The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components

In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (P[28]-P[35]), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3 (M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including, but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.

/pdf/uniformity-of-rotavirus-strain-nomenclature-proposed-by-the-4qpjav1aff.pdf

Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG).

Rolling circle amplification (RCA) is an isothermal enzymatic process where a short DNA or RNA primer is amplified to form a long single stranded DNA or RNA using a circular DNA template and special DNA or RNA polymerases. The RCA product is a concatemer containing tens to hundreds of tandem repeats that are complementary to the circular template. The power, simplicity, and versatility of the DNA amplification technique have made it an attractive tool for biomedical research and nanobiotechnology. Traditionally, RCA has been used to develop sensitive diagnostic methods for a variety of targets including nucleic acids (DNA, RNA), small molecules, proteins, and cells. RCA has also attracted significant attention in the field of nanotechnology and nanobiotechnology. The RCA-produced long, single-stranded DNA with repeating units has been used as template for the periodic assembly of nanospecies. Moreover, since RCA products can be tailor-designed by manipulating the circular template, RCA has been employed to generate complex DNA nanostructures such as DNA origami, nanotubes, nanoribbons and DNA based metamaterials. These functional RCA based nanotechnologies have been utilized for biodetection, drug delivery, designing bioelectronic circuits and bioseparation. In this review, we introduce the fundamental engineering principles used to design RCA nanotechnologies, discuss recently developed RCA-based diagnostics and bioanalytical tools, and summarize the use of RCA to construct multivalent molecular scaffolds and nanostructures for applications in biology, diagnostics and therapeutics.

Rolling circle amplification: A versatile tool for chemical biology, materials science and medicine

Hepatitis E virus (HEV) is a zoonotic agent, which is mainly transmitted by consumption of undercooked meat products originating from infected animals. Domestic pigs and wild boars are the major animal reservoirs, but HEV infections have been also repeatedly described in wild deer species. However, farmed deer has been only sparsely investigated so far. Here, 108 blood and 106 liver samples from fallow deer, red deer, and sika deer strictly hold in game enclosures from 11 farms in Germany were analyzed for markers of HEV infection. Using a commercial double antigen sandwich ELISA, 3/108 (2.7%) serum samples were scored borderline for HEV-specific antibodies, whereas the remaining samples were negative. No HEV-RNA (0%) was detected in the 106 liver samples. The results suggest a low risk of HEV infection in farmed deer in Germany.

No Evidence of Hepatitis E Virus Infection in Farmed Deer in Germany.

Spinareoviridae is a large family of icosahedral viruses that are usually regarded as non-enveloped with segmented (9-12 linear segments) dsRNA genomes of 23-29 kbp. Spinareovirids have a broad host range, infecting animals, fungi and plants. Some have important pathogenic potential for humans (e.g. Colorado tick fever virus), livestock (e.g. avian orthoreoviruses), fish (e.g. aquareoviruses) and plants (e.g. rice ragged stunt virus and rice black streaked dwarf virus). This is a summary of the ICTV Report on the family Spinareoviridae, which is available at ictv.global/report/spinareoviridae.

ICTV Virus Taxonomy Profile: Spinareoviridae 2022.

Two nightjars (Caprimulgus europaeus) from a bird park in the Netherlands died suddenly, with no clinical signs, within 1 month of each other. The main pathologic findings at necropsy were splenomegaly and hepatic necrosis. On histologic examination, intranuclear viral inclusion bodies consistent with avian Polyomavirus were observed in the liver, spleen, and kidneys. Polymerase chain reaction testing of samples from the liver, spleen, and kidneys detected avian polyomaviral DNA, and sequence analysis showed that the virus had a sequence homology of 99% to psittacine avian Polyomavirus strains. To our knowledge, this is the first report of avian Polyomavirus infection in the order Caprimulgiformes. Lovebirds (Agapornis species), which were housed near the nightjars, were considered as the possible source of infection.

Mortality Due To Polyomavirus Infection in Two Nightjars

Two nightjars (Caprimulgus europaeus) from a bird park in the Netherlands died suddenly, with no clinical signs, within 1 month of each other. The main pathologic findings at necropsy were splenomegaly and hepatic necrosis. On histologic examination, intranuclear viral inclusion bodies consistent with avian polyomavirus were observed in the liver, spleen, and kidneys. Polymerase chain reaction testing of samples from the liver, spleen, and kidneys detected avian polyomaviral DNA, and sequence analysis showed that the virus had a sequence homology of 99% to psittacine avian polyomavirus strains. To our knowledge, this is the first report of avian polyomavirus infection in the order Caprimulgiformes. Lovebirds (Agapornis species), which were housed near the nightjars, were considered as the possible source of infection.

Reimar Johne

Papers

No Evidence of Hepatitis E Virus Infection in Farmed Deer in Germany.

ICTV Virus Taxonomy Profile: Spinareoviridae 2022.

Mortality Due To Polyomavirus Infection in Two Nightjars

Mortality Due to Polyomavirus Infection in Two Nightjars (Caprimulgus europaeus)

Detection and genome characterization of bovine polyomaviruses in beef muscle and ground beef samples from Germany.