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Description

Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane

Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses.

Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3.

Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion.

Conclusions: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

ContributorsBoukari, Wardatou (Author) / Alcala-Briseno, Ricardo I. (Author) / Kraberger, Simona Joop (Author) / Fernandez, Emmanuel (Author) / Filloux, Denis (Author) / Daugrois, Jean-Heinrich (Author) / Comstock, Jack C. (Author) / Lett, Jean-Michel (Author) / Martin, Darren P. (Author) / Varsani, Arvind (Author) / Roumagnac, Philippe (Author) / Polston, Jane E. (Author) / Rott, Philippe C. (Author) / Biodesign Institute (Contributor)
Created2017-07-28
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Description

Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10. The AAPEc6 genome sequence shares 93% identity (with 92% coverage) to enterobacterial phage K1E (Sp6likevirus) in the Autographivirinae subfamily (Podoviridae).

ContributorsNonis, Judith (Author) / Premaratne, Aruni (Author) / Billington, Craig (Author) / Varsani, Arvind (Author) / Biodesign Institute (Contributor)
Created2017-08-03
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Description

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2–2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2–2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.

ContributorsVarsani, Arvind (Author) / Krupovic, Mart (Author) / Biodesign Institute (Contributor)
Created2017-02-02
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Description

Four genomovirus genomes were recovered from thrips (Echinothrips americanus) collected in Florida, USA. These represent four new species which are members of the Gemycircularvirus (n = 2), Gemyduguivirus (n = 1), and Gemykibivirus (n = 1) genera. This is the first record, to our knowledge, of genomoviruses associated with a

Four genomovirus genomes were recovered from thrips (Echinothrips americanus) collected in Florida, USA. These represent four new species which are members of the Gemycircularvirus (n = 2), Gemyduguivirus (n = 1), and Gemykibivirus (n = 1) genera. This is the first record, to our knowledge, of genomoviruses associated with a phytophagous insect.

ContributorsKraberger, Simona Joop (Author) / Polston, Jane E. (Author) / Capobianco, Heather M. (Author) / Alcala-Briseno, Ricardo I. (Author) / Fontenele, Rafaela Salgado (Author) / Varsani, Arvind (Author) / Biodesign Institute (Contributor)
Created2017-05-25
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Description

Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major cause of skin and soft tissue infections (SSTIs) in the US. We developed an age-structured compartmental model to study the spread of CA-MRSA at the population level and assess the effect of control intervention strategies. We used Monte-Carlo Markov Chain

Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major cause of skin and soft tissue infections (SSTIs) in the US. We developed an age-structured compartmental model to study the spread of CA-MRSA at the population level and assess the effect of control intervention strategies. We used Monte-Carlo Markov Chain (MCMC) techniques to parameterize our model using monthly time series data on SSTIs incidence in children (≤19 years) during January 2004 -December 2006 in Maricopa County, Arizona. Our model-based forecast for the period January 2007–December 2008 also provided a good fit to data. We also carried out an uncertainty and sensitivity analysis on the control reproduction number, Rc which we estimated at 1.3 (95% CI [1.2,1.4]) based on the model fit to data. Using our calibrated model, we evaluated the effect of typical intervention strategies namely reducing the contact rate of infected individuals owing to awareness of infection and decolonization strategies targeting symptomatic infected individuals on both and the long-term disease dynamics. We also evaluated the impact of hypothetical decolonization strategies targeting asymptomatic colonized individuals. We found that strategies focused on infected individuals were not capable of achieving disease control when implemented alone or in combination. In contrast, our results suggest that decolonization strategies targeting the pediatric population colonized with CA-MRSA have the potential of achieving disease elimination.

Created2013-11-21
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Description

Background: Extreme heat is a public health challenge. The scarcity of directly comparable studies on the association of heat with morbidity and mortality and the inconsistent identification of threshold temperatures for severe impacts hampers the development of comprehensive strategies aimed at reducing adverse heat-health events.

Objectives: This quantitative study was designed

Background: Extreme heat is a public health challenge. The scarcity of directly comparable studies on the association of heat with morbidity and mortality and the inconsistent identification of threshold temperatures for severe impacts hampers the development of comprehensive strategies aimed at reducing adverse heat-health events.

Objectives: This quantitative study was designed to link temperature with mortality and morbidity events in Maricopa County, Arizona, USA, with a focus on the summer season.
Methods: Using Poisson regression models that controlled for temporal confounders, we assessed daily temperature–health associations for a suite of mortality and morbidity events, diagnoses, and temperature metrics. Minimum risk temperatures, increasing risk temperatures, and excess risk temperatures were statistically identified to represent different “trigger points” at which heat-health intervention measures might be activated.

Results: We found significant and consistent associations of high environmental temperature with all-cause mortality, cardiovascular mortality, heat-related mortality, and mortality resulting from conditions that are consequences of heat and dehydration. Hospitalizations and emergency department visits due to heat-related conditions and conditions associated with consequences of heat and dehydration were also strongly associated with high temperatures, and there were several times more of those events than there were deaths. For each temperature metric, we observed large contrasts in trigger points (up to 22°C) across multiple health events and diagnoses.

Conclusion: Consideration of multiple health events and diagnoses together with a comprehensive approach to identifying threshold temperatures revealed large differences in trigger points for possible interventions related to heat. Providing an array of heat trigger points applicable for different end-users may improve the public health response to a problem that is projected to worsen in the coming decades.

Created2015-07-28
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Description

The ongoing Zika virus (ZIKV) epidemic in the Americas poses a major global public health emergency. While ZIKV is transmitted from human to human by bites of Aedes mosquitoes, recent evidence indicates that ZIKV can also be transmitted via sexual contact with cases of sexually transmitted ZIKV reported in Argentina,

The ongoing Zika virus (ZIKV) epidemic in the Americas poses a major global public health emergency. While ZIKV is transmitted from human to human by bites of Aedes mosquitoes, recent evidence indicates that ZIKV can also be transmitted via sexual contact with cases of sexually transmitted ZIKV reported in Argentina, Canada, Chile, France, Italy, New Zealand, Peru, Portugal, and the USA. Yet, the role of sexual transmission on the spread and control of ZIKV infection is not well-understood. We introduce a mathematical model to investigate the impact of mosquito-borne and sexual transmission on the spread and control of ZIKV and calibrate the model to ZIKV epidemic data from Brazil, Colombia, and El Salvador. Parameter estimates yielded a basic reproduction number R0 = 2.055 (95% CI: 0.523–6.300), in which the percentage contribution of sexual transmission is 3.044% (95% CI: 0.123–45.73). Our sensitivity analyses indicate that R0 is most sensitive to the biting rate and mortality rate of mosquitoes while sexual transmission increases the risk of infection and epidemic size and prolongs the outbreak. Prevention and control efforts against ZIKV should target both the mosquito-borne and sexual transmission routes.

ContributorsGao, Daozhou (Author) / Lou, Yijun (Author) / He, Daihai (Author) / Porco, Travis C. (Author) / Kuang, Yang (Author) / Chowell-Puente, Gerardo (Author) / Ruan, Shigui (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-06-17
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Description

Carefully calibrated transmission models have the potential to guide public health officials on the nature and scale of the interventions required to control epidemics. In the context of the ongoing Ebola virus disease (EVD) epidemic in Liberia, Drake and colleagues, in this issue of PLOS Biology, employed an elegant modeling

Carefully calibrated transmission models have the potential to guide public health officials on the nature and scale of the interventions required to control epidemics. In the context of the ongoing Ebola virus disease (EVD) epidemic in Liberia, Drake and colleagues, in this issue of PLOS Biology, employed an elegant modeling approach to capture the distributions of the number of secondary cases that arise in the community and health care settings in the context of changing population behaviors and increasing hospital capacity. Their findings underscore the role of increasing the rate of safe burials and the fractions of infectious individuals who seek hospitalization together with hospital capacity to achieve epidemic control. However, further modeling efforts of EVD transmission and control in West Africa should utilize the spatial-temporal patterns of spread in the region by incorporating spatial heterogeneity in the transmission process. Detailed datasets are urgently needed to characterize temporal changes in population behaviors, contact networks at different spatial scales, population mobility patterns, adherence to infection control measures in hospital settings, and hospitalization and reporting rates.

Created2015-01-21
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Description

Background: Ebola virus disease (EVD) has generated a large epidemic in West Africa since December 2013. This mini-review is aimed to clarify and illustrate different theoretical concepts of infectiousness in order to compare the infectiousness across different communicable diseases including EVD.

Methods: We employed a transmission model that rests on the

Background: Ebola virus disease (EVD) has generated a large epidemic in West Africa since December 2013. This mini-review is aimed to clarify and illustrate different theoretical concepts of infectiousness in order to compare the infectiousness across different communicable diseases including EVD.

Methods: We employed a transmission model that rests on the renewal process in order to clarify theoretical concepts on infectiousness, namely the basic reproduction number, R0, which measures the infectiousness per generation of cases, the force of infection (i.e. the hazard rate of infection), the intrinsic growth rate (i.e. infectiousness per unit time) and the per-contact probability of infection (i.e. infectiousness per effective contact).

Results: Whereas R0 of EVD is similar to that of influenza, the growth rate (i.e. the measure of infectiousness per unit time) for EVD was shown to be comparatively lower than that for influenza. Moreover, EVD and influenza differ in mode of transmission whereby the probability of transmission per contact is lower for EVD compared to that of influenza.

Conclusions: The slow spread of EVD associated with the need for physical contact with body fluids supports social distancing measures including contact tracing and case isolation. Descriptions and interpretations of different variables quantifying infectiousness need to be used clearly and objectively in the scientific community and for risk communication.

Created2015-01-06
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Description

Metagenomic approaches are rapidly expanding our knowledge of the diversity of viruses. In the fecal matter of Nigerian chimpanzees we recovered three gokushovirus genomes, one circular replication-associated protein encoding single-stranded DNA virus (CRESS), and a CRESS DNA molecule.

ContributorsWalters, Matthew (Author) / Bawuro, Musa (Author) / Christopher, Alfred (Author) / Knight, Alexander (Author) / Kraberger, Simona (Author) / Stainton, Daisy (Author) / Chapman, Hazel (Author) / Varsani, Arvind (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-03-02