Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen.

An increasing number of emerging tick-borne diseases has been reported in the United States since the 1970s. Using metagenomic next generation sequencing, we detected nucleic acid sequences from 2 novel viruses in the family Bunyaviridae and an emerging human rickettsial pathogen, Rickettsia philipii, in a population of the Pacific Coast tick, Dermacentor occidentalis in Mendocino County sampled annually from 2011 to 2014. A total of 250 adults of this human-biting, generalist tick were collected from contiguous chaparral and grassland habitats, and RNA from each individually extracted tick was deep sequenced to an average depth of 7.3 million reads. We detected a Francisella endosymbiont in 174 ticks (70%), and Rickettsia spp. in 19 ticks (8%); Rickettsia-infected ticks contained R. rhipicephali (16 of 250, 6.4%) or R. philipii (3 of 250,1.2%), the agent of eschar-associated febrile illness in humans. The genomes of 2 novel bunyaviruses (>99% complete) in the genera Nairovirus and Phlebovirus were also identified and found to be present in 20-91% of ticks, depending on the year of collection. The high prevalence of these bunyaviruses in sampled Dermacentor ticks suggests that they may be viral endosymbionts, although further studies are needed to determine whether they are infectious for vertebrate hosts, especially humans, and their potential role in tick ecology

ESA’s Soil Moisture and Ocean Salinity Mission - An overview on the mission’s performance and scientific results

European Geosciences Union General Assembly 2014 (EGU2014), 27 april - 2 may 2014, Vienna, Austria.-- 1 pageThe Soil Moisture and Ocean Salinity (SMOS) mission, launched on 2 November 2009, is the European Space Agency’s (ESA) second Earth Explorer Opportunity mission. The scientific objectives of the SMOS mission directly respond to the need for global observations of soil moisture and ocean salinity, two key variables used in predictive hydrological, oceanographic and atmospheric models. SMOS observations also provide information on the characterisation of ice and snow covered surfaces and the sea ice effect on ocean-atmosphere heat fluxes and dynamics, which affects large-scale processes of the Earth’s climate system. This paper will provide an overview on the various aspects of the SMOS mission, such as 1. The performance of the mission after more than 5 years in orbit: The SMOS mission has been in routine operations since May 2010, following the successful completion of the 6-months commissioning phase. The paper will summarise the technical and scientific status of the mission, including the status of the RFI detection and mitigation and its effect on the data products. SMOS has so far provided very reliable instrument operations, data processing and dissemination to users. The paper will also provide an overview on the MIRAS instrument performance, including the instrument calibration and level 1 brightness temperature data processing. 2. An overview on the SMOS data products: SMOS provides continuously level 1 (brightness temperature) and level 2 (soil moisture and ocean salinity) to its scientific user community since summer 2010. SMOS also provides brightness temperature data (level 1 data) to ECMWF in near-real time (NRT), who assimilates the data into their forecasting system. New services have been established to deliver a tailored NRT data product via the WMO’s GTS and EUMETSAT’s EUMETCast data dissemination systems to other operational agencies. This will open up new operational applications for SMOS data. Other data products are under development, responding to the requirements of the science community in particular in the area of hydrology, climate, land use and ship routing, namely a frozen soil indicator, data products for freeze/thaw periods, sea ice thickness and vegetation water content. 3. Provide an update on the overall validation approach and recent activities: SMOS data products are continuously improved and approach the scientific mission objectives. Validation activities are essential to ensure high data quality. ESA in collaboration with national agencies and institutions maintains a frame for validation activities such as reference sites, ground based observations as well as campaigns. The paper will provide an update on recent activities, such as the activities at DOME-C. 4. Summarise the collaboration with other space-borne L-band sensors, such as NASA’s Aquarius and SMAP missionsPeer Reviewe

Human Bocaviruses Are Highly Diverse, Dispersed, Recombination Prone, and Prevalent in Enteric Infections

International audienceA new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies

A Newly Identified Bocavirus Species in Human Stool

Viral metagenomic analysis was used to identify a previously uncharacterized parvovirus species, “HBoV2, ” whose closest phylogenetic relative is the human bocavirus (HBoV). HBoV2 has a genomic organization identical to that of HBoV but has only 78%, 67%, and 80 % identity, respectively, with the lat-ter’s NS1, NP1, and VP1/VP2 proteins. The study used poly-merase chain reaction to detect HBoV2 sequences in 5 of 98 stool samples from Pakistani children and in 3 of 699 stool samples from Edinburgh. Nearly-full-length genome se-quencing revealed the presence of 3HBoV2 genotypes and ev-idence of recombination between genotypes. Further studies are necessary to identify anatomical sites of HBoV2 replica-tion and potential associations with clinical symptoms or disease. The Parvoviridae family includes the Parvovirinae subfamily

Cellular Immune Responses and Viral Diversity in Individuals Treated during Acute and Early HIV-1 Infection

Immune responses induced during the early stages of chronic viral infections are thought to influence disease outcome. Using HIV as a model, we examined virus-specific cytotoxic T lymphocytes (CTLs), T helper cells, and viral genetic diversity in relation to duration of infection and subsequent response to antiviral therapy. Individuals with acute HIV-1 infection treated before seroconversion had weaker CTL responses directed at fewer epitopes than persons who were treated after seroconversion. However, treatment-induced control of viremia was associated with the development of strong T helper cell responses in both groups. After 1 yr of antiviral treatment initiated in acute or early infection, all epitope-specific CTL responses persisted despite undetectable viral loads. The breadth and magnitude of CTL responses remained significantly less in treated acute infection than in treated chronic infection, but viral diversity was also significantly less with immediate therapy. We conclude that early treatment of acute HIV infection leads to a more narrowly directed CTL response, stronger T helper cell responses, and a less diverse virus population. Given the need for T helper cells to maintain effective CTL responses and the ability of virus diversification to accommodate immune escape, we hypothesize that early therapy of primary infection may be beneficial despite induction of less robust CTL responses. These data also provide rationale for therapeutic immunization aimed at broadening CTL responses in treated primary HIV infection

The ancient evolutionary history of polyomaviruses

Author Summary: Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

<p>Abstract</p> <p>Background</p> <p>The occurrence of a genetic bottleneck in HIV sexual or mother-to-infant transmission has been well documented. This results in a majority of new infections being homogeneous, <it>i.e</it>., initiated by a single genetic strain. Early after infection, prior to the onset of the host immune response, the viral population grows exponentially. In this simple setting, an approach for estimating evolutionary and demographic parameters based on comparison of diversity measures is a feasible alternative to the existing Bayesian methods (<it>e.g</it>., BEAST), which are instead based on the simulation of genealogies.</p> <p>Results</p> <p>We have devised a web tool that analyzes genetic diversity in acutely infected HIV-1 patients by comparing it to a model of neutral growth. More specifically, we consider a homogeneous infection (<it>i.e</it>., initiated by a unique genetic strain) prior to the onset of host-induced selection, where we can assume a random accumulation of mutations. Previously, we have shown that such a model successfully describes about 80% of sexual HIV-1 transmissions provided the samples are drawn early enough in the infection. Violation of the model is an indicator of either heterogeneous infections or the initiation of selection.</p> <p>Conclusions</p> <p>When the underlying assumptions of our model (homogeneous infection prior to selection and fast exponential growth) are met, we are under a very particular scenario for which we can use a forward approach (instead of backwards in time as provided by coalescent methods). This allows for more computationally efficient methods to derive the time since the most recent common ancestor. Furthermore, the tool performs statistical tests on the Hamming distance frequency distribution, and outputs summary statistics (mean of the best fitting Poisson distribution, goodness of fit p-value, etc). The tool runs within minutes and can readily accommodate the tens of thousands of sequences generated through new ultradeep pyrosequencing technologies. The tool is available on the LANL website.</p

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify