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"Petrone, Mary"
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Everyday life in Russia past and present
\"In these original essays on long-term patterns of everyday life in pre-revolutionary, Soviet, and contemporary Russia, distinguished scholars survey the cultural practices, power relations, and behaviors that characterized daily existence for Russians through the post-Soviet present. Microanalyses and transnational perspectives shed new light on the formation and elaboration of gender, ethnicity, class, nationalism, and subjectivity. Changes in consumption and communication patterns, the restructuring of familial and social relations, systems of cultural meanings, and evolving practices in the home, at the workplace, and at sites of leisure are among the topics explored\"-- Provided by publisher.
Book
We shouldn’t worry when a virus mutates during disease outbreaks
Mutation. The word naturally conjures fears of unexpected and freakish changes. Ill-informed discussions of mutations thrive during virus outbreaks, including the ongoing spread of SARS-CoV-2. In reality, mutations are a natural part of the virus life cycle and rarely impact outbreaks dramatically.
Journal Article
Metatranscriptomic Identification of Trubanaman Virus Sequences in Patient with Encephalitis, Australia
Using metatranscriptomics, we identified Trubanaman virus in cerebrospinal fluid from a severely immunocompromised man who died of encephalitis in Queensland, Australia. Virus sequences were related to orthobunyaviruses previously detected in mosquitoes in Australia. Testing for other causes yielded negative results, suggesting that Trubanaman virus was the cause of this fatal encephalitis case.
Journal Article
Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Mosquito-borne viruses threaten the Caribbean due to the region’s tropical climate and seasonal reception of international tourists. Outbreaks of chikungunya and Zika have demonstrated the rapidity with which these viruses can spread. Concurrently, dengue fever cases have climbed over the past decade. Sustainable disease control measures are urgently needed to quell virus transmission and prevent future outbreaks. Here, to improve upon current control methods, we analyze temporal and spatial patterns of chikungunya, Zika, and dengue outbreaks reported in the Dominican Republic between 2012 and 2018. The viruses that cause these outbreaks are transmitted by
Aedes
mosquitoes, which are sensitive to seasonal climatological variability. We evaluate whether climate and the spatio-temporal dynamics of dengue outbreaks could explain patterns of emerging disease outbreaks. We find that emerging disease outbreaks were robust to the climatological and spatio-temporal constraints defining seasonal dengue outbreak dynamics, indicating that constant surveillance is required to prevent future health crises.
Dengue is endemic in the Dominican Republic, and causes regular outbreaks, whereas Zika and chikungunya are emerging infections in the area. Here, the authors show that outbreaks of the emerging infections could not be predicted by seasonal dengue dynamics.
Journal Article
New experimental insights into the biology of avian malaria parasites
Despite much research on avian malaria, the details of development of Plasmodium species in birds remain insufficiently investigated. This study aimed to gain new experimental information on avian malaria parasites regarding their host specificity, molecular characterization, persistence, and association with Matryoshka RNA viruses (MaRNAV), which are linked to haemosporidian infections.
Three species of widespread avian Plasmodium-P. circumflexum pTURDUS1, P. vaughani pSYAT05, and P. relictum pCOLL7-were found in naturally infected wild birds of the Muscicapidae, Turdidae and Phylloscopidae, respectively. The parasites were transferred to non-infected Eurasian siskins Spinus spinus (Fringillidae) by inoculation of infected blood, and infections were monitored up to 185 days. Microscopy, histology, chromogenic in situ hybridization (CISH), PCR, RNA sequencing and bioinformatic methods were applied in this study.
All recipient birds were susceptible to these pathogens. Extensive histology and CISH testing did not detect any tissue stages in all birds, suggesting that long-lasting persistence is mainly due to erythrocytic merogony. However, in the case of pCOLL7, parasitaemia consisted almost exclusively of gametocytes, presenting an unusual mode of parasitaemia in avian malaria. Based on morphological and phylogenetic data, pCOLL7 was linked to P. relictum. Morphological characterization showed that taxonomic characters of blood stages of all three parasite species are relatively stable across host species, supporting the value of the morphological characters of blood stages in Plasmodium species identification in birds belonging to different families. Furthermore, this study detected and associated a Matryoshka RNA virus (MaRNAV-9) with avian Plasmodium parasites for the first time. This virus was found in association with the bird malaria parasite P. (Giovannolaia) circumflexum (pTURDUS1) widespread in Eurasia, which can be used as a model host-parasite system to better understand the biology of MaRNAVs and their relationship with haemosporidians.
This study provides new information to better understand diagnostics and persistence of avian malaria parasites in avian hosts. It also contributes to new knowledge about the diversity of MaRNAVs associated with Plasmodium pathogens, opening opportunities for detecting these viruses in association with malaria parasites.
Journal Article
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
The current quantitative reverse transcription PCR (RT-qPCR) assay recommended for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in the United States requires analysis of 3 genomic targets per sample: 2 viral and 1 host. To simplify testing and reduce the volume of required reagents, we devised a multiplex RT-qPCR assay to detect SARS-CoV-2 in a single reaction. We used existing N1, N2, and RP primer and probe sets by the Centers for Disease Control and Prevention, but substituted fluorophores to allow multiplexing of the assay. The cycle threshold (Ct) values of our multiplex RT-qPCR were comparable to those obtained by the single assay adapted for research purposes. Low copy numbers (≥500 copies/reaction) of SARS-CoV-2 RNA were consistently detected by the multiplex RT-qPCR. Our novel multiplex RT-qPCR improves upon current single diagnostics by saving reagents, costs, time, and labor.
Journal Article
Real-time public health communication of local SARS-CoV-2 genomic epidemiology
Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted on a national or global scale. Here, we propose a new paradigm: Phylogenetic analyses performed on a local level (municipal, county, or state), with results communicated in a clear, timely, and actionable manner to strengthen public health responses. We believe that presenting results rapidly, and tailored to a non-expert audience, can serve as a template for effective public health response to COVID-19 and other emerging viral diseases.
Journal Article
Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
Background
There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance of medical professionals, impeding the implementation of large-scale testing. Self-collection of saliva may solve these problems, as it can be completed without specialized training and uses generic materials.
Methods
We observed 30 individuals who self-collected saliva using four different collection devices and analyzed their feedback. Two of these devices, a funnel and bulb pipette, were used to evaluate at-home saliva collection by 60 individuals. SARS-CoV-2-spiked saliva samples were subjected to temperature cycles designed to simulate the conditions the samples might be exposed to during the summer and winter seasons and sensitivity of detection was evaluated.
Results
All devices enabled the safe, unsupervised self-collection of saliva. The quantity and quality of the samples received were acceptable for SARS-CoV-2 diagnostic testing, as determined by human RNase P detection. There was no significant difference in SARS-CoV-2 nucleocapsid gene (N1) detection between the freshly spiked samples and those incubated with the summer and winter profiles.
Conclusion
We demonstrate inexpensive, generic, buffer free collection devices suitable for unsupervised and home saliva self-collection.
Journal Article
Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals
Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6-12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies.
Journal Article
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians
Abstract
The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus–host co-divergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750–800 million years ago.
Journal Article