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

Angehorige der Familien Papillomaviridae und Polyoma-viridae verursachen Erkrankungen bei Zier- und Wildvogeln. Papillomviren werden als Erreger von Hautwarzen an un-befiederten Stellen des Kopfes und der Stander vor allem bei Finken und Kanarienvogeln, selten auch bei Papageien, gefunden. Das Krankheitsbild der »internen Papillomatose der Papageien«, das durch die Ausbildung von Papillomen im Kloaken- und Schnabelbereich, aber auch im gesamten Gastrointestinaltrakt gekennzeichnet ist, tritt vor allem bei Amazonen und Aras auf. Die Atiologie dieser Erkrankung ist noch nicht geklart; neuere Untersuchungen weisen eher auf Herpes- als auf Papillomviren als atiologisches Agens hin. Infektionen mit dem »aviaren Polyomavirus« verursachen vor allem bei Wellensittichen und Agaporniden Erkrankun-gen, oft mit akutem bis perakutem Verlauf und hoher Todes-rate bei Nestlingen, wahrend altere Vogel zumeist Feder-missbildungen zeigen. Ahnliche Krankheitsbilder konnen auch bei der Infektion anderer Papageienarten sowie bei Sperlings- und Greifvogeln auftreten. Die vorliegende Arbeit gibt einen aktuellen Uberblick uber Klinik, Diagnostik und Bekampfung dieser Virusinfektionen.

Papillomavirus and polyomavirus infections of pet birds and wild birds: an overview

Infections with hepatitis E virus (HEV) have led to several large epidemic outbreaks of acute hepatitis in Central and South Asia, North and West Africa as well as in Mexico in the past. In general, the course of disease is moderate with a case/fatality rate of 0.5 % to 4 %, however, for pregnant women rates between 15 % and 25 % have been recorded due to fulminant hepatitis. Most of the hepatitis E cases in Central Europe (72 cases have been notified in 2007 in Germany) are infections imported from the endemic regions; however, there is increasing evidence of sporadic infections without a history of travel. HEV is related to Caliciviruses and possesses a high stability in the environment. It is transmitted via the faecal-oral route, in most cases by faecal contamination of water and in some cases by contaminated food. HEV strains closely related to human isolates have been detected in several animal species, especially in pigs. Reports on hepatitis E following consumption of uncooked meat from wild animals indicate a zoonotic potential of HEV. The virus seems to be highly prevalent in pig farms of several European countries; a first report shows that a high percentage of wild boars are also infected with HEV in Germany. Further research is needed to enable an estimation of the risk of a zoonotic transmission of HEV from the animal population to humans.

Hepatitis E : eine über Lebensmittel übertragbare virale Zoonose in Deutschland?

Rotavirus A (RVA) is an important cause of diarrhea in humans and animals. However, RVA in wild animals has only scarcely been investigated so far. Here, the presence of RVA in wild ungulates hunted between 2019 and 2022 in Brandenburg, Germany, was investigated using real-time RT-PCR and sequencing of RT-PCR products. By analyzing intestinal contents, RVA-RNA was detected in 1.0% (2/197) of wild boar (Sus scrofa), 1.3% (2/152) of roe deer (Capreolus capreolus), and 2.1% (2/95) of fallow deer (Dama dama) but not in 28 red deer (Cervus elaphus) samples. Genotyping identified G3P[13] strains in wild boar, which were closely related to previously described pig and wild boar strains. Genotype G10P[15] strains, closely related to strains from roe deer, sheep, or cattle, were found in roe deer. The strains of fallow deer represented genotype G3P[3], clustering in a group containing different strains from several hosts. The results indicated a low prevalence of RVA in wild ungulates in Germany. Associations of specific genotypes with certain ungulate species seem to exist but should be confirmed by analyses of more samples in the future.

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Reimar Johne

Papers

Papillomavirus and polyomavirus infections of pet birds and wild birds: an overview

Hepatitis E : eine über Lebensmittel übertragbare virale Zoonose in Deutschland?

Rotaviruses in Wild Ungulates from Germany, 2019–2022

Papillomvirus- und Polyomavirus-Infektionen bei Zier- und Wildvögeln: eine Übersicht

Detection of recurring antibody titres to avian polyoma virus in a captive population of Spix's macaws (Cyanopsitta spixii)