A novel astrovirus identified in wild rhesus monkey feces in China

Abstract

The discovery and analysis of pathogens carried by non-human primates are important for understanding zoonotic infections in humans. We identified a highly divergent astrovirus (AstV) from fecal matter from a rhesus monkey in China, which has been tentatively named “monkey-feces-associated AstV” (MkAstV). The full-length genome of MkAstV was determined to be 7377 nt in length. It exhibits the standard genomic AstV organization of three open reading frames (ORFs) and is most closely related to duck AstV (28%, 49%, and 35% amino acid sequence identity in ORF1a, ORF1b, and ORF2, respectively). Coincidentally, while this report was being prepared, an astrovirus sequence from Hainan black-spectacled toad became available in the GenBank database, showing 95%, 94% and 92% aa sequence identity in ORF1a, ORF1b and ORF2, respectively, to the corresponding ORFs of MkAstV. Phylogenetic analysis of ORF1a, ORF1b, and ORF2 indicated that MkAstV and the amphibian-related astroviruses formed an independent cluster in the genus Avastrovirus. The host of MkAstV remains unknown. Epidemiological and serological studies of this novel virus should be undertaken in primates, including humans.

Characterization and genome analysis of novel Klebsiella phage Henu1 with lytic activity against clinical strains of Klebsiella pneumoniae

Abstract

Klebsiella pneumoniae is an important human pathogen that is associated with a wide range of diseases, including pneumonia and septicemia. Because of the threat of drug-resistant K. pneumoniae to humans, especially carbapenem-resistant K. pneumoniae,which is becoming a growing threat to hospitalized patients, the potential use of phage therapy has generated considerable interest. Henu1, isolated from a sewage sample, was identified as a linear double-stranded DNA phage of 40,352 bp with 53.14% G + C content and 143-bp terminal repeats. The Henu1 genome contains 45 open reading frames, and no tRNA genes were found. K. pneumoniae clinical strains with the capsular types K-1, K-2, and K-57 could be infected by Henu1. No human-virulence-related genes or lysogen-formation gene clusters were detected in this phage genome, suggesting that Henu1 is a virulent phage in its bacterial host and is safe for humans.

Complete genome sequence of a previously undescribed badnavirus occurring in Polyscias fruticosa L. (Ming aralia)

Abstract

A previously undescribed badnavirus was identified in plants of Polyscias fruticosa (Ming aralia) showing symptoms of mild mosaic and leaf senescence. Characteristic bacilliform virions of the Polyscias badnavirus averaging 30 × 120 nm in size were observed by transmission electron microscopy in partially purified leaf tissue extracts from symptomatic but not asymptomatic plants collected in the USA and Nigeria. The isolate from the USA was complete sequenced. The genome is 7592 bp in length and contains three open reading frames with an arrangement similar to that of other members of the genus Badnavirus. The largest open reading frame (ORF3) encodes a putative polyprotein, with predicted domains including zinc finger, aspartic protease, reverse transcriptase (RT) and RNase H, in that order. The USA and Nigeria isolates of the virus had a high level (98%) of nucleotide sequence identity in the RT+RNase H region. Within the genus Badnavirus, these viruses were most closely related to schefflera ringspot virus (SRV), sharing 63% identity at the nucleotide level. Based on the ICTV species demarcation criteria for the genus Badnavirus (more than 20% nucleotide sequence divergence in the RT+RNase H region), the Polyscias virus is proposed to be a new member of the genus, and the name polyscias mosaic virus (PoMV) is proposed. The complete genome sequence was deposited in the NCBI GenBank database under accession no. MH475918.

Questions surrounding the taxonomic validity of the species Garlic mite-borne filamentous virus (genus Allexivirus )

Abstract

Garlic mite-borne filamentous virus is one of the oldest recognized allexivirus species but, paradoxically, one with the least well studied member viruses. In this paper, we review the history of this taxon and highlight problems in designating a holotype (exemplar isolate). Analyses are presented that suggest that GarMbFV is conspecific with Garlic virus A, and therefore the former taxon should be abolished.

Novel smacoviruses identified in the faeces of two wild felids: North American bobcat and African lion

Abstract

Smacoviruses are small circular single-stranded DNA viruses that appear to be prevalent in faeces of a range of animals and have also been found in a few insect species. In this study, we report the first viral genomes from faeces of free-roaming wild felids on two continents. Two smacoviruses were recovered from the faeces of two North American bobcats (Lynx rufus), and one was recovered from an African lion (Panthera leo). All three genomes are genetically different, sharing 59-69% genome-wide sequence identity to other smacoviruses. These are the first full smacovirus genome sequences associated with a large top-end feline predator, and their presence in these samples suggests that feline faeces are a natural niche for the organisms that these viruses infect.

Complete genome sequence of a tentative new umbravirus isolated from Patrinia scabiosaefolia

Abstract

The complete genomic RNA sequence of a tentative new umbravirus from Patrinia scabiosaefolia, tentatively named “patrinia mild mottle virus” (PatMMoV), was determined. The genome of PatMMoV consists of 4,214 nucleotides and has a typical umbravirus genome organization with four open reading frames. BLAST searches showed that the complete nucleotide sequence of PatMMoV had the highest identity (72%; 50% query coverage) to Ixeridium yellow mottle-associated virus 2 (IxYMaV-2; an unclassified umbravirus). In addition, phylogenetic analysis and pairwise comparisons showed that PatMMoV and IxYMaV-2 were the most closely related and placed in the same clade within a group of umbraviruses. These results suggest that PatMMoV is a putative new member of the genus Umbravirus in the family Tombusviridae.

DNA of diverse adenoviruses detected in Cameroonian rodent and shrew species

Abstract

Rodent adenoviruses are important models for human disease. In contrast to the over 70 adenovirus types isolated from humans, few rodent adenoviruses are known, despite the vast diversity of rodent species. PCR and Sanger sequencing were used to investigate adenovirus diversity in wild rodents and shrews in Cameroon. Adenovirus DNA was detected in 13.8% of animals (n = 218). All detected sequences differ from known adenovirus types by more than 10% at the amino acid level, thus indicating up to 14 novel adenovirus species. These results highlight the diversity of rodent adenoviruses, their phylogeny, and opportunities for studying alternative adenovirus rodent models.

Elimination of multidrug-resistant Proteus mirabilis biofilms using bacteriophages

Abstract

Proteus mirabilis is responsible for a wide range of infections that affect the urinary tract, the respiratory tract, burns, wounds and the feet of individuals with diabetes. They are highly resistant to antimicrobial agents, and new therapeutic options are therefore needed to combat this pathogen. The use of bacteriophages is one option that may be useful in treating multidrug-resistant (MDR) Proteus mirabilis infections, especially biofilm-based infections. The aim of this study was to control biofilms formed by MDR Proteus mirabilis using bacteriophages. Proteus mirabilis isolates were identified based on biochemical tests, and their resistance profiles were determined by the disk diffusion method. The biofilm-forming capacity of the isolates was assessed by the spectrophotometric method. Bacteriophages attacking Proteus mirabilis were isolated from sewage. The effect of phage on biofilm formation was investigated by the viable count method. A high rate of drug resistance was found (87.2%). Strong biofilm formation was observed in 80.5% of isolates, while moderate production was found in 19.5%. Five bacteriophages were isolated from sewage and were tested for their ability to eliminate biofilms. Significant disruption of pre-formed biofilms was observed that reached up to 99.9% decrease in the number of viable cells. The use of bacteriophages is considered a promising strategy against the biofilm infections caused by MDR Proteus mirabilis isolates.