skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Viral genomic features predict Orthopoxvirus reservoir hosts
Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs.Wedemonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.  more » « less
Award ID(s):
2515340
PAR ID:
10595291
Author(s) / Creator(s):
; ; ; ; ; ;
Publisher / Repository:
Nature
Date Published:
Journal Name:
Communications Biology
Volume:
8
Issue:
1
ISSN:
2399-3642
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; (, mSphere)
    Imperiale, Michael J (Ed.)
    ABSTRACT Mpox disease, caused by the monkeypox virus (MPXV), was recently classified as a public health emergency of international concern due to its high lethality and pandemic potential. MPXV is a zoonotic disease that emerged and is primarily spread by small rodents. Historically, it was considered mainly zoonotic and not likely to sustain human-to-human transmission. However, the worldwide outbreak of Clade IIb MPXV from 2020 to 2022 and ongoing Clade I MPXV epidemics in the Democratic Republic of the Congo and surrounding areas are a warning that human-adapted MPXVs will continually arise. Understanding the viral genetic determinants of host range, pathogenesis, and immune evasion is imperative for developing control strategies and predicting the future of Mpox. Here, we delve into the MPXV genome to detail genes involved in host immune evasion strategies for this zoonotic rodent-borne and human-circulating virus. We compare MPXV gene content to related Orthopoxviruses, which have narrow host ranges, to identify potential genes involved in species-specific pathogenesis and host tropism. In addition, we cover the key virulence factor differences that distinguish the MPXV clade lineages. Finally, we dissect how genomic reduction of Orthopoxviruses, through various molecular mechanisms, is contributing to the generation of novel MPXV lineages with increased human adaptation. This review aims to highlight gene content that defines the MPXV species, MPXV clades, and novel MPXV lineages that have culminated in this virus being elevated to a public health emergency of national concern. 
    more » « less
  2. ; ; ; ; (, Agronomy)
    null (Ed.)
    Recognizing the growing interest in the application of organic photovoltaics (OPVs) with greenhouse crop production systems, in this study we used flexible, roll-to-roll printed, semi-transparent OPV arrays as a roof shade for a greenhouse hydroponic tomato production system during a spring and summer production season in the arid southwestern U.S. The wavelength-selective OPV arrays were installed in a contiguous area on a section of the greenhouse roof, decreasing the transmittance of all solar radiation wavelengths and photosynthetically active radiation (PAR) wavelengths (400–700 nm) to the OPV-shaded area by approximately 40% and 37%, respectively. Microclimate conditions and tomato crop growth and yield parameters were measured in both the OPV-shaded (‘OPV’) and non-OPV-shaded (‘Control’) sections of the greenhouse. The OPV shade stabilized the canopy temperature during midday periods with the highest solar radiation intensities, performing the function of a conventional shading method. Although delayed fruit development and ripening in the OPV section resulted in lower total yields compared to the Control section (24.6 kg m−2 and 27.7 kg m−2, respectively), after the fourth (of 10 total) harvests, the average weekly yield, fruit number, and fruit mass were not significantly different between the treatment (OPV-shaded) and control group. Light use efficiency (LUE), defined as the ratio of total fruit yield to accumulated PAR received by the plant canopy, was nearly twice as high as the Control section, with 21.4 g of fruit per mole of PAR for plants in the OPV-covered section compared to 10.1 g in the Control section. Overall, this study demonstrated that the use of semi-transparent OPVs as a seasonal shade element for greenhouse production in a high-light region is feasible. However, a higher transmission of PAR and greater OPV device efficiency and durability could make OPV shades more economically viable, providing a desirable solution for co-located greenhouse crop production and renewable energy generation in hot and high-light intensity regions. 
    more » « less
  3. ; ; ; ; (, Agronomy)
    Recognizing the growing interest in the application of organic photovoltaics (OPVs) with greenhouse crop production systems, in this study we used flexible, roll-to-roll printed, semitransparent OPV arrays as a roof shade for a greenhouse hydroponic tomato production system during a spring and summer production season in the arid southwestern U.S. The wavelength-selective OPV arrays were installed in a contiguous area on a section of the greenhouse roof, decreasing the transmittance of all solar radiation wavelengths and photosynthetically active radiation (PAR) wavelengths (400–700 nm) to the OPV-shaded area by approximately 40% and 37%, respectively. Microclimate conditions and tomato crop growth and yield parameters were measured in both the OPV-shaded (‘OPV’) and non-OPV-shaded (‘Control’) sections of the greenhouse. The OPV shade stabilized the canopy temperature during midday periods with the highest solar radiation intensities, performing the function of a conventional shading method. Although delayed fruit development and ripening in the OPV section resulted in lower total yields compared to the Control section (24.6 kg m−2 and 27.7 kg m−2, respectively), after the fourth (of 10 total) harvests, the average weekly yield, fruit number, and fruit mass were not significantly different between the treatment (OPV-shaded) and control group. Light use efficiency (LUE), defined as the ratio of total fruit yield to accumulated PAR received by the plant canopy, was nearly twice as high as the Control section, with 21.4 g of fruit per mole of PAR for plants in the OPV-covered section compared to 10.1 g in the Control section. Overall, this study demonstrated that the use of semi-transparent OPVs as a seasonal shade element for greenhouse production in a high-light region is feasible. However, a higher transmission of PAR and greater OPV device efficiency and durability could make OPV shades more economically viable, providing a desirable solution for co-located greenhouse crop production and renewable energy generation in hot and high-light intensity regions. 
    more » « less
  4. ; ; ; ; ; ; ; (, Open Forum Infectious Diseases)
    Background The 2022 monkeypox (mpox) outbreak in Los Angeles County (LAC) emphasized the need to prepare for emergent infectious disease outbreaks. Vaccination and promotion of sexual risk reduction practices appeared successful in LAC, as mpox cases declined starting in August. Nonetheless, questions persisted regarding the effectiveness of targeting vaccinations and the role of sexual risk reduction in reducing mpox cases. Methods We collaborated with the LAC Department of Public Health to develop a microsimulation for men who have sex with men (MSM). This model tracked mpox dynamics by age, race/ethnicity, and HIV status and was calibrated and validated against surveillance data. We simulated counterfactual scenarios to understand the effects of variation in vaccination rates, timing of vaccination rollout, vaccine allocation, and sexual contact rates. Results In the simulation, doubling the vaccination rate reduced cumulative cases over a 40-week time horizon by 13% but would necessitate 88 995 additional doses. Initiating vaccination 2 weeks earlier decreased cases by 11%, while an 8-week delay yielded a 20% increase in cases. A 3-week earlier decrease in sexual contact rates reduced cumulative cases by 60%, while a 3-week delay resulted in a 95% increase. Prioritizing people with HIV (PWH) for vaccination reduced cumulative cases, while allocating vaccines to a single racial/ethnic group was not effective. Conclusions Our study highlights the significance of policies to support timely vaccination and sexual partnership reduction to address mpox outbreaks among MSM. These findings also underscore the need to target vulnerable risk groups, such as PWH. 
    more » « less
  5. ; ; ; ; ; (, Scientific Reports)
    Abstract SARS-CoV-2 (CoV) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. We divided the CoV genome into 29 constituent regions and applied novel analytical approaches to identify associations between CoV genomic features and epidemiological metadata. Our results show that nonstructural protein 3 (nsp3) and Spike protein (S) have the highest variation and greatest correlation with the viral whole-genome variation. S protein variation is correlated with nsp3, nsp6, and 3′-to-5′ exonuclease variation. Country of origin and time since the start of the pandemic were the most influential metadata associated with genomic variation, while host sex and age were the least influential. We define a novel statistic—coherence—and show its utility in identifying geographic regions (populations) with unusually high (many new variants) or low (isolated) viral phylogenetic diversity. Interestingly, at both global and regional scales, we identify geographic locations with high coherence neighboring regions of low coherence; this emphasizes the utility of this metric to inform public health measures for disease spread. Our results provide a direction to prioritize genes associated with outcome predictors (e.g., health, therapeutic, and vaccine outcomes) and to improve DNA tests for predicting disease status. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email