Novel coronaviruses and astroviruses in bats

Zoonotic transmissions of emerging pathogens from wildlife to human have shaped the history of mankind. These events have also highlighted our poor understanding of microorganisms circulated in wild animals. Coronaviruses and astroviruses, which can be found from a wide range of mammals, were recently detected in bats. Strikingly, these bat viruses are genetically highly diverse and these interesting findings might help to better understand the evolution and ecology of these viruses. The discoveries of these novel bats viruses not only suggested that bats are important hosts for these virus families, but also reiterated the role of bats as a reservoir of viruses that might pose a zoonotic threat to human health.     

The release of genetically engineered micro-organisms and viruses into the environment

This review considers the reasons for, and research governing, the regulation and monitoring of genetically engineered micro-organisms and viruses (GEMs) released into the environment. The hazards associated with releasing GEMs into the environment are the creation and evolution of new pests and diseases, and damage to the ecosystem and non target species. The similarities and differences between GEMs and conventional micro-organisms are discussed in relation to risk assessment. Other issues covered include the persistence of micro-organisms in the environment, transgene dispersal to non-engineered microbes and other organisms, the effects of transgenes and transformation on fitness, and the evolution of pests and pathogens that are given or acquire transgenes. Areas requiring further research are identified and recommendations for risk assessment made.     

Does fumagillin control the recently detected invasive parasite Nosema ceranae in western honey bees (Apis mellifera)?

Western honey bee (Apis mellifera) colonies in Nova Scotia, Canada were sampled in spring and late summer 2007 to evaluate efficacy of fumagillin dicyclohexylammonium (hereafter, fumagillin) against Nosema ceranae. Colonies treated with fumagillin in September 2006 (n = 94) had significantly lower Nosema intensity in spring 2007 than did colonies that received no treatment (n = 51), but by late summer 2007 no difference existed between groups. Molecular sequencing of 15 infected colonies identified N. ceranae in 93.3% of cases, suggesting that fumagillin is successful at temporarily reducing this recent invasive parasite in western honey bees.     

Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus

Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from the largest virus discovered to date (the Mimivirus) that is also a causative agent of pneumonia in humans. Mimicyp adopts a typical cyclophilin-fold, yet it also forms trimers unlike any previously characterized homologue. Strikingly, immunofluorescence assays reveal that mimicyp localizes to the surface of the mature virion, as recently proposed for several viruses that recruit host cell cyclophilins such as SARS and HIV-1. Additionally mimicyp lacks peptidyl-prolyl isomerase activity in contrast to human cyclophilins. Thus, this study suggests that cyclophilins, whether recruited from host cells (i.e. HIV-1 and SARS) or virally encoded (i.e. Mimivirus), are localized on viral surfaces for at least a subset of viruses.     

Discovery of novel DNA viruses in small mammals from Kenya

Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.     

土壤含水量驱动土壤病毒和细菌多度及其与土壤异养呼吸关系的变化

土壤微生物是维持陆地生态系统稳定性和功能的重要组成部分。病毒是地球上数量最多的生物实体,也是若干类型生境中微生物数量的重要调节者。因此,了解病毒与微生物的相互作用,对深入认识包括碳循环在内的生态系统过程具有重要意义。在实验室建立土壤微宇宙实验系统,跟踪调查恒定低含水量、恒定高含水量和波动含水量3种水分处理下土壤病毒和细菌多度的变化,以及土壤异养呼吸速率对土壤病毒-细菌相互作用的响应。相较于低水分处理,高水分处理显著增加了病毒多度（P<0.001）和病毒-细菌多度比（P=0.0026）,波动水分处理显著增加了病毒多度（P<0.001）。在高水分处理的土壤微宇宙中,细菌和病毒多度呈现出随时间动荡的信号,即细菌多度表现出增加-降低-增加的趋势,而病毒多度则表现出增加-降低的趋势,且其变化滞后于细菌。土壤异养呼吸速率与土壤含水量（P<0.001）、细菌多度（P=0.0045）和病毒多度（P<0.001）都具有显著的正相关关系。这些结果说明：病毒导致的下行控制可能是细菌多度的重要影响因子,在水分增加情形下,病毒有可能通过加速细菌的更新速率进而加速土壤呼吸。因此,病毒与细菌的相互作用可能是碳循环的重要决定因素。     

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10⁴–10⁵ genomes ml⁻¹ for the samples from the photic zone and 10²–10³ genomes ml⁻¹ for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.     

Tick-Borne Viruses

Ticks are important vectors for the transmission of pathogens including viruses. The viruses carried by ticks also known as tick-borne viruses (TBVs), contain a large group of viruses with diverse genetic properties and are concluded in two orders, nine families, and at least 12 genera. Some members of the TBVs are notorious agents causing severe diseases with high mortality rates in humans and livestock, while some others may pose risks to public health that are still unclear to us. Herein, we review the current knowledge of TBVs with emphases on the history of virus isolation and identification, tick vectors, and potential pathogenicity to humans and animals, including assigned species as well as the recently discovered and unassigned species. All these will promote our understanding of the diversity of TBVs, and will facilitate the further investigation of TBVs in association with both ticks and vertebrate hosts.