Comparison of gut viral communities in diarrhoea and healthy dairy calves

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.

Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom

There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.

Intraspecific host variation plays a key role in virus community assembly

Infection by multiple pathogens of the same host is ubiquitous in both natural and managed habitats. While intraspecific variation in disease resistance is known to affect pathogen occurrence, how differences among host genotypes affect the assembly of pathogen communities remains untested. In our experiment using cloned replicates of naive Plantago lanceolata plants as sentinels during a seasonal virus epidemic, we find non-random co-occurrence patterns of five focal viruses. Using joint species distribution modelling, we attribute the non-random virus occurrence patterns primarily to differences among host genotypes and local population context. Our results show that intraspecific variation among host genotypes may play a large, previously unquantified role in pathogen community structure.

Structural and Functional Characteristics of Soil Microbial Community in a Pinus Massoniana Forest at Different Elevations

BackgroundIn spite of the ecological importance of soil microbial communities, very little data is available on different soil microorganism types along altitudinal gradients on a mountain system with a forest ecosystem to identify the distribution patterns of soil microbial diversity and function. This study aimed to determine the diversity patterns of different soil microorganism types (archaea, bacteria, fungi, viruses) along an altitudinal gradient on Mt. Leigong, a typical mid-subtropical mountain forest ecosystem.ResultsThe richness of bacterial, fungal, and virus community changed in a unimodal pattern, while archaeal community changed in a bimodal pattern with increasing altitude. Euryarchaeota and Thaumarchaeota, Proteobacteria and Acidobacteria, Ascomycota and Basidiomycota, Myoviridae and Podoviridae were abundant taxa in archaeal, bacterial, fungal, and virus community, respectively. Amino acid transport and metabolism, and energy production and conversion were the predominant categories as per Nonsupervised Orthologous Groups (NOG) function gene-annotation. Carbohydrate metabolism, global and overview map, and amino acid metabolism, were predominant categories in the Kyoto encyclopedia of genes and genomes-based (KEGG) pathways. Glycosyl transferase and glycoside hydrolase were predominant categories among carbohydrate enzyme-functional genes. Cluster analysis, redundancy analysis, and Network analysis showed obvious differences in composition, structure, and function of different soil microorganism types in the P. massoniana forest on Mt. Leigong.ConclusionsThese results indicate that different soil microorganism types (archaea, bacteria, fungi, viruses) along the altitudinal gradient have an obvious different distribution patterns in the typical mid-subtropical mountain coniferous forest soil.

Virome Structure of the Small Aral Sea

ABSTRACT Here, we present a virome analysis of the surface waters of the Small Aral Sea. In this case, shotgun metagenomic sequencing of the RNA and DNA virus community was used.

Influence of countries adopted policies for COVID-19 reduction under the view of the airborne transmission framework (Preprint)

UNSTRUCTURED Daily new cases dataset since January 2020 were used to search for evidences of SARS-CoV-2 community transmission as the main nowadays cause of constant infection rates among countries. Despite traditional forms of transmission of this virus (droplets and aerosols in medical facilities), new evidence suggests aerosols forming patterns in the atmosphere as a main factor of community transmission outside medical spaces. Following these findings, this research focused on comparing some countries and the adopted policy used as preventive framework for virus community transmission. Countries social distancing policy aspect, of one to two meters of physical distance, was statistically analyzed from January to early May 2020, and countries were divided into those implementing only social physical distance and those implementing distancing with additional transmission isolation (with masks and city disinfection). Correlating countries social distancing policy adoption with other preventive measures such as social isolation and COVID-19 testing, a new indicator results, derived from SIR models and Weibull parameterization, show that only social physical distance measure could act as a factor for SARS-CoV-2 transmission with respect to atmosphere carrier potential. In this sense, the type of social distancing framework adopted by some countries without additional measures might represent a main model for the constant reproductive spread patterns of SARS-CoV-2 within the community transmission. Finally, the findings have important implications for the policy making to be adopted globally as well as individual-scale preventive methods. INTERNATIONAL REGISTERED REPORT RR2-https://doi.org/10.1101/2020.05.20.20107763

Influence of countries adopted policies for COVID-19 reduction under the view of the airborne transmission framework

Daily new cases dataset since January 2020 were used to search for evidences of SARS-CoV-2 community transmission as the main nowadays cause of constant infection rates among countries. Despite traditional forms of transmission of this virus (droplets and aerosols in medical facilities), new evidence suggests aerosols forming patterns in the atmosphere as a main factor of community transmission outside medical spaces. Following these findings, this research focused on comparing some countries and the adopted policy used as preventive framework for virus community transmission. Countries social distancing policy aspect, of one to two meters of physical distance, was statistically analyzed from January to early May 2020, and countries were divided into those implementing only social physical distance and those implementing distancing with additional transmission isolation (with masks and city disinfection). Correlating countries social distancing policy adoption with other preventive measures such as social isolation and COVID-19 testing, a new indicator results, derived from SIR models and Weibull parameterization, show that only social physical distance measure could act as a factor for SARS-CoV-2 transmission with respect to atmosphere carrier potential. In this sense, the type of social distancing framework adopted by some countries without additional measures might represent a main model for the constant reproductive spread patterns of SARS-CoV-2 within the community transmission. Finally, the findings have important implications for the policy making to be adopted globally as well as individual-scale preventive methods.

Virome of riverside phytocommunity ecosystem of an ancient canal

Background The virus community in plants in a local plant ecosystem has remained largely unknown. In this study, we investigated the virus community in these wild and cultivated plants in Zhenjiang ancient canal ecosystem. Results using viral metagenomic approach, we investigated the viral community in leaf tissues of 161 plant species belonging in 38 different orders in a local riverside plant ecosystem. We discovered 251 different plant-associated virus genomes which included 88 DNA and 163 RNA viruses belonging to 27 different virus families, orders or unclassified virus groups. The identified viruses include some that are sufficiently divergent to comprise new genera, families, or even orders. Our data indicated that some groups of viruses known to infect non-plant organisms had host switching to infecting plants. Cross-species infection and co-infection of viruses were common in this plant ecosystem. Conclusions these data present a view of the viral community in plants present in a local plant ecosystem which is more diverse than that depicted in current classification of plant viruses and provide a solid foundation for studies in virus ecology and evolution in plants.