Safety and efficacy of subthreshold micropulse yellow laser for persistent subretinal fluid after scleral bucking a randomized clinical trial.

Persistent subretinal fluid (PSF) after scleral bucking of rhegmatogenous retinal detachment may delay recovery and affect the final visual quality, but with no effective treatment. This study firstly investigated the safety and efficacy of 577 nm yellow subthreshold micropulse laser (SML) on PSF after scleral bucking surgery. This double-masked randomized clinical trial was conducted from December 2020 to October 2022 at Chongqing Aier Eye Hospital. Participants with PSF last for 1 month after scleral bucking surgery with break closed and retina reattachment were recruitment. These participants were treated by 577 nm yellow SML or sham treatment. Funduscopy, optical coherence tomography (OCT) volume change, best corrected vision acuity (BCVA) and visual field test were evaluated for six mouths follow-up. A total of 24 participants were randomized into SML group or Sham group equally. Compared with Sham group, the OCT volume within 6 mm of macular fovea was significantly less in SML group 6 months after therapy (P = 0.048). There were no statistically significant differences of OCT volume at 1, 2 and 3 months from baseline between groups. BCVA of ETDRS letters had no statistically significant difference. Pattern Standard Deviation amelioration (P = 0.039) had statistically significance in SML group compared with Sham group. There were no complications in the 2 groups. These preliminary findings suggest that 577 nm yellow SML therapy could accelerate PSF absorption after scleral bucking surgery.Trial registration: Chinese Clinical Trial Registry No. ChiCTR2000037838, 02/09/2020, https://www.chictr.org.cn/showproj.html?proj=51885 .

Generating synthetic computed tomography for radiotherapy: SynthRAD2023 challenge report.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information, while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: (1) MRI-to-CT and (2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (≥0.87/0.90) and gamma pass rates for photon (≥98.1%/99.0%) and proton (≥97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy. It showcased the growing capacity of deep learning to produce high-quality sCT, reducing reliance on conventional CT for treatment planning.

DoseDiff: Distance-Aware Diffusion Model for Dose Prediction in Radiotherapy.

Treatment planning, which is a critical component of the radiotherapy workflow, is typically carried out by a medical physicist in a time-consuming trial-and-error manner. Previous studies have proposed knowledge-based or deep-learning-based methods for predicting dose distribution maps to assist medical physicists in improving the efficiency of treatment planning. However, these dose prediction methods usually fail to effectively utilize distance information between surrounding tissues and targets or organs-at-risk (OARs). Moreover, they are poor at maintaining the distribution characteristics of ray paths in the predicted dose distribution maps, resulting in a loss of valuable information. In this paper, we propose a distance-aware diffusion model (DoseDiff) for precise prediction of dose distribution. We define dose prediction as a sequence of denoising steps, wherein the predicted dose distribution map is generated with the conditions of the computed tomography (CT) image and signed distance maps (SDMs). The SDMs are obtained by distance transformation from the masks of targets or OARs, which provide the distance from each pixel in the image to the outline of the targets or OARs. We further propose a multi-encoder and multi-scale fusion network (MMFNet) that incorporates multi-scale and transformer-based fusion modules to enhance information fusion between the CT image and SDMs at the feature level. We evaluate our model on two in-house datasets and a public dataset, respectively. The results demonstrate that our DoseDiff method outperforms state-of-the-art dose prediction methods in terms of both quantitative performance and visual quality.

Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China.

The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.

Multi-Scale Tokens-Aware Transformer Network for Multi-Region and Multi-Sequence MR-to-CT Synthesis in a Single Model.

The superiority of magnetic resonance (MR)-only radiotherapy treatment planning (RTP) has been well demonstrated, benefiting from the synthesis of computed tomography (CT) images which supplements electron density and eliminates the errors of multi-modal images registration. An increasing number of methods has been proposed for MR-to-CT synthesis. However, synthesizing CT images of different anatomical regions from MR images with different sequences using a single model is challenging due to the large differences between these regions and the limitations of convolutional neural networks in capturing global context information. In this paper, we propose a multi-scale tokens-aware Transformer network (MTT-Net) for multi-region and multi-sequence MR-to-CT synthesis in a single model. Specifically, we develop a multi-scale image tokens Transformer to capture multi-scale global spatial information between different anatomical structures in different regions. Besides, to address the limited attention areas of tokens in Transformer, we introduce a multi-shape window self-attention into Transformer to enlarge the receptive fields for learning the multi-directional spatial representations. Moreover, we adopt a domain classifier in generator to introduce the domain knowledge for distinguishing the MR images of different regions and sequences. The proposed MTT-Net is evaluated on a multi-center dataset and an unseen region, and remarkable performance was achieved with MAE of 69.33 ± 10.39 HU, SSIM of 0.778 ± 0.028, and PSNR of 29.04 ± 1.32 dB in head & neck region, and MAE of 62.80 ± 7.65 HU, SSIM of 0.617 ± 0.058 and PSNR of 25.94 ± 1.02 dB in abdomen region. The proposed MTT-Net outperforms state-of-the-art methods in both accuracy and visual quality.

First report of Lily virus X infecting Paris polyphylla var. yunnanensis in Yunnnan, China.

Lily virus X (LVX) is a positive-sense ssRNA virus belonging to the genus Potexvirus in the family Alphaflexiviridae. LVX is known to infect plants of the genera Lilium and Tricyrtis in the family Liliacea. LVX was first reported in an asymptomatic lily (Lilium formosanum) from England (Stone, 1980), but has been shown to infect plants in the Netherlands (Chen et al. 2005), the United States (Jordan et al. 2008) and Japan (Nijo et al. 2018). To date, the complete genomes of two LVX isolates from the Netherlands and Japan have been reported. Paris polyphylla var. yunnanensis, known as Dianchonglou in China, is a perennial plant of the family Melanthiaceae (formerly belonging to the family Trillium). In China, its rhizome is commonly used as an antispasmodic agent for stroke and cancer treatment (Chang et al. 2017). From 2019 to 2022, leaf mottle and shrinkage which are typical symptoms of viral infections were observed on the leaves of P. polyphylla var. yunnanensis plants in Dianchonglou fields in Qujing, Yunnan. Disease incidence ranged from 19% to 45% across 5 fields (90 plants per field) in Qujing. To identify the possible viral pathogen(s) associated with the disease, the mirVanaTM miRNA isolation Kit was used to extract total RNA was from a mixed sample pool of 5 symptomatic leaf samples collected from the 5 fields. RNA sequencing library was constructed using TruSeqTM RNA sample preparation kit. Sequencing on the Illumina HiSeqTM 2500 platform (Illumina, USA) with 125-bp paired-end reads yielded 23,077,786 raw reads. 22,534,100 clean reads were obtained by removing reads of low quality and poly-N using Trimmomatic software (Bolger et al. 2014). By utilizing the paired-end splicing method in Trinity software (Grabherr et al. 2011) the the raw reads were De novo assembled into 184,596 contigs, of which 303 were related to viruses, including Paris mosaic necrosis virus (PMNV), Pear alphapartitivirus (PAPV), Dahlia mosaic virus (DMV), and Lily virus X (LVX). BLASTn analysis revealed that 12 contigs (lengths ranging from 344 nt to 5,981 nt, query cover 6% to 99%) were most similar (57.32% to 91.67% nt identities) to the genome sequences of LVX, suggesting a possible infection of LVX in the plants. To confirm the result, a full-length genomic sequence of LVX was obtained by reverse transcription polymerase chain reaction (RT-PCR) using specific primers designed based on the sequence of the assembled contigs. The PCR products were cloned into pGEM-T vector (Promega Corporation, USA) and sequenced using the Sanger method (Sangon Biotech, Shanghai, China). The obtained full-length genomic sequence of the LVX isolate (LVX-PP, accession number OM100017) was 5,981 nt in length. BLASTp analysis demonstrated that the putative Rep and CP of LVX-PP shared 76.27% to 81.05% and 80.81% to 81.82% aa sequence similarities with that of other LVX isolates, respectively. Maximum-likelihood phylogenetic trees inferred from the Rep and CP aa sequences showed that LVX-PP clustered closely with LVX isolates. The leaf samples were further analyzed using a lily virus X (LVX) ELISA kit (DEIAPV181, Creative Diagnostics, U.S.A.). Healthy P. polyphylla var. yunnanensis leaves were taken as a negative control and buffer solution as a blank control. The results showed a positive reaction for all five symptomatic plants (OD = 1.259 ± 0.007) relative to the negative (OD = 0.099) and blank (OD = 0.073) controls. These results indicate that LVX can infect P. polyphylla var. yunnanensis. To our knowledge, this is the first report that LVX has been detected in P. polyphylla var. yunnannensis. This study will serve as an important reference for the study of the host range of LVX. Further studies will be required to determine how LVX spreads between P. polyphylla var. yunnannensis and other host plants.

Complete genome sequence analysis of Valeriana jatamansi tymovirus 1: a novel member of the genus Tymovirus infecting Valeriana jatamansi Jones.

A new positive-sense, single-stranded RNA virus, tentatively named "Valeriana jatamansi tymovirus 1" (VaJV1, OQ730267), was isolated from Valeriana jatamansi Jones displaying symptoms of vein-clearing in Yunnan Province, China. The complete genome of VaJV1 consists of 6,215 nucleotides and contains three open reading frames (ORFs). The genome structure of VaJV1 is typical of members of the genus Tymovirus. BLASTn analysis and multiple sequence alignments showed that the complete genome and coat protein of VaJV1 shared the most sequence similarity (65.5% nucleotides and 50.5% amino acid sequence identity) with an isolate of the tymovirus okra mosaic virus (NC_009532). Phylogenetic analysis confirmed that VaJV1 clustered most closely with other tymoviruses. We propose that Valeriana jatamansi tymovirus 1 represents a new species within the genus Tymovirus.

Complete genome sequence of a novel fusarivirus from the phytopathogenic fungus Fusarium sp.

Fusarium diseases include wilts, blights, rots, and cankers of many horticultural, field, ornamental, and forest crops in both agricultural and natural ecosystems, and they significantly hinder food plant production. Here, we describe a novel mycovirus, tentatively designated as "Fusarium fusarivirus 1" (FuFV1), which was discovered in an isolate of the phytopathogenic fungus Fusarium sp. FuFV1 has a positive-sense single-stranded RNA (+ssRNA) genome of 6,391 nucleotides (nt) containing three open reading frames (ORFs). ORF1 encodes a large polypeptide of 1,501 amino acids (aa) with conserved RNA-dependent RNA polymerase (RdRp) and helicase (Hel) domains. ORF2, overlapping ORF1 by 122 nucleotides, encodes a polypeptide with a conserved Smc domain. The third and smaller ORF (ORF3) encodes a polypeptide with an unknown function. BLASTp analysis of the ORF1-encoded polypeptide revealed that FuFV1 shares the highest aa sequence similarity (68.5% identity, E-value 0.0) with Fusarium poae fusarivirus 1 (FpFV1, genus Alphafusarivirus). Phylogenetic analysis of the RdRp and helicase (Hel) sequences indicated that FuFV1 clustered closely with FpFV1 in a separate branch within the clade containing members of the genus Alphafusarivirus. Based on these results, we propose that FuFV1 should be considered a novel mycovirus belonging to the genus Alphafusarivirus of the family Fusariviridae.

Complete genome sequence of a novel closterovirus isolated from Dregea volubilis.

The complete genome sequence of a putative novel closterovirus, tentatively named "Dregea volubilis closterovirus 1" (DvCV1, GenBank accession no. MZ779122), infecting Dregea volubilis in China was determined using high-throughput sequencing (HTS). The complete genome sequence of DvCV1 consists of 16,165 nucleotides (nt) and contains nine ORFs. The genome structure of DvCV1 is typical of members of the genus Closterovirus. Complete genome sequence analysis showed that DvCV1 shares 41.4-48.4% nucleotide sequence identity with other known closteroviruses. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70-like protein (HSP70h), and coat protein (CP) of DvCV1 share 46.80-62.65%, 31.06-51.80%, and 28.34-37.37% amino acid sequence identity, respectively, with the RdRp, HSP70h and CP of other closteroviruses. Phylogenetic analysis based on HSP70h aa sequences placed DvCV1 alongside other members of the genus Closterovirus in the family Closteroviridae. These results suggest that DvCV1 is a new member of the genus Closterovirus. This is the first report of a closterovirus infecting D. volubilis.

Complete genome sequence analysis of a novel citlodavirus isolated from the leaves of Myrica rubra in Yunnan.

Through high-throughput sequencing, a novel citlodavirus, tentatively named "Myrica rubra citlodavirus 1" (MRV1, accession no. OP374189), was isolated from the leaves of Myrica rubra in Yunnan exhibiting narrow deformity of leaf tips, shrinkage, and chlorosis along the veins. The complete genome sequence was determined and analyzed using cloning and Sanger sequencing. MRV1 is a single-stranded circular non-enveloped DNA virus with a genome size of 3775 nucleotides and contains six open reading frames (ORFs). The virion-sense genome strand encodes a coat protein (CP, nt 750-1,493, 247 aa), two hypothetical movement proteins (V3, nt 382-666, 94 aa; and V2, nt 461-895, 144 aa), and one movement protein (MP, nt 1,527-2,438, 303 aa). The complementary strand of the genome encodes two replication proteins (RepA, nt 3,712-2,834, 292 aa; Rep, nt 2,867-2,553, 104 aa). The MRV1 genome contains the stem-loop motif 5'-TAATATTAC-3', which is a highly conserved nonanucleotide motif found in the origin of virion-strand replication in geminiviruses. Genome sequence alignment analysis showed that citrus chlorotic dwarf associated virus (CCDaV, accession no. JQ920490) shared the highest nucleotide sequence similarity (66.10% identity) with MRV1. Phylogenetic analysis showed that CCDaV is the closest known relative of MRV1, and that these viruses clustered in a single branch within a clade consisting of citlodaviruses. These results indicate that MRV1 should be regarded as a new species of the genus Citlodavirus in the family Geminiviridae.

Modified hydrodissection as a safe and effective treatment modality for rotating lens in cataract surgery.

We describe in this article an effective and safe modification of hydrodissection technique in cataract surgery. The hydrodissection cannula tip is inserted into the capsulorhexis edge near the primary incision, with the cannula elbow resisting on the upper lip of the primary incision. Hydrodissection is then completed effectively and safely by squirting fluid to cleave the lens and capsular. This modified hydrodissection technique can be performed with high reproducibility and in a short practice period.

QACL: Quartet attention aware closed-loop learning for abdominal MR-to-CT synthesis via simultaneous registration.

Synthesis of computed tomography (CT) images from magnetic resonance (MR) images is an important task to overcome the lack of electron density information in MR-only radiotherapy treatment planning (RTP). Some innovative methods have been proposed for abdominal MR-to-CT synthesis. However, it is still challenging due to the large misalignment between preprocessed abdominal MR and CT images and the insufficient feature information learned by models. Although several studies have used the MR-to-CT synthesis to alleviate the difficulty of multi-modal registration, this misalignment remains unsolved when training the MR-to-CT synthesis model. In this paper, we propose an end-to-end quartet attention aware closed-loop learning (QACL) framework for MR-to-CT synthesis via simultaneous registration. Specifically, the proposed quartet attention generator and mono-modal registration network form a closed-loop to improve the performance of MR-to-CT synthesis via simultaneous registration. In particular, a quartet-attention mechanism is developed to enlarge the receptive fields in networks to extract the long-range and cross-dimension spatial dependencies. Experimental results on two independent abdominal datasets demonstrate that our QACL achieves impressive results with MAE of 55.30±10.59 HU, PSNR of 22.85±1.43 dB, and SSIM of 0.83±0.04 for synthesis, and with Dice of 0.799±0.129 for registration. The proposed QACL outperforms the state-of-the-art MR-to-CT synthesis and multi-modal registration methods.

External validation and comparison of MR-based radiomics models for predicting pathological complete response in locally advanced rectal cancer: a two-centre, multi-vendor study.

OBJECTIVES: The aim of this study was two-fold: (1) to develop and externally validate a multiparameter MR-based machine learning model to predict the pathological complete response (pCR) in locally advanced rectal cancer (LARC) patients after neoadjuvant chemoradiotherapy (nCRT), and (2) to compare different classifiers' discriminative performance for pCR prediction. METHODS: This retrospective study includes 151 LARC patients divided into internal (centre A, n = 100) and external validation set (centre B, n = 51). The clinical and MR radiomics features were derived to construct clinical, radiomics, and clinical-radiomics model. Random forest (RF), support vector machine (SVM), logistic regression (LR), K-nearest neighbor (KNN), naive Bayes (NB), and extreme gradient boosting (XGBoost) were used as classifiers. The predictive performance was assessed using the receiver operating characteristic (ROC) curve. RESULTS: Eleven radiomics and four clinical features were chosen as pCR-related signatures. In the radiomics model, the RF algorithm achieved 74.0% accuracy (an AUC of 0.863) and 84.4% (an AUC of 0.829) in the internal and external validation sets. In the clinical-radiomics model, RF algorithm exhibited high and stable predictive performance in the internal and external validation datasets with an AUC of 0.906 (87.3% sensitivity, 73.7% specificity, 76.0% accuracy) and 0.872 (77.3% sensitivity, 88.2% specificity, 86.3% accuracy), respectively. RF showed a better predictive performance than the other classifiers in the external validation datasets of three models. CONCLUSIONS: The multiparametric clinical-radiomics model combined with RF algorithm is optimal for predicting pCR in the internal and external sets, and might help improve clinical stratifying management of LARC patients. KEY POINTS: • A two-centre study showed that radiomics analysis of pre- and post-nCRT multiparameter MR images could predict pCR in patients with LARC. • The combined model was superior to the clinical and radiomics model in predicting pCR in locally advanced rectal cancer. • The RF classifier performed best in the current study.

The CADM2 Gene and Behavior: A Phenome-Wide Scan in UK-Biobank.

The cell adhesion molecule 2 (CADM2) gene has appeared among the top associations in a wide range of genome-wide association studies (GWASs). This study aims to: (1) examine how widespread the role of CADM2 is in behavioural traits, and (2) investigate trait-specific effects on CADM2 expression levels across tissues. We conducted a phenome-wide association study in UK Biobank (N = 12,211-453,349) on 242 psycho-behavioral traits, both at the SNP and the gene-level. For comparison, we repeated the analyses for other large (and high LD) genes. We found significant associations between CADM2 and 50 traits (including cognitive, risk taking, and dietary traits), many more than for the comparison genes. We show that many trait associations are reduced when taking geographical stratification into account. S-Predixcan revealed that CADM2 expression in brain tissues was significantly associated with many traits; highly significant effects were also observed for lung, mammary, and adipose tissues. In conclusion, this study shows that the role of CADM2 extends to a wide range of psycho-behavioral traits, suggesting these traits may share a common biological denominator.

Complete genome sequence analysis of Paris alphapartitivirus 1: a novel member of the genus Alphapartitivirus infecting Paris polyphylla var. yunnanensis.

A novel double-stranded RNA (dsRNA) virus, tentatively named "Paris alphapartitivirus 1" (ParAPV1, OL960006-OL960007), was detected in Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and shrinkage symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. ParAPV1 has a bipartite genome that consists of dsRNA1 (1,917 bp) encoding the viral RNA-dependent RNA polymerase (RdRp), and dsRNA2 (1,818 bp) encoding the putative coat protein (CP). Sequence comparisons showed that the RdRp and CP of ParAPV1 are most similar to those of pear alphapartitivirus (PpPV2), with 69.97% and 54.21% amino acid sequence identities respectively. Phylogenetic analysis of the RdRp amino acid sequences of ParAPV1 and other partitiviruses showed that ParAPV1 cluster with viruses in a clade containing alphapartitiviruses, and that its closest known relatives are PpPV2 (BBA66577) and rose partitivirus (RoPV, ANQ45203S). Taken together, these results suggest that ParAPV1 should be regarded as a new member of genus Alphapartitivirus in the family Partitiviridae. This is the first report of a partitivirus infecting P. polyphylla var. yunnanensis.

Adjusted femtosecond laser capsulotomy distance in white cataracts to decrease incomplete capsulotomy: a randomized comparative cohort study.

BACKGROUND: To compare safety and effectiveness between standard position and adjusted distance pre- and post-anterior capsule of femtosecond laser capsulotomy in white cataracts surgery. METHODS: Selected white cataracts that underwent LenSx femtosecond laser capsulotomy were randomized into groups A (standard position, with 300 µm symmetrically pre- and post-anterior capsule), B (increased distance with 400 µm symmetrically pre- and post-anterior capsule), and C (unsymmetrical distances of 200 µm pre- and 400 µm post-anterior capsule, respectively). All these surgeries were performed by the same experienced surgeon. Complications, including incomplete capsulotomy and capsule tears, were recorded. In addition, femtosecond capsulotomy and phacoemulsification parameters, IOLs centrality and corrected distance visual acuity were assessed. RESULTS: A total of 113 eyes were included in this study. There were 8 (21.6%) incomplete capsulotomy and 1 anterior capsule tear in group A. Meanwhile, only 2 eyes (5.1%) had incomplete capsulotomy with none showing capsule tear in group B. In group C, only 1 eye (2.7%) had incomplete capsulotomy and no capsule tear occurred. Mean femtosecond laser capsulotomy time was longer in group B compared with groups A and C. Average cumulative dispersed energy, IOL centrality and corrected distance visual acuity were similar in all groups. CONCLUSIONS: Appropriate adjustment on femtosecond laser capsulotomy distance by reducing pre-anterior capsule and increasing post-anterior distance, may decrease incomplete capsulotomy and be more effective in white cataracts surgery. TRIAL REGISTRATION: Clinical trial registration number: ChiCTR2100043863.

Complete genome sequence of a novel mitovirus detected in Paris polyphylla var. yunnanensis.

Paris mitovirus 1 (ParMV1) is a positive-sense RNA virus that was detected in diseased Paris polyphylla var. yunnanensis plants in Wenshan, Yunnan. The complete genome sequence of ParMV1 is 2,751 nucleotides in length, and the genome structure is typical of mitoviruses. The ParMV1 genome has a single open reading frame (ORF; nt 358-2,637) that encodes an RNA-dependent RNA polymerase (RdRp) with a predicted molecular mass of 86.42 kDa. ParMV1 contains six conserved motifs (Ι-VΙ) that are unique to mitoviruses. The 5' and 3' termini of the genome are predicted to have a stable secondary structure, with the reverse complementary sequence forming a panhandle structure. Comparative genome analysis revealed that the RdRp of ParMV1 shares 23.1-40.6% amino acid (aa) and 32.3-45.7% nucleotide (nt) sequence identity with those of other mitoviruses. Phylogenetic analysis based on RdRp aa sequences showed that ParMV1 clusters with mitoviruses and hence should be considered a new member of the genus Mitovirus in the family Mitoviridae. This is the first report of a novel mitovirus infecting Paris polyphylla var. yunnanensis.

Characterization of a novel Tombusviridae species isolated from Paris polyphylla var. yunnanensis.

A novel virus, Paris virus 2 (ParV2), was isolated from diseased Paris polyphylla var. yunnanensis, and its complete genome sequence was determined and analyzed. ParV2 is a positive-sense single-stranded RNA (+ssRNA) virus with a genome size of 4,118 nucleotides. The ParV2 genome contains six putative open reading frames (ORFs) that encode proteins with predicted molecular weights of 40.14, 100.26, 7.31, 7.85, 26.09, and 8.77 kDa. The first ORF (ORF1) of ParV2 encodes a putative protein of 40.14 kDa (P40, nt: 20-1,096), whiles the second ORF (ORF2, 888 aa) containing the GDD motif encodes the highly conserved RNA-dependent RNA polymerase protein (RdRP, nt:20-2,683, P100, 100.26 kDa) of viruses in the family Tombusviridae. Multiple sequence alignments analysis showed that the complete genome sequence of ParV2 shares 31.7-55.5% nucleotide sequence identities with viruses in the family Tombusviridae. Ginger chlorotic fleck-associated tombusvirus (GCFaV-1, Accession No. QKE30557) had the highest sequence identity (55.5%) with ParV2. GCFaV-1 also shares 59.2% RdRP and 34.9% CP amino acid sequence identities with ParV2. Sequence comparisons and phylogenetic analysis of RdRP suggested that ParV2 is a novel member of the family Tombusviridae, and its closest known relative is GCFaV-1.

Complete genome sequence analysis of a novel coguvirus isolated from Paris polyphylla var. yunnanensis.

A novel negative-stranded (ns) RNA virus tentatively named "Yunnan paris negative-stranded virus" (YPNSV), was isolated from Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. YPNSV has a bipartite genome that consists of a negative-stranded (ns) RNA1 encoding the viral RNA-dependent RNA polymerase (RdRp, p251), an ambisense RNA2 coding for the putative movement protein (MP, p46) and nucleocapsid protein (NP, p39), with the two open reading frames separated by a long intergenic region that is rich in A and U. Sequence comparisons showed that the RdRp, MP, and NP of YPNSV are most similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4%, and 60.9% amino acid sequence identity, respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP showed that YPNSV clustered in a clade with coguviruses and that its closest known relative is WCLaV-2. Based on the above results, YPNSV should be regarded as a new member of genus Coguvirus, family Phenuiviridae.