayed and altered disease course with decreased respiratory disease and increased terminal neurological disease associated with altered in vitro inflammatory cytokine production. This study confirms the V protein as the major determinant of pathogenesis, also being the first in vivo study to show that the W protein modulates the inflammatory host immune response in a manner that determines the disease course.
| S-EPMC4482017 | biostudies-literature