Evidence of Influenza A Virus RNA in Siberian Lake Ice
Ontology highlight
ABSTRACT:
SUBMITTER: Zhang G
PROVIDER: S-EPMC1865937 | biostudies-literature | 2007 Mar
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Influenza A virus infects a large proportion of the human population annually, sometimes leading to the deaths of millions. The biotic cycles of infection are well characterized in the literature, including in studies of populations of humans, poultry, swine, and migratory waterfowl. However, there are few studies of abiotic reservoirs for this virus. Here, we report the preservation of influenza A virus genes in ice and water from high-latitude lakes that are visited by large numbers of migratory birds. The lakes are along the migratory flight paths of birds flying into Asia, North America, Europe, and Africa. The data suggest that influenza A virus, deposited as the birds begin their autumn migration, can be preserved in lake ice. As birds return in the spring, the ice melts, releasing the viruses. Therefore, temporal gene flow is facilitated between the viruses shed during the previous year and the viruses newly acquired by birds during winter months spent in the south. Above the Arctic Circle, the cycles of entrapment in the ice and release by melting can be variable in length, because some ice persists for several years, decades, or longer. This type of temporal gene flow might be a feature common to viruses that can survive entrapment in environmental ice and snow.
| S-EPMC1676296 | biostudies-literature
Project description:The late Pleistocene Ice Complex (also known as Yedoma) encompasses ice-rich permafrost formed when alluvial and/or aeolian sediments accumulated under cold climatic conditions. Three metagenomes obtained from Yedoma deposits continually frozen for periods up to 60,000 years are reported here.
| S-EPMC6813392 | biostudies-literature
Project description:The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.
| S-EPMC11421388 | biostudies-literature
Project description:BACKGROUND: Wild birds, especially those in wetlands and aquatic environments, are considered to be natural reservoirs of avian influenza viruses. It is accepted that water is an important component in the transmission cycle of avian influenza virus. Monitoring the water at aggregation and breeding sites of migratory waterfowl, mainly wetland, is very important for early detection of avian influenza virus. The epidemiology investigation of avian influenza virus was performed in Dongting lake wetland which is an international important wetland. RESULTS: An H10N8 influenza virus was isolated from Dongting Lake wetland in 2007. Phylogenetic analysis indicated that the virus was generated by multiple gene segment reassortment. The isolate was lowly pathogenic for chickens. However, it replicated efficiently in the mouse lung without prior adaptation, and the virulence to mice increased rapidly during adaptation in mouse lung. Sequence analysis of the genome of viruses from different passages showed that multiple amino acid changes were involved in the adaptation of the isolates to mice. CONCLUSIONS: The water might be an important component in the transmission cycle of avian influenza virus, and other subtypes of avian influenza viruses (other than H5, H7 and H9) might evolve to pose a potential threat to mammals and even humans.
| S-EPMC3038951 | biostudies-literature
Project description:Lakes are a key geographical feature in Canada and have an impact on the regional climate. In the winter, they are important for recreational activities such as snowmobiling and ice fishing and act as part of an important supply route for northern communities. The ability to accurately report lake ice characteristics such as thickness is vital, however, it is underreported in Canada and there is a lack of lake ice thickness records for temperate latitude areas such as Central Ontario. Here, we evaluate the application of previously developed temperature models and RADARSAT-2 for estimating lake ice thickness in Central Ontario and provide insight into the regions long term ice thickness variability. The ALS Environmental Science Shallow Water Ice Profiler (SWIP) was used for validation of both temperature and radar-based models. Results indicate that the traditional approach that uses temperatures to predict ice thickness during ice growth has low RMSE values of 2.3 cm and correlations of greater than 0.9. For ice decay, similar low RMSE values of 2.1 cm and high correlations of 0.97 were found. Using RADARSAT-2 to estimate ice thickness results in R2 values of 0.6 (p < 0.01) but high RMSE values of 11.7 cm. Uncertainty in the RADARSAT-2 approach may be linked to unexplored questions about scattering mechanisms and the interaction of radar signal with mid-latitude lake ice. The application of optimized temperature models to a long-term temperature record revealed a thinning of ice cover by 0.81 cm per decade.
| S-EPMC6283572 | biostudies-literature
Project description:Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity.
| S-EPMC6470161 | biostudies-literature
Project description:Temperate lakes worldwide are losing ice cover but the implications for under-ice thermal dynamics are poorly constrained. Using a 92-year record of ice phenology from a temperate and historically dimictic lake, we examined trends, variability, and drivers of ice phenology and under-ice temperatures. The onset of ice formation decreased by 23 days century-1, which can be largely attributed to warming air temperatures. Ice-off date has become substantially more variable with spring air temperatures and cumulative February through April snowfall explaining over 80% of the variation in timing. As a result of changing ice phenology, total ice duration contracted by a month and more than doubled in interannual variability. Using weekly under-ice temperature profiles for the most recent 36 years, we found that shorter ice duration decreased winter inverse stratification and was associated with an extended spring mixing period. We illustrate the limitations of relying on discrete ice clearance dates in our assumptions around under-ice thermal dynamics by presenting high-frequency under-ice observations in two recent winters: one with intermittent ice cover and a year with slow spring ice clearance.
| S-EPMC11584988 | biostudies-literature
Project description:The emergence of drug-resistant strains of influenza virus makes exploring new classes of inhibitors that target universally conserved viral targets a highly important goal. The influenza A viral genome is made up of eight single-stranded RNA-negative segments. The RNA promoter, consisting of the conserved sequences at the 3' and 5' end of each RNA genomic segment, is universally conserved among influenza A virus strains and in all segments. Previously, we reported on the identification and NMR structure of DPQ (6,7-dimethoxy-2-(1-piperazinyl)-4-quinazolinamine) (compound 1) in complex with the RNA promoter. Here, we report on additional screening and SAR studies with compound 1, including ex vivo anti-influenza activity assays, resulted in improved cellular activity against influenza A virus in the micromolar range.
| S-EPMC4531110 | biostudies-literature
Project description: Not available
| S-EPMC3166005 | biostudies-literature
Project description:In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
| S-EPMC10418309 | biostudies-literature