Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify the viruses infecting oats in this country. In this study, we carried out RNA-sequencing followed by bioinformatics analyses to understand the virosphere in six different geographical locations in Korea where oats are cultivated. We identified three different virus species, namely, barley yellow dwarf virus (BYDV) (BYDV-PAV and BYDV-PAS), cereal yellow dwarf virus (CYDV) (CYDV-RPS and CYDV-RPV), and rice black-streaked dwarf virus (RBSDV). Based on the number of virus-associated reads and contigs, BYDV-PAV was a dominant virus infecting winter oats in Korea. Interestingly, RBSDV was identified in only a single region, and this is the first report of this virus infecting oats in Korea. Single nucleotide polymorphisms analyses indicated that most BYDV, CYDV, and RBSDV isolates show considerable genetic variations. Phylogenetic analyses indicated that BYDVs and CYDVs were largely grouped in isolates from Asia and USA, whereas RBSDV was genetically similar to isolates from China. Overall, the findings of this study provide a preliminary characterization of the types of plant viruses infecting oats in six geographical regions of Korea.Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats ( Plant viruses cause significant yield reduction and economic losses in many crops worldwide. Such viruses can be devastating, especially for varieties with no virus resistance ,2. Thus,Avena sativa), of the family Poaceae, is generally cultivated as a secondary crop. Oat was derived from a weed of the primary cereal and is ranked 7th in terms of cereal production after maize, wheat, barley, and sorghum [Oat  and CYDV (genus Polerovirus) are single-stranded RNA viruses in the family Luteoviridae, which can detrimentally affect more than 150 species of the Poaceae family [Luteovirusa: BYDV-PAV, BYDV-PAS, BYDV-MAV, BYDV-kerII, and BYDV-kerIII [Polerovirus, five species of viruses infect cereals or grasses: CYDV-RPV, CYDV-RPS, maize yellow dwarf virus, maize yellow mosaic virus, and sugarcane yellow leaf virus [In common with other crop plants, the production of oats can be severely affected by the invasion of emerging plant pathogens . Of identified viruses infecting oat, barley yellow dwarf virus (BYDV), cereal yellow dwarf virus (CYDV), oat blue dwarf virus (OBDV), and oat mosaic virus (OMV) have been widely documented worldwide. The most frequently identified viruses, BYDV , quantitative real time polymerase chain reaction, enzyme-linked immunosorbent assay, and loop-mediated isothermal amplification can be conducted for specific viral diseases, given prior knowledge of the sequence or antibody. In contrast, next-generation sequencing (NGS) can detect pathogens without prior knowledge of the disease ,23. ThusIn the early 2000s, high-throughput sequencing (HTS)-based approaches using RNA-sequencing analysis were developed and used to identify viruses infecting different plant species ,26,27,28Several viruses infecting cereal crops have been previously studied using RNA-sequencing (RNA-seq) ,30. AlthTo examine viruses infecting oat plants, we collected 323 oat samples from plantations located in six different regions of Korea from March to June 2020 a. We namThe number of raw reads bases ranged from 5,504,951,432 (YP library) to 6,811,937,066 (JE library). The raw reads obtained by RNA-seq from the six libraries were individually de novo assembled using the gsAssembler program. The number of assembled contigs ranged from 365,264 (library IG) to 618,180 (library SW). These libraries were deposited in an SRA database with accession numbers .To examine virus-associated reads and contigs, the raw reads and assembled contigs were used for a BLASTN search against a virus reference genome database obtained from the NCBI database. The number of virus-associated reads ranged from 107,106 (HN) to 618,395 (YP) A. AdditiThe virus-associated contigs from the dataset were first combined and then classified. We identified three different viruses, BYDV, CYDV, and RBSDV in all libraries C. Of theThrough de novo assembly, we obtained virus consensus sequences mapped to each reference virus genome from the six libraries . Virus-aThe number of identified SNPs among each identified virus genome was diverse; these were analyzed by reads mapping to the virus reference genome . In the We performed phylogenetic analyses with assembled viral genomes for BYDV isolates, CYDV isolates, and RBSDV isolates identified using RNA-seq. For phylogenetic analyses, we retrieved CP sequences of 16 BYDV isolates, 14 CYDV isolates, and 14 RBSDV isolates from the NCBI database. After nucleotide sequence alignment, three phylogenetic trees were constructed using MEGA 7 .A phylogenetic analysis of the CP sequences of the BYDV isolated from all six libraries, in addition to other isolates from various countries, showed two separated clades. In the blue colored clade, the identified isolates  obtained from RNA-seq were grouped into the same clade; they were closely related to BYDV-PAV isolates from USA (EF521840) and Australia . In the orange clade, BYDV isolate  was closely related to the China isolate (AY855920) A.For CYDV, the phylogenetic tree of CYDV showed two defined groups, and four CYDV isolates identified from RNA-seq were separated into two clades B. Two CYTo confirm the presence of viruses identified by RNA-seq, we carried out RT-PCR using specific primers previously used for the detection of these viruses . The RT-We are becoming increasingly familiar with the concept that a variety of organisms, including plants, co-exist with a rich diversity of microorganisms—the microbiome. However, a somewhat less-considered notion is that organisms also interact with a considerable diversity of viruses, designated the virome, which can be defined as virus-associated nucleic acids existing anywhere in plants, animals, or the environment. Recently, the generic detection and analyses of highly diverse viruses in a range of sample types have been performed using HTS as a platform offering an ideal and unique approach ,41. The Luteovirus [In the present study, we pooled all samples collected from sites in the six surveyed provinces to monitor virus infections in a large number of samples. The pooling of samples not only reduces HTS costs and analysis time, but also provides broad-scale information on the structure of viral communities affecting oats in different geographical locations . Our RNAteovirus ,50. Giveteovirus .Rhopalosiphum padi, Sitobion avenae, Metopolophium dirhodum and Sitobion fragariae; BYDV-PAS by Rhopalosiphum maidis; CYDV-RPV by Rhopalosiphum padi, Schizaphis graminum; and CYDV-RPS by Rhopalosiphum padi [BYDV and CYDV are the most economically important viruses infecting cereal crops worldwide. These viruses differ in terms of ease of transmission by different aphid species. Among the viruses identified to infect oats, BYDV and CYDV are the most common viruses transmitted by aphids. For example, it has been reported that BYDV-PAV is transmitted by hum padi . Among thum padi ,53,54. Uhum padi . RBSDVs,hum padi ,56. RBSDhum padi . In thishum padi . Such dihum padi . To dateViruses can evolve rapidly by mutation and recombination during replication, and thus, it can be expected that large-scale genome rearrangements and SNP mutations will occur naturally among virus isolates or strains. To confirm such variability in our Korean isolates, we examined SNPs for the eight assembled BYDVs, four assembled CYDVs, and ten segments of RBSDV genomes. The SNP analyses suggested that most BYDVs, CYDVs, and RBSDVs showed strong genetic variations. Among these, BYDV-PAS (983 SNPs) and CYDV-RPV (677) identified from JE exhibited the highest number of SNPs. An increased genetic variation in one region compared to very low genetic variation in another region can be thought of as a pooled oat sample for library construction. For example, in the case of JE library, which pooled the largest number (128) of samples, it was found that the largest number of SNPs were identified. In addition, the library with the lowest number of SNPs in BYDV-PAV was the SW library that pooled the fewest samples (16). However, BYDV-PAV identified in the YP library pooled with a small number (16) of samples showed a high number of SNPs. This suggests that there is no overall correlation with the number of pooled samples. Virus mutation is closely related to host type, complexity of plant–virus–insect relationships, and environmental conditions; thus, the correlations between the SNPs and geographical regions should be further examined. With respect to RBSDV, we found that the number of SNPs identified among YP isolates ranged from 12 (segment 9) to 47 (segment 7), indicating that there were no strong genetic variations among the genome segments.Isolates of BYDVs and CYDVs collected in different countries have been found to show diversity with respect to their genome sequences and pathogenicity , and in In view of the genetic diversity and variability among the genomes of B/CYDV species, it has been suggested that the primers for each species are extremely important criteria. In this regard, a detection method for BYDV species has previously been developed based on the use of multiplex RT-PCR . AccordiIn summary, in this study, we identified viruses infecting oats in different geographical regions of Korea. Our findings will contribute to gaining a more comprehensive understanding of the viral communities infecting this crop and thereby provide information that could be used to develop management strategies for the control of viral diseases in oats cultivated in Korea. However, given the limited scope of this study, we did not seek to estimate the direct crop losses attributable to these viruses nationwide. Given the current and predicted changes in global climate and the increasing diversity of insect vectors, HTS-based studies of the viromes of cultivated crops and alternative hosts as virus reservoirs are urgently needed to assess the prevalence and potential impact of viruses and to provide further insights on their epidemiological status.From March to May 2020, oat leaves were collected from six different geographical regions in Korea. A total of 322 samples were collected from various cultivars . The symptomatic oat leaves showed reddening and dwarfing characteristics. Samples were frozen in liquid nitrogen and stored at −80 °C in a deep freezer until used. Samples were pooled based on geographical province for total RNA extraction and library preparation.Total RNA was extracted from the ground pooling samples using the Clear-S Total RNA Extraction Kit , according to the manufacturer’s instructions. The quality and quantity of extracted total RNA were determined using an Agilent 2100 Bioanalyzer . The confirmed total RNA was used in the preparation of a cDNA library after ribosomal RNA was removed using a Ribo-zero rRNA removal kit  and purified and collected using RNA Clean XP. Purified mRNAs were fragmented and used for the synthesis of cDNA. Briefly, mRNAs with poly-A tail were extracted, and the first strand of cDNA was synthesized using the purified mRNAs followed by the second strand of cDNA. Then, the adenylation of 3′ ends was conducted using A-tailing mix, followed by washing using AMPure XP beads. To enrich DNA fragments that were ligated with adaptors, PCR was conducted. The quality and quantity of the generated libraries were determined using an Agilent D5000 ScreenTape system . Finally, oat leaves collected from Yeoncheon and Pocheon were named YP, Suwon as SW, Iksan and Gimje as IG, Jeongeup as JE, Haenam as HN, and Gangjin as GJ. The six libraries were loaded into flow cells, forming a library cluster. Then, five flow cell libraries were paired-end sequenced using a HiSeq 4000 sequencer, generating 200 bp paired-end reads . All raw sequences were deposited in the SRA database in NCBI.https://www.ncbi.nlm.nih.gov/genome/viruses/ accessed on 16 April 2021) using BLASTX with a cutoff E-value of 1 × 10−5 [−10 against the mitochondria, chloroplast, and other contaminated oat host sequences of less than 200 bp derived from the NCBI database. Finally, only virus-associated contigs were selected for further virome analyses.A workstation (two six-core CPUs and 256 GB RAM) with the Ubuntu 12.04.5 LTS operating system was used for the de novo transcriptome assembly and BLAST search. Raw sequence reads obtained from each library were subjected to de novo transcriptome assembly using gsAssembler v2.8  with default parameters . To iden1 × 10−5 . The obtThe sequences of all virus-associated contigs were compared with the identified virus reference genomes using BLAST. Contigs with the highest similarity matches to specific viruses were selected. The virus-associated contigs were mapped to identified reference virus genome sequences using Geneious v. 11.1.5 , and conFor phylogenetic tree analyses, we generated complete coat protein (CP) gene sequences for BYDV, CYDV, and rice black-streaked dwarf virus (RBSDV) based on mapping consensus sequences. Phylogenetic trees for each virus were constructed with other viral CP sequences downloaded from GenBank. NCBI accession numbers of all viral genomes are indicated in the phylogenetic trees. Nucleotide sequences were aligned using CLUSTALW in BioEdit version 7.0.5.3., and the aligned nucleotide sequences were used to construct phylogenetic trees using 1000 bootstrap replicates based on either the neighbor-joining or the Kimura 2-parameter method in MEGA 7 .Single nucleotide polymorphisms (SNPs) were identified by mapping reads sequence data to the consensus sequences for each complete or nearly complete viral genome, using Geneious v. 11.1.5 with default parameters, and then Geneious v. 11.1.5 was used to perform SNP-calling and to export an Excel file containing the SNP data . The posTo confirm the presence of identified viruses by RNA-seq in oat samples, the total RNAs were extracted from leaf pooling samples based on province using the Clear-S Total RNA Extraction Kit . Three specific primer sets were designed to amplify genomic regions corresponding to the CP genes from BYDV, CYDV, and RBSDV. The RT-PCR was performed using the SuPrimeScript RT-PCR Premix , according to the manufacturer’s recommendations. Each of the 20 μL reaction mixtures included 0.4 μM forward primer, 0.4 μM reverse primer, 10 μL SuPrimeScript RT Premix, 2 μL RNA template, and 6 μL DEPC-treated water. The thermocycling conditions were as follows: a reverse transcription stage of 50 °C for 30 min; an initial denaturation step of 95 °C for 5 min; 35 cycles of 95 °C for 30 s, 56 °C for 60 s, and 72 °C for 60 s; and a final extension step of 72 °C for 10 min. After conducting RT-PCR, the amplification products were visualized by gel electrophoresis using 1.2% agarose gels under UV light. Furthermore, the amplicons were individually cloned into the pGEM-T Easy Vector , followed by Sanger sequencing.The raw dataset generated in the present study will be available upon publication in the NCBI Sequence Read Archive (SRA) repository under accession numbers SRR13259170, SRR13259239, SRR13259172, SRR13259168, SRR13259171, and SRR13259240. The viral genome sequences obtained from this study were also deposited in GenBank with individual accession numbers.


Hysteroscopic morcellation is an alternative approach for the removal of placental remnants, given its advantages of safety, efficiency and good reproductive outcomes. This superiority can be even more obvious for removing persistent placental remnants in the lateral angle of the uterine cavity after repeated dilation and curettage (D&C) of an angular pregnancy, which is rarely reported.Two patients who were both initially misdiagnosed as having missed intrauterine miscarriages underwent repeated suction-assisted D&C procedures and were found to have persistent placental remnants in the lateral angles of the uterine cavity.Ultrasound and hysteroscopy evaluations showed that placental remnants in both cases were in the lateral uterine angles and protruding to the interstitial myometrium around the fallopian tube. We corrected the diagnosis to that of angular pregnancy according to a comprehensive consideration of the ultrasound, hysteroscopy and pathology results.We performed MyoSure hysteroscopic morcellation for both patients and the placental remnants were removed completely without any complication.The patients were both scheduled for a second-look hysteroscopy 1 to 3 months after surgery, which revealed normal morphology of the uterine cavities and tubal ostia. The patients both achieved normal intrauterine pregnancies several months after surgery.Hysteroscopic morcellation is a good alternative approach for the removal of placental remnants and should be considered in cases in which there might be a high risk of incomplete evacuation or a high risk of uterine perforation, especially in cases of angular pregnancy. These account for 2% to 4% of all ectopic pregnancies. Women with an angular pregnancy have a rate of spontaneous or missed miscarriage of 38.5%, and the rate of uterine rupture is 13.6%. Hysteroscopic morcellation and loop resection are more efficient for the selective removal of placental remnants under direct visualization.–6 As a novel technique, hysteroscopic morcellation is associated with a shorter operative time and possibly lower odds of incomplete lesion removal than loop resection.,8 However, its use in cases of placental remnants in patients with an angular pregnancy has rarely been reported.Placental remnants often occur after dilation and curettage (D&C), when the angular pregnancy is misdiagnosed as a normal intrauterine pregnancy. There are many methods for removal of placental remnants, such as “blind” D&C, hysteroscopy with D&C, ultrasound-guided curettage, hysteroscopic loop resection, and hysteroscopic morcellation.Here, we present 2 cases of persistent placental remnants in the uterine cornu after repeated suction-assisted D&C procedures, as angular pregnancies had not been diagnosed initially. We performed hysteroscopic morcellation for the 2 patients using the MyoSure device  and the placental remnants were removed completely without any complications. Both patients proceeded to have normal intrauterine pregnancies within a few months.22.12.1.1A 28-year-old woman, gravida 3, para 1, was diagnosed with a missed miscarriage at 8 weeks’ gestation in a local hospital. A D&C with vacuum aspiration was performed and the presence of chorionic villi was confirmed by histology. She returned to the same hospital 4 weeks later, complaining of persistent vaginal bleeding. Transvaginal ultrasonography revealed placental remnants and a second suction-assisted D&C was performed together with diagnostic hysteroscopy. This showed the retained placental tissue to be located in the left lateral angle of the uterine cavity with mild adhesions. The evacuation failed because the metal D&C catheter could not reach the retained tissue. Two weeks later, she was referred to our hospital for further treatment. Another transvaginal ultrasound scan was done, which showed a 2.07 ’ 1.18 cm mass of mixed echogenic material suggestive of placental remnants extending to the left angle of the uterus. The left angular myometrial mantle was thinned to approximately 6 mm  or under ultrasound guidance (Case 2). Direct vision-guided removal of uterine pathology is recommended over conventional “blind” D&C to achieve targeted removal of pathological material.–6 Both techniques are safe and show high rates of complete removal and tissue availability and low rates of intrauterine adhesions (IUAs). Hysteroscopic morcellation is faster than loop resection because it uses continuous suction of resected chips as it cuts, which keeps the field clear and requires only a single insertion of the instrument.,6 Another advantage of the MyoSure instrument is that the outer sheath is only 6.25 mm in diameter and cervical dilation is mostly avoidable. In both cases, the procedure times were short according to the mean procedure time of 11.7 minutes for removing placental remnants of mean diameter of 1.7 cm reported by Hamerlynck et al. In Case 2, the procedure time was 20 minutes; however, the volume of retained placental tissue was large, with a maximum diameter of 3.78 cm.Hysteroscopic morcellation and loop resection have been proven to be efficient for the selective removal of placental remnants under direct visualization. Furthermore, the MyoSure instrument has a smaller 3-mm outer tubular cutting device, which enabled us to reach tissues in the lateral angle. In our experience, intrauterine pressure should be reduced so that the uterine cavity is just visible. If uterine bleeding obscures the surgical field, oxytocin or pituitrin can be used. In both of our cases, there was minimal bleeding that did not need to be managed further.The angular placental remnants in our 2 cases were noted by hysteroscopy to protrude to the tubal interstitial myometrium. Because of the deep and limited space in the lateral uterine horn and the tightly adhering placental tissues, the evacuation could have been very difficult, especially in Case 1. Nevertheless, the tissues were removed precisely and completely under direct vision with minimal blood loss and without uterine perforation. It is thought that the use of a hysteroscopic morcellator for this indication might reduce the risk of perforation not only by precise removal but also by utilizing the instrument's closed blunted tip and lateral operative window. significantly fewer episodes of IUAs were encountered after hysteroscopic evacuation compared with after D&C procedures: 13% vs 30%. The major advantage of hysteroscopic evacuation is the possibility of selective removal of the placental remnants without damaging surrounding healthy endometrium and with a trend towards earlier conception.–12 This advantage is more obvious for hysteroscopic morcellation using mechanical excision, which avoids electrical and thermal injury to the endometrium. In both cases, second-look hysteroscopies showed that there were only mild IUAs and old adhesive scars. Moreover, normal intrauterine pregnancies were obtained several months after surgery in both of our cases.As reported in a systematic review,4Our cases demonstrate the value of hysteroscopic morcellation, both in confirming the diagnosis of an angular pregnancy and in completely removing placental remnants from the uterine cornu. Thanks to the advantages of safety, efficiency and good reproductive outcomes, hysteroscopic morcellation has emerged as an alternative approach for the removal of placental remnants, and this method should be considered in cases in which there might be high risks of incomplete evacuation or of uterine perforation, especially in cases of angular pregnancy.Informed and signed consents were obtained from the patients to publish this case report, which is greatly appreciated.Resources: Zhimin Li, Yi Wang, Zhen Yue, Yuanyue Zhong, Liqin Zeng.Writing – original draft: Fan Yu.Writing – review & editing: Liqin Zeng.


Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework.The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive-sense RNA viruses have been classified in two genera ( Allassoviricetes (TaxoProp 2020.095B.R.Leviviricetes), written by the authors of this article [ICTV (ictvonline.org).The taxonomic proposal (TaxoProp) on the reorganization and renaming of lenarviricot class  article  and subsLeviviricetes within phylum Lenarviricota, hidden Markov models (HMMs) generated from the expanded number of available bacteria-infecting positive-sense single-stranded RNA (+ssRNA) virus proteins are available at Figshare: https://doi.org/10.6084/m9.figshare.12745394.v1.To support the continued expansion of the newly organized class The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.Leviviricetes. Furthermore, this work presents a case study adopting a Latinised binomial species nomenclature for all 882 species as a standardized nomenclature for all viruses. Looking forward, the methods and resources developed in this study support future phylogenetic analyses and taxonomic classifications of newly isolated viruses and metagenomic viral sequences.This work describes a taxonomic framework for the classification of bacteria-infecting positive-sense, single-stranded RNA (+ssRNA) viruses and is the largest proposal submitted to the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) to date. Both metagenomic-sourced sequences and known isolates of +ssRNA viruses were incorporated into a taxonomic scheme using novel algorithms and automated systems. The existing hierarchical organization of bacteria-infecting +ssRNA viruses was overhauled to capture their vast diversity uncovered through metagenomic approaches and these viruses are now unified in the class Escherichia coli bacteria, was the first of any biological entity ever to be sequenced [E. coli +ssRNA phages, the family was slightly expanded. Most recently (prior to 2021), family Leviviridae included two genera for a total of four viruses. Those four viruses remained the only classified viruses in Leviviridae-including class Allassoviricetes – one of four classes in phylum Lenarviricota  [The genome of the positive-sense single-stranded RNA (+ssRNA) phage MS2, which infects equenced . In the equenced , which iequenced . Throughviricota , althougnaviria) .Leviviridae contain three core genes encoding a maturation protein (MP), a coat protein (CP) and a catalytic subunit of an RNA-directed RNA polymerase (RdRP), respectively; leviviruses were distinguished from alloleviviruses by additional encoding a lysis protein as opposed to a unique ‘read-through’ protein [Allassaviricetes and resulted in a more robust taxonomic framework that will aid future progress in our understanding of bacteria-infecting +ssRNA virus diversity, evolution and ecological significance.The genomes of all viruses previously classified in  protein . Whereas protein . This diTo create a novel taxonomic framework for bacteria-infecting +ssRNA viruses, 1868 genomic sequences tentatively identified as such in  were obtLeviviricetes taxon by incorporating metagenome-assembled genomes  to retain the Levi- word stem, reflecting the colloquial use of the term ‘levivirus(es)”. This class now includes all +ssRNA viruses encoding the specific pattern of three +ssRNA virus core proteins: MP, CP and RdRP. In a recent analysis of +ssRNA virus genomes, 1868 sequences fit this genome architectural criterion. Additionally, the encoded MP and RdRP were required to meet a minimum length threshold of 350 and 500 amino acid residues, respectively, to ensure only near-complete (coding-complete) genomes were investigated. The 1868 sequences originated from sequences available through the National Center for Biotechnology Information (NCBI) and the studies of Callanan et al., Starr et al., Shi et al. and Krishnamurthy et al. [The previously established class y et al. .We adopted clustering and separation of the RdRP into distinct phylogenetic clades as the order demarcation criterium because the RdRP is the most conserved protein across leviviricetes with the strongest phylogenetic signal . Orders Norzivirales  is based on the phylogeny and clustering of bacterial +ssRNA virus RdRP protein sequences. It is named after Norton Zinder (1928–2012), who isolated the first bacterial virus with an RNA genome and who continued to make crucial findings regarding these entities [Norzivirales order. Tying in with its original description, the profile HMM output additionally describes Norzivirales hits as cluster RdRP_A [The order entities . A totalr 1928–20, who isoTimlovirales: This order is based on the phylogeny and clustering of bacterial +ssRNA virus RdRP protein sequences (cluster RdRP_B). It is named after Timothy Loeb (1935–2016) who, with Norton Zinder, isolated the first +ssRNA bacterial virus [Timlovirales.b 1935–20 who, witAtkinsviridae, Duinviridae, Fiersviridae and Solspiviridae are the new families created within the Norzivirales order, whereas Blumeviridae and Steitzviridae are the new families in the Timlovirales order.Familial taxonomic groups were based on the distinct phylogeny of bacterial +ssRNA virus CP sequences, as either a single cluster or collection of clusters generated from orthoMCL . Out of Atkinsviridae is named after John Atkins (1944–present) for his discovery of the lysin protein from Escherichia virus MS2 [Atkinsviridae.irus MS2 . This faBlumeviridae is named after Thomas Blumenthal (1943–present) for his findings on the replication of bacterial +ssRNA viruses, in particular the structure and function of the replicase [Blumeviridae.Duinviridae is named after Jan van Duin (1937–2017) for his discoveries related to novel bacterial +ssRNA viruses, and the RNA folding within bacterial +ssRNA virus genomes to control gene expression [Duinviridae.pression . This faFiersviridae is named after Walter Fiers (1931–2019) who sequenced the first gene and genome of any organism, MS2, previously assigned to the species Escherichia virus MS2 (3). This family encompasses +ssRNA viruses predicted to encode a CP corresponding to CP clusters A, B and H . There are 298 viruses currently assigned to Fiersviridae.Solspiviridae is named after Sol Spiegelman (1914–1983), who discovered an RNA chain of only 218 nucleotides that could be reproduced by an RdRP [Solspiviridae family (HMM profile CP_G). an RdRP . This faSteitzviridae is named after Joan Argetsinger Steitz (1941–present) for her determination of an initiation sequence that is central to modern-day ribosome profiling [Steitzviridae.rofiling . This faICTV (ictvonline.org) [We chose 50 % pairwise amino-acid identity (PAAI) of the viral encoded RdRP as the criterion for establishing genera based on an analysis of the previous ICTV classification of known bacteria-infecting +ssRNA viruses . Exemplaine.org) .ICTV (ictvonline.org) [Emesvirus zinderi and phage BZ13 is now assigned to Emesvirus japonicum, whereas phage Qbeta is assigned to Qubevirus durum and FI 4184 b is assigned to Qubevirus faecium. The new naming scheme no longer necessitates knowledge of host bacteria and is therefore well-suited to the incorporation of sequence-only or uncultured virus genomes.We chose 80 % PAAI of the RdRP as the species demarcation criterion . This cuine.org) . For exaLeviviricetes taxonomic proposal detailed here is the first to systematically include metagenomic sequences to build a class-rank taxonomy incorporating automatic approaches. This effort supports incorporation of metagenomic sequences within ICTV’s framework in future taxonomic proposals and subsequent expansion of established virus taxonomic groups – thus advancing a holistic understanding of viral diversity. At present, the expansion and restructuring of Leviviricetes has been one of the largest-ever proposals submitted to and approved by the ICTV. However, as the incorporation of metagenome-assembled genomes into ICTV taxonomic proposals become more frequent, due to the immense unexplored diversity of the virosphere, this record will likely be short-lived.The massive expansion in the discovery of novel bacteria-infecting +ssRNA virus genomes is now complemented with a timely update to their associated taxonomy. Fitting with phage MS2 being the first organism to have its genome completely sequenced, the presented ICTV-approved


To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyperlinks to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a convenient resource for researchers to browse and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights in our understanding and treatment of respiratory virus infection. Database URL:  Common Human responses to respiratory virus infection differ from uninfected, asymptomatic, mild, moderate, severe to fatal outcome. The wide variations in susceptibility and severity are not only attributed to the different transmissibility and virulence of different virus strains, but also attributed to host factors like age, sex, premature birth, pregnancy, obesity and comorbidity –11. AmonThough great progress has been made in this area, there is a lack of database systematically collecting, formatting, annotating, storing and displaying studies of human susceptibility and severity in respiratory virus. Searching and reading related papers scattered in PubMed are time-consuming, hindering convenient access to useful information.http://www.ehbio.com/dbGSRV/front/. We anticipate that this resource will a useful tool for researchers to query and retrieve genetic association studies of respiratory viruses.Therefore, we present the first database of Genetic Susceptibility to Respiratory Virus (dbGSRV), which integrates published genetic studies relating susceptibility and severity in respiratory virus infection. It contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Comprehensive information about reference, infection, samples, mutations and their relationships are available at We searched for literatures that describe genetic associations with susceptibility or severity of respiratory virus infections in PubMed, using keywords of ‘variant’, ‘polymorphism’, ‘susceptibility’ combined with names of specific respiratory virus like ‘adenovirus’, ‘bocavirus’, ‘influenza’, ‘measles’, ‘MERS’, ‘metapneumovirus’, ‘mumps’, ‘parainfluenza virus’, ‘respiratory syncytial virus’, ‘rhinovirus’, ‘rubella’, ‘SARS’ and ‘SARS-CoV-2’. We selected these viruses because they are the most common respiratory viruses that infect humans. The searching results were manually examined to only leave English publications that study associations between human single nucleotide variants (SNVs), multiple nucleotide variants (MNVs) or indels with susceptibility or severity of explicit respiratory virus in case-control researches. Meta-analysis and researches that did not test which virus the cases were infected with were excluded. As for these related publications, we collected publication information like paper title, first and corresponding author, year and journal published and PubMed Unique Identifier (PMID).We defined one record of genetic association study based on the virus type, case-control sample and variant. As for each record, respiratory virus type information was extracted from the full text of the paper. Virus subtype was also extracted if specified. The number, country, ethnicity and clinical severity information of samples were collected. Based on the ethnicity, we determined the superpopulation of 1000 Genomics that the sample population belonged to. If the sample belonged to multiple superpopulation, marked as ‘Mixed’. No matter whether the variant was associated with virus susceptibility or not, all the studied variants mentioned in the main text were included, to provide a more comprehensive and unbiased scope of genetic association studies.For sake of uniformity, the name, reference allele and alternate allele of each variant were based on the dbSNP database. Many early publications did not offer dbSNP rs ID of the variant. We manually annotated the rs ID of these variants by genomic mapping. The original names of these variants in the publication were also included in the database as old name. The genomic position of the variants was annotated based on hg38 human genome. Annotation of variants relative to genes were based the following order: exon, 5’ UTR, 3’ UTR, intron, promoter (within 2kb upstream), upstream (2-5kb upstream), downstream (within 2kb downstream).The alternate allele frequencies of cases and controls, statistic method, odds ratio (OR), 95% confidence interval (CI) and p value for the allele association were extracted from the full-text or supplementary materials. If only genotype frequency was given in the paper, then alternate allele frequency was calculated manually. As for p value, ‘> 0.05%’ was marked if the paper did not give a specific value but claimed that there was no statistically significant difference or association. The allele, genotype, and haplotype association results were each classified into one of the following four categories: ‘severity’, ‘susceptibility’, ‘no association’ and ‘NA’. If at least of one of the allele, genotype or haplotype association result reported ‘severity’ or ‘susceptibility’, then the overall association status was determined as ‘severity’ or ‘susceptibility’, otherwise the overall association status was determined as ‘no association’. Additional noteworthy information about sample, variant and disease association was included in notes.https://vuejs.org/) for the main front-end framework, vis.js (https://visjs.org) for Network viewer, plotly.js (https://plotly.com/) for Lollipop charts. High-level web framework Django (https://www.djangoproject.com/) was used for back-end data preprocess and data analysis. The global search function was based on Elasticsearch module. Open source data management system MySQL was used for table-data saving and accessing.dbGSRV database was implemented as a web application using JavaScript and HTML for front-end development. The used core JavaScript libraries included Vue.js (https://david.ncifcrf.gov/).Gene Ontology (GO) and pathway analysis of associated genes were conducted using Database for Annotation, Visualization and Integrated Discovery , Year (the year that the paper is published) and PMID (the PMID of the paper in PubMed database). Third, each column could be ranked in ascending or descending by clicking the triangle on the right side of the column header. Fourth, for each record, clicking the Variant dbSNP, Position, Gene and PMID column will take users to the corresponding page in the dbSNP, UCSC, GeneCards and PubMed database respectively. Clicking ‘More’ will jump to the Details page of the record in the database, which consists of more detail information about the reference, infection, population, mutation and disease relationship .The Network page provides a visual overview of the topological relationship between respiratory viruses and associated genes . Nodes rAt last, dbGSRV provides a detailed tutorial for usage of the database in the Help page.For a more comprehensive and unbiased understanding of the genetic association studies with respiratory viruses, the database not only includes positive results of association, but also includes negative results reported in the main text of the paper.In total, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. The seven respiratory viruses are adenovirus, influenza virus, measle virus, rhinovirus, RSV, SARS-CoV and SARS-CoV-2, of which influenza virus, SARS-CoV-2, RSV and SARS-CoV have the most records, with 718, 486, 433 and 221 records respectively . BesidesThe Network page in the database provides a visual overview of the topological relationship between respiratory viruses and associated genes as shown in We performed GO and pathway analysis of associated genes using Database for Annotation, Visualization and Integrated Discovery (DAVID). The top 10 significantly enriched GO terms and pathways were shown in Tables GO analysis revealed ‘immune response’ and ‘inflammatory response’ were top enriched terms. In addition, other enriched terms such as ‘positive regulation of T cell proliferation’, ‘positive regulation of interferon-gamma production’, ‘regulation of complement activation’, ‘type I interferon signaling pathway’, ‘cytokine activity’ and ‘positive regulation of inflammatory response’ are also related with immune response and inflammatory response, highlighting the central role of these processes against respiratory virus infection . NotablyPathway analysis revealed a significant enrichment for pathways directly related to pathogens and autoimmune diseases such as ‘Influenza A’, ‘Inflammatory bowel disease (IBD)’, ‘Herpes simplex infection’, ‘Measles’, ‘Rheumatoid arthritis’ and ‘Leishmaniasis’. There were three enriched pathways related to cytokines, ‘Cytokine-cytokine receptor interaction’, ‘Jak-STAT signaling pathway’ which is the downstream signaling pathway of cytokine interferon  and ‘CytTo our knowledge, dbGSRV is the first manually curated database containing comprehensive human genetic association information with respiratory viruses. It is composed of several characteristic features worth noting.First, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses with a user-friendly interface, which is convenient for researchers to browse and retrieve the data, access more information of public databases by hyperlinks and visualize the network of respiratory viruses and associated genes. Users could make use of the database to familiarize themselves with respiratory virus genetics, explore genes implicated in virus infection, select variants to further confirm and check whether significant variants discovered in their studies have been reported previously.Second, inconsistent results are frequently found in replication studies of genetic association , 30, thuThird, users should recognize that there are certain limitations in the database. Among all kinds of common respiratory viruses, only seven respiratory viruses have been studied of human genetic susceptibility or severity and thus included in the database, and a majority of the studies are candidate gene studies. This might lead to a biased representation of certain variants and associations in the database. Therefore, more and more studies, especially GWAS studies, on a wider range of respiratory viruses are anticipated in the future, and dbGSRV will be updated about once in a year according to newly available data. In addition, we find that many genetic association studies with respiration viruses have limited sample size and statistic power, which might be compensated with meta-analysis . TherefoIn summary, dbGSRV will be a convenient resource for researchers to query and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights into our understanding and treatment of respiratory virus infection.


Background: Cervical cancer rates in North Africa have risen in the last 10 years, suggesting that this region might benefit from cervical cancer screening and HPV vaccination programs. To assess the potential benefits of cervical cancer screening and HPV vaccination in North African countries, country-specific data on the prevalence and burden of HPV-related conditions are needed.Objectives: To describe the patterns and estimate the costs of management of cervical cancer, cervical intraepithelial neoplasia (CIN), and genital warts in Algeria.Methods: This was a descriptive analysis of questionnaire data obtained from a panel of 15 oncologists, gynecologists, and dermatologists (n=5 each). Data on diagnostic and treatment patterns, recurrence, and healthcare resource use (HCRU) were obtained. The costs (in Algerian dinars) associated with diagnosis, treatment, and recurrence were estimated.Results: Diagnosis of CIN was obtained by cytology tests or lesion biopsies; for cervical cancer, lesion biopsies, MRI, and CT scans were the most common diagnostic tests. For CIN, 70% of gynecologists and/or oncologists regularly or always used conization as a treatment. Treatments used regularly or always for cervical cancer included chemotherapy (80%), hysterectomy (70%), and radiation (70%). Annual HCRU per institution included 20 outpatient visits and 15 hospitalizations for CIN, and 50 outpatient visits and 11 hospitalizations for cervical cancer. For genital warts, diagnostic tests performed regularly or always included assays for hepatitis B, hepatitis C, HIV, and syphilis; cervical cytology; and colposcopy. Cryotherapy was the universal first-line treatment. Median per-patient costs associated with diagnosis, treatment, and recurrence were 6750, 19 750, and 77 750, respectively, for CIN; 53 750, 650 000, and 431 250, respectively, for cervical cancer; and 16 075, 15 500, and 9250, respectively, for genital warts.Discussion: These results give an estimate of the HCRU and cost of cervical cancer, CIN, and genital warts and highlight the need to assess more precisely the epidemiology of these diseases in Algeria.Conclusions: This study investigated the management of patients with cervical cancer, CIN, or genital warts in Algeria and provided the first estimates of diagnosis and treatment patterns, HCRU, and costs associated with these conditions. These resource use and cost estimates highlight the need to develop prevention strategies for HPV-related pathologies. Human papillomavirus (HPV) is a sexually transmitted virus that infects >10% of women and ≥19% of men globally.Relative to the rest of the world, North Africa is a low-risk region regarding cervical cancer,To assess the potential benefits of cervical cancer screening and HPV vaccination in North African countries, country-specific data on the prevalence and burden of HPV-related conditions are needed. Currently, there are no data on the healthcare resource utilization (HCRU) patterns among patients diagnosed with cervical cancer, cervical neoplasia, or genital warts in Algeria. Similarly, the economic impact of these diseases on patients and the healthcare system in Algeria is unknown. The purpose of this study was to describe the patterns and estimate the costs of management of cervical cancer, cervical intraepithelial neoplasia (CIN), and genital warts in Algeria.This was a descriptive analysis of questionnaire data obtained via a Delphi panel. A Delphi panel was chosen because there is a lack of reliable chart data for the management of genital warts in Algeria. In addition, electronic medical reports are not yet available in the country. Questionnaires were completed by participating physicians from December 2019 to March 2020 in 2 rounds. The study protocol was approved by the Beni Messous Ethics Committee on December 12, 2019.There is no optimal number of participants on a Delphi panel in the literature; for feasibility, we chose to recruit 15 experts in the fields of cervical cancer, CIN, and genital warts in Algeria, specifically, oncologists, gynecologists, and dermatologists. Individual subject matter experts were identified via publication records, lists of conference organizers and presenters, and membership in relevant medical associations. Qualifying physicians had to (1) be based in Algeria; (2) have an active practice where patients with cervical cancer, CIN, and genital warts were treated; and (3) work at least part-time in the public sector. Individuals who (1) might be involved in the inclusion of HPV vaccination in the national immunization program, (2) only worked in private medical offices and/or private clinics, or (3) did not complete the confidentiality disclosure agreement for the study were excluded.After identifying a list of 15 potential subject matter experts among department heads at the 14 academic hospitals in Algeria, the third-party vendor contacted each one, requesting their participation in the Delphi panel. Panelists were informed prior to their engagement that Merck Sharp & Dohme, Algeria was sponsoring the research. All 15 experts agreed to participate, and an initiation visit was performed for each site to describe the Delphi technique and the reimbursement offered for participation (25.35 Algerian dinars [DZD]). The initiation visit concluded with a request to complete the initial study questionnaire (on paper). The second round of the Delphi process was done via email and consisted of circulation of the results of round 1, along with a request for panelists to review and confirm their answers from round 1. Panelists were responsible for recording and verifying the accuracy of their data. Data from the paper copies of the questionnaires were entered into a secure electronic database by the third-party vendor.Appendix. Questions about CIN/cervical cancer were directed to gynecologists/oncologists; questions about genital warts were directed to dermatologists. Main themes of each questionnaire were (1) panelists’ demographic characteristics ; (2) characteristics of panelists’ practices pertaining to either CIN/cervical cancer (for gynecologists/oncologists) or genital warts (for dermatologists) ; (3) institutional information ; and (4) HCRU . The questionnaire also asked about side effects and complications of treatment, referrals to other medical specialties, frequency and duration of follow-up, and recurrences. Questions generally took one of two forms, asking either for a number  or a categorical designation .The questionnaires are shown in the Answers to the questionnaire were analyzed descriptively using SAS 9.4/STAT 15.3 . Continuous quantitative variables were described by the number of documented values, number of missing values, mean, standard deviation of the mean, median, first and third quartiles (interquartile range [IQR]), and range. Due to the small sample size, the results for continuous variables are generally reported in this paper as the median and IQR, with exceptions indicated in the table footnotes. Categorical variables were described by the number and the percentage of answers in each category, with the latter presented in the text.The goal of cost estimation was to quantify the cost of treatment of each disease, not necessarily over a fixed time period, but rather according to clinical presentation, ie, per case. No national nomenclature of treatment costs is available in Algeria, so several public (n=3) and private (n=7) institutions were contacted by phone to obtain local cost information in DZD. The collected costs for each diagnostic test and treatment were aggregated to estimate the total cost of diagnosis, treatment, and management of recurrence of cervical cancer, CIN, and genital warts. Costs for hospitalization and outpatient visits were estimated for cervical cancer and CIN only.Supplementary Table S1. As the numbers of patients at each institution were not available, cost analyses were performed for a single hypothetical case at each institution and averaged across all participating institutions. For questionnaire items with 4 possible answers, the following frequencies were assumed: never, zero patients; sometimes, 25% of patients; regularly, 50% of patients; always, 100% of patients. Therefore, the cost per patient of each diagnostic test and treatment was adjusted by multiplying the individual cost by 0, 0.25, 0.5, or 1 depending on the answer to the item by the physician. Costs of diagnosis, treatment, and recurrence are reported per patient, and costs for hospitalizations and outpatient visits are reported per institution per year.The specific questions used to calculate the costs are shown in All 15 experts agreed to participate in the study. The median (range) age of panel participants was 54 (40-74) years. Eleven panelists were male (73%), and 4 were female (27%). Specialties included gynecology, oncology, and dermatology . The median (range) time in medical practice was 30 (12-48) years.. Panelists estimated that 18% of the CIN patients were at stage 1, 28% were at stage 2, and 23% were at stage 3. The median duration of care for a single patient with CIN/cervical cancer was 10 years. Among CIN patients, 10% were under age 30, and among cervical cancer patients, 18% were under age 40. Panelists estimated the incidence of cervical cancer in Algeria to be 2800 cases per year.Among gynecologists and oncologists, it was estimated that 11% of their monthly caseload involved patients with CIN/cervical cancer . The median time in clinical practice treating patients with genital warts was 25 years. Among patients with genital warts, an estimated 65% were men and 35% were women, and 13% were under age 20. A median of 70% of patients were presenting with genital warts for the first time. Panelists estimated the prevalence of genital warts at their institution to range from 2% to 8% in men and 2% to 3% in women.Among dermatologists, it was estimated that 4% of their monthly caseload involved patients with genital warts . For the diagnosis of cervical cancer, lesion biopsies, magnetic resonance imaging (MRI), and computed tomography (CT) scans were the most common diagnostic tests, according to the percentage of panelists ranking them as being performed regularly or always . Forty percent of panelists reported that systematic screening for CIN/cervical cancer was performed regularly or always (not shown). Systematic screening typically occurred 2-3 times per year in women of median age 25 .Among gynecologists and oncologists, 60% reported that cytology tests were performed regularly or always for the diagnosis of CIN, and 40% said the same about lesion biopsies . Most panelists reported that revision  was conducted (80%) and laboratory tests were requested (60%) regularly or always for the sexual partners of patients with genital warts (not shown).Among dermatologists, diagnostic tests reported to be performed regularly or always in patients with genital warts included assays for hepatitis B, hepatitis C, HIV, and syphilis; anoscopy; and, in women, cervical cytology tests and colposcopy Most gynecologists and oncologists (60%) reported the availability of treatment guidelines for CIN/cervical cancer at their institution, and 80% reported the availability of all resources needed to treat CIN/cervical cancer according to the guidelines. In contrast, most dermatologists (80%) reported that treatment guidelines for genital warts were not available at their institution, with 3 of 4 reporting that at least some resources for treating genital warts were lacking.. The number of hospitalizations per year was estimated at 15 for CIN and 11 for cervical cancer. The estimated length of hospitalization was 1 day for CIN and 7 days for cervical cancer. Panelists reported an average of 4 follow-up visits for CIN/cervical cancer per patient per year.Gynecologists and oncologists estimated an institution-wide total of 20 outpatient visits  per year for CIN and 50 outpatient visits per year for cervical cancer Among dermatologists, the majority (60%) reported that patients with genital warts were never admitted to the hospital for treatment, although 2 panelists reported that hospitalization occurred sometimes (n=1) or always (n=1). Panelists estimated that patients with genital warts had an average of 12 follow-up visits per year.. The majority of panelists reported that large loop excision of the transformation zone (60%), trichloroacetic acid (70%), and laser surgery (90%) were never used as treatments for CIN. Treatments used regularly or always for cervical cancer included chemotherapy (80%), hysterectomy (70%), and radiation (70%) . According to 80% of panelists, complications of treatment for CIN/cervical cancer occurred “sometimes.” Complications occurring sometimes or regularly included bleeding (90%) and infection (100%). Recurrence of disease after treatment for CIN/cervical cancer occurred sometimes (80%) or regularly (10%). For recurrence of CIN, conization (40%) and hysterectomy (40%) were the treatments used regularly or always . For recurrence of cervical cancer, hysterectomy, chemotherapy, and radiation became less frequent than during initial treatment but were still used by the majority of panelists at least sometimes .For CIN, 70% of gynecologists and oncologists reported that conization was regularly or always used as a treatment  Cryotherapy remained in routine use as a second-line therapy , but excision and laser surgery became second-line options for regular use by 25% and 20% of panelists, respectively . According to 60% of panelists, complications occurred sometimes or regularly in patients treated for genital warts. Complications included bleeding (40% regularly), infection (60% sometimes), and deformity (40% sometimes). Recurrence after treatment for genital warts was reported to occur sometimes (40%) or regularly (40%). All panelists reported using cryotherapy  for recurring cases of genital warts .For genital warts, 100% of dermatologists reported cryotherapy to be the first-line treatment of choice  or always (20%). Specialties to which these panelists refer patients with CIN/cervical cancer regularly or always include surgeons (10%), gynecologists , and psychologists (40%). All dermatologists sometimes (80%) or regularly (20%) referred patients with genital warts to other specialists, generally to other dermatologists or to gynecologists.The estimated costs for diagnosis, treatment, and recurrence of CIN/cervical cancer and genital warts are shown in This study gives a first estimation of the diagnosis and treatment patterns, HCRU, and costs associated with cervical cancer, CIN, and genital warts in Algeria. Diagnosis and treatment patterns and HCRU estimates were obtained from a panel of experts practicing in Algeria, and total costs were calculated by synthesizing panelist responses with public and private data sources on individual cost line items.The diagnosis and treatment patterns reported by the panelists in this study were generally in line with international recommendations. The European Society for Medical Oncology’s guidelines on the diagnosis, treatment, and follow-up of cervical cancer state that colposcopy, biopsy, or excisional procedures are appropriate responses to an abnormal cytology result or a positive HPV test.The 2019 International Union Against Sexually Transmitted Infections (IUSTI)-Europe guideline for the management of anogenital warts recommends visual inspection as the best method for diagnosis, stating that biopsy and HPV testing are not necessary.In estimates of HCRU for genital warts in Algeria, most panelists reported that patients with genital warts were never admitted to the hospital and that each case of genital warts required an average of 12 follow-up visits per year. A systematic review of studies published through 2010 found that physician visits per genital warts episode ranged from 2.8 to 4.7.The total estimated cost per patient with genital warts in Algeria  was 40 825 DZD, which is equivalent to US $308 . The systematic review mentioned above reported a range of costs per episode of genital warts in different countries, from $168 to $1196 (in 2009 US dollars).The panelists in this study provided estimates of the incidence of cervical cancer and the prevalence of genital warts in Algeria. Other sources of data on cervical cancer in Algeria include the HPV Information CentreAccording to the HPV Information Centre, Algeria has a national cervical cancer screening program.Considering the scarcity of data from Algeria on the management of HPV-related diseases, the current study provides valuable new and novel information on the prevalence of genital warts and the management of cervical cancer, CIN, and genital warts. The panelists’ answers offer insight into the current diagnosis and treatment patterns for cervical cancer, CIN, and genital warts in Algeria, as well as estimates of the resource use associated with each condition.Despite these strengths, this study has several limitations. First and foremost, the results are based on answers to a questionnaire that, due to lack of other data, could not be compared or verified against other sources such as electronic medical records or health insurance databases. However, we note that previous studies of the HCRU and costs associated with warts in other countries have used expert opinion as a data source.In conclusion, this study investigated the management of patients with cervical cancer, CIN, or genital warts in Algeria and provided the first estimates of diagnosis and treatment patterns, HCRU, and costs associated with these conditions. These resource use and cost estimates highlight the need to develop prevention strategies for HPV-related pathologies.


Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases. In astronomy, for example, multiple measures of planetary positions across seasons provided compelling evidence for a universe that was heliocentric rather than geocentric . In biol-to-PFU) . Althoug-to-PFU)  or drug -to-PFU) . By reviThe counting of virus and virus-like particles of a laboratory, environmental, or clinical sample exploits physical, chemical, or biological aspects of the virus. These include the size, shape and electrical conductivity of virus particles, their propensity to be specifically labeled with one or more fluorophores, and the ability of the virus particle to infect a host cell, cause cell death, or produce virus progeny. Chemical and physical methods of particle quantification are summarized in Transmission electron microscopy (TEM) has been used to identify, classify, and quantify different viruses based on morphology . HistoriTEM focuses an accelerated electron beam upon a thin specimen that transmits an image onto a screen. It has a higher resolution than light microscopy, owing to the shorter wavelength of electrons (0.1 angstrom). Thus, TEM can capture atomic scale resolution of viruses, which are typically 20-to-200 nm in size. Before the establishment of electron microscopy for determining particle-to-PFU ratios, the first ratio between the count of infectious particles and the count of physical virus particles was measured for vaccinia virus, with the quantity of “elementary bodies” being calculated using the dry weight of a sample . ElementFor virus quantification, samples are often mixed with latex beads of known size and concentration ,30. Manu7 particles per mL; samples may need to be concentrated prior to analysis. Specimen preparation can be complex and tedious, typically requiring several hours, and artifacts in the images may result from the preparation steps. The virus is purified from cell debris, and a suitable supporting film needs to be prepared to hold the sample, often using a coated copper grid [While TEM can produce high-resolution images, its throughput is limited by its field of view. Higher magnification enables greater confidence in particle identification, but the sampling field is then smaller. Interpretation of TEM images depends on the operator, and during virus quantification the accidental counting of debris can cause overestimation. Owing to its dependence on human counting, TEM quantification has a relatively low throughput. Particle counting requires a high enough number of particles to reflect the average number in the sample, but not so high as to overwhelm the manual counter. In practice, such counting has a lower detection limit of 10per grid . Three mper grid ; direct In epifluorescence microscopy (EFM) virus particles are stained with fluorescent dyes that can bind nucleic acids and proteins of the virus. Fluorescence microscopy uses dyes that will produce a distinguishable signal, with the requirement being a signal-to-noise ratio higher than five . DAPI, YCompared to TEM, EFM equipment is less expensive, and sample preparation is relatively simple, making EFM a favored method for analyzing samples in the field. EFM has been most commonly used to count viruses in marine samples. Collecting and fixing samples takes 15–20 min, slide preparation takes one hour, and enumeration takes 30 min . The EFMResistive pulse sensing (RPS) is a particle detection method based on the Coulter principle, first developed and released by Wallace Coulter more than sixty years ago . The pri7 to 1010 particles/mL [Tunable resistive pulse sensing (TRPS) is a variant of RPS techniques that uses an elastic membrane containing a pore that can be stretched or relaxed, differing from the standard fixed solid-state pores. The resulting size of the pore aperture can be fine-tuned to better match different sizes of particles, which is especially important for polydisperse populations of viruses that have a wide range of sizes. The ability to determine the size of blockade events can also allow for the determination of coincidence and aggregate events, for example, when the pulse magnitude is an integer multiple of the typical individual pulses . The pulicles/mL .Flow cytometry combined the Coulter principle with fluorescence detection as a high-throughput method to measure the nucleic acid content and size of cells . Cells aA powerful feature of flow virometry is the ability to characterize heterogeneity at the level of individual virions. By taking advantage of multiple fluorescent labels, a flow virometer can characterize multiple characteristics of individual virus particles. For example, magnetic nanoparticles (MNPs) coupled with specific monoclonal antibodies have been used to capture and separate virions, and the separated complexes have been analyzed by flow virometry. This technique has been used to analyze the maturation of Dengue virus particles produced from different sources , and ther is the flow rate (particles per second) through the detection volume and t is the time spent within the detection volume. Typically, a high concentration of about 6 × 108 particles/mL gives 10 percent probability of two particles occupying the detection volume at the same time, with higher concentrations resulting in greater probability of coincidence. The lowest limit of detection of flow virometry is around 100 nm [Because flow virometry is flow-based and non-visualization based, flow virometry is a fast technique that relies less on the operator than EFM, with throughput up to 2000–6000 particles per second and producing results for a sample in less than 1 h. Operating a viral flow cytometer is less technically demanding than other methods such as TEM, and many steps of the process are automated ,48. DisaInfectious virus particles are quantified by plaque assay or end-point dilution, which both involve visualization of macroscopic regions of cytopathology. Virus particles that infect cells and kill them without making virus progeny can be quantified by their ability to prevent formation of cell colonies, called the clonogenic assay. These methods are summarized in The plaque assay is the most widely used method for the quantification of infectious particles or virus titers. The assay is carried out by preparing serial dilutions of a virus stock of unknown titer and applying them to susceptible cell monolayers. After adsorption and infection initiation, cells are overlaid with agar to localize the spread of subsequent rounds of infection to the vicinity of initial infected cells; macroscopic regions of cell death called ‘plaques’ can be made visible by crystal violet, which stains intact cells and leaves dead-cell or infected areas unstained. Since each plaque arises from the amplification of an initial single infectious particle, plaque counts, combined with known volumes of known dilutions can be used to calculate the concentration of infectious particles in the stock sample. The infectious virus titer is reported in plaque forming foci (PFF) or plaque forming units (PFU) per ml of solution.50) per mL. A virus stock of unknown titer is used to produce 10-fold dilutions, where one milliliter of each dilution is applied to multiple (say ten) cell cultures. After incubation, plates are inspected for cell death or cytopathic effects (CPE). The dilution at which 50% of the cultures exhibit CPE is considered the end point; for example, if 50 percent of the cultures at 104-fold dilution exhibit CPE, then the stock has a titer of approximately 104 TCID50 per ml. In practice, the TCID50 is determined from this dilution by calculation using the Spearman–Karber or Reed–Muench method, though other methods exist [50/mL and PFU/mL are not equivalent, but are comparable [An alternative to the plaque assay, the end-point dilution assay, is also used to quantify infectious virus titer. End-point dilution measures viral titer based on the dilution at which half of the total cell cultures become infected, expressed as a 50 percent tissue culture infectious dose  and other RNA viruses were used to recover DIPs , and polDIPs arise as byproducts of virus replication and infection. When a cell is infected by a virus, the viral replication complex uses the virus genome or anti-genome as a template to instruct the synthesis of full-length genomic templates for eventual packaging into virus progeny particles. Stretches of the template that are flanked by similar or identical short (less than 20 nucleotide) repeat sequences can enable hopping of the elongating replication complex between the repeats, causing within-strand or between-strand recombination, leaving a deletion in the resulting genomic template ,67,68. I−8-to-10−6 per replication have been estimated for the polymerase complex of the T7 phage [The structure and evolution of DVG populations will depend on their rates of generation. Here, it is useful to distinguish between rates and frequencies of mutation , defined by Drake and Holland ,72. SpecT7 phage ; larger −8-to-10−7, a value that will reflect a combination of rates RNA recombination to form DVGs, and the fraction of DVGs that can be packaged and co-infect cells with intact virus to replicate and spread as DIPs. Similarly, a deletion frequency of about 10−8 was estimated for DVGs of phage T7 that deleted their gene encoding T7 RNA polymerase [In contrast to the mutation rate, the mutation frequency depends on both the mutation rate as well as the ability of the resulting DVG to enrich relative to other genomes in the population . In shorlymerase . Such DVlymerase . This eslymerase . By emplOther aspects of DVG and DIP evolution have been revealed by other serial-passage or continuous cell and virus cultures. Such cultures have been shown to promote the emergence, enrichment, and displacement of longer DVGs by shorter higher fitness DVG variants. Such evolution of DVGs has been demonstrated by tomato bushy stunt virus (TBSV) during serial propagation on plants , by phagThe spatial distribution in cells of full-length viral genomes and their DVGs has been elucidated for Sendai virus by fluorescent in situ hybridization (FISH). In cells enriched with the full-length viral genomes, the viral genomes interacted with the cellular trafficking machinery and clustered in the perinuclear region. In contrast, in cells enriched in DVGs, the defective genomes showed no evidence of interaction with the trafficking machinery, and they were diffusely distributed around throughout the cytoplasm . ResultaMore complex evolutionary dynamics of viruses and their defective genomes can exhibit co-evolution. The emergence of DVGs and DIPs can create an environment that selects for intact virus that resist interference. For example, mutants of intact VSV can resist DVG and DIP interference by mutations that impact genome replication and encapsidation . MoreoveFinally, DVGs can evolve to cooperate in a manner that frees them from any dependence on intact virus for their growth. Serial-passage cultures of foot-and-mouth-disease virus (FMDV) at high multiplicities of infection enable the emergence and enrichment of DVGs and DIPs that are infectious by complementation; by co-infecting the same cell, they provide in trans the replication, encapsidation, and other functions needed to propagate their DVGs and their associated defective cooperating particles . Such coThe simplest models of DIP interference with virus growth assume single-hit behavior, where a cell co-infected with intact virus and at least one DI particle can only produce DI particle progeny ,100,101,Quantitative studies of VSV have provided evidence for complex feedback of interfering processes on DI genome and particle production. Using radioisotopes to metabolically label both DI and standard particles, density-based separation by ultracentrifugation, and quantification of both DI and standard particle populations, increasing inputs of DI particles were found to dramatically reduce production of standard particles, but the highest yields DI particles were under input doses that exhibited minimal interference with standard particle production . Furtherin vitro include vesicular stomatitis virus [DIPs have been found for many DNA and RNA viruses. DIP-forming DNA viruses include herpes simplex virus , pseudoris virus , Newcastis virus , measlesis virus , influenis virus , mouse his virus , and moris virus . Defectiis virus , but it in vitro [in vivo. For example, short fragments of Dengue viral RNA containing only key regulatory elements for packaging at 3′ and 5′ ends and large internal deletions were found in serum from infected patients. Patient sera were used to infect mosquito cultures which developed identical RNA fragments, opening the possibility that the RNA fragments were transmitted as fully packaged DIPs. Transcribed in vitro, RNA corresponding to the in vivo samples were shown to be packaged into virus-like particles and transmitted over three passages in the presence of the wild-type virus. In preparations of Dengue virus with these short RNA fragments, yields of wild-type virus were reduced [in vivo. More recently, the same RNA from the serum was used to infect cell lines that support dengue virus growth, and again, infectious virus production was reduced; moreover, the RNA was shown to induce activity of RIG-I, MDA5, and interferon, consistent with the immunostimulatory activity characteristic of DIPs  of human respiratory syncytial virus (RSV) were found in human cells which triggered an antiviral immune response , charactDirect sequencing of a nasopharyngeal sample from a patient infected with Middle East respiratory syndrome (MERS) coronavirus revealed two virus variants with internal deletions that resulted in the truncation of viral proteins, and bioinformatic analysis suggested the variants were defective in packaging ,126. FunRecent reviews have summarized the role of DIPs in activating the immune response ,116. SpeBeyond activating IFN associated innate immune responses, DIPs can also suppress IFN . Eight sMost recently, DVGs detected in nasal secretions of RSV have been associated with clinical patient responses to the virus. In children, DVGs were associated with a higher viral load and more robust pro-inflammatory response. In adults, however, the clinical response was based on the time at which DVGs were detected, rather than solely their presence. DVGs detected early in the course of infection were associated with mild disease, and DVGs detected later were linked to severe disease. Patients with DVGs had heightened expression of cytokines, including IFN alpha, which aligned with past studies linking induction of IFN to DVGs and DIPs .Aside from their roles in triggering innate immune responses, work on Sendai virus has provided evidence of roles DIPs and DVGs play in adaptive immunity. Sendai stocks rich with DIPs were shown to induce dendritic cell maturation in human and mouse cells by helping upregulate cytokine activity. This pathway worked independently of IFN, and suggests possible applications of DIPs as vaccine adjuvants, stimulating dendritic cell maturation . SubsequOwing to their ability to interfere with standard virus infections, DIPs have been proposed as potentially transmissible antiviral therapies. For example, a cloned DI virus of IAV with a large internal deletion, called 244 DI virus, has been administered intranasally to mice and found to protect against infections by several strains of IAV. In ferrets, intranasal administration of 244 DI reduced fever, weight loss, respiratory symptoms, and the infectious load of the standard virus relative to infected controls, providing further evidence that 244 DI virus can act as an effective antiviral . A diffe0R) that is greater than 1; the TIP would generate more genomic RNA (gRNA) than the wild type virus, exploit viral resources made by the wild type virus, driving down wild type virus replication, disease progression, and transmission on large scale [Engineered DIPs from human immunodeficiency virus (HIV) have been shown to reduce wild-type HIV replication ,146,147.ge scale .Recently, DIPs have been explored as therapeutics against flaviviruses. A production cell line used a combination of lentiviral and retroviral vectors to stably produce virus-free DIPs of dengue virus; following purification and concentration, the DIPs displayed antiviral activity in cells co-infected with dengue virus. Such production systems and DIP activities might well be realized for diverse viruses, providing a potential platform technology for DIP-based antiviral therapeutics . For ZikThe COVID-19 pandemic has spurred the development of synthetic DVGs and DIPs against human coronaviruses, specifically SARS-CoV-2. Based on known DIPs of coronaviruses ,152, a dFinally, engineered DIPs may contribute toward a new paradigm to promote public health: specifically, vaccines that reduce infectious disease owing to their broad protective effects . For exaInfluenza A virus (IAV) typically exhibits particle-to-PFU ratios of 10-to-100 , so moreGenerally, SIPs differ from DIPs. SIPs do not interfere with standard virus production during co-infections, and they lack the large internal deletions that are genomic signatures for DIPs . FurtherHigh particle-to-PFU ratios can arise from the particles that lack essential functions for infection, such as DIPs, but also from SIPs, which one might expect to be fully functional based on their genome sequences, biomolecular composition, and structure. However, single-cell measures and quantitative models indicate an important role for stochastic or noisy processes in the mixed on/off behaviors of IAV SIPs and other viruses.Common measures of average-cell behavior measured from a population of cells mask significant heterogeneity that can best be appreciated by measurements at the single-cell level ,163,164.Noteworthy effects of noisy behavior have been revealed by computational models of different intracellular processes associated with virus-cell interactions: stochastic gene expression in the lysis-lysogeny decision , heterogThe need for cooperation between virus particles is not limited to IAV. Elegant single-cell studies of vaccinia virus have combined nanoscale fluidic manipulation, detection of recombinant fluorescent virus particles, and atomic force microscopy (AFM) to dissect early stages of infection . Based oBeyond the noisy or stochastic behavior, which is inescapable for single infected cells, other mechanisms may also contribute to the semi-infectious phenotype. For example, electron microscopy has shown that packaging of genomic segments for IAV can be incomplete , often oInfectious virus particles typically kill their host cell as a byproduct of producing virus progeny. Particles that kill their host cell but fail to make detectable progeny have been called non-infectious cell killing particles (NiCKPs), as shown in 9, across passages [Evidence for NiCKPs was based on differences between measures of cell-killing and plaque-forming by particles of VSV. The CKPs that failed to produce detectable progeny by plaque assay were “defective cell killing particles” or NiCKPs, which were produced at 5 to 9-fold higher concentrations than PFPs . Furtherpassages .Tobacco etch potyvirus [Although descriptions of virus particles as infectious or cell-killing suggest all-or-nothing behaviors, such descriptions are simplifications for a continuum of behaviors. The fitness of a virus under specified conditions typically refers to its replicative ability, while its virulence refers to its capacity to kill cells . The fitotyvirus .Virus-like particles that span a broad range of virulence or cell-killing may have useful applications in human health. Non-infectious CKPs, which have low fitness but remain virulent, may be useful as therapeutics where cell killing is desirable but not infection-spread, as in oncolytic therapies to treat cancer. For example, engineered highly attenuated VSV, which makes few progeny and small plaques, selectively infected and killed human gliomas implanted in SCID mice ; oncolytParticle-to-PFU ratios. What significance should one assign ratios of particle-to-PFU or genome-to-PFU that are far greater than one? The ability to quantify such ratios require total particle or genome levels, in addition to PFUs measured from the same sample. Such multiple measures are most often performed on samples from “clean” laboratory cultures of cells and virus rather than from “dirty” or uncultivated environmental samples. Such cultures also typically use transformed cell lines to host the infection, as they can give robust virus titers or enable easy visualization and quantification of infectious particles by plaque counting. The virus strains are often far removed from their natural counterparts, having been selected over multiple generations of passage cultures in the lab to yield robust titers or easily visualized plaques. The broad ranges of reported particle-to-PFU ratios also reflect a lack of reference ratios and standardization [dization . NeverthDefective viral genomes in nature. We have highlighted compelling examples of diverse biological activities of virus-like particles and DVGs in vivo or from natural and clinical isolates. These include semi-infectious particles, which must infect the same cell with multiple particles in order to give a productive infection for influenza A virus in mice [ in mice . Further in mice . More re in mice  and link in mice . Finally in mice . We antiEngineered study of viruses and virus-like particles. Engineered experimental systems can enable the study of virus-cell behaviors at a deeper level than would be practical or ethical for natural or patient infections. For example, engineering includes design, synthesis and application of reporter genomes. Single-reporter viruses can be used to infect cells at low MOI, combined with fluorescent-activated cell sorting (FACS) to isolate single cells infected by single virus particles, which can be further studied to study infections start viral gene expression but fail to produce virus, as well as distributions of yields from productive infections [fections . Engineefections ; micro-wfections . Alternafections . Finallyfections ; co-infefections .How can a virus be “semi-infectious?” Mathematical modeling of single cell behaviors has highlighted how noisy or stochastic degradation of virus genomes can cause otherwise identical infected cells to either produce virus or not [s or not . More mes or not , which hs or not ,166,190.s or not . More brs or not . In otheReturning to nature. Transformed cell lines commonly used to culture viruses are often defective in innate immune signaling and suppression of virus growth; these include, for example, Vero [le, Vero ,193, BHKle, Vero ,195, HEKle, Vero , and HeLle, Vero . Al-thoule, Vero , such stTo culture primary cells is technically challenging, and their infections by viruses tend to be less productive and highly variable. However, it is plausible that the low productivities and variability reflect features of infection that are a step closer to their behaviors in nature. Other more natural and challenging to implement culture environments include conditions that promote primary cell differentiation. For example, air–liquid interface (ALI) cultures of primary human airway epithelial cells promote their differentiation to create a pseudostratified epithelium; goblet and mucus-producing cells are present, as well as functional cilia, and the epithelium is susceptible to infection by human rhinovirus-C . The fieConclusion. Large particle-to-PFU ratios measured for many viruses suggest that the vast majority of virus-like particles are unable to productively infect their host cells. However, despite being “dead”, virus-like particles can be very much alive in other facets: parasitizing the resources within host cells that intact viruses establish for growth, interfering with normal virus growth, activating or inhibiting innate immune signaling of their host cells, killing their host cells, and teaming with other “dead” viruses to produce infectious progeny. Such understanding of virus-like particles has been largely gleaned from studies at the level of particles and host cells. A grand challenge remains to understand how such functions and activities impact the development, severity, transmission, and persistence of infectious disease in their plant, animal, and human hosts.


Zhang Z. et al. describes the occurrence and distribution of orthotospoviral diseases and their possible management strategies in China.The International Committee on Taxonomy of Viruses (ICTV) lists nearly 2,000 different species of plant viruses. Plant viruses are recognized as economically important plant pathogens, because they cause significant losses in a variety of crops that we rely on. Due to the global transportation of agricultural products and planting materials and intensive agricultural farming practices, emerging new viruses and reemerging known viruses significantly threat food security. There is currently no efficient or long-term control measures for many of the plant viruses that cause serious diseases. On these lines, Maclot et al. highlights the many opportunities that careful use of the HTS method opens up in understanding the behavior of plant virus populations in cultivated and wild plants. Velasco and Padilla consider the possibility to use HTS in certification schemes based on the results of a comparison between HTS of small RNAs and other diagnostic methods in grapevine plants. The prospects of HTS based diagnosis in controlling plant virus diseases are bright.A big advancement in ecological plant virus research has been achieved by high throughput sequencing (HTS). HTS allows quick identification of most, if not all, viruses in plants without a need for prior information, which viruses might be present. In their expert review, Zhang L. et al., discuss fijivirus outbreaks, which occur in connection to migrations of the planthopper vectors. The authors give insights into several aspects of vector transmission including the effects of viruses on the behavior and physiology of vector insects. An interesting finding presented by Du et al., is that the RNA-silencing suppressor NSs of tomato spotted wilt virus reduces the monoterpene volatiles in a way that increases the attractiveness of the plant for the transmission vector thrip Frankliniella occidentalis. In their paper, McGreal et al. studied the possibility to use ground cover plants as an alternative controlling strategy to reduce transmission of grapevine leafroll-associated virus 3 by mealybugs. Zhang J. et al., asked the question about the role of virus-induced expression of circular RNAs in the vector Laodelphax striatellus on rice black-streaked dwarf virus infection. Chen et al., found that the virus concentrations in the salivary gland of the leafhopper vector Nephotettix cincticeps were higher during the intermittent period than during the transmitting period of rice dwarf virus, a plant reovirus, which led the authors to discuss a threshold-regulated release of viruses from the insect vectors.Plant viruses enter the plant cell by mechanical injury, when transported by insects or nematodes feeding on them or via parasitic agents such as fungi. Virus-insect vector interaction studies are essential for understanding the connections between plant viral transmission routes and virus epidemics. In their review, Domingo-Calap et al.). The authors demonstrate reduced RNA silencing suppression activity of the crinivirus P25 in this interaction. An interaction that reduced the activity of RNA silencing suppressor of another crinivirus cucurbit chlorotic yellows virus was discovered by Yang et al., In this case the interactor was a ribosomal protein that could negatively affect virus accumulation. These studies suggest that the silencing suppressor proteins interact with various proteins and many antiviral defense pathways during crinivirus infections. It also simply is amazing in how many ways geminiviral AC2 silencing suppressor proteins interfere with post-transcriptional gene silencing, transcriptional gene silencing and other plant defense pathways as can be learned from the review article by Veluthambi and Sunitha.Plant responses to mixed infections vary, but because of their many possible adverse consequences, it is important to understand how viruses interact in co-infected susceptible plants. A previously undescribed interaction of a potyvirus watermelon mosaic virus protein P1 with a crinivirus cucurbit yellow stunting disorder virus protein P25 was proposed to contribute to the complex response of the host to this virus pair  and CRISPR-associated Cas nucleases are reviewed by Cao et al. They discuss the challenges and opportunities provided by CRISPR/Cas systems for controlling different plant viruses by targeting either viral sequences or host susceptibility genes.Basal immunity of non-host plant species protects plants against most plant virus diseases. Also host plants may express basal resistance at certain developmental stages. The factors underlying the mechanism of age-related resistance against a geminivirus, tomato leaf curl virus, were studied by against a geminvirus tomato yellow leaf curl virus were studied by Finally, we would like to show our gratitude to all the authors who contributed to the Research Topic. The articles cover a broad spectrum of plant host-virus interactions and management strategies and open several channels for study by providing major insights into these complex relationships.All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.