Virology

Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy Abstract The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.

Genetic diversity of group A rotaviruses in Moscow in 2018-2019 Abstract Here, we present the results of a study in which 639 samples obtained between October 2018 and April 2019 from patients with symptoms of acute gastroenteritis were tested for the presence of a rotavirus infection. The antigen of group A rotavirus was detected in 160 samples (25% of those tested). To study the genetic diversity of group A rotavirus, RNA was isolated from the samples, and polymerase chain reaction combined with reverse transcription (RT-PCR) with primers specific for the VP4, VP6, and VP7 genes of group A rotaviruses was performed. At least one fragment of the group A rotavirus genome was found in 101 samples (15.8%). These fragments were sequenced, and their G and P genotypes—as well as their combinations—were determined. The predominant G genotypes were G9 (35.8% of all genotyped samples) and G4 (28.4%), but the rare G12 genotype was also found (3.0%). The dominant P genotype was P[8]. The spectrum of certain G/P combinations of genotypes included seven variants. The most common variants were G9P[8] (37.2%) and G4P[8] (30.2%).

Protective cellular immune response against hepatitis C virus elicited by chimeric protein formulations in BALB/c mice Abstract The eradication of hepatitis C virus (HCV) infection is a public health priority. Despite the efficiency of treatment with direct-acting antivirals, the high cost of the therapy and the lack of accurate data about the HCV-infected population worldwide constitute important factors hampering this task. Hence, an affordable preventive vaccine is still necessary for reducing transmission and the future disease burden globally. In this work, chimeric proteins (EnvCNS3 and NS3EnvCo) encompassing conserved and immunogenic epitopes from the HCV core, E1, E2 and NS3 proteins were produced in Escherichia coli, and their immunogenicity was evaluated in BALB/c mice. The impact of recombinant HCV E2.680 protein and oligodeoxynucleotide 39M (ODN39M) on the immune response to chimeric proteins was also assessed. Immunization with chimeric proteins mixed with E2.680 enhanced the antibody and cellular response against HCV antigens and chimeric proteins. Interestingly, the combination of NS3EnvCo with E2.680 and ODN39M as adjuvant elicited a potent antibody response characterized by an increase in antibodies of the IgG2a subclass against E2.680, NS3 and chimeric proteins, suggesting the induction of a Th1-type response. Moreover, a cytotoxic T lymphocyte response and a broad response of IFN-γ-secreting cells against HCV antigens were induced with this formulation as well. This T cell response was able to protect vaccinated mice against challenge with a surrogate model based on HCV recombinant vaccinia virus. Overall, the vaccine candidate NS3EnvCo/E2.680/ODN39M might constitute an effective immunogen against HCV with potential for reducing the likelihood of viral persistence.

Novel positive-sense single-stranded RNA virus related to alphavirus-like viruses from Fusarium graminearum Abstract A putative novel positive-sense (+) RNA virus was detected in isolate CF16158 of the fungus Fusarium graminearum, the causal agent of Fusarium head blight and crown rot in wheat in China. The full genome of this virus was sequenced and characterized. The complete cDNA sequence is 7,051 nt long and contains four open reading frames (ORFs). ORF2 is predicted to encode helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains that are conserved among the alphavirus-like viruses. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of Hel and RdRp indicated that this (+) RNA mycovirus is a novel member of a new, yet to be established family of alphavirus-like viruses. Therefore, we named this virus “Fusarium graminearum alphavirus-like virus 1” (FgALV1). This is the first report of a full-length genomic sequence of a putative alphavirus-like virus in F. graminearum.

Complete genome sequence of a novel polerovirus in Ornithogalum thyrsoides from South Africa Abstract Ornithogalum thyrsoides, commonly known as chincherinchee, is an indigenous ornamental plant widely cultivated in South Africa. It is commercially valued as a flowering pot plant and for the production of cut flowers. Virus infections resulting in the development of severe necrotic mosaic symptoms threaten the success of commercial cultivation. The virome of an O. thyrsoides plant displaying necrotic mosaic symptoms was determined using high-throughput sequencing (HTS). In this plant, ornithogalum mosaic virus and ornithogalum virus 3 were identified, as well as a previously unknown virus. The full genome sequence of this virus was confirmed by Sanger sequencing using overlapping amplicons combined with rapid amplification of cDNA ends (RACE). Based on genome organisation and phylogenetic analysis, this novel virus can be classified as a polerovirus.

Nonstructural p26 proteins encoded by the 3’-proximal genes of velariviruses and criniviruses are orthologs Abstract The 3’-most genes in RNA-2 of the Crinivirus genus members (family Closteroviridae) code for non-structural p26 proteins that share amino acid sequence similarity [Stewart LR, Hwang MS, Falk BW (2009) Virus Res 145:293-299]. In this study, sensitive bioinformatic tools have been used to identify the homologous p26 proteins encoded by the 3’ genes in monopartite genomes of the members of Velarivirus, another Closteroviridae genus, and mint vein banding-associated virus, an unassigned member of the family. The p26 proteins showed similarity in their predicted secondary structures, but an amino acid sequence alignment showed no strictly conserved positions, thus indicating a high plasticity of these non-structural proteins. The implications of the sequence analysis for possible functions of the crinivirus and velarivirus p26 proteins are discussed.

First detection and genetic characterization of a novel kirkovirus from a dead thoroughbred mare in northern Xinjiang, China, in 2018 Abstract Background In May 2018, a 8 year old thoroughbred mare died at an equestrian club in Changji, Xinjiang, China. The horse had been imported from the United States in 2013. She became pregnant in December 2016 but, after foaling, gradually lost weight and died in May 2018. This study aim to identify the pathogen, who cause of horse death, using virome. Results We have identified an Equ1-like virus from the fecal virome of a dead thoroughbred mare in China. Full genomic sequencing and phylogenetic analysis of the virus, tentatively named “kirkovirus Cj-7-7”, showed that it was closely related to kirkovirus Equ1 and clustered together with po-circo-like viruses 21, 22, 41, and 51, suggesting that it should be assigned to the proposed family “Kirkoviridae”. An epidemiological investigation showed that kirkovirus Cj-7-7 circulates in horses of northern Xinjiang and may specifically infect intestinal cells. Conclusions Our findings demonstrate the genetic diversity and geographic distribution of Kirkoviruses, and the prevalence of Kirkovirus Cj-7-7 in Xinjiang, China.

Genomic characterization of Malus domestica virus A (MdoVA), a novel velarivirus infecting apple Abstract Screening of apple samples using a high-throughput sequencing (HTS) approach led to the discovery of a novel virus, tentatively named “Malus domestica virus A” (MdoVA). Its genomic organisation and phylogenetic relationship showed relatedness to viruses of the genus Velarivirus in the family Closteroviridae. It is not clear whether MdoVA has any impact on its host, as the analysed apple tree contained other viruses and a viroid.

Phage vB_BmeM-Goe8 infecting Bacillus megaterium DSM319 Abstract vB_BmeM-Goe8 is a phage preying on Bacillus megaterium. Its genome has a GC content of 38.9%, is 161,583 bp in size, and has defined ends consisting of 7436-bp-long terminal repeats. It harbours 11 genes encoding tRNAs and 246 coding DNA sequences, 66 of which were annotated. The particle reveals Myoviridae morphology, and the formation of a double baseplate upon tail sheath contraction indicates morphological relatedness to the group of SPO1-like phages. BLASTn comparison against the NCBI non-redundant nucleotide database revealed that Bacillus phage Mater is the closest relative of vB_BmeM-Goe8.

Complete genomic sequence of crow-dipper mosaic-associated virus, a novel macluravirus infecting Pinellia ternata Abstract A new macluravirus infecting Pinellia ternata in China was identified by high-throughput sequencing (HTS) and tentatively named “crow-dipper mosaic-associated virus” (CrdMV). The complete genome sequence of CrdMV was determined by reverse transcription (RT) PCR and rapid amplification of cDNA ends (RACE) PCR. The genomic RNA of CrdMV consists of 8,454 nucleotides (nt), excluding the poly(A) tail at the 3′ end. CrdMV has a genomic structure typical of macluraviruses, with large open reading frame encoding a polyprotein of 2,696 amino acids (aa). CrdMV shares 54.40%–59.37% nt sequence identity at the genome sequence level, 48.00%–58.58% aa sequence identity, at the polyprotein sequence level and 37.27%–49.22% aa sequence identity at the CP sequence level with other members of the genus Macluravirus. These values are well below the species demarcation threshold for the family Potyviridae. Phylogenetic analysis based on the amino acid sequences of polyproteins confirmed that CrdMV clusters closely with broad-leafed dock virus A (BDVA, GenBank accession no. KU053507). These results suggest that CrdMV should be considered a distinct member of the genus Macluravirus.