The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China

In September 2017, a yellow spot leaf disease was noted on the leaves of Prunus davidiana (Carr.) Franch. plants in Liaoning, China, and spherical virions (approx. 30 nm in diameter) were later observed in preparations of symptomatic leaves. Subsequent deep sequencing of small RNA revealed the presence of a virus in these symptomatic leaves The complete genome of this viral isolate consists of 6,072 nucleotides, excluding the poly(A) tail. The virus showed the closest genetic relationship to grapevine-associated tymo-like virus, reported in Colmar, France (GaTLV, MH383239), which is the sole member of the newly proposed genus "Gratylivirus" within the order Tymovirales, which is currently unassigned to a particular family. The virus clustered closely with GaTLV in a phylogenetic tree constructed based on complete genomic sequences. On the basis of the nucleotide and amino acid sequences of the replicase and coat protein genes, this virus shares the highest (although still relatively low) sequence similarity with those of GaTLV (41.6%-60.8% identity), indicating that the virus is a distinct member of the order Tymovirales, for which the name "prunus yellow spot-associated virus" (PYSaV) is proposed. To our knowledge, this is the first report of a virus naturally infecting P. davidiana.

Complete genome sequence of a novel member of the family Potyviridae isolated from Phellodendron amurense Rupr. in Liaoning, China

In September 2017, Phellodendron amurense Rupr. plants showing yellow ringspots on leaves were observed in Liaoning, China. Flexuous filamentous particles (~1000 × 13 nm) were observed in the sap prepared from symptomatic leaves. A virus was detected in the symptomatic leaves by sequencing small RNAs and assembling the genome sequence. The complete genomic RNA was found to be 10,457 nucleotides in length excluding the poly(A) tail and to have the closest phylogenetic relationship to rose yellow mosaic virus (RoYMV), the sole member of newly established genus Roymovirus in the family Potyviridae. The coat protein gene (CP) of this virus shares 49.2% nucleotide and 55.1% amino acid sequence identity with that of RoYMV. These results suggest that this virus, which was named "phellodendron yellow ringspot-associated virus" (PYRaV) is a new member of the genus Roymovirus.

Correction to: Molecular characterization of a novel citrivirus from citrus using next‑generation sequencing

Unfortunately, the Acknowledgement, ethical statement and the Conflict of interest statements were not included in the online publication and updated here in this Erratum.

Sequence analysis and genomic organization of a novel chuvirus, Tàiyuán leafhopper virus

A novel unsegmented chuvirus was found in a leafhopper (Psammotettix alienus) and tentatively named "Tàiyuán leafhopper virus" (TYLeV). The full genome of TYLeV is 14,670 nucleotides in length and includes four ORFs encoding glycoprotein, nucleocapsid protein, RNA-dependent RNA polymerase and an uncharacterized protein, respectively. These genomic features are similar to those of the chuvirus Scaldis River bee virus, but the virus is highly divergent from known chuviruses and other members in the order Mononegavirales, with amino acid sequence identities of only 13.6-33% for the RNA-dependent RNA polymerase (RdRp). On the basis of genomic features, phylogenetic analysis and comparisons of RdRp sequences, we suggest that this virus is a member of a new species of chuvirus in the proposed genus Mivirus.

Full genome sequence of a novel iflavirus from the leafhopper Psammotettix alienus

A novel iflavirus was discovered in Psammotettix alienus by RNA sequencing. The virus genome has 10,826 nucleotides (nt) excluding the poly A tail, encodes a 3187-amino-acid polyprotein, and is tentatively named "Psammotettix alienus iflavirus 1" (PaIV1). PaIV1 has a similar genomic structure, conserved motifs, and a close phylogenetic relationship to members of the genus Iflavirus, but it shows only 41.9-55.2% sequence identity in the full genome and 16.2-49% in the deduced polyprotein. Thus, we suggest that it is a new member of the genus Iflavirus, family Iflaviridae.

Efficacy of Nd-YAG laser for treatment of pyogenic granuloma on the fingers and toes

Pyogenic granuloma (PG) is a common benign vascular proliferation which often occurs on the head, neck, hands, and feet. Among the various treatment options for PG, surgical excision is the most effective treatment which offers the lowest overall recurrence rates and also provides the exact diagnosis. However, it could have difficulties to do the surgery when lesions are located on the fingers and toes, especially very near to the nails, so laser may be a very good alternative choice. In this article, we evaluated the clinical efficacy and safety of neodymium-yttrium aluminum garnet (Nd:YAG) laser for treatment of PG located on the fingers and toes. Twenty-one patients with 21 PGs located on the fingers and toes were treated by multispot Nd-YAG laser. We chose monopulse (pulse width 10.5-13.5 ms; energy 100-125 J/cm²); treatment interval was 3-4 weeks. All lesions disappeared after one or two treatments. There was no apparent scar formation, no impact on the function of the fingers and toes, no damage to nail growth, and no recurrence in more than 12-month follow-up. Nd-YAG is an effective and safety treatment option for treatment of PG located on the fingers and toes.

Transcriptome sequencing reveals novel Citrus bark cracking viroid (CBCVd) variants from citrus and their molecular characterization

Citrus bark cracking viroid (CBCVd), previously called Citrus viroid IV, belongs to the genus Cocadviroid within the family Pospiviroidae. CBCVd has been identified as an important causative agent in citrus and hops. In this study, we obtained the full-length genomes of different variants of all detected citrus viroids from Pakistan through transcriptome sequencing. Different CBCVd variants were first found in Pakistan. These newly discovered Pakistani CBCVd variants were provisionally called "CBCVd-LSS" for their low sequence similarity (80.9%-88.9%) with the CBCVd RefSeq sequence (NC_003539). The two most predominant CBCVd sequences from Pakistan had the closest identity, 90.6% and 87.9%, with two CBCVd sequences isolated from hops. Identification and molecular characterization of CBCVd from citrus in Pakistan and China were also reported. The length of CBCVd from China ranged from 282 to 286 nucleotides, while that of the one from Pakistan ranged from 273 to 277 nucleotides. Based on genetic diversity and phylogenetic analysis, two main CBCVd clades were identified. CBCVd sequences from Pakistan, China, and other countries were further divided into six sub-clades. Sequence alignment revealed some nucleotide changes between these sub-clades, and analysis indicated that several mutations could significantly affect the primary and secondary structure of the viroid. Our results indicated that the CBCVd sequences from Pakistan and China were significantly different with respect to genome and secondary structure and Pakistan might be one of the independent geographical origins of CBCVd worldwide.

Characterization of a new apple luteovirus identified by high-throughput sequencing

Background

‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing.

Methods

Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5′/3’ RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus.

Results

Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards.

Conclusions

A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-0998-3) contains supplementary material, which is available to authorized users.

Complete genome sequence of yam chlorotic necrosis virus, a novel macluravirus infecting yam

The complete genome sequence of a novel member of the genus Macluravirus was determined from yam plants with chlorotic and necrotic symptoms in China. The genomic RNA consists of 8,261 nucleotides (nt) excluding the 3'-terminal poly(A) tail, containing one long open reading frame (ORF) encoding a large putative polyprotein of 2,627 amino acids. Its genomic structure is typical of macluraviruses, which lack the P1 protein, N-terminal HC-Pro, and D-A-G motif for aphid transmission that are found in potyviruses. The virus shares 56.3-63.8% sequence identity at the genome sequence level and 49.7-63.9% at the polyprotein sequence level with other members of the genus Macluravirus. Phylogenetic analysis based on the complete polyprotein sequence of representative members of the family Potyviridae clearly places the virus within the genus Macluravirus. These results suggest that the virus, tentatively named "yam chlorotic necrosis virus" (YCNV), should be considered a member of a novel species in the genus Macluravirus.

Safety and efficacy of telbivudine in late pregnancy to prevent mother-to-child transmission of hepatitis B virus: A multicenter prospective cohort study

Infection of hepatitis B virus (HBV) occurs in ~10% of infants of HBV-infected mothers with positive hepatitis B e antigen (HBeAg) after immunoprophylaxis. We aimed to evaluate the safety and efficacy of telbivudine used during late pregnancy for preventing mother-to-child transmission of HBV. We conducted a multicenter prospective cohort study in 5 hospitals from 2012 to 2014, which enrolled HBV-infected singleton pregnant women with positive HBeAg. By their choice, women were divided into therapy (telbivudine 600 mg/day, from gestation 28-32 weeks to 3-4 weeks postpartum) and control (no antiviral agent) groups. Infants received passive-active immunoprophylaxis and follow-up at the age of 7-14 months. Totally, 328 pregnant women were included: 149 in the telbivudine group and 179 in the control group. Baseline HBV DNA levels were similar in the 2 groups (7.43 vs 7.37 log₁₀ IU/mL, P = .711). At delivery, HBV DNA levels in the telbivudine and control groups were 3.80 and 7.26 log₁₀ IU/mL, respectively (P < .0001). Of the infants, 128 (85.9%) in the telbivudine group and 156 (87.2%) in the control group were followed up. No infant in the telbivudine group had chronic infection, while 2 (1.28%) infants in the control group did (P = .503). Three (2.34%) infants in the telbivudine group, but none in the control group, had severe congenital or developmental abnormalities (P = .090). The data indicate that telbivudine may block perinatal HBV transmission. However, larger studies are required to clarify whether anti-HBV therapy in pregnancy is associated with severe adverse effects in the foetuses and infants.

Non-invasive acquisition of fetal ECG from the maternal xyphoid process: a feasibility study in pregnant sheep and a call for open data sets

OBJECTIVE

The utility of fetal heart rate (FHR) monitoring can only be achieved with an acquisition sampling rate that preserves the underlying physiological information on the millisecond time scale (1000 Hz rather than 4 Hz). For such acquisition, fetal ECG (fECG) is required, rather than the ultrasound to derive FHR. We tested one recently developed algorithm, SAVER, and two widely applied algorithms to extract fECG from a single-channel maternal ECG signal recorded over the xyphoid process rather than the routine abdominal signal.

APPROACH

At 126dG, ECG was attached to near-term ewe and fetal shoulders, manubrium and xyphoid processes (n  =  12). fECG served as the ground-truth to which the fetal ECG signal extracted from the simultaneously-acquired maternal ECG was compared. All fetuses were in good health during surgery (pH 7.29  ±  0.03, pO₂ 33.2  ±  8.4, pCO₂ 56.0  ±  7.8, O₂Sat 78.3  ±  7.6, lactate 2.8  ±  0.6, BE  -0.3  ±  2.4).

MAIN RESULT

In all animals, single lead fECG extraction algorithm could not extract fECG from the maternal ECG signal over the xyphoid process with the F1 less than 50%.

SIGNIFICANCE

The applied fECG extraction algorithms might be unsuitable for the maternal ECG signal over the xyphoid process, or the latter does not contain strong enough fECG signal, although the lead is near the mother's abdomen. Fetal sheep model is widely used to mimic various fetal conditions, yet ECG recordings in a public data set form are not available to test the predictive ability of fECG and FHR. We are making this data set openly available to other researchers to foster non-invasive fECG acquisition in this animal model.

Two novel totiviruses in the white-backed planthopper, Sogatella furcifera

There is little information about commensal viruses in the white-backed planthopper, Sogatella furcifera, although it is an important agricultural insect. Here, two novel double-stranded RNA viruses related to the viruses in the family Totiviridae were identified using next-generation sequencing and tentatively named Sogatella furcifera totivirus 1 and 2 (SfTV1 and SfTV2). Their complete genomes consist of 6310 and 6303 nt, respectively, showing typical genomic features with viruses in the family Totiviridae. Identity, phylogenetic and conserved sequence analyses showed that SfTV1, SfTV2 and three other insect viruses may form a proposed novel genus of the family Totiviridae. Vertical transmission of the two viruses was highly efficient, and they were detected in all insect tissues and developmental stages, with the highest titres in the adult and in the haemolymph and reproductive organs. To our knowledge, this is the first report of viruses in the family Totiviridae found in a hemipteran insect.

Sequence analysis and genomic organization of a new insect iflavirus, Sogatella furcifera honeydew virus 1

A novel iflavirus, tentatively named "Sogatella furcifera honeydew virus 1" (SFHV1), discovered through transcriptome sequencing analysis of white-backed planthoppers (Sogatella furcifera) collected in southern China, is described here. The full genome of SFHV1 is 10,837 nucleotides (nt) long, including the polyA tail, and shares 65.5% and 64.5% genomic identity with Laodelphax striatellus picorna-like virus 2 and Laodelphax striatella honeydew virus 1, respectively. On the basis of the phylogenetic analysis of the complete genomic sequence and the deduced RdRp amino acid sequence of SFHV1 with other iflaviruses, we suggest that it is a member of a new species in the genus Iflavirus, family Iflaviridae.

Magnetic field application or mechanical stimulation via magnetic microparticles does not enhance chondrogenesis in mesenchymal stem cell sheets

Using a novel magnetic field bioreactor, this work evaluated the chondrogenesis of scaffold-free human mesenchymal stem cell sheets in response to static and variable magnetic fields, as well as mechanical stimulation via 4.4 μm magnetic particles. Neither static nor variable magnetic fields generated by 1.44-1.45 T permanent magnets affected cartilage formation. Notably, magnetic field-induced mechanical stimulation by magnetic particles, which applied forces to the cells and ECM statically (4.39 pN) or cyclically (1.06-63.6 pN; 16.7 mHz), also did not affect cartilage formation.

Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat

A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180-210 nm length and 35-40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers P. alienus. The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3' leader RNA and a 258-nt 5' trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus Nucleorhabdovirus. Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper P. alienus transmission.

Discovery of a novel geminivirus associated with camellia chlorotic dwarf disease

Next-generation sequencing of small RNAs and PCR amplification with two pairs of back-to-back primers, followed by cloning and sequencing, allowed identification of a novel geminivirus isolate provisionally named camellia chlorotic dwarf-associated virus (CaCDaV). The complete genome sequence of CaCDaV comprises 3,687 nucleotides (nts) and six open reading frames (ORFs). The genome and putative proteins of CaCDaV were most closely related to those of two unclassified geminiviruses: citrus chlorotic dwarf-associated virus (CCDaV, 3,640 nt) and mulberry mosaic dwarf-associated virus (MMDaV, 2,952 nt). Phylogenetic analysis revealed a distinct clade for CaCDaV, CCDaV and MMDaV, supporting their inclusion in a new genus within the family Geminiviridae. Because CaCDaV and CCDaV shared a high genome nucleotide sequence identity (54.8%), we propose that the CaCDaV should be included as a member in this new genus.

No effect of AR polyG polymorphism on spinal and bulbar muscular atrophy phenotype

BACKGROUND AND PURPOSE

Disease severity varies considerably among patients with Spinal and Bulbar Muscular Atrophy (SBMA). Our aim was to investigate the role of androgen receptor (AR) polymorphic repeats in SBMA phenotype.

METHODS

We analyzed the length of AR polyQ and polyG tracts in 159 SBMA patients.

RESULTS

No relationship between polyG size or polyG/polyQ haplotypes and clinical phenotype was found. An independent negative correlation between polyQ-length and onset of weakness was confirmed (P < 0.001).

CONCLUSIONS

The negative results of our study prompt to continue the search for potential disease modifiers in SBMA outside the AR gene.